Sample records for accurately reproduce observed

  1. Can cancer researchers accurately judge whether preclinical reports will reproduce?

    PubMed Central

    Mandel, David R.; Kimmelman, Jonathan

    2017-01-01

    There is vigorous debate about the reproducibility of research findings in cancer biology. Whether scientists can accurately assess which experiments will reproduce original findings is important to determining the pace at which science self-corrects. We collected forecasts from basic and preclinical cancer researchers on the first 6 replication studies conducted by the Reproducibility Project: Cancer Biology (RP:CB) to assess the accuracy of expert judgments on specific replication outcomes. On average, researchers forecasted a 75% probability of replicating the statistical significance and a 50% probability of replicating the effect size, yet none of these studies successfully replicated on either criterion (for the 5 studies with results reported). Accuracy was related to expertise: experts with higher h-indices were more accurate, whereas experts with more topic-specific expertise were less accurate. Our findings suggest that experts, especially those with specialized knowledge, were overconfident about the RP:CB replicating individual experiments within published reports; researcher optimism likely reflects a combination of overestimating the validity of original studies and underestimating the difficulties of repeating their methodologies. PMID:28662052

  2. Accurate and reproducible measurements of RhoA activation in small samples of primary cells.

    PubMed

    Nini, Lylia; Dagnino, Lina

    2010-03-01

    Rho GTPase activation is essential in a wide variety of cellular processes. Measurement of Rho GTPase activation is difficult with limited material, such as tissues or primary cells that exhibit stringent culture requirements for growth and survival. We defined parameters to accurately and reproducibly measure RhoA activation (i.e., RhoA-GTP) in cultured primary keratinocytes in response to serum and growth factor stimulation using enzyme-linked immunosorbent assay (ELISA)-based G-LISA assays. We also established conditions that minimize RhoA-GTP in unstimulated cells without affecting viability, allowing accurate measurements of RhoA activation on stimulation or induction of exogenous GTPase expression. Copyright 2009 Elsevier Inc. All rights reserved.

  3. Dysplastic naevus: histological criteria and their inter-observer reproducibility.

    PubMed

    Hastrup, N; Clemmensen, O J; Spaun, E; Søndergaard, K

    1994-06-01

    Forty melanocytic lesions were examined in a pilot study, which was followed by a final series of 100 consecutive melanocytic lesions, in order to evaluate the inter-observer reproducibility of the histological criteria proposed for the dysplastic naevus. The specimens were examined in a blind fashion by four observers. Analysis by kappa statistics showed poor reproducibility of nuclear features, while reproducibility of architectural features was acceptable, improving in the final series. Consequently, we cannot apply the combined criteria of cytological and architectural features with any confidence in the diagnosis of dysplastic naevus, and, until further studies have documented that architectural criteria alone will suffice in the diagnosis of dysplastic naevus, we, as pathologists, shall avoid this term.

  4. Intra-observer reproducibility and diagnostic performance of breast shear-wave elastography in Asian women.

    PubMed

    Park, Hye Young; Han, Kyung Hwa; Yoon, Jung Hyun; Moon, Hee Jung; Kim, Min Jung; Kim, Eun-Kyung

    2014-06-01

    Our aim was to evaluate intra-observer reproducibility of shear-wave elastography (SWE) in Asian women. Sixty-four breast masses (24 malignant, 40 benign) were examined with SWE in 53 consecutive Asian women (mean age, 44.9 y old). Two SWE images were obtained for each of the lesions. The intra-observer reproducibility was assessed by intra-class correlation coefficients (ICC). We also evaluated various clinicoradiologic factors that can influence reproducibility in SWE. The ICC of intra-observer reproducibility was 0.789. In clinicoradiologic factor evaluation, masses surrounded by mixed fatty and glandular tissue (ICC: 0.619) showed lower intra-observer reproducibility compared with lesions that were surrounded by glandular tissue alone (ICC: 0.937; p < 0.05). Overall, the intra-observer reproducibility of breast SWE was excellent in Asian women. However, it may decrease when breast tissue is in a heterogeneous background. Therefore, SWE should be performed carefully in these cases. Copyright © 2014 World Federation for Ultrasound in Medicine & Biology. Published by Elsevier Inc. All rights reserved.

  5. Digital image analysis: improving accuracy and reproducibility of radiographic measurement.

    PubMed

    Bould, M; Barnard, S; Learmonth, I D; Cunningham, J L; Hardy, J R

    1999-07-01

    To assess the accuracy and reproducibility of a digital image analyser and the human eye, in measuring radiographic dimensions. We experimentally compared radiographic measurement using either an image analyser system or the human eye with digital caliper. The assessment of total hip arthroplasty wear from radiographs relies on both the accuracy of radiographic images and the accuracy of radiographic measurement. Radiographs were taken of a slip gauge (30+/-0.00036 mm) and slip gauge with a femoral stem. The projected dimensions of the radiographic images were calculated by trigonometry. The radiographic dimensions were then measured by blinded observers using both techniques. For a single radiograph, the human eye was accurate to 0.26 mm and reproducible to +/-0.1 mm. In comparison the digital image analyser system was accurate to 0.01 mm with a reproducibility of +/-0.08 mm. In an arthroplasty model, where the dimensions of an object were corrected for magnification by the known dimensions of a femoral head, the human eye was accurate to 0.19 mm, whereas the image analyser system was accurate to 0.04 mm. The digital image analysis system is up to 20 times more accurate than the human eye, and in an arthroplasty model the accuracy of measurement increases four-fold. We believe such image analysis may allow more accurate and reproducible measurement of wear from standard follow-up radiographs.

  6. Reproducibility of Regional Pulse Wave Velocity in Healthy Subjects

    PubMed Central

    Lee, Nak Bum

    2009-01-01

    Background/Aims Despite the clinical importance and widespread use of pulse wave velocity (PWV), there are no standards for pulse sensors or for system requirements to ensure accurate pulse wave measurement. We assessed the reproducibility of PWV values using a newly developed PWV measurement system. Methods The system used in this study was the PP-1000, which simultaneously provides regional PWV values from arteries at four different sites (carotid, femoral, radial, and dorsalis pedis). Seventeen healthy male subjects without any cardiovascular disease participated in this study. Two observers performed two consecutive measurements in the same subject in random order. To evaluate the reproducibility of the system, two sets of analyses (within-observer and between-observer) were performed. Results The means±SD of PWV for the aorta, arm, and leg were 7.0±1.48, 8.43±1.14, and 8.09±0.98 m/s as measured by observer A and 6.76±1.00, 7.97±0.80, and 7.97±0.72 m/s by observer B, respectively. Between-observer differences for the aorta, arm, and leg were 0.14±0.62, 0.18±0.84, and 0.07±0.86 m/s, respectively, and the correlation coefficients were high, especially for aortic PWV (r=0.93). All the measurements showed significant correlation coefficients, ranging from 0.94 to 0.99. Conclusions The PWV measurement system used in this study provides accurate analysis results with high reproducibility. It is necessary to provide an accurate algorithm for the detection of additional features such as flow wave, reflection wave, and dicrotic notch from a pulse waveform. PMID:19270477

  7. The NANOGrav Observing Program: Automation and Reproducibility

    NASA Astrophysics Data System (ADS)

    Brazier, Adam; Cordes, James; Demorest, Paul; Dolch, Timothy; Ferdman, Robert; Garver-Daniels, Nathaniel; Hawkins, Steven; Lam, Michael Timothy; Lazio, T. Joseph W.

    2018-01-01

    The NANOGrav Observing Program is a decades-long search for gravitational waves using pulsar timing which relies, for its sensitivity, on large data sets from observations of many pulsars. These are constructed through an intensive, long-term observing campaign. The nature of the program requires automation in the transfer and archiving of the large volume of raw telescope data, the calibration of those data, and making these resulting data products—required for diagnostic and data exploration purposes—available to NANOGrav members. Reproducibility of results is a key goal in this project, and essential to its success; it requires treating the software itself as a data product of the research, while ensuring easy access by, and collaboration between, members of NANOGrav, the International Pulsar Timing Array consortium (of which NANOGrav is a key member), as well as the wider astronomy community and the public.

  8. Intra-observer reproducibility and interobserver reliability of the radiographic parameters in the Spinal Deformity Study Group's AIS Radiographic Measurement Manual.

    PubMed

    Dang, Natasha Radhika; Moreau, Marc J; Hill, Douglas L; Mahood, James K; Raso, James

    2005-05-01

    Retrospective cross-sectional assessment of the reproducibility and reliability of radiographic parameters. To measure the intra-examiner and interexaminer reproducibility and reliability of salient radiographic features. The management and treatment of adolescent idiopathic scoliosis (AIS) depends on accurate and reproducible radiographic measurements of the deformity. Ten sets of radiographs were randomly selected from a sample of patients with AIS, with initial curves between 20 degrees and 45 degrees. Fourteen measures of the deformity were measured from posteroanterior and lateral radiographs by 2 examiners, and were repeated 5 times at intervals of 3-5 days. Intra-examiner and interexaminer differences were examined. The parameters include measures of curve size, spinal imbalance, sagittal kyphosis and alignment, maximum apical vertebral rotation, T1 tilt, spondylolysis/spondylolisthesis, and skeletal age. Intra-examiner reproducibility was generally excellent for parameters measured from the posteroanterior radiographs but only fair to good for parameters from the lateral radiographs, in which some landmarks were not clearly visible. Of the 13 parameters observed, 7 had excellent interobserver reliability. The measurements from the lateral radiograph were less reproducible and reliable and, thus, may not add value to the assessment of AIS. Taking additional measures encourages a systematic and comprehensive assessment of spinal radiographs.

  9. Three-dimensional endoanal ultrasound is accurate and reproducible in determining type and height of anal fistulas.

    PubMed

    Kołodziejczak, M; Santoro, G A; Obcowska, A; Lorenc, Z; Mańczak, M; Sudoł-Szopińska, I

    2017-04-01

    Surgical treatment of high anal fistulas is associated with the potential risk of faecal incontinence and recurrence. The primary aim of this study was to determine the accuracy of three-dimensional endoanal ultrasound (3D-EAUS) in the assessment of height and type of anal fistulas, compared to the intra-operative findings (gold standard). The secondary aim was to evaluate the inter-observer reproducibility of 3D-EAUS. The study design was a prospective analysis of retrospective data. 299 patients (202 men), mean age 45.3 years, who underwent surgery for anal fistulas, were included. All patients were preoperatively assessed by 3D-EAUS. Two readers independently reviewed the volumes to determine the type and height of fistulas. Sensitivity, specificity, positive and negative predictive values, proportion of agreements and Cohen's kappa coefficient (κ) were calculated for both examiners. Ultrasound findings were compared with intra-operative data (reference standard), evaluated blindly by the surgeons. At surgery, 201 (67%) were transsphincteric, 49 (16%) suprasphincteric, 47 (16%) intersphincteric and two (1%) extrasphincteric fistulas. Intra-operatively, 177 (59%) were low and 122 (41%) high fistulas. The overall accuracy of 3D-EAUS was 91% for fistula type (271/299 fistulas: 97% transsphincteric, 100% intersphincteric, 57% suprasphincteric, 0% extrasphincteric) and 92% for fistula height (275/299 fistulas: 80% high and 100% low). Both readers reported very good agreement with surgery in the assessment of fistula type (proportion of agreement 0.88, κ = 0.89) and height (proportion of agreement 0.90, κ = 0.91). 3D-EAUS is an accurate and reproducible modality for the assessment of type and height of anal fistulas. Colorectal Disease © 2016 The Association of Coloproctology of Great Britain and Ireland.

  10. Feasibility and observer reproducibility of speckle tracking echocardiography in congenital heart disease patients.

    PubMed

    Mokhles, Palwasha; van den Bosch, Annemien E; Vletter-McGhie, Jackie S; Van Domburg, Ron T; Ruys, Titia P E; Kauer, Floris; Geleijnse, Marcel L; Roos-Hesselink, Jolien W

    2013-09-01

    The twisting motion of the heart has an important role in the function of the left ventricle. Speckle tracking echocardiography is able to quantify left ventricular (LV) rotation and twist. So far this new technique has not been used in congenital heart disease patients. The aim of our study was to investigate the feasibility and the intra- and inter-observer reproducibility of LV rotation parameters in adult patients with congenital heart disease. The study population consisted of 66 consecutive patients seen in the outpatient clinic (67% male, mean age 31 ± 7.7 years, NYHA class 1 ± 0.3) with a variety of congenital heart disease. First, feasibility was assessed in all patients. Intra- and inter-observer reproducibility was assessed for the patients in which speckle tracking echocardiography was feasible. Adequate image quality, for performing speckle echocardiography, was found in 80% of patients. The bias for the intra-observer reproducibility of the LV twist was 0.0°, with 95% limits of agreement of -2.5° and 2.5° and for interobserver reproducibility the bias was 0.0°, with 95% limits of agreement of -3.0° and 3.0°. Intra- and inter-observer measurements showed a strong correlation (0.86 and 0.79, respectively). Also a good repeatability was seen. The mean time to complete full analysis per subject for the first and second measurement was 9 and 5 minutes, respectively. Speckle tracking echocardiography is feasible in 80% of adult patients with congenital heart disease and shows excellent intra- and inter-observer reproducibility. © 2013, Wiley Periodicals, Inc.

  11. Evaluation of Oceanic Surface Observation for Reproducing the Upper Ocean Structure in ECHAM5/MPI-OM

    NASA Astrophysics Data System (ADS)

    Luo, Hao; Zheng, Fei; Zhu, Jiang

    2017-12-01

    Better constraints of initial conditions from data assimilation are necessary for climate simulations and predictions, and they are particularly important for the ocean due to its long climate memory; as such, ocean data assimilation (ODA) is regarded as an effective tool for seasonal to decadal predictions. In this work, an ODA system is established for a coupled climate model (ECHAM5/MPI-OM), which can assimilate all available oceanic observations using an ensemble optimal interpolation approach. To validate and isolate the performance of different surface observations in reproducing air-sea climate variations in the model, a set of observing system simulation experiments (OSSEs) was performed over 150 model years. Generally, assimilating sea surface temperature, sea surface salinity, and sea surface height (SSH) can reasonably reproduce the climate variability and vertical structure of the upper ocean, and assimilating SSH achieves the best results compared to the true states. For the El Niño-Southern Oscillation (ENSO), assimilating different surface observations captures true aspects of ENSO well, but assimilating SSH can further enhance the accuracy of ENSO-related feedback processes in the coupled model, leading to a more reasonable ENSO evolution and air-sea interaction over the tropical Pacific. For ocean heat content, there are still limitations in reproducing the long time-scale variability in the North Atlantic, even if SSH has been taken into consideration. These results demonstrate the effectiveness of assimilating surface observations in capturing the interannual signal and, to some extent, the decadal signal but still highlight the necessity of assimilating profile data to reproduce specific decadal variability.

  12. Automated morphometry provides accurate and reproducible virtual staging of liver fibrosis in chronic hepatitis C

    PubMed Central

    Calès, Paul; Chaigneau, Julien; Hunault, Gilles; Michalak, Sophie; Cavaro-Menard, Christine; Fasquel, Jean-Baptiste; Bertrais, Sandrine; Rousselet, Marie-Christine

    2015-01-01

    morphometric scores provide reproducible and accurate diagnoses of fibrosis stages via “virtual expert pathologist.” PMID:26110088

  13. Accurate and reproducible functional maps in 127 human cell types via 2D genome segmentation

    PubMed Central

    Hardison, Ross C.

    2017-01-01

    Abstract The Roadmap Epigenomics Consortium has published whole-genome functional annotation maps in 127 human cell types by integrating data from studies of multiple epigenetic marks. These maps have been widely used for studying gene regulation in cell type-specific contexts and predicting the functional impact of DNA mutations on disease. Here, we present a new map of functional elements produced by applying a method called IDEAS on the same data. The method has several unique advantages and outperforms existing methods, including that used by the Roadmap Epigenomics Consortium. Using five categories of independent experimental datasets, we compared the IDEAS and Roadmap Epigenomics maps. While the overall concordance between the two maps is high, the maps differ substantially in the prediction details and in their consistency of annotation of a given genomic position across cell types. The annotation from IDEAS is uniformly more accurate than the Roadmap Epigenomics annotation and the improvement is substantial based on several criteria. We further introduce a pipeline that improves the reproducibility of functional annotation maps. Thus, we provide a high-quality map of candidate functional regions across 127 human cell types and compare the quality of different annotation methods in order to facilitate biomedical research in epigenomics. PMID:28973456

  14. Panel-based Genetic Diagnostic Testing for Inherited Eye Diseases is Highly Accurate and Reproducible and More Sensitive for Variant Detection Than Exome Sequencing

    PubMed Central

    Bujakowska, Kinga M.; Sousa, Maria E.; Fonseca-Kelly, Zoë D.; Taub, Daniel G.; Janessian, Maria; Wang, Dan Yi; Au, Elizabeth D.; Sims, Katherine B.; Sweetser, David A.; Fulton, Anne B.; Liu, Qin; Wiggs, Janey L.; Gai, Xiaowu; Pierce, Eric A.

    2015-01-01

    Purpose Next-generation sequencing (NGS) based methods are being adopted broadly for genetic diagnostic testing, but the performance characteristics of these techniques have not been fully defined with regard to test accuracy and reproducibility. Methods We developed a targeted enrichment and NGS approach for genetic diagnostic testing of patients with inherited eye disorders, including inherited retinal degenerations, optic atrophy and glaucoma. In preparation for providing this Genetic Eye Disease (GEDi) test on a CLIA-certified basis, we performed experiments to measure the sensitivity, specificity, reproducibility as well as the clinical sensitivity of the test. Results The GEDi test is highly reproducible and accurate, with sensitivity and specificity for single nucleotide variant detection of 97.9% and 100%, respectively. The sensitivity for variant detection was notably better than the 88.3% achieved by whole exome sequencing (WES) using the same metrics, due to better coverage of targeted genes in the GEDi test compared to commercially available exome capture sets. Prospective testing of 192 patients with IRDs indicated that the clinical sensitivity of the GEDi test is high, with a diagnostic rate of 51%. Conclusion The data suggest that based on quantified performance metrics, selective targeted enrichment is preferable to WES for genetic diagnostic testing. PMID:25412400

  15. Many participants in inpatient rehabilitation can quantify their exercise dosage accurately: an observational study.

    PubMed

    Scrivener, Katharine; Sherrington, Catherine; Schurr, Karl; Treacy, Daniel

    2011-01-01

    Are inpatients undergoing rehabilitation who appear able to count exercises able to quantify accurately the amount of exercise they undertake? Observational study. Inpatients in an aged care rehabilitation unit and a neurological rehabilitation unit, who appeared able to count their exercises during a 1-2 min observation by their treating physiotherapist. Participants were observed for 30 min by an external observer while they exercised in the physiotherapy gymnasium. Both the participants and the observer counted exercise repetitions with a hand-held tally counter and the two tallies were compared. Of the 60 people admitted for aged care rehabilitation during the study period, 49 (82%) were judged by their treating therapist to be able to count their own exercise repetitions accurately. Of the 30 people admitted for neurological rehabilitation during the study period, 20 (67%) were judged by their treating therapist to be able to count their repetitions accurately. Of the 69 people judged to be accurate, 40 underwent observation while exercising. There was excellent agreement between these participants' counts of their exercise repetitions and the observers' counts, ICC (3,1) of 0.99 (95% CI 0.98 to 0.99). Eleven participants (28%) were in complete agreement with the observer. A further 19 participants (48%) varied from the observer by less than 10%. Therapists were able to identify a group of rehabilitation participants who were accurate in counting their exercise repetitions. Counting of exercise repetitions by therapist-selected patients is a valid means of quantifying exercise dosage during inpatient rehabilitation. Copyright © 2011 Australian Physiotherapy Association. Published by .. All rights reserved.

  16. Accuracy, repeatability, and reproducibility of Artemis very high-frequency digital ultrasound arc-scan lateral dimension measurements

    PubMed Central

    Reinstein, Dan Z.; Archer, Timothy J.; Silverman, Ronald H.; Coleman, D. Jackson

    2008-01-01

    Purpose To determine the accuracy, repeatability, and reproducibility of measurement of lateral dimensions using the Artemis (Ultralink LLC) very high-frequency (VHF) digital ultrasound (US) arc scanner. Setting London Vision Clinic, London, United Kingdom. Methods A test object was measured first with a micrometer and then with the Artemis arc scanner. Five sets of 10 consecutive B-scans of the test object were performed with the scanner. The test object was removed from the system between each scan set. One expert observer and one newly trained observer separately measured the lateral dimension of the test object. Two-factor analysis of variance was performed. The accuracy was calculated as the average bias of the scan set averages. The repeatability and reproducibility coefficients were calculated. The coefficient of variation (CV) was calculated for repeatability and reproducibility. Results The test object was measured to be 10.80 mm wide. The mean lateral dimension bias was 0.00 mm. The repeatability coefficient was 0.114 mm. The reproducibility coefficient was 0.026 mm. The repeatability CV was 0.38%, and the reproducibility CV was 0.09%. There was no statistically significant variation between observers (P = .0965). There was a statistically significant variation between scan sets (P = .0036) attributed to minor vertical changes in the alignment of the test object between consecutive scan sets. Conclusion The Artemis VHF digital US arc scanner obtained accurate, repeatable, and reproducible measurements of lateral dimensions of the size commonly found in the anterior segment. PMID:17081860

  17. NNLOPS accurate associated HW production

    NASA Astrophysics Data System (ADS)

    Astill, William; Bizon, Wojciech; Re, Emanuele; Zanderighi, Giulia

    2016-06-01

    We present a next-to-next-to-leading order accurate description of associated HW production consistently matched to a parton shower. The method is based on reweighting events obtained with the HW plus one jet NLO accurate calculation implemented in POWHEG, extended with the MiNLO procedure, to reproduce NNLO accurate Born distributions. Since the Born kinematics is more complex than the cases treated before, we use a parametrization of the Collins-Soper angles to reduce the number of variables required for the reweighting. We present phenomenological results at 13 TeV, with cuts suggested by the Higgs Cross section Working Group.

  18. Reproducible analyses of microbial food for advanced life support systems

    NASA Technical Reports Server (NTRS)

    Petersen, Gene R.

    1988-01-01

    The use of yeasts in controlled ecological life support systems (CELSS) for microbial food regeneration in space required the accurate and reproducible analysis of intracellular carbohydrate and protein levels. The reproducible analysis of glycogen was a key element in estimating overall content of edibles in candidate yeast strains. Typical analytical methods for estimating glycogen in Saccharomyces were not found to be entirely aplicable to other candidate strains. Rigorous cell lysis coupled with acid/base fractionation followed by specific enzymatic glycogen analyses were required to obtain accurate results in two strains of Candida. A profile of edible fractions of these strains was then determined. The suitability of yeasts as food sources in CELSS food production processes is discussed.

  19. The ability of different materials to reproduce accurate records of interocclusal relationships in the vertical dimension.

    PubMed

    Ghazal, M; Albashaireh, Z S; Kern, M

    2008-11-01

    Restorations made on incorrectly mounted casts might require considerable intra-oral adjustments to correct the occlusion or might even necessitate a remake of the restoration. The aim of this study was to evaluate interocclusal recording materials for their ability to reproduce accurate vertical interocclusal relationships after a storage time of 1 and 48 h, respectively. A custom-made apparatus was used to simulate the maxilla and mandible. Eight interocclusal records were made in each of the following groups: G1: Aluwax (aluminium wax), G2: Beauty Pink wax (hydrocarbon wax compound), G3: Futar D, G4: Futar D Fast, G5: Futar Scan (G3-G5: vinyl polysiloxane), G6: Ramitec (polyether). The vertical discrepancies were measured by an inductive displacement transducer connected to a carrier frequency amplifier after storage of the records for two periods of 1 and 48 h. Two-way anova was used for statistical analysis. The mean vertical discrepancies in mum (1/48 h) for G1 (31/35) and G2 (35/38) were statistically significantly higher than for the other groups G3 (8/10), G4 (11/12), G5 (6/8) and G6 (5/8) (P < or = 0.05). There were no statistically significant differences between the elastomers tested. The effect of storage on the vertical discrepancies was statistically significant (P < 0.001). Vinyl polysiloxane and polyether interocclusal records can be used to relate working casts during mounting procedures without significant vertical displacement of the casts.

  20. Investigation of random walks knee cartilage segmentation model using inter-observer reproducibility: Data from the osteoarthritis initiative.

    PubMed

    Hong-Seng, Gan; Sayuti, Khairil Amir; Karim, Ahmad Helmy Abdul

    2017-01-01

    Existing knee cartilage segmentation methods have reported several technical drawbacks. In essence, graph cuts remains highly susceptible to image noise despite extended research interest; active shape model is often constraint by the selection of training data while shortest path have demonstrated shortcut problem in the presence of weak boundary, which is a common problem in medical images. The aims of this study is to investigate the capability of random walks as knee cartilage segmentation method. Experts would scribble on knee cartilage image to initialize random walks segmentation. Then, reproducibility of the method is assessed against manual segmentation by using Dice Similarity Index. The evaluation consists of normal cartilage and diseased cartilage sections which is divided into whole and single cartilage categories. A total of 15 normal images and 10 osteoarthritic images were included. The results showed that random walks method has demonstrated high reproducibility in both normal cartilage (observer 1: 0.83±0.028 and observer 2: 0.82±0.026) and osteoarthritic cartilage (observer 1: 0.80±0.069 and observer 2: 0.83±0.029). Besides, results from both experts were found to be consistent with each other, suggesting the inter-observer variation is insignificant (Normal: P=0.21; Diseased: P=0.15). The proposed segmentation model has overcame technical problems reported by existing semi-automated techniques and demonstrated highly reproducible and consistent results against manual segmentation method.

  1. Evolvix BEST Names for semantic reproducibility across code2brain interfaces

    PubMed Central

    Scheuer, Katherine S.; Keel, Seth A.; Vyas, Vaibhav; Liblit, Ben; Hanlon, Bret; Ferris, Michael C.; Yin, John; Dutra, Inês; Pietsch, Anthony; Javid, Christine G.; Moog, Cecilia L.; Meyer, Jocelyn; Dresel, Jerdon; McLoone, Brian; Loberger, Sonya; Movaghar, Arezoo; Gilchrist‐Scott, Morgaine; Sabri, Yazeed; Sescleifer, Dave; Pereda‐Zorrilla, Ivan; Zietlow, Andrew; Smith, Rodrigo; Pietenpol, Samantha; Goldfinger, Jacob; Atzen, Sarah L.; Freiberg, Erika; Waters, Noah P.; Nusbaum, Claire; Nolan, Erik; Hotz, Alyssa; Kliman, Richard M.; Mentewab, Ayalew; Fregien, Nathan; Loewe, Martha

    2016-01-01

    Names in programming are vital for understanding the meaning of code and big data. We define code2brain (C2B) interfaces as maps in compilers and brains between meaning and naming syntax, which help to understand executable code. While working toward an Evolvix syntax for general‐purpose programming that makes accurate modeling easy for biologists, we observed how names affect C2B quality. To protect learning and coding investments, C2B interfaces require long‐term backward compatibility and semantic reproducibility (accurate reproduction of computational meaning from coder‐brains to reader‐brains by code alone). Semantic reproducibility is often assumed until confusing synonyms degrade modeling in biology to deciphering exercises. We highlight empirical naming priorities from diverse individuals and roles of names in different modes of computing to show how naming easily becomes impossibly difficult. We present the Evolvix BEST (Brief, Explicit, Summarizing, Technical) Names concept for reducing naming priority conflicts, test it on a real challenge by naming subfolders for the Project Organization Stabilizing Tool system, and provide naming questionnaires designed to facilitate C2B debugging by improving names used as keywords in a stabilizing programming language. Our experiences inspired us to develop Evolvix using a flipped programming language design approach with some unexpected features and BEST Names at its core. PMID:27918836

  2. Reproducible segmentation of white matter hyperintensities using a new statistical definition.

    PubMed

    Damangir, Soheil; Westman, Eric; Simmons, Andrew; Vrenken, Hugo; Wahlund, Lars-Olof; Spulber, Gabriela

    2017-06-01

    We present a method based on a proposed statistical definition of white matter hyperintensities (WMH), which can work with any combination of conventional magnetic resonance (MR) sequences without depending on manually delineated samples. T1-weighted, T2-weighted, FLAIR, and PD sequences acquired at 1.5 Tesla from 119 subjects from the Kings Health Partners-Dementia Case Register (healthy controls, mild cognitive impairment, Alzheimer's disease) were used. The segmentation was performed using a proposed definition for WMH based on the one-tailed Kolmogorov-Smirnov test. The presented method was verified, given all possible combinations of input sequences, against manual segmentations and a high similarity (Dice 0.85-0.91) was observed. Comparing segmentations with different input sequences to one another also yielded a high similarity (Dice 0.83-0.94) that exceeded intra-rater similarity (Dice 0.75-0.91). We compared the results with those of other available methods and showed that the segmentation based on the proposed definition has better accuracy and reproducibility in the test dataset used. Overall, the presented definition is shown to produce accurate results with higher reproducibility than manual delineation. This approach can be an alternative to other manual or automatic methods not only because of its accuracy, but also due to its good reproducibility.

  3. Accuracy of femoral templating in reproducing anatomical femoral offset in total hip replacement.

    PubMed

    Davies, H; Foote, J; Spencer, R F

    2007-01-01

    Restoration of hip biomechanics is a crucial component of successful total hip replacement. Preoperative templating is recommended to ensure that the size and orientation of implants is optimised. We studied how closely natural femoral offset could be reproduced using the manufacturers' templates for 10 femoral stems in common use in the UK. A series of 23 consecutive preoperative radiographs from patients who had undergone unilateral total hip replacement for unilateral osteoarthritis of the hip was employed. The change in offset between the templated position of the best-fitting template and the anatomical centre of the hip was measured. The templates were then ranked according to their ability to reproduce the normal anatomical offset. The most accurate was the CPS-Plus (Root Mean Square Error 2.0 mm) followed in rank order by: C stem (2.16), CPT (2.40), Exeter (3.23), Stanmore (3.28), Charnley (3.65), Corail (3.72), ABG II (4.30), Furlong HAC (5.08) and Furlong modular (7.14). A similar pattern of results was achieved when the standard error of variability of offset was analysed. We observed a wide variation in the ability of the femoral prosthesis templates to reproduce normal femoral offset. This variation was independent of the seniority of the observer. The templates of modern polished tapered stems with high modularity were best able to reproduce femoral offset. The current move towards digitisation of X-rays may offer manufacturers an opportunity to improve template designs in certain instances, and to develop appropriate computer software.

  4. Evolvix BEST Names for semantic reproducibility across code2brain interfaces.

    PubMed

    Loewe, Laurence; Scheuer, Katherine S; Keel, Seth A; Vyas, Vaibhav; Liblit, Ben; Hanlon, Bret; Ferris, Michael C; Yin, John; Dutra, Inês; Pietsch, Anthony; Javid, Christine G; Moog, Cecilia L; Meyer, Jocelyn; Dresel, Jerdon; McLoone, Brian; Loberger, Sonya; Movaghar, Arezoo; Gilchrist-Scott, Morgaine; Sabri, Yazeed; Sescleifer, Dave; Pereda-Zorrilla, Ivan; Zietlow, Andrew; Smith, Rodrigo; Pietenpol, Samantha; Goldfinger, Jacob; Atzen, Sarah L; Freiberg, Erika; Waters, Noah P; Nusbaum, Claire; Nolan, Erik; Hotz, Alyssa; Kliman, Richard M; Mentewab, Ayalew; Fregien, Nathan; Loewe, Martha

    2017-01-01

    Names in programming are vital for understanding the meaning of code and big data. We define code2brain (C2B) interfaces as maps in compilers and brains between meaning and naming syntax, which help to understand executable code. While working toward an Evolvix syntax for general-purpose programming that makes accurate modeling easy for biologists, we observed how names affect C2B quality. To protect learning and coding investments, C2B interfaces require long-term backward compatibility and semantic reproducibility (accurate reproduction of computational meaning from coder-brains to reader-brains by code alone). Semantic reproducibility is often assumed until confusing synonyms degrade modeling in biology to deciphering exercises. We highlight empirical naming priorities from diverse individuals and roles of names in different modes of computing to show how naming easily becomes impossibly difficult. We present the Evolvix BEST (Brief, Explicit, Summarizing, Technical) Names concept for reducing naming priority conflicts, test it on a real challenge by naming subfolders for the Project Organization Stabilizing Tool system, and provide naming questionnaires designed to facilitate C2B debugging by improving names used as keywords in a stabilizing programming language. Our experiences inspired us to develop Evolvix using a flipped programming language design approach with some unexpected features and BEST Names at its core. © 2016 The Authors. Annals of the New York Academy of Sciences published by Wiley Periodicals, Inc. on behalf of New York Academy of Sciences.

  5. Reproducibility of MRI-determined proton density fat fraction across two different MR scanner platforms.

    PubMed

    Kang, Geraldine H; Cruite, Irene; Shiehmorteza, Masoud; Wolfson, Tanya; Gamst, Anthony C; Hamilton, Gavin; Bydder, Mark; Middleton, Michael S; Sirlin, Claude B

    2011-10-01

    To evaluate magnetic resonance imaging (MRI)-determined proton density fat fraction (PDFF) reproducibility across two MR scanner platforms and, using MR spectroscopy (MRS)-determined PDFF as reference standard, to confirm MRI-determined PDFF estimation accuracy. This prospective, cross-sectional, crossover, observational pilot study was approved by an Institutional Review Board. Twenty-one subjects gave written informed consent and underwent liver MRI and MRS at both 1.5T (Siemens Symphony scanner) and 3T (GE Signa Excite HD scanner). MRI-determined PDFF was estimated using an axial 2D spoiled gradient-recalled echo sequence with low flip-angle to minimize T1 bias and six echo-times to permit correction of T2* and fat-water signal interference effects. MRS-determined PDFF was estimated using a stimulated-echo acquisition mode sequence with long repetition time to minimize T1 bias and five echo times to permit T2 correction. Interscanner reproducibility of MRI determined PDFF was assessed by correlation analysis; accuracy was assessed separately at each field strength by linear regression analysis using MRS-determined PDFF as reference standard. 1.5T and 3T MRI-determined PDFF estimates were highly correlated (r = 0.992). MRI-determined PDFF estimates were accurate at both 1.5T (regression slope/intercept = 0.958/-0.48) and 3T (slope/intercept = 1.020/0.925) against the MRS-determined PDFF reference. MRI-determined PDFF estimation is reproducible and, using MRS-determined PDFF as reference standard, accurate across two MR scanner platforms at 1.5T and 3T. Copyright © 2011 Wiley-Liss, Inc.

  6. Understanding reproducibility of human IVF traits to predict next IVF cycle outcome.

    PubMed

    Wu, Bin; Shi, Juanzi; Zhao, Wanqiu; Lu, Suzhen; Silva, Marta; Gelety, Timothy J

    2014-10-01

    Evaluating the failed IVF cycle often provides useful prognostic information. Before undergoing another attempt, patients experiencing an unsuccessful IVF cycle frequently request information about the probability of future success. Here, we introduced the concept of reproducibility and formulae to predict the next IVF cycle outcome. The experimental design was based on the retrospective review of IVF cycle data from 2006 to 2013 in two different IVF centers and statistical analysis. The reproducibility coefficients (r) of IVF traits including number of oocytes retrieved, oocyte maturity, fertilization, embryo quality and pregnancy were estimated using the interclass correlation coefficient between the repeated IVF cycle measurements for the same patient by variance component analysis. The formulae were designed to predict next IVF cycle outcome. The number of oocytes retrieved from patients and their fertilization rate had the highest reproducibility coefficients (r = 0.81 ~ 0.84), which indicated a very close correlation between the first retrieval cycle and subsequent IVF cycles. Oocyte maturity and number of top quality embryos had middle level reproducibility (r = 0.38 ~ 0.76) and pregnancy rate had a relative lower reproducibility (r = 0.23 ~ 0.27). Based on these parameters, the next outcome for these IVF traits might be accurately predicted by the designed formulae. The introduction of the concept of reproducibility to our human IVF program allows us to predict future IVF cycle outcomes. The traits of oocyte numbers retrieved, oocyte maturity, fertilization, and top quality embryos had higher or middle reproducibility, which provides a basis for accurate prediction of future IVF outcomes. Based on this prediction, physicians may counsel their patients or change patient's stimulation plans, and laboratory embryologists may improve their IVF techniques accordingly.

  7. Reproducible Earth observation analytics: challenges, ideas, and a study case on containerized land use change detection

    NASA Astrophysics Data System (ADS)

    Appel, Marius; Nüst, Daniel; Pebesma, Edzer

    2017-04-01

    Geoscientific analyses of Earth observation data typically involve a long path from data acquisition to scientific results and conclusions. Before starting the actual processing, scenes must be downloaded from the providers' platforms and the computing infrastructure needs to be prepared. The computing environment often requires specialized software, which in turn might have lots of dependencies. The software is often highly customized and provided without commercial support, which leads to rather ad-hoc systems and irreproducible results. To let other scientists reproduce the analyses, the full workspace including data, code, the computing environment, and documentation must be bundled and shared. Technologies such as virtualization or containerization allow for the creation of identical computing environments with relatively little effort. Challenges, however, arise when the volume of the data is too large, when computations are done in a cluster environment, or when complex software components such as databases are used. We discuss these challenges for the example of scalable Land use change detection on Landsat imagery. We present a reproducible implementation that runs R and the scalable data management and analytical system SciDB within a Docker container. Thanks to an explicit container recipe (the Dockerfile), this enables the all-in-one reproduction including the installation of software components, the ingestion of the data, and the execution of the analysis in a well-defined environment. We furthermore discuss possibilities how the implementation could be transferred to multi-container environments in order to support reproducibility on large cluster environments.

  8. How Accurately Can We Map SEP Observations Using L*?

    NASA Astrophysics Data System (ADS)

    Young, S. L.; Kress, B. T.

    2016-12-01

    In a dipole the cutoff rigidities at a given location are inversely proportional to L2. Smart and Shea, 1967 showed that this was approximately true at low altitudes using the McIlwain L parameter (Lm) in realistic magnetospheric models and provided heuristic evidence that it was also true at high altitudes. Later models developed by Smart and Shea and others (Ogliore et al., 2001, Neal et al., 2013, Selesnick et al., 2015) also use this relationship at low altitudes. Only the Smart and Shea model (Smart and Shea, 2006) uses this relationship to extrapolate to high altitudes, but they introduce a correction that yields a 1 MeV proton vertical cutoff at geosynchronous. Recent work mapped POES observations to the Van Allen Probes locations as a function of L* (Young et al., 2015). The comparison between mapped and observed was reasonably good, but this mapping was along L* and only attempted to account for differences in shielding between high and low latitude. No attempt was made to map across L* so the inverse squared relationship was not tested. These previous results suggest that L* may be useful for mapping flux observations between satellites at high altitudes. In this study we calculate cutoffs and L* shells in a Tsyganenko 2005 + IGRF magnetic field model to examine how accurately L* based mapping can be used in different regions of the magnetosphere.

  9. Accurate Modeling of Galaxy Clustering on Small Scales: Testing the Standard ΛCDM + Halo Model

    NASA Astrophysics Data System (ADS)

    Sinha, Manodeep; Berlind, Andreas A.; McBride, Cameron; Scoccimarro, Roman

    2015-01-01

    The large-scale distribution of galaxies can be explained fairly simply by assuming (i) a cosmological model, which determines the dark matter halo distribution, and (ii) a simple connection between galaxies and the halos they inhabit. This conceptually simple framework, called the halo model, has been remarkably successful at reproducing the clustering of galaxies on all scales, as observed in various galaxy redshift surveys. However, none of these previous studies have carefully modeled the systematics and thus truly tested the halo model in a statistically rigorous sense. We present a new accurate and fully numerical halo model framework and test it against clustering measurements from two luminosity samples of galaxies drawn from the SDSS DR7. We show that the simple ΛCDM cosmology + halo model is not able to simultaneously reproduce the galaxy projected correlation function and the group multiplicity function. In particular, the more luminous sample shows significant tension with theory. We discuss the implications of our findings and how this work paves the way for constraining galaxy formation by accurate simultaneous modeling of multiple galaxy clustering statistics.

  10. Reproducibility of preclinical animal research improves with heterogeneity of study samples

    PubMed Central

    Vogt, Lucile; Sena, Emily S.; Würbel, Hanno

    2018-01-01

    Single-laboratory studies conducted under highly standardized conditions are the gold standard in preclinical animal research. Using simulations based on 440 preclinical studies across 13 different interventions in animal models of stroke, myocardial infarction, and breast cancer, we compared the accuracy of effect size estimates between single-laboratory and multi-laboratory study designs. Single-laboratory studies generally failed to predict effect size accurately, and larger sample sizes rendered effect size estimates even less accurate. By contrast, multi-laboratory designs including as few as 2 to 4 laboratories increased coverage probability by up to 42 percentage points without a need for larger sample sizes. These findings demonstrate that within-study standardization is a major cause of poor reproducibility. More representative study samples are required to improve the external validity and reproducibility of preclinical animal research and to prevent wasting animals and resources for inconclusive research. PMID:29470495

  11. Assessing the reproducibility of discriminant function analyses

    PubMed Central

    Andrew, Rose L.; Albert, Arianne Y.K.; Renaut, Sebastien; Rennison, Diana J.; Bock, Dan G.

    2015-01-01

    Data are the foundation of empirical research, yet all too often the datasets underlying published papers are unavailable, incorrect, or poorly curated. This is a serious issue, because future researchers are then unable to validate published results or reuse data to explore new ideas and hypotheses. Even if data files are securely stored and accessible, they must also be accompanied by accurate labels and identifiers. To assess how often problems with metadata or data curation affect the reproducibility of published results, we attempted to reproduce Discriminant Function Analyses (DFAs) from the field of organismal biology. DFA is a commonly used statistical analysis that has changed little since its inception almost eight decades ago, and therefore provides an opportunity to test reproducibility among datasets of varying ages. Out of 100 papers we initially surveyed, fourteen were excluded because they did not present the common types of quantitative result from their DFA or gave insufficient details of their DFA. Of the remaining 86 datasets, there were 15 cases for which we were unable to confidently relate the dataset we received to the one used in the published analysis. The reasons ranged from incomprehensible or absent variable labels, the DFA being performed on an unspecified subset of the data, or the dataset we received being incomplete. We focused on reproducing three common summary statistics from DFAs: the percent variance explained, the percentage correctly assigned and the largest discriminant function coefficient. The reproducibility of the first two was fairly high (20 of 26, and 44 of 60 datasets, respectively), whereas our success rate with the discriminant function coefficients was lower (15 of 26 datasets). When considering all three summary statistics, we were able to completely reproduce 46 (65%) of 71 datasets. While our results show that a majority of studies are reproducible, they highlight the fact that many studies still are not the

  12. Reproducibility of MRI-Determined Proton Density Fat Fraction Across Two Different MR Scanner Platforms

    PubMed Central

    Kang, Geraldine H.; Cruite, Irene; Shiehmorteza, Masoud; Wolfson, Tanya; Gamst, Anthony C.; Hamilton, Gavin; Bydder, Mark; Middleton, Michael S.; Sirlin, Claude B.

    2016-01-01

    Purpose To evaluate magnetic resonance imaging (MRI)-determined proton density fat fraction (PDFF) reproducibility across two MR scanner platforms and, using MR spectroscopy (MRS)-determined PDFF as reference standard, to confirm MRI-determined PDFF estimation accuracy. Materials and Methods This prospective, cross-sectional, crossover, observational pilot study was approved by an Institutional Review Board. Twenty-one subjects gave written informed consent and underwent liver MRI and MRS at both 1.5T (Siemens Symphony scanner) and 3T (GE Signa Excite HD scanner). MRI-determined PDFF was estimated using an axial 2D spoiled gradient-recalled echo sequence with low flip-angle to minimize T1 bias and six echo-times to permit correction of T2* and fat-water signal interference effects. MRS-determined PDFF was estimated using a stimulated-echo acquisition mode sequence with long repetition time to minimize T1 bias and five echo times to permit T2 correction. Interscanner reproducibility of MRI determined PDFF was assessed by correlation analysis; accuracy was assessed separately at each field strength by linear regression analysis using MRS-determined PDFF as reference standard. Results 1.5T and 3T MRI-determined PDFF estimates were highly correlated (r = 0.992). MRI-determined PDFF estimates were accurate at both 1.5T (regression slope/intercept = 0.958/−0.48) and 3T (slope/intercept = 1.020/0.925) against the MRS-determined PDFF reference. Conclusion MRI-determined PDFF estimation is reproducible and, using MRS-determined PDFF as reference standard, accurate across two MR scanner platforms at 1.5T and 3T. PMID:21769986

  13. Shear wave elastography for breast masses is highly reproducible.

    PubMed

    Cosgrove, David O; Berg, Wendie A; Doré, Caroline J; Skyba, Danny M; Henry, Jean-Pierre; Gay, Joel; Cohen-Bacrie, Claude

    2012-05-01

    To evaluate intra- and interobserver reproducibility of shear wave elastography (SWE) for breast masses. For intraobserver reproducibility, each observer obtained three consecutive SWE images of 758 masses that were visible on ultrasound. 144 (19%) were malignant. Weighted kappa was used to assess the agreement of qualitative elastographic features; the reliability of quantitative measurements was assessed by intraclass correlation coefficients (ICC). For the interobserver reproducibility, a blinded observer reviewed images and agreement on features was determined. Mean age was 50 years; mean mass size was 13 mm. Qualitatively, SWE images were at least reasonably similar for 666/758 (87.9%). Intraclass correlation for SWE diameter, area and perimeter was almost perfect (ICC ≥ 0.94). Intraobserver reliability for maximum and mean elasticity was almost perfect (ICC = 0.84 and 0.87) and was substantial for the ratio of mass-to-fat elasticity (ICC = 0.77). Interobserver agreement was moderate for SWE homogeneity (κ = 0.57), substantial for qualitative colour assessment of maximum elasticity (κ = 0.66), fair for SWE shape (κ = 0.40), fair for B-mode mass margins (κ = 0.38), and moderate for B-mode mass shape (κ = 0.58), orientation (κ = 0.53) and BI-RADS assessment (κ = 0.59). SWE is highly reproducible for assessing elastographic features of breast masses within and across observers. SWE interpretation is at least as consistent as that of BI-RADS ultrasound B-mode features. • Shear wave ultrasound elastography can measure the stiffness of breast tissue • It provides a qualitatively and quantitatively interpretable colour-coded map of tissue stiffness • Intraobserver reproducibility of SWE is almost perfect while intraobserver reproducibility of SWE proved to be moderate to substantial • The most reproducible SWE features between observers were SWE image homogeneity and maximum elasticity.

  14. Urinary incontinence self-report questions: reproducibility and agreement with bladder diary.

    PubMed

    Bradley, Catherine S; Brown, Jeanette S; Van Den Eeden, Stephen K; Schembri, Michael; Ragins, Arona; Thom, David H

    2011-12-01

    This study aims to measure self-report urinary incontinence questions' reproducibility and agreement with bladder diary. Data were analyzed from the Reproductive Risk of Incontinence Study at Kaiser. Participating women reporting at least weekly incontinence completed self-report incontinence questions and a 7-day bladder diary. Self-report question reproducibility was assessed and agreement between self-reported and diary-recorded voiding and incontinence frequency was measured. Test characteristics and area under the curve were calculated for self-reported incontinence types using diary as the gold standard. Five hundred ninety-one women were included and 425 completed a diary. The self-report questions had moderate reproducibility and self-reported and diary-recorded incontinence and voiding frequencies had moderate to good agreement. Self-reported incontinence types identified stress and urgency incontinence more accurately than mixed incontinence. Self-report incontinence questions have moderate reproducibility and agreement with diary, and considering their minimal burden, are acceptable research tools in epidemiologic studies.

  15. Achieving perceptually-accurate aural telepresence

    NASA Astrophysics Data System (ADS)

    Henderson, Paul D.

    Immersive multimedia requires not only realistic visual imagery but also a perceptually-accurate aural experience. A sound field may be presented simultaneously to a listener via a loudspeaker rendering system using the direct sound from acoustic sources as well as a simulation or "auralization" of room acoustics. Beginning with classical Wave-Field Synthesis (WFS), improvements are made to correct for asymmetries in loudspeaker array geometry. Presented is a new Spatially-Equalized WFS (SE-WFS) technique to maintain the energy-time balance of a simulated room by equalizing the reproduced spectrum at the listener for a distribution of possible source angles. Each reproduced source or reflection is filtered according to its incidence angle to the listener. An SE-WFS loudspeaker array of arbitrary geometry reproduces the sound field of a room with correct spectral and temporal balance, compared with classically-processed WFS systems. Localization accuracy of human listeners in SE-WFS sound fields is quantified by psychoacoustical testing. At a loudspeaker spacing of 0.17 m (equivalent to an aliasing cutoff frequency of 1 kHz), SE-WFS exhibits a localization blur of 3 degrees, nearly equal to real point sources. Increasing the loudspeaker spacing to 0.68 m (for a cutoff frequency of 170 Hz) results in a blur of less than 5 degrees. In contrast, stereophonic reproduction is less accurate with a blur of 7 degrees. The ventriloquist effect is psychometrically investigated to determine the effect of an intentional directional incongruence between audio and video stimuli. Subjects were presented with prerecorded full-spectrum speech and motion video of a talker's head as well as broadband noise bursts with a static image. The video image was displaced from the audio stimulus in azimuth by varying amounts, and the perceived auditory location measured. A strong bias was detectable for small angular discrepancies between audio and video stimuli for separations of less than 8

  16. Reproducibility and Accuracy of Quantitative Myocardial Blood Flow Using 82Rb-PET: Comparison with 13N-Ammonia

    PubMed Central

    Fakhri, Georges El

    2011-01-01

    =0.843) and stress (r2=0.761). The Bland-Altman plots show no significant presence of proportional error at rest or stress, nor a dependence of the variations on the amplitude of the myocardial blood flow at rest or stress. A small systematic overestimation of 13N-ammonia MBF was observed with 82Rb at rest (0.129 ml/g/min) and the opposite, i.e., underestimation, at stress (0.22 ml/g/min). Conclusions Our results show that absolute quantitation of myocardial bloof flow is reproducible and accurate with 82Rb dynamic cardiac PET as compared to 13N-ammonia. The reproducibility of the quantitation approach itself was very good as well as inter-observer reproducibility. PMID:19525467

  17. Do detailed simulations with size-resolved microphysics reproduce basic features of observed cirrus ice size distributions?

    NASA Astrophysics Data System (ADS)

    Fridlind, A. M.; Atlas, R.; van Diedenhoven, B.; Ackerman, A. S.; Rind, D. H.; Harrington, J. Y.; McFarquhar, G. M.; Um, J.; Jackson, R.; Lawson, P.

    2017-12-01

    It has recently been suggested that seeding synoptic cirrus could have desirable characteristics as a geoengineering approach, but surprisingly large uncertainties remain in the fundamental parameters that govern cirrus properties, such as mass accommodation coefficient, ice crystal physical properties, aggregation efficiency, and ice nucleation rate from typical upper tropospheric aerosol. Only one synoptic cirrus model intercomparison study has been published to date, and studies that compare the shapes of observed and simulated ice size distributions remain sparse. Here we amend a recent model intercomparison setup using observations during two 2010 SPARTICUS campaign flights. We take a quasi-Lagrangian column approach and introduce an ensemble of gravity wave scenarios derived from collocated Doppler cloud radar retrievals of vertical wind speed. We use ice crystal properties derived from in situ cloud particle images, for the first time allowing smoothly varying and internally consistent treatments of nonspherical ice capacitance, fall speed, gravitational collection, and optical properties over all particle sizes in our model. We test two new parameterizations for mass accommodation coefficient as a function of size, temperature and water vapor supersaturation, and several ice nucleation scenarios. Comparison of results with in situ ice particle size distribution data, corrected using state-of-the-art algorithms to remove shattering artifacts, indicate that poorly constrained uncertainties in the number concentration of crystals smaller than 100 µm in maximum dimension still prohibit distinguishing which parameter combinations are more realistic. When projected area is concentrated at such sizes, the only parameter combination that reproduces observed size distribution properties uses a fixed mass accommodation coefficient of 0.01, on the low end of recently reported values. No simulations reproduce the observed abundance of such small crystals when the

  18. Wringing the last drop of optically stimulated luminescence response for accurate dating of glacial sediments

    NASA Astrophysics Data System (ADS)

    Medialdea, Alicia; Bateman, Mark D.; Evans, David J.; Roberts, David H.; Chiverrell, Richard C.; Clark, Chris D.

    2017-04-01

    BRITICE-CHRONO is a NERC-funded consortium project of more than 40 researchers aiming to establish the retreat patterns of the last British and Irish Ice Sheet. For this purpose, optically stimulated luminescence (OSL) dating, among other dating techniques, has been used in order to establish accurate chronology. More than 150 samples from glacial environments have been dated and provide key information for modelling of the ice retreat. Nevertheless, luminescence dating of glacial sediments has proven to be challenging: first, glacial sediments were often affected by incomplete bleaching and secondly, quartz grains within the sediments sampled were often characterized by complex luminescence behaviour; characterized by dim signal and low reproducibility. Specific statistical approaches have been used to over come the former to enable the estimated ages to be based on grain populations most likely to have been well bleached. This latest work presents how issues surrounding complex luminescence behaviour were over-come in order to obtain accurate OSL ages. This study has been performed on two samples of bedded sand originated on an ice walled lake plain, in Lincolnshire, UK. Quartz extracts from each sample were artificially bleached and irradiated to known doses. Dose recovery tests have been carried out under different conditions to study the effect of: preheat temperature, thermal quenching, contribution of slow components, hot bleach after a measuring cycles and IR stimulation. Measurements have been performed on different luminescence readers to study the possible contribution of instrument reproducibility. These have shown that a great variability can be observed not only among the studied samples but also within a specific site and even a specific sample. In order to determine an accurate chronology and realistic uncertainties to the estimated ages, this variability must be taken into account. Tight acceptance criteria to measured doses from natural, not

  19. Reproducibility of techniques using Archimedes' principle in measuring cancellous bone volume.

    PubMed

    Zou, L; Bloebaum, R D; Bachus, K N

    1997-01-01

    Researchers have been interested in developing techniques to accurately and reproducibly measure the volume fraction of cancellous bone. Historically bone researchers have used Archimedes' principle with water to measure the volume fraction of cancellous bone. Preliminary results in our lab suggested that the calibrated water technique did not provide reproducible results. Because of this difficulty, it was decided to compare the conventional water method to a water with surfactant and a helium method using a micropycnometer. The water/surfactant and the helium methods were attempts to improve the fluid penetration into the small voids present in the cancellous bone structure. In order to compare the reproducibility of the new methods with the conventional water method, 16 cancellous bone specimens were obtained from femoral condyles of human and greyhound dog femora. The volume fraction measurements on each specimen were repeated three times with all three techniques. The results showed that the helium displacement method was more than an order of magnitudes more reproducible than the two other water methods (p < 0.05). Statistical analysis also showed that the conventional water method produced the lowest reproducibility (p < 0.05). The data from this study indicate that the helium displacement technique is a very useful, rapid and reproducible tool for quantitatively characterizing anisotropic porous tissue structures such as cancellous bone.

  20. Musical training generalises across modalities and reveals efficient and adaptive mechanisms for reproducing temporal intervals.

    PubMed

    Aagten-Murphy, David; Cappagli, Giulia; Burr, David

    2014-03-01

    Expert musicians are able to time their actions accurately and consistently during a musical performance. We investigated how musical expertise influences the ability to reproduce auditory intervals and how this generalises across different techniques and sensory modalities. We first compared various reproduction strategies and interval length, to examine the effects in general and to optimise experimental conditions for testing the effect of music, and found that the effects were robust and consistent across different paradigms. Focussing on a 'ready-set-go' paradigm subjects reproduced time intervals drawn from distributions varying in total length (176, 352 or 704 ms) or in the number of discrete intervals within the total length (3, 5, 11 or 21 discrete intervals). Overall, Musicians performed more veridical than Non-Musicians, and all subjects reproduced auditory-defined intervals more accurately than visually-defined intervals. However, Non-Musicians, particularly with visual stimuli, consistently exhibited a substantial and systematic regression towards the mean interval. When subjects judged intervals from distributions of longer total length they tended to regress more towards the mean, while the ability to discriminate between discrete intervals within the distribution had little influence on subject error. These results are consistent with a Bayesian model that minimizes reproduction errors by incorporating a central tendency prior weighted by the subject's own temporal precision relative to the current distribution of intervals. Finally a strong correlation was observed between all durations of formal musical training and total reproduction errors in both modalities (accounting for 30% of the variance). Taken together these results demonstrate that formal musical training improves temporal reproduction, and that this improvement transfers from audition to vision. They further demonstrate the flexibility of sensorimotor mechanisms in adapting to

  1. Optimal Design for Placements of Tsunami Observing Systems to Accurately Characterize the Inducing Earthquake

    NASA Astrophysics Data System (ADS)

    Mulia, Iyan E.; Gusman, Aditya Riadi; Satake, Kenji

    2017-12-01

    Recently, there are numerous tsunami observation networks deployed in several major tsunamigenic regions. However, guidance on where to optimally place the measurement devices is limited. This study presents a methodological approach to select strategic observation locations for the purpose of tsunami source characterizations, particularly in terms of the fault slip distribution. Initially, we identify favorable locations and determine the initial number of observations. These locations are selected based on extrema of empirical orthogonal function (EOF) spatial modes. To further improve the accuracy, we apply an optimization algorithm called a mesh adaptive direct search to remove redundant measurement locations from the EOF-generated points. We test the proposed approach using multiple hypothetical tsunami sources around the Nankai Trough, Japan. The results suggest that the optimized observation points can produce more accurate fault slip estimates with considerably less number of observations compared to the existing tsunami observation networks.

  2. On the Possibility to Combine the Order Effect with Sequential Reproducibility for Quantum Measurements

    NASA Astrophysics Data System (ADS)

    Basieva, Irina; Khrennikov, Andrei

    2015-10-01

    In this paper we study the problem of a possibility to use quantum observables to describe a possible combination of the order effect with sequential reproducibility for quantum measurements. By the order effect we mean a dependence of probability distributions (of measurement results) on the order of measurements. We consider two types of the sequential reproducibility: adjacent reproducibility (A-A) (the standard perfect repeatability) and separated reproducibility(A-B-A). The first one is reproducibility with probability 1 of a result of measurement of some observable A measured twice, one A measurement after the other. The second one, A-B-A, is reproducibility with probability 1 of a result of A measurement when another quantum observable B is measured between two A's. Heuristically, it is clear that the second type of reproducibility is complementary to the order effect. We show that, surprisingly, this may not be the case. The order effect can coexist with a separated reproducibility as well as adjacent reproducibility for both observables A and B. However, the additional constraint in the form of separated reproducibility of the B-A-B type makes this coexistence impossible. The problem under consideration was motivated by attempts to apply the quantum formalism outside of physics, especially, in cognitive psychology and psychophysics. However, it is also important for foundations of quantum physics as a part of the problem about the structure of sequential quantum measurements.

  3. A Simple and Accurate Method for Measuring Enzyme Activity.

    ERIC Educational Resources Information Center

    Yip, Din-Yan

    1997-01-01

    Presents methods commonly used for investigating enzyme activity using catalase and presents a new method for measuring catalase activity that is more reliable and accurate. Provides results that are readily reproduced and quantified. Can also be used for investigations of enzyme properties such as the effects of temperature, pH, inhibitors,…

  4. Using Copula Distributions to Support More Accurate Imaging-Based Diagnostic Classifiers for Neuropsychiatric Disorders

    PubMed Central

    Bansal, Ravi; Hao, Xuejun; Liu, Jun; Peterson, Bradley S.

    2014-01-01

    Many investigators have tried to apply machine learning techniques to magnetic resonance images (MRIs) of the brain in order to diagnose neuropsychiatric disorders. Usually the number of brain imaging measures (such as measures of cortical thickness and measures of local surface morphology) derived from the MRIs (i.e., their dimensionality) has been large (e.g. >10) relative to the number of participants who provide the MRI data (<100). Sparse data in a high dimensional space increases the variability of the classification rules that machine learning algorithms generate, thereby limiting the validity, reproducibility, and generalizability of those classifiers. The accuracy and stability of the classifiers can improve significantly if the multivariate distributions of the imaging measures can be estimated accurately. To accurately estimate the multivariate distributions using sparse data, we propose to estimate first the univariate distributions of imaging data and then combine them using a Copula to generate more accurate estimates of their multivariate distributions. We then sample the estimated Copula distributions to generate dense sets of imaging measures and use those measures to train classifiers. We hypothesize that the dense sets of brain imaging measures will generate classifiers that are stable to variations in brain imaging measures, thereby improving the reproducibility, validity, and generalizability of diagnostic classification algorithms in imaging datasets from clinical populations. In our experiments, we used both computer-generated and real-world brain imaging datasets to assess the accuracy of multivariate Copula distributions in estimating the corresponding multivariate distributions of real-world imaging data. Our experiments showed that diagnostic classifiers generated using imaging measures sampled from the Copula were significantly more accurate and more reproducible than were the classifiers generated using either the real-world imaging

  5. Cycle accurate and cycle reproducible memory for an FPGA based hardware accelerator

    DOEpatents

    Asaad, Sameh W.; Kapur, Mohit

    2016-03-15

    A method, system and computer program product are disclosed for using a Field Programmable Gate Array (FPGA) to simulate operations of a device under test (DUT). The DUT includes a device memory having a number of input ports, and the FPGA is associated with a target memory having a second number of input ports, the second number being less than the first number. In one embodiment, a given set of inputs is applied to the device memory at a frequency Fd and in a defined cycle of time, and the given set of inputs is applied to the target memory at a frequency Ft. Ft is greater than Fd and cycle accuracy is maintained between the device memory and the target memory. In an embodiment, a cycle accurate model of the DUT memory is created by separating the DUT memory interface protocol from the target memory storage array.

  6. Enhancing reproducibility: Failures from Reproducibility Initiatives underline core challenges.

    PubMed

    Mullane, Kevin; Williams, Michael

    2017-08-15

    Efforts to address reproducibility concerns in biomedical research include: initiatives to improve journal publication standards and peer review; increased attention to publishing methodological details that enable experiments to be reconstructed; guidelines on standards for study design, implementation, analysis and execution; meta-analyses of multiple studies within a field to synthesize a common conclusion and; the formation of consortia to adopt uniform protocols and internally reproduce data. Another approach to addressing reproducibility are Reproducibility Initiatives (RIs), well-intended, high-profile, systematically peer-vetted initiatives that are intended to replace the traditional process of scientific self-correction. Outcomes from the RIs reported to date have questioned the usefulness of this approach, particularly when the RI outcome differs from other independent self-correction studies that have reproduced the original finding. As a failed RI attempt is a single outcome distinct from the original study, it cannot provide any definitive conclusions necessitating additional studies that the RI approach has neither the ability nor intent of conducting making it a questionable replacement for self-correction. A failed RI attempt also has the potential to damage the reputation of the author of the original finding. Reproduction is frequently confused with replication, an issue that is more than semantic with the former denoting "similarity" and the latter an "exact copy" - an impossible outcome in research because of known and unknown technical, environmental and motivational differences between the original and reproduction studies. To date, the RI framework has negatively impacted efforts to improve reproducibility, confounding attempts to determine whether a research finding is real. Copyright © 2017 Elsevier Inc. All rights reserved.

  7. Reproducibility in science.

    PubMed

    Yaffe, Michael B

    2015-04-07

    The issue of reproducibility and reliability in science has come to the forefront in light of several high-profile studies that could not be reproduced. Whereas some errors in reliability can be attributed to the application of new techniques that have unappreciated caveats, some problems with reproducibility lie in the climate of intense pressure for funding and to publish faced by many researchers. Copyright © 2015, American Association for the Advancement of Science.

  8. Accuracy and Reproducibility of Adipose Tissue Measurements in Young Infants by Whole Body Magnetic Resonance Imaging

    PubMed Central

    Bauer, Jan Stefan; Noël, Peter Benjamin; Vollhardt, Christiane; Much, Daniela; Degirmenci, Saliha; Brunner, Stefanie; Rummeny, Ernst Josef; Hauner, Hans

    2015-01-01

    Purpose MR might be well suited to obtain reproducible and accurate measures of fat tissues in infants. This study evaluates MR-measurements of adipose tissue in young infants in vitro and in vivo. Material and Methods MR images of ten phantoms simulating subcutaneous fat of an infant’s torso were obtained using a 1.5T MR scanner with and without simulated breathing. Scans consisted of a cartesian water-suppression turbo spin echo (wsTSE) sequence, and a PROPELLER wsTSE sequence. Fat volume was quantified directly and by MR imaging using k-means clustering and threshold-based segmentation procedures to calculate accuracy in vitro. Whole body MR was obtained in sleeping young infants (average age 67±30 days). This study was approved by the local review board. All parents gave written informed consent. To obtain reproducibility in vivo, cartesian and PROPELLER wsTSE sequences were repeated in seven and four young infants, respectively. Overall, 21 repetitions were performed for the cartesian sequence and 13 repetitions for the PROPELLER sequence. Results In vitro accuracy errors depended on the chosen segmentation procedure, ranging from 5.4% to 76%, while the sequence showed no significant influence. Artificial breathing increased the minimal accuracy error to 9.1%. In vivo reproducibility errors for total fat volume of the sleeping infants ranged from 2.6% to 3.4%. Neither segmentation nor sequence significantly influenced reproducibility. Conclusion With both cartesian and PROPELLER sequences an accurate and reproducible measure of body fat was achieved. Adequate segmentation was mandatory for high accuracy. PMID:25706876

  9. Accuracy and reproducibility of adipose tissue measurements in young infants by whole body magnetic resonance imaging.

    PubMed

    Bauer, Jan Stefan; Noël, Peter Benjamin; Vollhardt, Christiane; Much, Daniela; Degirmenci, Saliha; Brunner, Stefanie; Rummeny, Ernst Josef; Hauner, Hans

    2015-01-01

    MR might be well suited to obtain reproducible and accurate measures of fat tissues in infants. This study evaluates MR-measurements of adipose tissue in young infants in vitro and in vivo. MR images of ten phantoms simulating subcutaneous fat of an infant's torso were obtained using a 1.5T MR scanner with and without simulated breathing. Scans consisted of a cartesian water-suppression turbo spin echo (wsTSE) sequence, and a PROPELLER wsTSE sequence. Fat volume was quantified directly and by MR imaging using k-means clustering and threshold-based segmentation procedures to calculate accuracy in vitro. Whole body MR was obtained in sleeping young infants (average age 67±30 days). This study was approved by the local review board. All parents gave written informed consent. To obtain reproducibility in vivo, cartesian and PROPELLER wsTSE sequences were repeated in seven and four young infants, respectively. Overall, 21 repetitions were performed for the cartesian sequence and 13 repetitions for the PROPELLER sequence. In vitro accuracy errors depended on the chosen segmentation procedure, ranging from 5.4% to 76%, while the sequence showed no significant influence. Artificial breathing increased the minimal accuracy error to 9.1%. In vivo reproducibility errors for total fat volume of the sleeping infants ranged from 2.6% to 3.4%. Neither segmentation nor sequence significantly influenced reproducibility. With both cartesian and PROPELLER sequences an accurate and reproducible measure of body fat was achieved. Adequate segmentation was mandatory for high accuracy.

  10. The Need for Reproducibility

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Robey, Robert W.

    2016-06-27

    The purpose of this presentation is to consider issues of reproducibility, specifically it determines whether bitwise reproducible computation is possible, if computational research in DOE improves its publication process, and if reproducible results can be achieved apart from the peer review process?

  11. Quantized correlation coefficient for measuring reproducibility of ChIP-chip data.

    PubMed

    Peng, Shouyong; Kuroda, Mitzi I; Park, Peter J

    2010-07-27

    Chromatin immunoprecipitation followed by microarray hybridization (ChIP-chip) is used to study protein-DNA interactions and histone modifications on a genome-scale. To ensure data quality, these experiments are usually performed in replicates, and a correlation coefficient between replicates is used often to assess reproducibility. However, the correlation coefficient can be misleading because it is affected not only by the reproducibility of the signal but also by the amount of binding signal present in the data. We develop the Quantized correlation coefficient (QCC) that is much less dependent on the amount of signal. This involves discretization of data into set of quantiles (quantization), a merging procedure to group the background probes, and recalculation of the Pearson correlation coefficient. This procedure reduces the influence of the background noise on the statistic, which then properly focuses more on the reproducibility of the signal. The performance of this procedure is tested in both simulated and real ChIP-chip data. For replicates with different levels of enrichment over background and coverage, we find that QCC reflects reproducibility more accurately and is more robust than the standard Pearson or Spearman correlation coefficients. The quantization and the merging procedure can also suggest a proper quantile threshold for separating signal from background for further analysis. To measure reproducibility of ChIP-chip data correctly, a correlation coefficient that is robust to the amount of signal present should be used. QCC is one such measure. The QCC statistic can also be applied in a variety of other contexts for measuring reproducibility, including analysis of array CGH data for DNA copy number and gene expression data.

  12. Accurate Modelling of Surface Currents and Internal Tides in a Semi-enclosed Coastal Sea

    NASA Astrophysics Data System (ADS)

    Allen, S. E.; Soontiens, N. K.; Dunn, M. B. H.; Liu, J.; Olson, E.; Halverson, M. J.; Pawlowicz, R.

    2016-02-01

    The Strait of Georgia is a deep (400 m), strongly stratified, semi-enclosed coastal sea on the west coast of North America. We have configured a baroclinic model of the Strait of Georgia and surrounding coastal waters using the NEMO ocean community model. We run daily nowcasts and forecasts and publish our sea-surface results (including storm surge warnings) to the web (salishsea.eos.ubc.ca/storm-surge). Tides in the Strait of Georgia are mixed and large. The baroclinic model and previous barotropic models accurately represent tidal sea-level variations and depth mean currents. The baroclinic model reproduces accurately the diurnal but not the semi-diurnal baroclinic tidal currents. In the Southern Strait of Georgia, strong internal tidal currents at the semi-diurnal frequency are observed. Strong semi-diurnal tides are also produced in the model, but are almost 180 degrees out of phase with the observations. In the model, in the surface, the barotropic and baroclinic tides reinforce, whereas the observations show that at the surface the baroclinic tides oppose the barotropic. As such the surface currents are very poorly modelled. Here we will present evidence of the internal tidal field from observations. We will discuss the generation regions of the tides, the necessary modifications to the model required to correct the phase, the resulting baroclinic tides and the improvements in the surface currents.

  13. Inter-observer variability in fetal biometric measurements.

    PubMed

    Kilani, Rami; Aleyadeh, Wesam; Atieleh, Luay Abu; Al Suleimat, Abdul Mane; Khadra, Maysa; Hawamdeh, Hassan M

    2018-02-01

    To evaluate inter-observer variability and reproducibility of ultrasound measurements for fetal biometric parameters. A prospective cohort study was implemented in two tertiary care hospitals in Amman, Jordan; Prince Hamza Hospital and Albashir Hospital. 192 women with a singleton pregnancy at a gestational age of 18-36 weeks were the participants in the study. Transabdominal scans for fetal biometric parameter measurement were performed on study participants from the period of November 2014 to March 2015. Women who agreed to participate in the study were administered two ultrasound scans for head circumference, abdominal circumference and femur length. The correlation coefficient was calculated. Bland-Altman plots were used to analyze the degree of measurement agreement between observers. Limits of agreement ± 2 SD for the differences in fetal biometry measurements in proportions of the mean of the measurements were derived. Main outcome measures examine the reproducibility of fetal biometric measurements by different observers. High inter-observer inter-class correlation coefficient (ICC) was found for femur length (0.990) and abdominal circumference (0.996) where Bland-Altman plots showed high degrees of agreement. The highest degrees of agreement were noted in the measurement of abdominal circumference followed by head circumference. The lowest degree of agreement was found for femur length measurement. We used a paired-sample t-test and found that the mean difference between duplicate measurements was not significant (P > 0.05). Biometric fetal parameter measurements may be reproducible by different operators in the clinical setting with similar results. Fetal head circumference, abdominal circumference and femur length were highly reproducible. Large organized studies are needed to ensure accurate fetal measurements due to the important clinical implications of inaccurate measurements. Copyright © 2018. Published by Elsevier B.V.

  14. NetBenchmark: a bioconductor package for reproducible benchmarks of gene regulatory network inference.

    PubMed

    Bellot, Pau; Olsen, Catharina; Salembier, Philippe; Oliveras-Vergés, Albert; Meyer, Patrick E

    2015-09-29

    In the last decade, a great number of methods for reconstructing gene regulatory networks from expression data have been proposed. However, very few tools and datasets allow to evaluate accurately and reproducibly those methods. Hence, we propose here a new tool, able to perform a systematic, yet fully reproducible, evaluation of transcriptional network inference methods. Our open-source and freely available Bioconductor package aggregates a large set of tools to assess the robustness of network inference algorithms against different simulators, topologies, sample sizes and noise intensities. The benchmarking framework that uses various datasets highlights the specialization of some methods toward network types and data. As a result, it is possible to identify the techniques that have broad overall performances.

  15. Quantifying reproducibility in computational biology: the case of the tuberculosis drugome.

    PubMed

    Garijo, Daniel; Kinnings, Sarah; Xie, Li; Xie, Lei; Zhang, Yinliang; Bourne, Philip E; Gil, Yolanda

    2013-01-01

    How easy is it to reproduce the results found in a typical computational biology paper? Either through experience or intuition the reader will already know that the answer is with difficulty or not at all. In this paper we attempt to quantify this difficulty by reproducing a previously published paper for different classes of users (ranging from users with little expertise to domain experts) and suggest ways in which the situation might be improved. Quantification is achieved by estimating the time required to reproduce each of the steps in the method described in the original paper and make them part of an explicit workflow that reproduces the original results. Reproducing the method took several months of effort, and required using new versions and new software that posed challenges to reconstructing and validating the results. The quantification leads to "reproducibility maps" that reveal that novice researchers would only be able to reproduce a few of the steps in the method, and that only expert researchers with advance knowledge of the domain would be able to reproduce the method in its entirety. The workflow itself is published as an online resource together with supporting software and data. The paper concludes with a brief discussion of the complexities of requiring reproducibility in terms of cost versus benefit, and a desiderata with our observations and guidelines for improving reproducibility. This has implications not only in reproducing the work of others from published papers, but reproducing work from one's own laboratory.

  16. Generating clock signals for a cycle accurate, cycle reproducible FPGA based hardware accelerator

    DOEpatents

    Asaad, Sameth W.; Kapur, Mohit

    2016-01-05

    A method, system and computer program product are disclosed for generating clock signals for a cycle accurate FPGA based hardware accelerator used to simulate operations of a device-under-test (DUT). In one embodiment, the DUT includes multiple device clocks generating multiple device clock signals at multiple frequencies and at a defined frequency ratio; and the FPG hardware accelerator includes multiple accelerator clocks generating multiple accelerator clock signals to operate the FPGA hardware accelerator to simulate the operations of the DUT. In one embodiment, operations of the DUT are mapped to the FPGA hardware accelerator, and the accelerator clock signals are generated at multiple frequencies and at the defined frequency ratio of the frequencies of the multiple device clocks, to maintain cycle accuracy between the DUT and the FPGA hardware accelerator. In an embodiment, the FPGA hardware accelerator may be used to control the frequencies of the multiple device clocks.

  17. Infrared Imaging of Carbon and Ceramic Composites: Data Reproducibility

    NASA Astrophysics Data System (ADS)

    Knight, B.; Howard, D. R.; Ringermacher, H. I.; Hudson, L. D.

    2010-02-01

    Infrared NDE techniques have proven to be superior for imaging of flaws in ceramic matrix composites (CMC) and carbon silicon carbide composites (C/SiC). Not only can one obtain accurate depth gauging of flaws such as delaminations and layered porosity in complex-shaped components such as airfoils and other aeronautical components, but also excellent reproducibility of image data is obtainable using the STTOF (Synthetic Thermal Time-of-Flight) methodology. The imaging of large complex shapes is fast and reliable. This methodology as applied to large C/SiC flight components at the NASA Dryden Flight Research Center will be described.

  18. Three-dimensional reproducibility of natural head position.

    PubMed

    Weber, Diana W; Fallis, Drew W; Packer, Mark D

    2013-05-01

    Although natural head position has proven to be reliable in the sagittal plane, with an increasing interest in 3-dimensional craniofacial analysis, a determination of its reproducibility in the coronal and axial planes is essential. This study was designed to evaluate the reproducibility of natural head position over time in the sagittal, coronal, and axial planes of space with 3-dimensional imaging. Three-dimensional photographs were taken of 28 adult volunteers (ages, 18-40 years) in natural head position at 5 times: baseline, 4 hours, 8 hours, 24 hours, and 1 week. Using the true vertical and horizontal laser lines projected in an iCAT cone-beam computed tomography machine (Imaging Sciences International, Hatfield, Pa) for orientation, we recorded references for natural head position on the patient's face with semipermanent markers. By using a 3-dimensional camera system, photographs were taken at each time point to capture the orientation of the reference points. By superimposing each of the 5 photographs on stable anatomic surfaces, changes in the position of the markers were recorded and assessed for parallelism by using 3dMDvultus (3dMD, Atlanta, Ga) and software (Dolphin Imaging & Management Solutions, Chatsworth, Calif). No statistically significant differences were observed between the 5 time points in any of the 3 planes of space. However, a statistically significant difference was observed between the mean angular deviations of 3 reference planes, with a hierarchy of natural head position reproducibility established as coronal > axial > sagittal. Within the parameters of this study, natural head position was found to be reproducible in the sagittal, coronal, and axial planes of space. The coronal plane had the least variation over time, followed by the axial and sagittal planes. Copyright © 2013 American Association of Orthodontists. Published by Mosby, Inc. All rights reserved.

  19. NIHAO - XIV. Reproducing the observed diversity of dwarf galaxy rotation curve shapes in ΛCDM

    NASA Astrophysics Data System (ADS)

    Santos-Santos, Isabel M.; Di Cintio, Arianna; Brook, Chris B.; Macciò, Andrea; Dutton, Aaron; Domínguez-Tenreiro, Rosa

    2018-02-01

    The significant diversity of rotation curve (RC) shapes in dwarf galaxies has recently emerged as a challenge to Λ cold dark matter (ΛCDM): in dark matter (DM) only simulations, DM haloes have a universal cuspy density profile that results in self-similar RC shapes. We compare RC shapes of simulated galaxies from the NIHAO (Numerical Investigation of a Hundred Astrophysical Objects) project with observed galaxies from the homogeneous SPARC data set. The DM haloes of the NIHAO galaxies can expand to form cores, with the degree of expansion depending on their stellar-to-halo mass ratio. By means of the V2kpc-VRlast relation (where VRlast is the outermost measured rotation velocity), we show that both the average trend and the scatter in RC shapes of NIHAO galaxies are in reasonable agreement with SPARC: this represents a significant improvement compared to simulations that do not result in DM core formation, suggesting that halo expansion is a key process in matching the diversity of dwarf galaxy RCs. Note that NIHAO galaxies can reproduce even the extremely slowly rising RCs of IC 2574 and UGC 5750. Revealingly, the range where observed galaxies show the highest diversity corresponds to the range where core formation is most efficient in NIHAO simulations, 50 < VRlast/km s-1 < 100. A few observed galaxies in this range cannot be matched by any NIHAO RC nor by simulations that predict a universal halo profile. Interestingly, the majority of these are starbursts or emission-line galaxies, with steep RCs and small effective radii. Such galaxies represent an interesting observational target providing new clues to the process/viability of cusp-core transformation, the relationship between starburst and inner potential well, and the nature of DM.

  20. A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control consortium

    PubMed Central

    2014-01-01

    We present primary results from the Sequencing Quality Control (SEQC) project, coordinated by the United States Food and Drug Administration. Examining Illumina HiSeq, Life Technologies SOLiD and Roche 454 platforms at multiple laboratory sites using reference RNA samples with built-in controls, we assess RNA sequencing (RNA-seq) performance for junction discovery and differential expression profiling and compare it to microarray and quantitative PCR (qPCR) data using complementary metrics. At all sequencing depths, we discover unannotated exon-exon junctions, with >80% validated by qPCR. We find that measurements of relative expression are accurate and reproducible across sites and platforms if specific filters are used. In contrast, RNA-seq and microarrays do not provide accurate absolute measurements, and gene-specific biases are observed, for these and qPCR. Measurement performance depends on the platform and data analysis pipeline, and variation is large for transcript-level profiling. The complete SEQC data sets, comprising >100 billion reads (10Tb), provide unique resources for evaluating RNA-seq analyses for clinical and regulatory settings. PMID:25150838

  1. Decadal variability of surface incident solar radiation over China: Observations, satellite retrievals, and reanalyses

    NASA Astrophysics Data System (ADS)

    Wang, Kaicun; Ma, Qian; Li, Zhijun; Wang, Jiankai

    2015-07-01

    Existing studies have shown that observed surface incident solar radiation (Rs) over China may have important inhomogeneity issues. This study provides metadata and reference data to homogenize observed Rs, from which the decadal variability of Rs over China can be accurately derived. From 1958 to 1990, diffuse solar radiation (Rsdif) and direct solar radiation (Rsdir) were measured separately, and Rs was calculated as their sum. The pyranometers used to measure Rsdif had a strong sensitivity drift problem, which introduced a spurious decreasing trend into the observed Rsdif and Rs data, whereas the observed Rsdir did not suffer from this sensitivity drift problem. From 1990 to 1993, instruments and measurement methods were replaced and measuring stations were restructured in China, which introduced an abrupt increase in the observed Rs. Intercomparisons between observation-based and model-based Rs performed in this research show that sunshine duration (SunDu)-derived Rs is of high quality and can be used as reference data to homogenize observed Rs data. The homogenized and adjusted data of observed Rs combines the advantages of observed Rs in quantifying hourly to monthly variability and SunDu-derived Rs in depicting decadal variability and trend. Rs averaged over 105 stations in China decreased at -2.9 W m-2 per decade from 1961 to 1990 and remained stable afterward. This decadal variability is confirmed by the observed Rsdir and diurnal temperature ranges, and can be reproduced by high-quality Earth System Models. However, neither satellite retrievals nor reanalyses can accurately reproduce such decadal variability over China.

  2. Enhancing reproducibility of ultrasonic measurements by new users

    NASA Astrophysics Data System (ADS)

    Pramanik, Manojit; Gupta, Madhumita; Krishnan, Kajoli Banerjee

    2013-03-01

    Perception of operator influences ultrasound image acquisition and processing. Lower costs are attracting new users to medical ultrasound. Anticipating an increase in this trend, we conducted a study to quantify the variability in ultrasonic measurements made by novice users and identify methods to reduce it. We designed a protocol with four presets and trained four new users to scan and manually measure the head circumference of a fetal phantom with an ultrasound scanner. In the first phase, the users followed this protocol in seven distinct sessions. They then received feedback on the quality of the scans from an expert. In the second phase, two of the users repeated the entire protocol aided by visual cues provided to them during scanning. We performed off-line measurements on all the images using a fully automated algorithm capable of measuring the head circumference from fetal phantom images. The ground truth (198.1±1.6 mm) was based on sixteen scans and measurements made by an expert. Our analysis shows that: (1) the inter-observer variability of manual measurements was 5.5 mm, whereas the inter-observer variability of automated measurements was only 0.6 mm in the first phase (2) consistency of image appearance improved and mean manual measurements was 4-5 mm closer to the ground truth in the second phase (3) automated measurements were more precise, accurate and less sensitive to different presets compared to manual measurements in both phases. Our results show that visual aids and automation can bring more reproducibility to ultrasonic measurements made by new users.

  3. Intraobserver Repeatability and Interobserver Reproducibility of Ellipsoid Zone Measurements in Retinitis Pigmentosa.

    PubMed

    Strampe, Margaret R; Huckenpahler, Alison L; Higgins, Brian P; Tarima, Sergey; Visotcky, Alexis; Stepien, Kimberly E; Kay, Christine N; Carroll, Joseph

    2018-05-01

    To examine repeatability and reproducibility of ellipsoid zone (EZ) width measurements in patients with retinitis pigmentosa (RP) using a longitudinal reflectivity profile (LRP) analysis. We examined Bioptigen optical coherence tomography (OCT) scans from 48 subjects with RP or Usher syndrome. Nominal scan lengths were 6, 7, or 10 mm, and the lateral scale of each scan was calculated using axial length measurements. LRPs were generated from OCT line scans, and the peak corresponding to EZ was manually identified using ImageJ. The locations at which the EZ peak disappeared were used to calculate EZ width. Each scan was analyzed twice by each of two observers, who were masked to their previous measurements and those of the other observer. On average, horizontal width (HW) was significantly greater than vertical width (VW), and there was high interocular symmetry for both HW and VW. We observed excellent intraobserver repeatability with intraclass correlation coefficients (ICCs) ranging from 0.996 to 0.998 for HW and VW measurements. Interobserver reproducibility was also excellent for both HW (ICC = 0.989; 95% confidence interval [CI] = 0.983-0.995) and VW (ICC = 0.991; 95% CI = 0.985-0.996), with no significant bias observed between observers. EZ width can be measured using LRPs with excellent repeatability and reproducibility. Our observation of greater HW than VW is consistent with previous observations in RP, though the reason for this anisotropy remains unclear. We describe repeatability and reproducibility of a method for measuring EZ width in patients with RP or Usher syndrome. This approach could facilitate measurement of retinal band thickness and/or intensity.

  4. Can the Λ CDM model reproduce MOND-like behavior?

    NASA Astrophysics Data System (ADS)

    Dai, De-Chang; Lu, Chunyu

    2017-12-01

    It is usually believed that MOND can describe the galactic rotational curves with only baryonic matter and without any dark matter very well, while the Λ CDM model is expected to have difficulty in reproducing MOND-like behavior. Here, we use EAGLE's data to learn whether the Λ CDM model can reproduce MOND-like behavior. EAGLE's simulation result clearly reproduces the MOND-like behavior for ab⪆10-12 m/s 2 at z =0 , although the acceleration constant, a0, is a little larger than the observational data indicate. We find that a0 increases with the redshift in a way different from what Milgrom proposed (a0∝H ). Therefore, while galaxy rotation curves can be fitted by MOND's empirical function in the Λ CDM model, there is no clear connection between a0 and the Hubble constant. We also find that a0 at z ⪆1 is well separated from a0 at z =0 . Once we have enough galaxies observed at high redshifts, we will be able to rule out the modified gravity model based on MOND-like empirical function with a z -independent a0.

  5. Development of accurate potentials to explore the structure of water on 2D materials

    NASA Astrophysics Data System (ADS)

    Bejagam, Karteek; Singh, Samrendra; Deshmukh, Sanket; Deshmkuh Group Team; Samrendra Group Collaboration

    Water play an important role in many biological and non-biological process. Thus structure of water at various interfaces and under confinement has always been the topic of immense interest. 2-D materials have shown great potential in surface coating applications and nanofluidic devices. However, the exact atomic level understanding of the wettability of single layer of these 2-D materials is still lacking mainly due to lack of experimental techniques and computational methodologies including accurate force-field potentials and algorithms to measure the contact angle of water. In the present study, we have developed a new algorithm to measure the accurate contact angle between water and 2-D materials. The algorithm is based on fitting the best sphere to the shape of the droplet. This novel spherical fitting method accounts for every individual molecule of the droplet, rather than those at the surface only. We employ this method of contact angle measurements to develop the accurate non-bonded potentials between water and 2-D materials including graphene and boron nitride (BN) to reproduce the experimentally observed contact angle of water on these 2-D materials. Different water models such as SPC, SPC/Fw, and TIP3P were used to study the structure of water at the interfaces.

  6. Illusory Motion Reproduced by Deep Neural Networks Trained for Prediction.

    PubMed

    Watanabe, Eiji; Kitaoka, Akiyoshi; Sakamoto, Kiwako; Yasugi, Masaki; Tanaka, Kenta

    2018-01-01

    The cerebral cortex predicts visual motion to adapt human behavior to surrounding objects moving in real time. Although the underlying mechanisms are still unknown, predictive coding is one of the leading theories. Predictive coding assumes that the brain's internal models (which are acquired through learning) predict the visual world at all times and that errors between the prediction and the actual sensory input further refine the internal models. In the past year, deep neural networks based on predictive coding were reported for a video prediction machine called PredNet. If the theory substantially reproduces the visual information processing of the cerebral cortex, then PredNet can be expected to represent the human visual perception of motion. In this study, PredNet was trained with natural scene videos of the self-motion of the viewer, and the motion prediction ability of the obtained computer model was verified using unlearned videos. We found that the computer model accurately predicted the magnitude and direction of motion of a rotating propeller in unlearned videos. Surprisingly, it also represented the rotational motion for illusion images that were not moving physically, much like human visual perception. While the trained network accurately reproduced the direction of illusory rotation, it did not detect motion components in negative control pictures wherein people do not perceive illusory motion. This research supports the exciting idea that the mechanism assumed by the predictive coding theory is one of basis of motion illusion generation. Using sensory illusions as indicators of human perception, deep neural networks are expected to contribute significantly to the development of brain research.

  7. ACCURATE ORBITAL INTEGRATION OF THE GENERAL THREE-BODY PROBLEM BASED ON THE D'ALEMBERT-TYPE SCHEME

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Minesaki, Yukitaka

    2013-03-15

    We propose an accurate orbital integration scheme for the general three-body problem that retains all conserved quantities except angular momentum. The scheme is provided by an extension of the d'Alembert-type scheme for constrained autonomous Hamiltonian systems. Although the proposed scheme is merely second-order accurate, it can precisely reproduce some periodic, quasiperiodic, and escape orbits. The Levi-Civita transformation plays a role in designing the scheme.

  8. Compared to X-ray, three-dimensional computed tomography measurement is a reproducible radiographic method for normal proximal humerus.

    PubMed

    Jia, Xiaoyang; Chen, Yanxi; Qiang, Minfei; Zhang, Kun; Li, Haobo; Jiang, Yuchen; Zhang, Yijie

    2016-07-15

    Accurate comprehension of the normal humeral morphology is crucial for anatomical reconstruction in shoulder arthroplasty. However, traditional morphological measurements for humerus were mainly based on cadaver and radiography. The purpose of this study was to provide a series of precise and repeatable parameters of the normal proximal humerus for arthroplasty, based on the three-dimensional (3-D) measurements. Radiographic and 3-D computed tomography (CT) measurements of the proximal humerus were performed in a sample of 120 consecutive adults. Sex differences, two image modalities differences, and correlations of the parameters were evaluated. Intra- and inter-observer reproducibility was evaluated using intraclass correlation coefficients (ICCs). In the male group, all parameters except the neck-shaft angle of humerus, based on 3-D CT images, were greater than those in the female group (P < 0.05). All variables were significantly different between two image modalities (P < 0.05). In 3-D CT measurement, all parameters expect neck-shaft angle had correlation with each other (P < 0.001), particularly between two diameters of the humeral head (r = 0.907). All parameters in the 3-D CT measurement had excellent reproducibility (ICC range, 0.878 to 0.936) that was higher than those in the radiographs (ICC range, 0.741 to 0.858). The present study suggested that 3-D CT was more reproducible than plain radiography in the assessment of morphology of the normal proximal humerus. Therefore, this reproducible modality could be utilized in the preoperative planning. Our data could serve as an effective guideline for humeral component selection and improve the design of shoulder prosthesis.

  9. ITK: enabling reproducible research and open science

    PubMed Central

    McCormick, Matthew; Liu, Xiaoxiao; Jomier, Julien; Marion, Charles; Ibanez, Luis

    2014-01-01

    Reproducibility verification is essential to the practice of the scientific method. Researchers report their findings, which are strengthened as other independent groups in the scientific community share similar outcomes. In the many scientific fields where software has become a fundamental tool for capturing and analyzing data, this requirement of reproducibility implies that reliable and comprehensive software platforms and tools should be made available to the scientific community. The tools will empower them and the public to verify, through practice, the reproducibility of observations that are reported in the scientific literature. Medical image analysis is one of the fields in which the use of computational resources, both software and hardware, are an essential platform for performing experimental work. In this arena, the introduction of the Insight Toolkit (ITK) in 1999 has transformed the field and facilitates its progress by accelerating the rate at which algorithmic implementations are developed, tested, disseminated and improved. By building on the efficiency and quality of open source methodologies, ITK has provided the medical image community with an effective platform on which to build a daily workflow that incorporates the true scientific practices of reproducibility verification. This article describes the multiple tools, methodologies, and practices that the ITK community has adopted, refined, and followed during the past decade, in order to become one of the research communities with the most modern reproducibility verification infrastructure. For example, 207 contributors have created over 2400 unit tests that provide over 84% code line test coverage. The Insight Journal, an open publication journal associated with the toolkit, has seen over 360,000 publication downloads. The median normalized closeness centrality, a measure of knowledge flow, resulting from the distributed peer code review system was high, 0.46. PMID:24600387

  10. ITK: enabling reproducible research and open science.

    PubMed

    McCormick, Matthew; Liu, Xiaoxiao; Jomier, Julien; Marion, Charles; Ibanez, Luis

    2014-01-01

    Reproducibility verification is essential to the practice of the scientific method. Researchers report their findings, which are strengthened as other independent groups in the scientific community share similar outcomes. In the many scientific fields where software has become a fundamental tool for capturing and analyzing data, this requirement of reproducibility implies that reliable and comprehensive software platforms and tools should be made available to the scientific community. The tools will empower them and the public to verify, through practice, the reproducibility of observations that are reported in the scientific literature. Medical image analysis is one of the fields in which the use of computational resources, both software and hardware, are an essential platform for performing experimental work. In this arena, the introduction of the Insight Toolkit (ITK) in 1999 has transformed the field and facilitates its progress by accelerating the rate at which algorithmic implementations are developed, tested, disseminated and improved. By building on the efficiency and quality of open source methodologies, ITK has provided the medical image community with an effective platform on which to build a daily workflow that incorporates the true scientific practices of reproducibility verification. This article describes the multiple tools, methodologies, and practices that the ITK community has adopted, refined, and followed during the past decade, in order to become one of the research communities with the most modern reproducibility verification infrastructure. For example, 207 contributors have created over 2400 unit tests that provide over 84% code line test coverage. The Insight Journal, an open publication journal associated with the toolkit, has seen over 360,000 publication downloads. The median normalized closeness centrality, a measure of knowledge flow, resulting from the distributed peer code review system was high, 0.46.

  11. Reproducibility of gastrocnemius medialis muscle architecture during treadmill running.

    PubMed

    Giannakou, Erasmia; Aggeloussis, Nickos; Arampatzis, Adamantios

    2011-12-01

    The purpose of this study was to assess the reproducibility of fascicle length (FL) and pennation angle (PA) of gastrocnemius medialis (GM) muscle during running in vivo. Twelve male recreational long distance runners (mean±SD; age: 24±3 years, mass: 76±7kg) ran on a treadmill at a speed of 3.0m/s, wearing their own running shoes, for two different 10min sessions that were at least 2 days apart. For each test day 10 acceptable trials were recorded. Ankle and knee joint angle data were recorded by a Vicon 624 system with three cameras operating at 120Hz. B-mode ultrasonography was used to examine fascicle length and pennation angle of gastrocnemius medialis muscle. The ultrasound probe was firmly secured on the muscle belly using a lightweight foam fixation. The results indicated that fascicle length and pennation angle demonstrated high reproducibility values during treadmill running both for within and between test days. The root mean square scores between the repeated waveforms of pennation angle and fascicle length were small (∼2° and ∼3.5mm, respectively). However, ∼14 trials for pennation angle and ∼9 trials for fascicle length may be required in order to record accurate data from muscle architecture parameters. In conclusion, ultrasound measurements may be highly reproducible during dynamic movements such as treadmill running, provided that a proper fixation is used in order to assure the constant location and orientation of the ultrasound probe throughout the movement. Copyright © 2011 Elsevier Ltd. All rights reserved.

  12. Reproducing the observed energy-dependent structure of Earth's electron radiation belts during storm recovery with an event-specific diffusion model

    DOE PAGES

    Ripoll, J. -F.; Reeves, Geoffrey D.; Cunningham, Gregory Scott; ...

    2016-06-11

    Here, we present dynamic simulations of energy-dependent losses in the radiation belt “slot region” and the formation of the two-belt structure for the quiet days after the 1 March storm. The simulations combine radial diffusion with a realistic scattering model, based data-driven spatially and temporally resolved whistler-mode hiss wave observations from the Van Allen Probes satellites. The simulations reproduce Van Allen Probes observations for all energies and L shells (2–6) including (a) the strong energy dependence to the radiation belt dynamics (b) an energy-dependent outer boundary to the inner zone that extends to higher L shells at lower energies andmore » (c) an “S-shaped” energy-dependent inner boundary to the outer zone that results from the competition between diffusive radial transport and losses. We find that the characteristic energy-dependent structure of the radiation belts and slot region is dynamic and can be formed gradually in ~15 days, although the “S shape” can also be reproduced by assuming equilibrium conditions. The highest-energy electrons (E > 300 keV) of the inner region of the outer belt (L ~ 4–5) also constantly decay, demonstrating that hiss wave scattering affects the outer belt during times of extended plasmasphere. Through these simulations, we explain the full structure in energy and L shell of the belts and the slot formation by hiss scattering during storm recovery. We show the power and complexity of looking dynamically at the effects over all energies and L shells and the need for using data-driven and event-specific conditions.« less

  13. Inflow-vascular space occupancy (iVASO) reproducibility in the hippocampus and cortex at different blood water nulling times.

    PubMed

    Rane, Swati; Talati, Pratik; Donahue, Manus J; Heckers, Stephan

    2016-06-01

    Inflow-vascular space occupancy (iVASO) measures arterial cerebral blood volume (aCBV) using accurate blood water nulling (inversion time [TI]) when arterial blood reaches the capillary, i.e., at the arterial arrival time. This work assessed the reproducibility of iVASO measurements in the hippocampus and cortex at multiple TIs. The iVASO approach was implemented at multiple TIs in 10 healthy volunteers at 3 Tesla. aCBV values were measured at each TI in the left and right hippocampus, and the cortex. Reproducibility of aCBV measurements within scans (same day) and across sessions (different days) was assessed using the intraclass correlation coefficient (ICC). Overall hippocampal aCBV was significantly higher than cortical aCBV, likely due to higher gray matter volume. Hippocampal ICC values were high at short TIs (≤914 ms; intrascan values = 0.80-0.96, interscan values = 0.61-0.91). Cortically, high ICC values were observed at intermediate TIs of 914 (intra: 0.93, inter: 0.87) and 1034 ms (intra: 0.96, inter: 0.86). The ICC values were comparable to established contrast-based CBV measures. iVASO measurements are reproducible within and across sessions. TIs for iVASO measurements should be chosen carefully, taking into account heterogeneous arterial arrival times in different brain regions. Magn Reson Med 75:2379-2387, 2016. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

  14. Opinion: Is science really facing a reproducibility crisis, and do we need it to?

    PubMed Central

    Fanelli, Daniele

    2018-01-01

    Efforts to improve the reproducibility and integrity of science are typically justified by a narrative of crisis, according to which most published results are unreliable due to growing problems with research and publication practices. This article provides an overview of recent evidence suggesting that this narrative is mistaken, and argues that a narrative of epochal changes and empowerment of scientists would be more accurate, inspiring, and compelling. PMID:29531051

  15. STEM VQ Method, Using Scanning Transmission Electron Microscopy (STEM) for Accurate Virus Quantification

    DTIC Science & Technology

    2017-02-02

    Corresponding Author Abstract Accurate virus quantification is sought, but a perfect method still eludes the scientific community. Electron...unlimited. UNCLASSIFIED 2 provides morphology data and counts all viral particles, including partial or noninfectious particles; however, EM methods ...consistent, reproducible virus quantification method called Scanning Transmission Electron Microscopy – Virus Quantification (STEM-VQ) which simplifies

  16. On the accuracy and reproducibility of a novel probabilistic atlas-based generation for calculation of head attenuation maps on integrated PET/MR scanners.

    PubMed

    Chen, Kevin T; Izquierdo-Garcia, David; Poynton, Clare B; Chonde, Daniel B; Catana, Ciprian

    2017-03-01

    To propose an MR-based method for generating continuous-valued head attenuation maps and to assess its accuracy and reproducibility. Demonstrating that novel MR-based photon attenuation correction methods are both accurate and reproducible is essential prior to using them routinely in research and clinical studies on integrated PET/MR scanners. Continuous-valued linear attenuation coefficient maps ("μ-maps") were generated by combining atlases that provided the prior probability of voxel positions belonging to a certain tissue class (air, soft tissue, or bone) and an MR intensity-based likelihood classifier to produce posterior probability maps of tissue classes. These probabilities were used as weights to generate the μ-maps. The accuracy of this probabilistic atlas-based continuous-valued μ-map ("PAC-map") generation method was assessed by calculating the voxel-wise absolute relative change (RC) between the MR-based and scaled CT-based attenuation-corrected PET images. To assess reproducibility, we performed pair-wise comparisons of the RC values obtained from the PET images reconstructed using the μ-maps generated from the data acquired at three time points. The proposed method produced continuous-valued μ-maps that qualitatively reflected the variable anatomy in patients with brain tumor and agreed well with the scaled CT-based μ-maps. The absolute RC comparing the resulting PET volumes was 1.76 ± 2.33 %, quantitatively demonstrating that the method is accurate. Additionally, we also showed that the method is highly reproducible, the mean RC value for the PET images reconstructed using the μ-maps obtained at the three visits being 0.65 ± 0.95 %. Accurate and highly reproducible continuous-valued head μ-maps can be generated from MR data using a probabilistic atlas-based approach.

  17. Automated Generation of Technical Documentation and Provenance for Reproducible Research

    NASA Astrophysics Data System (ADS)

    Jolly, B.; Medyckyj-Scott, D.; Spiekermann, R.; Ausseil, A. G.

    2017-12-01

    Data provenance and detailed technical documentation are essential components of high-quality reproducible research, however are often only partially addressed during a research project. Recording and maintaining this information during the course of a project can be a difficult task to get right as it is a time consuming and often boring process for the researchers involved. As a result, provenance records and technical documentation provided alongside research results can be incomplete or may not be completely consistent with the actual processes followed. While providing access to the data and code used by the original researchers goes some way toward enabling reproducibility, this does not count as, or replace, data provenance. Additionally, this can be a poor substitute for good technical documentation and is often more difficult for a third-party to understand - particularly if they do not understand the programming language(s) used. We present and discuss a tool built from the ground up for the production of well-documented and reproducible spatial datasets that are created by applying a series of classification rules to a number of input layers. The internal model of the classification rules required by the tool to process the input data is exploited to also produce technical documentation and provenance records with minimal additional user input. Available provenance records that accompany input datasets are incorporated into those that describe the current process. As a result, each time a new iteration of the analysis is performed the documentation and provenance records are re-generated to provide an accurate description of the exact process followed. The generic nature of this tool, and the lessons learned during its creation, have wider application to other fields where the production of derivative datasets must be done in an open, defensible, and reproducible way.

  18. Illusory Motion Reproduced by Deep Neural Networks Trained for Prediction

    PubMed Central

    Watanabe, Eiji; Kitaoka, Akiyoshi; Sakamoto, Kiwako; Yasugi, Masaki; Tanaka, Kenta

    2018-01-01

    The cerebral cortex predicts visual motion to adapt human behavior to surrounding objects moving in real time. Although the underlying mechanisms are still unknown, predictive coding is one of the leading theories. Predictive coding assumes that the brain's internal models (which are acquired through learning) predict the visual world at all times and that errors between the prediction and the actual sensory input further refine the internal models. In the past year, deep neural networks based on predictive coding were reported for a video prediction machine called PredNet. If the theory substantially reproduces the visual information processing of the cerebral cortex, then PredNet can be expected to represent the human visual perception of motion. In this study, PredNet was trained with natural scene videos of the self-motion of the viewer, and the motion prediction ability of the obtained computer model was verified using unlearned videos. We found that the computer model accurately predicted the magnitude and direction of motion of a rotating propeller in unlearned videos. Surprisingly, it also represented the rotational motion for illusion images that were not moving physically, much like human visual perception. While the trained network accurately reproduced the direction of illusory rotation, it did not detect motion components in negative control pictures wherein people do not perceive illusory motion. This research supports the exciting idea that the mechanism assumed by the predictive coding theory is one of basis of motion illusion generation. Using sensory illusions as indicators of human perception, deep neural networks are expected to contribute significantly to the development of brain research. PMID:29599739

  19. Reproducibility in a multiprocessor system

    DOEpatents

    Bellofatto, Ralph A; Chen, Dong; Coteus, Paul W; Eisley, Noel A; Gara, Alan; Gooding, Thomas M; Haring, Rudolf A; Heidelberger, Philip; Kopcsay, Gerard V; Liebsch, Thomas A; Ohmacht, Martin; Reed, Don D; Senger, Robert M; Steinmacher-Burow, Burkhard; Sugawara, Yutaka

    2013-11-26

    Fixing a problem is usually greatly aided if the problem is reproducible. To ensure reproducibility of a multiprocessor system, the following aspects are proposed; a deterministic system start state, a single system clock, phase alignment of clocks in the system, system-wide synchronization events, reproducible execution of system components, deterministic chip interfaces, zero-impact communication with the system, precise stop of the system and a scan of the system state.

  20. Ensemble MD simulations restrained via crystallographic data: Accurate structure leads to accurate dynamics

    PubMed Central

    Xue, Yi; Skrynnikov, Nikolai R

    2014-01-01

    Currently, the best existing molecular dynamics (MD) force fields cannot accurately reproduce the global free-energy minimum which realizes the experimental protein structure. As a result, long MD trajectories tend to drift away from the starting coordinates (e.g., crystallographic structures). To address this problem, we have devised a new simulation strategy aimed at protein crystals. An MD simulation of protein crystal is essentially an ensemble simulation involving multiple protein molecules in a crystal unit cell (or a block of unit cells). To ensure that average protein coordinates remain correct during the simulation, we introduced crystallography-based restraints into the MD protocol. Because these restraints are aimed at the ensemble-average structure, they have only minimal impact on conformational dynamics of the individual protein molecules. So long as the average structure remains reasonable, the proteins move in a native-like fashion as dictated by the original force field. To validate this approach, we have used the data from solid-state NMR spectroscopy, which is the orthogonal experimental technique uniquely sensitive to protein local dynamics. The new method has been tested on the well-established model protein, ubiquitin. The ensemble-restrained MD simulations produced lower crystallographic R factors than conventional simulations; they also led to more accurate predictions for crystallographic temperature factors, solid-state chemical shifts, and backbone order parameters. The predictions for 15N R1 relaxation rates are at least as accurate as those obtained from conventional simulations. Taken together, these results suggest that the presented trajectories may be among the most realistic protein MD simulations ever reported. In this context, the ensemble restraints based on high-resolution crystallographic data can be viewed as protein-specific empirical corrections to the standard force fields. PMID:24452989

  1. Reliability and reproducibility of disc-foveal angle measurements by non-mydriatic fundus photography.

    PubMed

    Le Jeune, Caroline; Chebli, Fayçal; Leon, Lorette; Anthoine, Emmanuelle; Weber, Michel; Péchereau, Alain; Lebranchu, Pierre

    2018-01-01

    Abnormal torsion could be associated with cyclovertical strabismus, but torsion measurements are not reliable in children. To assess an objective fundus torsion evaluation in a paediatric population, we used Non-Mydriatic Fundus photography (NMFP) in healthy and cyclovertical strabismus patients to evaluate the disc-foveal angle over time and observers. We used a retrospective set of NMFP including 24 A or V-pattern strabismus and 27 age-matched normal children (mean age 6.4 and 6.7 years respectively), taken during 2 distinct follow-up consultations (separated by 251 and 479 days respectively). Each disc-foveal angle measurement (from which the ocular torsion can be assessed) was performed by 5 different observers, using graphical software and based on reproducible fundus anatomical marks. Statistical analysis was performed with a multivariate ANOVA using group, time and observers as factors, in addition to intraclass coefficient correlation (ICC) to assess measurement reproducibility. A significant difference of disc-foveal angle measures was observed between groups (p<0,001): 18.73° (SD = 6.42), -3,25° (SD = 5.51) and 6,89° (SD = 4,41) respectively for V-pattern, A- pattern and normal subjects. Neither observers (F = 0,2028 p = 0,9369) nor time between 1st and 2nd NMFP (F = 0,6312 p = 0,4271) seem to influence the measure of disc-foveal angle. The evaluation of disc-foveal angle was very reproducible between observers (ICC>0,97). Abnormal amount of objective torsion could be associated with alphabet-pattern strabismus. Disc-foveal angle evaluation by NMFP in a children population appears as a non-invasive, reliable and reproducible method.

  2. Contextual sensitivity in scientific reproducibility

    PubMed Central

    Van Bavel, Jay J.; Mende-Siedlecki, Peter; Brady, William J.; Reinero, Diego A.

    2016-01-01

    In recent years, scientists have paid increasing attention to reproducibility. For example, the Reproducibility Project, a large-scale replication attempt of 100 studies published in top psychology journals found that only 39% could be unambiguously reproduced. There is a growing consensus among scientists that the lack of reproducibility in psychology and other fields stems from various methodological factors, including low statistical power, researcher’s degrees of freedom, and an emphasis on publishing surprising positive results. However, there is a contentious debate about the extent to which failures to reproduce certain results might also reflect contextual differences (often termed “hidden moderators”) between the original research and the replication attempt. Although psychologists have found extensive evidence that contextual factors alter behavior, some have argued that context is unlikely to influence the results of direct replications precisely because these studies use the same methods as those used in the original research. To help resolve this debate, we recoded the 100 original studies from the Reproducibility Project on the extent to which the research topic of each study was contextually sensitive. Results suggested that the contextual sensitivity of the research topic was associated with replication success, even after statistically adjusting for several methodological characteristics (e.g., statistical power, effect size). The association between contextual sensitivity and replication success did not differ across psychological subdisciplines. These results suggest that researchers, replicators, and consumers should be mindful of contextual factors that might influence a psychological process. We offer several guidelines for dealing with contextual sensitivity in reproducibility. PMID:27217556

  3. Contextual sensitivity in scientific reproducibility.

    PubMed

    Van Bavel, Jay J; Mende-Siedlecki, Peter; Brady, William J; Reinero, Diego A

    2016-06-07

    In recent years, scientists have paid increasing attention to reproducibility. For example, the Reproducibility Project, a large-scale replication attempt of 100 studies published in top psychology journals found that only 39% could be unambiguously reproduced. There is a growing consensus among scientists that the lack of reproducibility in psychology and other fields stems from various methodological factors, including low statistical power, researcher's degrees of freedom, and an emphasis on publishing surprising positive results. However, there is a contentious debate about the extent to which failures to reproduce certain results might also reflect contextual differences (often termed "hidden moderators") between the original research and the replication attempt. Although psychologists have found extensive evidence that contextual factors alter behavior, some have argued that context is unlikely to influence the results of direct replications precisely because these studies use the same methods as those used in the original research. To help resolve this debate, we recoded the 100 original studies from the Reproducibility Project on the extent to which the research topic of each study was contextually sensitive. Results suggested that the contextual sensitivity of the research topic was associated with replication success, even after statistically adjusting for several methodological characteristics (e.g., statistical power, effect size). The association between contextual sensitivity and replication success did not differ across psychological subdisciplines. These results suggest that researchers, replicators, and consumers should be mindful of contextual factors that might influence a psychological process. We offer several guidelines for dealing with contextual sensitivity in reproducibility.

  4. Low-dimensional, morphologically accurate models of subthreshold membrane potential

    PubMed Central

    Kellems, Anthony R.; Roos, Derrick; Xiao, Nan; Cox, Steven J.

    2009-01-01

    The accurate simulation of a neuron’s ability to integrate distributed synaptic input typically requires the simultaneous solution of tens of thousands of ordinary differential equations. For, in order to understand how a cell distinguishes between input patterns we apparently need a model that is biophysically accurate down to the space scale of a single spine, i.e., 1 μm. We argue here that one can retain this highly detailed input structure while dramatically reducing the overall system dimension if one is content to accurately reproduce the associated membrane potential at a small number of places, e.g., at the site of action potential initiation, under subthreshold stimulation. The latter hypothesis permits us to approximate the active cell model with an associated quasi-active model, which in turn we reduce by both time-domain (Balanced Truncation) and frequency-domain (ℋ2 approximation of the transfer function) methods. We apply and contrast these methods on a suite of typical cells, achieving up to four orders of magnitude in dimension reduction and an associated speed-up in the simulation of dendritic democratization and resonance. We also append a threshold mechanism and indicate that this reduction has the potential to deliver an accurate quasi-integrate and fire model. PMID:19172386

  5. Central Corneal Thickness Reproducibility among Ten Different Instruments.

    PubMed

    Pierro, Luisa; Iuliano, Lorenzo; Gagliardi, Marco; Ambrosi, Alessandro; Rama, Paolo; Bandello, Francesco

    2016-11-01

    To assess agreement between one ultrasonic (US) and nine optical instruments for the measurement of central corneal thickness (CCT), and to evaluate intra- and inter-operator reproducibility. In this observational cross-sectional study, two masked operators measured CCT thickness twice in 28 healthy eyes. We used seven spectral-domain optical coherence tomography (SD-OCT) devices, one time-domain OCT, one Scheimpflug camera, and one US-based instrument. Inter- and intra-operator reproducibility was evaluated by intraclass correlation coefficient (ICC), coefficient of variation (CV), and Bland-Altman test analysis. Instrument-to-instrument reproducibility was determined by ANOVA for repeated measurements. We also tested how the devices disagreed regarding systemic bias and random error using a structural equation model. Mean CCT of all instruments ranged from 536 ± 42 μm to 577 ± 40 μm. An instrument-to-instrument correlation test showed high values among the 10 investigated devices (correlation coefficient range 0.852-0.995; p values <0.0001 in all cases). The highest correlation coefficient values were registered between 3D OCT-2000 Topcon-Spectral OCT/SLO Opko (0.995) and Cirrus HD-OCT Zeiss-RS-3000 Nidek (0.995), whereas the lowest were seen between SS-1000 CASIA and Spectral OCT/SLO Opko (0.852). ICC and CV showed excellent inter- and intra-operator reproducibility for all optic-based devices, except for the US-based device. Bland-Altman analysis demonstrated low mean biases between operators. Despite highlighting good intra- and inter-operator reproducibility, we found that a scale bias between instruments might interfere with thorough CCT monitoring. We suggest that optimal monitoring is achieved with the same operator and the same device.

  6. Reproducibility of a four-point clinical severity score for glabellar frown lines.

    PubMed

    Honeck, P; Weiss, C; Sterry, W; Rzany, B

    2003-08-01

    Focal injections of botulinum toxin A are used successfully for the treatment of hyperkinetic facial wrinkles. Efficacy can be measured by several methods. However, so far none has been investigated for its reproducibility. Objectives To investigate the reproducibility of a clinical 0-3 score for glabellar frown lines. In the first part of the study, a standardized photographic documentation of glabellar frown lines was produced. Based on the results of this phase, a consensus atlas of glabellar frown lines was developed and participants were trained using this atlas. In the main study, 50 standardized photographs were shown on two consecutive days to 28 dermatologists. The reproducibility of the score was investigated by conventional kappa statistics. In the main study, we found an unweighted kappa according to Fleiss of 0.62 for interobserver reproducibility. Intraobserver reproducibility showed an unweighted kappa according to Cohen of between 0.57 and 0.91 for each observer, and a weighted kappa according to Cicchetti and Allison of between 0.68 and 0.94. The clinical 0-3 score for glabellar frown lines shows a good inter- and intraobserver reproducibility.

  7. The use of a robotic tibial rotation device and an electromagnetic tracking system to accurately reproduce the clinical dial test.

    PubMed

    Stinton, S K; Siebold, R; Freedberg, H; Jacobs, C; Branch, T P

    2016-03-01

    The purpose of this study was to: (1) determine whether a robotic tibial rotation device and an electromagnetic tracking system could accurately reproduce the clinical dial test at 30° of knee flexion; (2) compare rotation data captured at the footplates of the robotic device to tibial rotation data measured using an electromagnetic sensor on the proximal tibia. Thirty-two unilateral ACL-reconstructed patients were examined using a robotic tibial rotation device that mimicked the dial test. The data reported in this study is only from the healthy legs of these patients. Torque was applied through footplates and was measured using servomotors. Lower leg motion was measured at the foot using the motors. Tibial motion was also measured through an electromagnetic tracking system and a sensor on the proximal tibia. Load-deformation curves representing rotational motion of the foot and tibia were compared using Pearson's correlation coefficients. Off-axis motions including medial-lateral translation and anterior-posterior translation were also measured using the electromagnetic system. The robotic device and electromagnetic system were able to provide axial rotation data and translational data for the tibia during the dial test. Motion measured at the foot was not correlated to motion of the tibial tubercle in internal rotation or in external rotation. The position of the tibial tubercle was 26.9° ± 11.6° more internally rotated than the foot at torque 0 Nm. Medial-lateral translation and anterior-posterior translation were combined to show the path of the tubercle in the coronal plane during tibial rotation. The information captured during a manual dial test includes both rotation of the tibia and proximal tibia translation. All of this information can be captured using a robotic tibial axial rotation device with an electromagnetic tracking system. The pathway of the tibial tubercle during tibial axial rotation can provide additional information about knee

  8. Analytical Validation of a Highly Quantitative, Sensitive, Accurate, and Reproducible Assay (HERmark) for the Measurement of HER2 Total Protein and HER2 Homodimers in FFPE Breast Cancer Tumor Specimens.

    PubMed

    Larson, Jeffrey S; Goodman, Laurie J; Tan, Yuping; Defazio-Eli, Lisa; Paquet, Agnes C; Cook, Jennifer W; Rivera, Amber; Frankson, Kristi; Bose, Jolly; Chen, Lili; Cheung, Judy; Shi, Yining; Irwin, Sarah; Kiss, Linda D B; Huang, Weidong; Utter, Shannon; Sherwood, Thomas; Bates, Michael; Weidler, Jodi; Parry, Gordon; Winslow, John; Petropoulos, Christos J; Whitcomb, Jeannette M

    2010-06-28

    We report here the results of the analytical validation of assays that measure HER2 total protein (H2T) and HER2 homodimer (H2D) expression in Formalin Fixed Paraffin Embedded (FFPE) breast cancer tumors as well as cell line controls. The assays are based on the VeraTag technology platform and are commercially available through a central CAP-accredited clinical reference laboratory. The accuracy of H2T measurements spans a broad dynamic range (2-3 logs) as evaluated by comparison with cross-validating technologies. The measurement of H2T expression demonstrates a sensitivity that is approximately 7-10 times greater than conventional immunohistochemistry (IHC) (HercepTest). The HERmark assay is a quantitative assay that sensitively and reproducibly measures continuous H2T and H2D protein expression levels and therefore may have the potential to stratify patients more accurately with respect to response to HER2-targeted therapies than current methods which rely on semiquantitative protein measurements (IHC) or on indirect assessments of gene amplification (FISH).

  9. Reproducibility2020: Progress and priorities

    PubMed Central

    Freedman, Leonard P.; Venugopalan, Gautham; Wisman, Rosann

    2017-01-01

    The preclinical research process is a cycle of idea generation, experimentation, and reporting of results. The biomedical research community relies on the reproducibility of published discoveries to create new lines of research and to translate research findings into therapeutic applications. Since 2012, when scientists from Amgen reported that they were able to reproduce only 6 of 53 “landmark” preclinical studies, the biomedical research community began discussing the scale of the reproducibility problem and developing initiatives to address critical challenges. Global Biological Standards Institute (GBSI) released the “Case for Standards” in 2013, one of the first comprehensive reports to address the rising concern of irreproducible biomedical research. Further attention was drawn to issues that limit scientific self-correction, including reporting and publication bias, underpowered studies, lack of open access to methods and data, and lack of clearly defined standards and guidelines in areas such as reagent validation. To evaluate the progress made towards reproducibility since 2013, GBSI identified and examined initiatives designed to advance quality and reproducibility. Through this process, we identified key roles for funders, journals, researchers and other stakeholders and recommended actions for future progress. This paper describes our findings and conclusions. PMID:28620458

  10. Evaluation of NASA's MERRA Precipitation Product in Reproducing the Observed Trend and Distribution of Extreme Precipitation Events in the United States

    NASA Technical Reports Server (NTRS)

    Ashouri, Hamed; Sorooshian, Soroosh; Hsu, Kuo-Lin; Bosilovich, Michael G.; Lee, Jaechoul; Wehner, Michael F.; Collow, Allison

    2016-01-01

    This study evaluates the performance of NASA's Modern-Era Retrospective Analysis for Research and Applications (MERRA) precipitation product in reproducing the trend and distribution of extreme precipitation events. Utilizing the extreme value theory, time-invariant and time-variant extreme value distributions are developed to model the trends and changes in the patterns of extreme precipitation events over the contiguous United States during 1979-2010. The Climate Prediction Center (CPC) U.S.Unified gridded observation data are used as the observational dataset. The CPC analysis shows that the eastern and western parts of the United States are experiencing positive and negative trends in annual maxima, respectively. The continental-scale patterns of change found in MERRA seem to reasonably mirror the observed patterns of change found in CPC. This is not previously expected, given the difficulty in constraining precipitation in reanalysis products. MERRA tends to overestimate the frequency at which the 99th percentile of precipitation is exceeded because this threshold tends to be lower in MERRA, making it easier to be exceeded. This feature is dominant during the summer months. MERRA tends to reproduce spatial patterns of the scale and location parameters of the generalized extreme value and generalized Pareto distributions. However, MERRA underestimates these parameters, particularly over the Gulf Coast states, leading to lower magnitudes in extreme precipitation events. Two issues in MERRA are identified: 1) MERRA shows a spurious negative trend in Nebraska and Kansas, which is most likely related to the changes in the satellite observing system over time that has apparently affected the water cycle in the central United States, and 2) the patterns of positive trend over the Gulf Coast states and along the East Coast seem to be correlated with the tropical cyclones in these regions. The analysis of the trends in the seasonal precipitation extremes indicates that

  11. An International Ki67 Reproducibility Study

    PubMed Central

    2013-01-01

    Background In breast cancer, immunohistochemical assessment of proliferation using the marker Ki67 has potential use in both research and clinical management. However, lack of consistency across laboratories has limited Ki67’s value. A working group was assembled to devise a strategy to harmonize Ki67 analysis and increase scoring concordance. Toward that goal, we conducted a Ki67 reproducibility study. Methods Eight laboratories received 100 breast cancer cases arranged into 1-mm core tissue microarrays—one set stained by the participating laboratory and one set stained by the central laboratory, both using antibody MIB-1. Each laboratory scored Ki67 as percentage of positively stained invasive tumor cells using its own method. Six laboratories repeated scoring of 50 locally stained cases on 3 different days. Sources of variation were analyzed using random effects models with log2-transformed measurements. Reproducibility was quantified by intraclass correlation coefficient (ICC), and the approximate two-sided 95% confidence intervals (CIs) for the true intraclass correlation coefficients in these experiments were provided. Results Intralaboratory reproducibility was high (ICC = 0.94; 95% CI = 0.93 to 0.97). Interlaboratory reproducibility was only moderate (central staining: ICC = 0.71, 95% CI = 0.47 to 0.78; local staining: ICC = 0.59, 95% CI = 0.37 to 0.68). Geometric mean of Ki67 values for each laboratory across the 100 cases ranged 7.1% to 23.9% with central staining and 6.1% to 30.1% with local staining. Factors contributing to interlaboratory discordance included tumor region selection, counting method, and subjective assessment of staining positivity. Formal counting methods gave more consistent results than visual estimation. Conclusions Substantial variability in Ki67 scoring was observed among some of the world’s most experienced laboratories. Ki67 values and cutoffs for clinical decision-making cannot be transferred between laboratories without

  12. Tau-independent Phase Analysis: A Novel Method for Accurately Determining Phase Shifts.

    PubMed

    Tackenberg, Michael C; Jones, Jeff R; Page, Terry L; Hughey, Jacob J

    2018-06-01

    Estimations of period and phase are essential in circadian biology. While many techniques exist for estimating period, comparatively few methods are available for estimating phase. Current approaches to analyzing phase often vary between studies and are sensitive to coincident changes in period and the stage of the circadian cycle at which the stimulus occurs. Here we propose a new technique, tau-independent phase analysis (TIPA), for quantifying phase shifts in multiple types of circadian time-course data. Through comprehensive simulations, we show that TIPA is both more accurate and more precise than the standard actogram approach. TIPA is computationally simple and therefore will enable accurate and reproducible quantification of phase shifts across multiple subfields of chronobiology.

  13. Reproducible surface-enhanced Raman quantification of biomarkers in multicomponent mixtures.

    PubMed

    De Luca, Anna Chiara; Reader-Harris, Peter; Mazilu, Michael; Mariggiò, Stefania; Corda, Daniela; Di Falco, Andrea

    2014-03-25

    Direct and quantitative detection of unlabeled glycerophosphoinositol (GroPIns), an abundant cytosolic phosphoinositide derivative, would allow rapid evaluation of several malignant cell transformations. Here we report label-free analysis of GroPIns via surface-enhanced Raman spectroscopy (SERS) with a sensitivity of 200 nM, well below its apparent concentration in cells. Crucially, our SERS substrates, based on lithographically defined gold nanofeatures, can be used to predict accurately the GroPIns concentration even in multicomponent mixtures, avoiding the preliminary separation of individual compounds. Our results represent a critical step toward the creation of SERS-based biosensor for rapid, label-free, and reproducible detection of specific molecules, overcoming limits of current experimental methods.

  14. Repeatability and reproducibility of corneal thickness using SOCT Copernicus HR.

    PubMed

    Vidal, Silvia; Viqueira, Valentín; Mas, David; Domenech, Begoña

    2013-05-01

    The aim of this study is to determine the reliability of corneal thickness measurements derived from SOCT Copernicus HR (Fourier domain OCT). Thirty healthy eyes of 30 subjects were evaluated. One eye of each patient was chosen randomly. Images were obtained of the central (up to 2.0 mm from the corneal apex) and paracentral (2.0 to 4.0 mm) cornea. We assessed corneal thickness (central and paracentral) and epithelium thickness. The intra-observer repeatability data were analysed using the intra-class correlation coefficient (ICC) for a range of 95 per cent within-subject standard deviation (S(W)) and the within-subject coefficient of variation (C(W)). The level of agreement by Bland-Altman analysis was also represented for the study of the reproducibility between observers and agreement between methods of measurement (automatic versus manual). The mean value of the central corneal thickness (CCT) was 542.4 ± 30.1 μm (SD). There was a high intra-observer agreement, finding the best result in the central sector with an intra-class correlation coefficient of 0.99, 95 per cent CI (0.989 to 0.997) and the worst, in the minimum corneal thickness, with an intra-class correlation coefficient of 0.672, 95 per cent CI (0.417 to 0.829). Reproducibility between observers was very high. The best result was found in the central sector thickness obtained both manually and automatically with an intra-class correlation coefficient of 0.990 in both cases and the worst result in the maximum corneal thickness with an intra-class correlation coefficient of 0.827. The agreement between measurement methods was also very high with intra-class correlation coefficient greater than 0.91. On the other hand the repeatability and reproducibility for epithelial measurements was poor. Pachymetric mapping with SOCT Copernicus HR was found to be highly repeatable and reproducible. We found that the device lacks an appropriate ergonomic design as proper focusing of the laser beam onto the

  15. Exploring the reproducibility of functional connectivity alterations in Parkinson’s disease

    PubMed Central

    Onu, Mihaela; Wu, Tao; Roceanu, Adina; Bajenaru, Ovidiu

    2017-01-01

    Since anatomic MRI is presently not able to directly discern neuronal loss in Parkinson’s Disease (PD), studying the associated functional connectivity (FC) changes seems a promising approach toward developing non-invasive and non-radioactive neuroimaging markers for this disease. While several groups have reported such FC changes in PD, there are also significant discrepancies between studies. Investigating the reproducibility of PD-related FC changes on independent datasets is therefore of crucial importance. We acquired resting-state fMRI scans for 43 subjects (27 patients and 16 normal controls, with 2 replicate scans per subject) and compared the observed FC changes with those obtained in two independent datasets, one made available by the PPMI consortium (91 patients, 18 controls) and a second one by the group of Tao Wu (20 patients, 20 controls). Unfortunately, PD-related functional connectivity changes turned out to be non-reproducible across datasets. This could be due to disease heterogeneity, but also to technical differences. To distinguish between the two, we devised a method to directly check for disease heterogeneity using random splits of a single dataset. Since we still observe non-reproducibility in a large fraction of random splits of the same dataset, we conclude that functional heterogeneity may be a dominating factor behind the lack of reproducibility of FC alterations in different rs-fMRI studies of PD. While global PD-related functional connectivity changes were non-reproducible across datasets, we identified a few individual brain region pairs with marginally consistent FC changes across all three datasets. However, training classifiers on each one of the three datasets to discriminate PD scans from controls produced only low accuracies on the remaining two test datasets. Moreover, classifiers trained and tested on random splits of the same dataset (which are technically homogeneous) also had low test accuracies, directly substantiating

  16. Reproducibility of cine displacement encoding with stimulated echoes (DENSE) cardiovascular magnetic resonance for measuring left ventricular strains, torsion, and synchrony in mice.

    PubMed

    Haggerty, Christopher M; Kramer, Sage P; Binkley, Cassi M; Powell, David K; Mattingly, Andrea C; Charnigo, Richard; Epstein, Frederick H; Fornwalt, Brandon K

    2013-08-27

    Advanced measures of cardiac function are increasingly important to clinical assessment due to their superior diagnostic and predictive capabilities. Cine DENSE cardiovascular magnetic resonance (CMR) is ideal for quantifying advanced measures of cardiac function based on its high spatial resolution and streamlined post-processing. While many studies have utilized cine DENSE in both humans and small-animal models, the inter-test and inter-observer reproducibility for quantification of advanced cardiac function in mice has not been evaluated. This represents a critical knowledge gap for both understanding the capabilities of this technique and for the design of future experiments. We hypothesized that cine DENSE CMR would show excellent inter-test and inter-observer reproducibility for advanced measures of left ventricular (LV) function in mice. Five normal mice (C57BL/6) and four mice with depressed cardiac function (diet-induced obesity) were imaged twice, two days apart, on a 7T ClinScan MR system. Images were acquired with 15-20 frames per cardiac cycle in three short-axis (basal, mid, apical) and two long-axis orientations (4-chamber and 2-chamber). LV strain, twist, torsion, and measures of synchrony were quantified. Images from both days were analyzed by one observer to quantify inter-test reproducibility, while inter-observer reproducibility was assessed by a second observer's analysis of day-1 images. The coefficient of variation (CoV) was used to quantify reproducibility. LV strains and torsion were highly reproducible on both inter-observer and inter-test bases with CoVs ≤ 15%, and inter-observer reproducibility was generally better than inter-test reproducibility. However, end-systolic twist angles showed much higher variance, likely due to the sensitivity of slice location within the sharp longitudinal gradient in twist angle. Measures of synchrony including the circumferential (CURE) and radial (RURE) uniformity of strain indices, showed excellent

  17. Properties of galaxies reproduced by a hydrodynamic simulation

    NASA Astrophysics Data System (ADS)

    Vogelsberger, M.; Genel, S.; Springel, V.; Torrey, P.; Sijacki, D.; Xu, D.; Snyder, G.; Bird, S.; Nelson, D.; Hernquist, L.

    2014-05-01

    Previous simulations of the growth of cosmic structures have broadly reproduced the `cosmic web' of galaxies that we see in the Universe, but failed to create a mixed population of elliptical and spiral galaxies, because of numerical inaccuracies and incomplete physical models. Moreover, they were unable to track the small-scale evolution of gas and stars to the present epoch within a representative portion of the Universe. Here we report a simulation that starts 12 million years after the Big Bang, and traces 13 billion years of cosmic evolution with 12 billion resolution elements in a cube of 106.5 megaparsecs a side. It yields a reasonable population of ellipticals and spirals, reproduces the observed distribution of galaxies in clusters and characteristics of hydrogen on large scales, and at the same time matches the `metal' and hydrogen content of galaxies on small scales.

  18. Reproducibility of positive results for the detection of serum galactomannan by Platelia™ aspergillus EIA.

    PubMed

    Pedroza, Kelly C M C; de Matos, Sócrates B; de Moura, Daniel L; Oliveira, Mônica B B; Araújo, Marco A S; Nascimento, Roberto J M; Lima, Fernanda W M

    2013-10-01

    Galactomannan (GM) was recently included in consensus guidelines as an indirect mycological criterion for the diagnosis of invasive aspergillosis. Currently, there is an enzyme immunoassay available to detect GM in biological samples, the Platelia™ Aspergillus EIA. In this study, the reproducibility of positive results obtained using this assay was evaluated using serum samples from neutropenic patients. A trend toward lower values was observed, and 55 %(27/49) of positive results were negative after retesting. A low reproducibility of positive results for the detection of GM in serum was observed.

  19. In Spite of Indeterminacy Many Common Factor Score Estimates Yield an Identical Reproduced Covariance Matrix

    ERIC Educational Resources Information Center

    Beauducel, Andre

    2007-01-01

    It was investigated whether commonly used factor score estimates lead to the same reproduced covariance matrix of observed variables. This was achieved by means of Schonemann and Steiger's (1976) regression component analysis, since it is possible to compute the reproduced covariance matrices of the regression components corresponding to different…

  20. Reproducibility in Data-Scarce Environments

    NASA Astrophysics Data System (ADS)

    Darch, P. T.

    2016-12-01

    Among the usual requirements for reproducibility are large volumes of data and computationally intensive methods. Many fields within earth sciences, however, do not meet these requirements. Data are scarce and data-intensive methods are not well established. How can science be reproducible under these conditions? What changes, both infrastructural and cultural, are needed to advance reproducibility? This paper presents findings from a long-term social scientific case study of an emergent and data scarce field, the deep subseafloor biosphere. This field studies interactions between microbial communities living in the seafloor and the physical environments they inhabit. Factors such as these make reproducibility seem a distant goal for this community: - The relative newness of the field. Serious study began in the late 1990s; - The highly multidisciplinary nature of the field. Researchers come from a range of physical and life science backgrounds; - Data scarcity. Domain researchers produce much of these data in their own onshore laboratories by analyzing cores from international ocean drilling expeditions. Allocation of cores is negotiated between researchers from many fields. These factors interact in multiple ways to inhibit reproducibility: - Incentive structures emphasize producing new data and new knowledge rather than reanalysing extant data; - Only a few steps of laboratory analyses can be reproduced - such as analysis of DNA sequences, but not extraction of DNA from cores -, due to scarcity of cores; - Methodological heterogeneity is a consequence of multidisciplinarity, as researchers bring different techniques from diverse fields. - Few standards for data collection or analysis are available at this early stage of the field; - While datasets from multiple biological and physical phenomena can be integrated into a single workflow, curation tends to be divergent. Each type of dataset may be subject to different disparate policies and contributed to different

  1. Composting in small laboratory pilots: Performance and reproducibility

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Lashermes, G.; Barriuso, E.; Le Villio-Poitrenaud, M.

    2012-02-15

    final compost. The TOM losses, compost stabilisation and evolution of the biochemical fractions were similar to observed in large reactors or on-site experiments, excluding the lignin degradation, which was less important than in full-scale systems. The reproducibility of the process and the quality of the final compost make it possible to propose the use of this experimental device for research requiring a mass reduction of the initial composted waste mixtures.« less

  2. Accurate SERS detection of malachite green in aquatic products on basis of graphene wrapped flexible sensor.

    PubMed

    Ouyang, Lei; Yao, Ling; Zhou, Taohong; Zhu, Lihua

    2018-10-16

    Malachite Green (MG) is a banned pesticide for aquaculture products. As a required inspection item, its fast and accurate determination before the products' accessing market is very important. Surface enhanced Raman scattering (SERS) is a promising tool for MG sensing, but it requires the overcoming of several problems such as fairly poor sensitivity and reproducibility, especially laser induced chemical conversion and photo-bleaching during SERS observation. By using a graphene wrapped Ag array based flexible membrane sensor, a modified SERS strategy was proposed for the sensitive and accurate detection of MG. The graphene layer functioned as an inert protector for impeding chemical transferring of the bioproduct Leucomalachite Green (LMG) to MG during the SERS detection, and as a heat transmitter for preventing laser induced photo-bleaching, which enables the separate detection of MG and LMG in fish extracts. The combination of the Ag array and the graphene cover also produced plentiful densely and uniformly distributed hot spots, leading to analytical enhancement factor up to 3.9 × 10 8 and excellent reproducibility (relative standard deviation low to 5.8% for 70 runs). The proposed method was easily used for MG detection with limit of detection (LOD) as low as 2.7 × 10 -11  mol L -1 . The flexibility of the sensor enable it have a merit for in-field fast detection of MG residues on the scale of a living fish through a surface extraction and paste transferring manner. The developed strategy was successfully applied in the analysis of real samples, showing good prospects for both the fast inspection and quantitative detection of MG. Copyright © 2018 Elsevier B.V. All rights reserved.

  3. Reproducing (and Disrupting) Heteronormativity: Gendered Sexual Socialization in Preschool Classrooms

    ERIC Educational Resources Information Center

    Gansen, Heidi M.

    2017-01-01

    Using ethnographic data from 10 months of observations in nine preschool classrooms, I examine gendered sexual socialization children receive from teachers' practices and reproduce through peer interactions. I find heteronormativity permeates preschool classrooms, where teachers construct (and occasionally disrupt) gendered sexuality in a number…

  4. Accurate Nanoscale Crystallography in Real-Space Using Scanning Transmission Electron Microscopy.

    PubMed

    Dycus, J Houston; Harris, Joshua S; Sang, Xiahan; Fancher, Chris M; Findlay, Scott D; Oni, Adedapo A; Chan, Tsung-Ta E; Koch, Carl C; Jones, Jacob L; Allen, Leslie J; Irving, Douglas L; LeBeau, James M

    2015-08-01

    Here, we report reproducible and accurate measurement of crystallographic parameters using scanning transmission electron microscopy. This is made possible by removing drift and residual scan distortion. We demonstrate real-space lattice parameter measurements with <0.1% error for complex-layered chalcogenides Bi2Te3, Bi2Se3, and a Bi2Te2.7Se0.3 nanostructured alloy. Pairing the technique with atomic resolution spectroscopy, we connect local structure with chemistry and bonding. Combining these results with density functional theory, we show that the incorporation of Se into Bi2Te3 causes charge redistribution that anomalously increases the van der Waals gap between building blocks of the layered structure. The results show that atomic resolution imaging with electrons can accurately and robustly quantify crystallography at the nanoscale.

  5. Analytical Validation of a Highly Quantitative, Sensitive, Accurate, and Reproducible Assay (HERmark®) for the Measurement of HER2 Total Protein and HER2 Homodimers in FFPE Breast Cancer Tumor Specimens

    PubMed Central

    Larson, Jeffrey S.; Goodman, Laurie J.; Tan, Yuping; Defazio-Eli, Lisa; Paquet, Agnes C.; Cook, Jennifer W.; Rivera, Amber; Frankson, Kristi; Bose, Jolly; Chen, Lili; Cheung, Judy; Shi, Yining; Irwin, Sarah; Kiss, Linda D. B.; Huang, Weidong; Utter, Shannon; Sherwood, Thomas; Bates, Michael; Weidler, Jodi; Parry, Gordon; Winslow, John; Petropoulos, Christos J.; Whitcomb, Jeannette M.

    2010-01-01

    We report here the results of the analytical validation of assays that measure HER2 total protein (H2T) and HER2 homodimer (H2D) expression in Formalin Fixed Paraffin Embedded (FFPE) breast cancer tumors as well as cell line controls. The assays are based on the VeraTag technology platform and are commercially available through a central CAP-accredited clinical reference laboratory. The accuracy of H2T measurements spans a broad dynamic range (2-3 logs) as evaluated by comparison with cross-validating technologies. The measurement of H2T expression demonstrates a sensitivity that is approximately 7–10 times greater than conventional immunohistochemistry (IHC) (HercepTest). The HERmark assay is a quantitative assay that sensitively and reproducibly measures continuous H2T and H2D protein expression levels and therefore may have the potential to stratify patients more accurately with respect to response to HER2-targeted therapies than current methods which rely on semiquantitative protein measurements (IHC) or on indirect assessments of gene amplification (FISH). PMID:21151530

  6. GeoTrust Hub: A Platform For Sharing And Reproducing Geoscience Applications

    NASA Astrophysics Data System (ADS)

    Malik, T.; Tarboton, D. G.; Goodall, J. L.; Choi, E.; Bhatt, A.; Peckham, S. D.; Foster, I.; Ton That, D. H.; Essawy, B.; Yuan, Z.; Dash, P. K.; Fils, G.; Gan, T.; Fadugba, O. I.; Saxena, A.; Valentic, T. A.

    2017-12-01

    Recent requirements of scholarly communication emphasize the reproducibility of scientific claims. Text-based research papers are considered poor mediums to establish reproducibility. Papers must be accompanied by "research objects", aggregation of digital artifacts that together with the paper provide an authoritative record of a piece of research. We will present GeoTrust Hub (http://geotrusthub.org), a platform for creating, sharing, and reproducing reusable research objects. GeoTrust Hub provides tools for scientists to create `geounits'--reusable research objects. Geounits are self-contained, annotated, and versioned containers that describe and package computational experiments in an efficient and light-weight manner. Geounits can be shared on public repositories such as HydroShare and FigShare, and also using their respective APIs reproduced on provisioned clouds. The latter feature enables science applications to have a lifetime beyond sharing, wherein they can be independently verified and trust be established as they are repeatedly reused. Through research use cases from several geoscience laboratories across the United States, we will demonstrate how tools provided from GeoTrust Hub along with Hydroshare as its public repository for geounits is advancing the state of reproducible research in the geosciences. For each use case, we will address different computational reproducibility requirements. Our first use case will be an example of setup reproducibility which enables a scientist to set up and reproduce an output from a model with complex configuration and development environments. Our second use case will be an example of algorithm/data reproducibility, where in a shared data science model/dataset can be substituted with an alternate one to verify model output results, and finally an example of interactive reproducibility, in which an experiment is dependent on specific versions of data to produce the result. Toward this we will use software and data

  7. Accurate CT-MR image registration for deep brain stimulation: a multi-observer evaluation study

    NASA Astrophysics Data System (ADS)

    Rühaak, Jan; Derksen, Alexander; Heldmann, Stefan; Hallmann, Marc; Meine, Hans

    2015-03-01

    Since the first clinical interventions in the late 1980s, Deep Brain Stimulation (DBS) of the subthalamic nucleus has evolved into a very effective treatment option for patients with severe Parkinson's disease. DBS entails the implantation of an electrode that performs high frequency stimulations to a target area deep inside the brain. A very accurate placement of the electrode is a prerequisite for positive therapy outcome. The assessment of the intervention result is of central importance in DBS treatment and involves the registration of pre- and postinterventional scans. In this paper, we present an image processing pipeline for highly accurate registration of postoperative CT to preoperative MR. Our method consists of two steps: a fully automatic pre-alignment using a detection of the skull tip in the CT based on fuzzy connectedness, and an intensity-based rigid registration. The registration uses the Normalized Gradient Fields distance measure in a multilevel Gauss-Newton optimization framework and focuses on a region around the subthalamic nucleus in the MR. The accuracy of our method was extensively evaluated on 20 DBS datasets from clinical routine and compared with manual expert registrations. For each dataset, three independent registrations were available, thus allowing to relate algorithmic with expert performance. Our method achieved an average registration error of 0.95mm in the target region around the subthalamic nucleus as compared to an inter-observer variability of 1.12 mm. Together with the short registration time of about five seconds on average, our method forms a very attractive package that can be considered ready for clinical use.

  8. Organ-on-a-Chip Technology for Reproducing Multiorgan Physiology.

    PubMed

    Lee, Seung Hwan; Sung, Jong Hwan

    2018-01-01

    In the drug development process, the accurate prediction of drug efficacy and toxicity is important in order to reduce the cost, labor, and effort involved. For this purpose, conventional 2D cell culture models are used in the early phase of drug development. However, the differences between the in vitro and the in vivo systems have caused the failure of drugs in the later phase of the drug-development process. Therefore, there is a need for a novel in vitro model system that can provide accurate information for evaluating the drug efficacy and toxicity through a closer recapitulation of the in vivo system. Recently, the idea of using microtechnology for mimicking the microscale tissue environment has become widespread, leading to the development of "organ-on-a-chip." Furthermore, the system is further developed for realizing a multiorgan model for mimicking interactions between multiple organs. These advancements are still ongoing and are aimed at ultimately developing "body-on-a-chip" or "human-on-a-chip" devices for predicting the response of the whole body. This review summarizes recently developed organ-on-a-chip technologies, and their applications for reproducing multiorgan functions. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Testing Reproducibility in Earth Sciences

    NASA Astrophysics Data System (ADS)

    Church, M. A.; Dudill, A. R.; Frey, P.; Venditti, J. G.

    2017-12-01

    Reproducibility represents how closely the results of independent tests agree when undertaken using the same materials but different conditions of measurement, such as operator, equipment or laboratory. The concept of reproducibility is fundamental to the scientific method as it prevents the persistence of incorrect or biased results. Yet currently the production of scientific knowledge emphasizes rapid publication of previously unreported findings, a culture that has emerged from pressures related to hiring, publication criteria and funding requirements. Awareness and critique of the disconnect between how scientific research should be undertaken, and how it actually is conducted, has been prominent in biomedicine for over a decade, with the fields of economics and psychology more recently joining the conversation. The purpose of this presentation is to stimulate the conversation in earth sciences where, despite implicit evidence in widely accepted classifications, formal testing of reproducibility is rare.As a formal test of reproducibility, two sets of experiments were undertaken with the same experimental procedure, at the same scale, but in different laboratories. Using narrow, steep flumes and spherical glass beads, grain size sorting was examined by introducing fine sediment of varying size and quantity into a mobile coarse bed. The general setup was identical, including flume width and slope; however, there were some variations in the materials, construction and lab environment. Comparison of the results includes examination of the infiltration profiles, sediment mobility and transport characteristics. The physical phenomena were qualitatively reproduced but not quantitatively replicated. Reproduction of results encourages more robust research and reporting, and facilitates exploration of possible variations in data in various specific contexts. Following the lead of other fields, testing of reproducibility can be incentivized through changes to journal

  10. High-Reproducibility and High-Accuracy Method for Automated Topic Classification

    NASA Astrophysics Data System (ADS)

    Lancichinetti, Andrea; Sirer, M. Irmak; Wang, Jane X.; Acuna, Daniel; Körding, Konrad; Amaral, Luís A. Nunes

    2015-01-01

    Much of human knowledge sits in large databases of unstructured text. Leveraging this knowledge requires algorithms that extract and record metadata on unstructured text documents. Assigning topics to documents will enable intelligent searching, statistical characterization, and meaningful classification. Latent Dirichlet allocation (LDA) is the state of the art in topic modeling. Here, we perform a systematic theoretical and numerical analysis that demonstrates that current optimization techniques for LDA often yield results that are not accurate in inferring the most suitable model parameters. Adapting approaches from community detection in networks, we propose a new algorithm that displays high reproducibility and high accuracy and also has high computational efficiency. We apply it to a large set of documents in the English Wikipedia and reveal its hierarchical structure.

  11. Evaluation of NASA’s MERRA Precipitation Product in Reproducing the Observed Trend and Distribution of Extreme Precipitation Events in the United States

    DOE PAGES

    Ashouri, Hamed; Sorooshian, Soroosh; Hsu, Kuo-Lin; ...

    2016-02-03

    This study evaluates the performance of NASA's Modern-Era Retrospective Analysis for Research and Applications (MERRA) precipitation product in reproducing the trend and distribution of extreme precipitation events. Utilizing the extreme value theory, time-invariant and time-variant extreme value distributions are developed to model the trends and changes in the patterns of extreme precipitation events over the contiguous United States during 1979-2010. The Climate Prediction Center (CPC)U.S.Unified gridded observation data are used as the observational dataset. The CPC analysis shows that the eastern and western parts of the United States are experiencing positive and negative trends in annual maxima, respectively. The continental-scalemore » patterns of change found in MERRA seem to reasonably mirror the observed patterns of change found in CPC. This is not previously expected, given the difficulty in constraining precipitation in reanalysis products. MERRA tends to overestimate the frequency at which the 99th percentile of precipitation is exceeded because this threshold tends to be lower in MERRA, making it easier to be exceeded. This feature is dominant during the summer months. MERRAtends to reproduce spatial patterns of the scale and location parameters of the generalized extreme value and generalized Pareto distributions. However, MERRA underestimates these parameters, particularly over the Gulf Coast states, leading to lower magnitudes in extreme precipitation events. Two issues in MERRA are identified: 1)MERRAshows a spurious negative trend in Nebraska andKansas, which ismost likely related to the changes in the satellite observing system over time that has apparently affected the water cycle in the central United States, and 2) the patterns of positive trend over theGulf Coast states and along the East Coast seem to be correlated with the tropical cyclones in these regions. The analysis of the trends in the seasonal precipitation extremes indicates

  12. Threshold level for measurement of UV sensitivity: reproducibility of phototest.

    PubMed

    Lock-Andersen, J; Wulf, H C

    1996-08-01

    The ultraviolet (UV) sensitivity is determined by a phototest where the skin is exposed to well-defined doses of UV radiation and the resulting erythema is graded by visual scoring after 20-24 h. In this study we wanted to estimate the reproducibility of erythema assessment in phototesting. Twenty-one healthy Caucasians with skin types I to IV were phototested on UV un-exposed buttock skin using a xenon lamp solar simulator. Twenty-four hours after UV exposure eight physicians independently graded the erythema reactions two times. Data were analysed using inter- and intra-observer agreement and kappa statistics, which adjusts for agreement that could be caused by chance alone. Observed agreement and kappa statistics were found to decrease with increasing intensity of erythema and to be lower for skin types III and IV compared to skin types I and II. Intra-observer agreement was uniformly better than inter-observer agreement. The difference between observers assessment could be as much as three clinical erythema grades. Physicians's previous experience with phototesting only had a minor influence on agreement. In conclusion, phototesting is based on subjective assessment of erythema and is not as precise and reproducible as expected. Agreement was better for barely perceptible erythema than for erythema with a well-defined border and we therefore recommend that the barely perceptible erythema reaction should be used for measurement of the minimal erythema dose.

  13. Properties of galaxies reproduced by a hydrodynamic simulation.

    PubMed

    Vogelsberger, M; Genel, S; Springel, V; Torrey, P; Sijacki, D; Xu, D; Snyder, G; Bird, S; Nelson, D; Hernquist, L

    2014-05-08

    Previous simulations of the growth of cosmic structures have broadly reproduced the 'cosmic web' of galaxies that we see in the Universe, but failed to create a mixed population of elliptical and spiral galaxies, because of numerical inaccuracies and incomplete physical models. Moreover, they were unable to track the small-scale evolution of gas and stars to the present epoch within a representative portion of the Universe. Here we report a simulation that starts 12 million years after the Big Bang, and traces 13 billion years of cosmic evolution with 12 billion resolution elements in a cube of 106.5 megaparsecs a side. It yields a reasonable population of ellipticals and spirals, reproduces the observed distribution of galaxies in clusters and characteristics of hydrogen on large scales, and at the same time matches the 'metal' and hydrogen content of galaxies on small scales.

  14. A numerical model to reproduce squeaking of ceramic-on-ceramic total hip arthroplasty. Influence of design and material.

    PubMed

    Piriou, P; Ouenzerfi, G; Migaud, H; Renault, E; Massi, F; Serrault, M

    2016-06-01

    Modern ceramic (CoC) bearings for hip arthroplasty (THA) have been used in younger patients who expect improved survivorship. However, audible squeaking produced by the implant is an annoying complication. Previous numerical simulations were not able to accurately reproduce in vitro and in vivo observations. Therefore, we developed a finite element model to: (1) reproduce in vitro squeaking and validate the model by comparing it with in vivo recordings, (2) determine why there are differences between in vivo and in vitro squeaking frequencies, (3) identify the stem's role in this squeaking, (4) predict which designs and materials are more likely to produce squeaking. A CoC THA numerical model can be developed that reproduces the squeaking frequencies observed in vivo. Numerical methods (finite element analysis [ANSYS]) and experimental methods (using a non-lubricated simulated hip with a cementless 32mm CoC THA) were developed to reproduce squeaking. Numerical analysis was performed to identify the frequencies that cause vibrations perceived as an acoustic emission. The finite element analysis (FEA) model was enhanced by adjusting periprosthetic bone and soft tissue elements in order to reproduce the squeaking frequencies recorded in vivo. A numerical method (complex eigenvalue analysis) was used to find the acoustic frequencies of the squeaking noise. The frequencies obtained from the model and the hip simulator were compared to those recorded in vivo. The numerical results were validated by experiments with the laboratory hip simulator. The frequencies obtained (mean 2790Hz with FEA, 2755Hz with simulator, decreasing to 1759Hz when bone and soft tissue were included in the FEA) were consistent with those of squeaking hips recorded in vivo (1521Hz). The cup and ceramic insert were the source of the vibration, but had little influence on the diffusion of the noise required to make the squeaking audible to the human ear. The FEA showed that diffusion of squeaking

  15. A new approach to compute accurate velocity of meteors

    NASA Astrophysics Data System (ADS)

    Egal, Auriane; Gural, Peter; Vaubaillon, Jeremie; Colas, Francois; Thuillot, William

    2016-10-01

    The CABERNET project was designed to push the limits of meteoroid orbit measurements by improving the determination of the meteors' velocities. Indeed, despite of the development of the cameras networks dedicated to the observation of meteors, there is still an important discrepancy between the measured orbits of meteoroids computed and the theoretical results. The gap between the observed and theoretic semi-major axis of the orbits is especially significant; an accurate determination of the orbits of meteoroids therefore largely depends on the computation of the pre-atmospheric velocities. It is then imperative to dig out how to increase the precision of the measurements of the velocity.In this work, we perform an analysis of different methods currently used to compute the velocities and trajectories of the meteors. They are based on the intersecting planes method developed by Ceplecha (1987), the least squares method of Borovicka (1990), and the multi-parameter fitting (MPF) method published by Gural (2012).In order to objectively compare the performances of these techniques, we have simulated realistic meteors ('fakeors') reproducing the different error measurements of many cameras networks. Some fakeors are built following the propagation models studied by Gural (2012), and others created by numerical integrations using the Borovicka et al. 2007 model. Different optimization techniques have also been investigated in order to pick the most suitable one to solve the MPF, and the influence of the geometry of the trajectory on the result is also presented.We will present here the results of an improved implementation of the multi-parameter fitting that allow an accurate orbit computation of meteors with CABERNET. The comparison of different velocities computation seems to show that if the MPF is by far the best method to solve the trajectory and the velocity of a meteor, the ill-conditioning of the costs functions used can lead to large estimate errors for noisy

  16. The effect of sample holder material on ion mobility spectrometry reproducibility

    NASA Technical Reports Server (NTRS)

    Jadamec, J. Richard; Su, Chih-Wu; Rigdon, Stephen; Norwood, Lavan

    1995-01-01

    When a positive detection of a narcotic occurs during the search of a vessel, a decision has to be made whether further intensive search is warranted. This decision is based in part on the results of a second sample collected from the same area. Therefore, the reproducibility of both sampling and instrumental analysis is critical in terms of justifying an in depth search. As reported at the 2nd Annual IMS Conference in Quebec City, the U.S. Coast Guard has determined that when paper is utilized as the sample desorption medium for the Barringer IONSCAN, the analytical results using standard reference samples are reproducible. A study was conducted utilizing papers of varying pore sizes and comparing their performance as a desorption material relative to the standard Barringer 50 micron Teflon. Nominal pore sizes ranged from 30 microns down to 2 microns. Results indicate that there is some peak instability in the first two to three windows during the analysis. The severity of the instability was observed to increase as the pore size of the paper is decreased. However, the observed peak instability does not create a situation that results in a decreased reliability or reproducibility in the analytical result.

  17. Gene expression profiling of whole blood: Comparison of target preparation methods for accurate and reproducible microarray analysis

    PubMed Central

    Vartanian, Kristina; Slottke, Rachel; Johnstone, Timothy; Casale, Amanda; Planck, Stephen R; Choi, Dongseok; Smith, Justine R; Rosenbaum, James T; Harrington, Christina A

    2009-01-01

    Background Peripheral blood is an accessible and informative source of transcriptomal information for many human disease and pharmacogenomic studies. While there can be significant advantages to analyzing RNA isolated from whole blood, particularly in clinical studies, the preparation of samples for microarray analysis is complicated by the need to minimize artifacts associated with highly abundant globin RNA transcripts. The impact of globin RNA transcripts on expression profiling data can potentially be reduced by using RNA preparation and labeling methods that remove or block globin RNA during the microarray assay. We compared four different methods for preparing microarray hybridization targets from human whole blood collected in PAXGene tubes. Three of the methods utilized the Affymetrix one-cycle cDNA synthesis/in vitro transcription protocol but varied treatment of input RNA as follows: i. no treatment; ii. treatment with GLOBINclear; or iii. treatment with globin PNA oligos. In the fourth method cDNA targets were prepared with the Ovation amplification and labeling system. Results We find that microarray targets generated with labeling methods that reduce globin mRNA levels or minimize the impact of globin transcripts during hybridization detect more transcripts in the microarray assay compared with the standard Affymetrix method. Comparison of microarray results with quantitative PCR analysis of a panel of genes from the NF-kappa B pathway shows good correlation of transcript measurements produced with all four target preparation methods, although method-specific differences in overall correlation were observed. The impact of freezing blood collected in PAXGene tubes on data reproducibility was also examined. Expression profiles show little or no difference when RNA is extracted from either fresh or frozen blood samples. Conclusion RNA preparation and labeling methods designed to reduce the impact of globin mRNA transcripts can significantly improve the

  18. Verification of land-atmosphere coupling in forecast models, reanalyses and land surface models using flux site observations.

    PubMed

    Dirmeyer, Paul A; Chen, Liang; Wu, Jiexia; Shin, Chul-Su; Huang, Bohua; Cash, Benjamin A; Bosilovich, Michael G; Mahanama, Sarith; Koster, Randal D; Santanello, Joseph A; Ek, Michael B; Balsamo, Gianpaolo; Dutra, Emanuel; Lawrence, D M

    2018-02-01

    We confront four model systems in three configurations (LSM, LSM+GCM, and reanalysis) with global flux tower observations to validate states, surface fluxes, and coupling indices between land and atmosphere. Models clearly under-represent the feedback of surface fluxes on boundary layer properties (the atmospheric leg of land-atmosphere coupling), and may over-represent the connection between soil moisture and surface fluxes (the terrestrial leg). Models generally under-represent spatial and temporal variability relative to observations, which is at least partially an artifact of the differences in spatial scale between model grid boxes and flux tower footprints. All models bias high in near-surface humidity and downward shortwave radiation, struggle to represent precipitation accurately, and show serious problems in reproducing surface albedos. These errors create challenges for models to partition surface energy properly and errors are traceable through the surface energy and water cycles. The spatial distribution of the amplitude and phase of annual cycles (first harmonic) are generally well reproduced, but the biases in means tend to reflect in these amplitudes. Interannual variability is also a challenge for models to reproduce. Our analysis illuminates targets for coupled land-atmosphere model development, as well as the value of long-term globally-distributed observational monitoring.

  19. [Reproducibility of subjective refraction measurement].

    PubMed

    Grein, H-J; Schmidt, O; Ritsche, A

    2014-11-01

    Reproducibility of subjective refraction measurement is limited by various factors. The main factors affecting reproducibility include the characteristics of the measurement method and of the subject and the examiner. This article presents the results of a study on this topic, focusing on the reproducibility of subjective refraction measurement in healthy eyes. The results of previous studies are not all presented in the same way by the respective authors and cannot be fully standardized without consulting the original scientific data. To the extent that they are comparable, the results of our study largely correspond largely with those of previous investigations: During repeated subjective refraction measurement, 95% of the deviation from the mean value was approximately ±0.2 D to ±0.65 D for the spherical equivalent and cylindrical power. The reproducibility of subjective refraction measurement in healthy eyes is limited, even under ideal conditions. Correct assessment of refraction results is only feasible after identifying individual variability. Several measurements are required. Refraction cannot be measured without a tolerance range. The English full-text version of this article is available at SpringerLink (under supplemental).

  20. Assessing the accuracy and reproducibility of modality independent elastography in a murine model of breast cancer

    PubMed Central

    Weis, Jared A.; Flint, Katelyn M.; Sanchez, Violeta; Yankeelov, Thomas E.; Miga, Michael I.

    2015-01-01

    Abstract. Cancer progression has been linked to mechanics. Therefore, there has been recent interest in developing noninvasive imaging tools for cancer assessment that are sensitive to changes in tissue mechanical properties. We have developed one such method, modality independent elastography (MIE), that estimates the relative elastic properties of tissue by fitting anatomical image volumes acquired before and after the application of compression to biomechanical models. The aim of this study was to assess the accuracy and reproducibility of the method using phantoms and a murine breast cancer model. Magnetic resonance imaging data were acquired, and the MIE method was used to estimate relative volumetric stiffness. Accuracy was assessed using phantom data by comparing to gold-standard mechanical testing of elasticity ratios. Validation error was <12%. Reproducibility analysis was performed on animal data, and within-subject coefficients of variation ranged from 2 to 13% at the bulk level and 32% at the voxel level. To our knowledge, this is the first study to assess the reproducibility of an elasticity imaging metric in a preclinical cancer model. Our results suggest that the MIE method can reproducibly generate accurate estimates of the relative mechanical stiffness and provide guidance on the degree of change needed in order to declare biological changes rather than experimental error in future therapeutic studies. PMID:26158120

  1. An inter-observer Ki67 reproducibility study applying two different assessment methods: on behalf of the Danish Scientific Committee of Pathology, Danish breast cancer cooperative group (DBCG).

    PubMed

    Laenkholm, Anne-Vibeke; Grabau, Dorthe; Møller Talman, Maj-Lis; Balslev, Eva; Bak Jylling, Anne Marie; Tabor, Tomasz Piotr; Johansen, Morten; Brügmann, Anja; Lelkaitis, Giedrius; Di Caterino, Tina; Mygind, Henrik; Poulsen, Thomas; Mertz, Henrik; Søndergaard, Gorm; Bruun Rasmussen, Birgitte

    2018-01-01

    In 2011, the St. Gallen Consensus Conference introduced the use of pathology to define the intrinsic breast cancer subtypes by application of immunohistochemical (IHC) surrogate markers ER, PR, HER2 and Ki67 with a specified Ki67 cutoff (>14%) for luminal B-like definition. Reports concerning impaired reproducibility of Ki67 estimation and threshold inconsistency led to the initiation of this quality assurance study (2013-2015). The aim of the study was to investigate inter-observer variation for Ki67 estimation in malignant breast tumors by two different quantification methods (assessment method and count method) including measure of agreement between methods. Fourteen experienced breast pathologists from 12 pathology departments evaluated 118 slides from a consecutive series of malignant breast tumors. The staining interpretation was performed according to both the Danish and Swedish guidelines. Reproducibility was quantified by intra-class correlation coefficient (ICC) and Lights Kappa with dichotomization of observations at the larger than (>) 20% threshold. The agreement between observations by the two quantification methods was evaluated by Bland-Altman plot. For the fourteen raters the median ranged from 20% to 40% by the assessment method and from 22.5% to 36.5% by the count method. Light's Kappa was 0.664 for observation by the assessment method and 0.649 by the count method. The ICC was 0.82 (95% CI: 0.77-0.86) by the assessment method vs. 0.84 (95% CI: 0.80-0.87) by the count method. Although the study in general showed a moderate to good inter-observer agreement according to both ICC and Lights Kappa, still major discrepancies were identified in especially the mid-range of observations. Consequently, for now Ki67 estimation is not implemented in the DBCG treatment algorithm.

  2. Reproducibility in light microscopy: Maintenance, standards and SOPs.

    PubMed

    Deagle, Rebecca C; Wee, Tse-Luen Erika; Brown, Claire M

    2017-08-01

    Light microscopy has grown to be a valuable asset in both the physical and life sciences. It is a highly quantitative method available in individual research laboratories and often centralized in core facilities. However, although quantitative microscopy is becoming a customary tool in research, it is rarely standardized. To achieve accurate quantitative microscopy data and reproducible results, three levels of standardization must be considered: (1) aspects of the microscope, (2) the sample, and (3) the detector. The accuracy of the data is only as reliable as the imaging system itself, thereby imposing the need for routine standard performance testing. Depending on the task some maintenance procedures should be performed once a month, some before each imaging session, while others conducted annually. This text should be implemented as a resource for researchers to integrate with their own standard operating procedures to ensure the highest quality quantitative microscopy data. Copyright © 2017. Published by Elsevier Ltd.

  3. Reproducing Epidemiologic Research and Ensuring Transparency.

    PubMed

    Coughlin, Steven S

    2017-08-15

    Measures for ensuring that epidemiologic studies are reproducible include making data sets and software available to other researchers so they can verify published findings, conduct alternative analyses of the data, and check for statistical errors or programming errors. Recent developments related to the reproducibility and transparency of epidemiologic studies include the creation of a global platform for sharing data from clinical trials and the anticipated future extension of the global platform to non-clinical trial data. Government agencies and departments such as the US Department of Veterans Affairs Cooperative Studies Program have also enhanced their data repositories and data sharing resources. The Institute of Medicine and the International Committee of Medical Journal Editors released guidance on sharing clinical trial data. The US National Institutes of Health has updated their data-sharing policies. In this issue of the Journal, Shepherd et al. (Am J Epidemiol. 2017;186:387-392) outline a pragmatic approach for reproducible research with sensitive data for studies for which data cannot be shared because of legal or ethical restrictions. Their proposed quasi-reproducible approach facilitates the dissemination of statistical methods and codes to independent researchers. Both reproducibility and quasi-reproducibility can increase transparency for critical evaluation, further dissemination of study methods, and expedite the exchange of ideas among researchers. © The Author(s) 2017. Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  4. Accurate bulk density determination of irregularly shaped translucent and opaque aerogels

    NASA Astrophysics Data System (ADS)

    Petkov, M. P.; Jones, S. M.

    2016-05-01

    We present a volumetric method for accurate determination of bulk density of aerogels, calculated from extrapolated weight of the dry pure solid and volume estimates based on the Archimedes' principle of volume displacement, using packed 100 μm-sized monodispersed glass spheres as a "quasi-fluid" media. Hard particle packing theory is invoked to demonstrate the reproducibility of the apparent density of the quasi-fluid. Accuracy rivaling that of the refractive index method is demonstrated for both translucent and opaque aerogels with different absorptive properties, as well as for aerogels with regular and irregular shapes.

  5. Composting in small laboratory pilots: performance and reproducibility.

    PubMed

    Lashermes, G; Barriuso, E; Le Villio-Poitrenaud, M; Houot, S

    2012-02-01

    Small-scale reactors (<10 l) have been employed in composting research, but few attempts have assessed the performance of composting considering the transformations of organic matter. Moreover, composting at small scales is often performed by imposing a fixed temperature, thus creating artificial conditions, and the reproducibility of composting has rarely been reported. The objectives of this study are to design an innovative small-scale composting device safeguarding self-heating to drive the composting process and to assess the performance and reproducibility of composting in small-scale pilots. The experimental setup included six 4-l reactors used for composting a mixture of sewage sludge and green wastes. The performance of the process was assessed by monitoring the temperature, O(2) consumption and CO(2) emissions, and characterising the biochemical evolution of organic matter. A good reproducibility was found for the six replicates with coefficients of variation for all parameters generally lower than 19%. An intense self-heating ensured the existence of a spontaneous thermophilic phase in all reactors. The average loss of total organic matter (TOM) was 46% of the initial content. Compared to the initial mixture, the hot water soluble fraction decreased by 62%, the hemicellulose-like fraction by 68%, the cellulose-like fraction by 50% and the lignin-like fractions by 12% in the final compost. The TOM losses, compost stabilisation and evolution of the biochemical fractions were similar to observed in large reactors or on-site experiments, excluding the lignin degradation, which was less important than in full-scale systems. The reproducibility of the process and the quality of the final compost make it possible to propose the use of this experimental device for research requiring a mass reduction of the initial composted waste mixtures. Copyright © 2011 Elsevier Ltd. All rights reserved.

  6. The Rényi divergence enables accurate and precise cluster analysis for localisation microscopy.

    PubMed

    Staszowska, Adela D; Fox-Roberts, Patrick; Hirvonen, Liisa M; Peddie, Christopher J; Collinson, Lucy M; Jones, Gareth E; Cox, Susan

    2018-06-01

    Clustering analysis is a key technique for quantitatively characterising structures in localisation microscopy images. To build up accurate information about biological structures, it is critical that the quantification is both accurate (close to the ground truth) and precise (has small scatter and is reproducible). Here we describe how the Rényi divergence can be used for cluster radius measurements in localisation microscopy data. We demonstrate that the Rényi divergence can operate with high levels of background and provides results which are more accurate than Ripley's functions, Voronoi tesselation or DBSCAN. Data supporting this research will be made accessible via a web link. Software codes developed for this work can be accessed via http://coxphysics.com/Renyi_divergence_software.zip. Implemented in C ++. Correspondence and requests for materials can be also addressed to the corresponding author. adela.staszowska@gmail.com or susan.cox@kcl.ac.uk. Supplementary data are available at Bioinformatics online.

  7. Using induced electroosmotic micromixer to enhance the reproducibility of chemiluminescence intensity.

    PubMed

    Chen, Hsiao-Ping; Yeh, Chun-Yi; Hung, Pei-Chin; Wang, Shau-Chun

    2014-02-01

    In this study, induced electroosmotic vortex flows were generated using an AC electric field by one pair of external electrodes to rapidly mix luminescence reagents in a 30 μL micromixer and enhance the reproducibility of chemiluminescence (CL) assays. A solution containing the catalyst reagent ferricyanide ions (4 μL) was pipetted into a reservoir containing luminol to produce CL in the presence of hydrogen peroxide. When the added ferricyanide aliquot contacted the reservoir solution, the CL began flashing, but rapidly diminished as the ferricyanide was consumed. In such a short illumination period, the solutes could not mix homogeneously. Therefore, the reproducibility of CL intensities collected using a CCD and multiple aliquot additions was determined to be inadequate. By contrast, when the solutes were efficiently mixed after adding a ferricyanide aliquot to a micromixer, the intensity reproducibility was significantly improved. When the CL temporal profile was analyzed using a PMT, a consistent improvement in reproducibility was observed between the CL intensity and estimated CL reaction rate. Replicating the proposed device would create a multiple well plate that contains a micromixer in each reservoir; this system is compatible with conventional CL instrumentation and requires no CL enhancer to slow a reaction. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Seeing and Being Seen: Predictors of Accurate Perceptions about Classmates’ Relationships

    PubMed Central

    Neal, Jennifer Watling; Neal, Zachary P.; Cappella, Elise

    2015-01-01

    This study examines predictors of observer accuracy (i.e. seeing) and target accuracy (i.e. being seen) in perceptions of classmates’ relationships in a predominantly African American sample of 420 second through fourth graders (ages 7 – 11). Girls, children in higher grades, and children in smaller classrooms were more accurate observers. Targets (i.e. pairs of children) were more accurately observed when they occurred in smaller classrooms of higher grades and involved same-sex, high-popularity, and similar-popularity children. Moreover, relationships between pairs of girls were more accurately observed than relationships between pairs of boys. As a set, these findings suggest the importance of both observer and target characteristics for children’s accurate perceptions of classroom relationships. Moreover, the substantial variation in observer accuracy and target accuracy has methodological implications for both peer-reported assessments of classroom relationships and the use of stochastic actor-based models to understand peer selection and socialization processes. PMID:26347582

  9. Reproducibility of the pink esthetic score--rating soft tissue esthetics around single-implant restorations with regard to dental observer specialization.

    PubMed

    Gehrke, Peter; Lobert, Markus; Dhom, Günter

    2008-01-01

    The pink esthetic score (PES) evaluates the esthetic outcome of soft tissue around implant-supported single crowns in the anterior zone by awarding seven points for the mesial and distal papilla, soft-tissue level, soft-tissue contour, soft-tissue color, soft-tissue texture, and alveolar process deficiency. The aim of this study was to measure the reproducibility of the PES and assess the influence exerted by the examiner's degree of dental specialization. Fifteen examiners (three general dentists, three oral maxillofacial surgeons, three orthodontists, three postgraduate students in implant dentistry, and three lay people) applied the PES to 30 implant-supported single restorations twice at an interval of 4 weeks. Using a 0-1-2 scoring system, 0 being the lowest, 2 being the highest value, the maximum achievable PES was 14. At the second assessment, the photographs were scored in reverse order. Differences between the two assessments were evaluated with the Spearman's rank correlation coefficient (R). The Wilcoxon signed-rank test was used for comparisons of differences between the ratings. A significance level of p < 0.05 was chosen for both tests. Observer results indicated that the agreement between the first and second rating for all occupational groups was 70.5%, with a broad correlation between the two ratings and a high statistical significance (Spearman's R = 0.58, p = 0; Wilcoxon T = 163,182, Z = 3.383599, p = 0.000716). The most agreement between the first and second rating was obtained by orthodontists with 73.5% (R = 0.67), and the least by lay people 65.9% (R = 0.50). Very poor and very esthetic restorations showed the smallest deviations. Orthodontists were found to have assigned significantly poorer ratings than any other group. The assessment of postgraduate students and laypersons were the most favorable. The PES allows for a more objective appraisal of the esthetic short- and long-term results of various surgical and prosthetic implant procedures

  10. Appearance Constrained Semi-Automatic Segmentation from DCE-MRI is Reproducible and Feasible for Breast Cancer Radiomics: A Feasibility Study.

    PubMed

    Veeraraghavan, Harini; Dashevsky, Brittany Z; Onishi, Natsuko; Sadinski, Meredith; Morris, Elizabeth; Deasy, Joseph O; Sutton, Elizabeth J

    2018-03-19

    We present a segmentation approach that combines GrowCut (GC) with cancer-specific multi-parametric Gaussian Mixture Model (GCGMM) to produce accurate and reproducible segmentations. We evaluated GCGMM using a retrospectively collected 75 invasive ductal carcinoma with ERPR+ HER2- (n = 15), triple negative (TN) (n = 9), and ER-HER2+ (n = 57) cancers with variable presentation (mass and non-mass enhancement) and background parenchymal enhancement (mild and marked). Expert delineated manual contours were used to assess the segmentation performance using Dice coefficient (DSC), mean surface distance (mSD), Hausdorff distance, and volume ratio (VR). GCGMM segmentations were significantly more accurate than GrowCut (GC) and fuzzy c-means clustering (FCM). GCGMM's segmentations and the texture features computed from those segmentations were the most reproducible compared with manual delineations and other analyzed segmentation methods. Finally, random forest (RF) classifier trained with leave-one-out cross-validation using features extracted from GCGMM segmentation resulted in the best accuracy for ER-HER2+ vs. ERPR+/TN (GCGMM 0.95, expert 0.95, GC 0.90, FCM 0.92) and for ERPR + HER2- vs. TN (GCGMM 0.92, expert 0.91, GC 0.77, FCM 0.83).

  11. Inferring Lower Boundary Driving Conditions Using Vector Magnetic Field Observations

    NASA Technical Reports Server (NTRS)

    Schuck, Peter W.; Linton, Mark; Leake, James; MacNeice, Peter; Allred, Joel

    2012-01-01

    Low-beta coronal MHD simulations of realistic CME events require the detailed specification of the magnetic fields, velocities, densities, temperatures, etc., in the low corona. Presently, the most accurate estimates of solar vector magnetic fields are made in the high-beta photosphere. Several techniques have been developed that provide accurate estimates of the associated photospheric plasma velocities such as the Differential Affine Velocity Estimator for Vector Magnetograms and the Poloidal/Toroidal Decomposition. Nominally, these velocities are consistent with the evolution of the radial magnetic field. To evolve the tangential magnetic field radial gradients must be specified. In addition to estimating the photospheric vector magnetic and velocity fields, a further challenge involves incorporating these fields into an MHD simulation. The simulation boundary must be driven, consistent with the numerical boundary equations, with the goal of accurately reproducing the observed magnetic fields and estimated velocities at some height within the simulation. Even if this goal is achieved, many unanswered questions remain. How can the photospheric magnetic fields and velocities be propagated to the low corona through the transition region? At what cadence must we observe the photosphere to realistically simulate the corona? How do we model the magnetic fields and plasma velocities in the quiet Sun? How sensitive are the solutions to other unknowns that must be specified, such as the global solar magnetic field, and the photospheric temperature and density?

  12. Thou Shalt Be Reproducible! A Technology Perspective

    PubMed Central

    Mair, Patrick

    2016-01-01

    This article elaborates on reproducibility in psychology from a technological viewpoint. Modern open source computational environments are shown and explained that foster reproducibility throughout the whole research life cycle, and to which emerging psychology researchers should be sensitized, are shown and explained. First, data archiving platforms that make datasets publicly available are presented. Second, R is advocated as the data-analytic lingua franca in psychology for achieving reproducible statistical analysis. Third, dynamic report generation environments for writing reproducible manuscripts that integrate text, data analysis, and statistical outputs such as figures and tables in a single document are described. Supplementary materials are provided in order to get the reader started with these technologies. PMID:27471486

  13. Accurate virus quantitation using a Scanning Transmission Electron Microscopy (STEM) detector in a scanning electron microscope.

    PubMed

    Blancett, Candace D; Fetterer, David P; Koistinen, Keith A; Morazzani, Elaine M; Monninger, Mitchell K; Piper, Ashley E; Kuehl, Kathleen A; Kearney, Brian J; Norris, Sarah L; Rossi, Cynthia A; Glass, Pamela J; Sun, Mei G

    2017-10-01

    A method for accurate quantitation of virus particles has long been sought, but a perfect method still eludes the scientific community. Electron Microscopy (EM) quantitation is a valuable technique because it provides direct morphology information and counts of all viral particles, whether or not they are infectious. In the past, EM negative stain quantitation methods have been cited as inaccurate, non-reproducible, and with detection limits that were too high to be useful. To improve accuracy and reproducibility, we have developed a method termed Scanning Transmission Electron Microscopy - Virus Quantitation (STEM-VQ), which simplifies sample preparation and uses a high throughput STEM detector in a Scanning Electron Microscope (SEM) coupled with commercially available software. In this paper, we demonstrate STEM-VQ with an alphavirus stock preparation to present the method's accuracy and reproducibility, including a comparison of STEM-VQ to viral plaque assay and the ViroCyt Virus Counter. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  14. In silico comparison of the reproducibility of full-arch implant provisional restorations to final restoration between a 3D Scan/CAD/CAM technique and the conventional method.

    PubMed

    Mino, Takuya; Maekawa, Kenji; Ueda, Akihiro; Higuchi, Shizuo; Sejima, Junichi; Takeuchi, Tetsuo; Hara, Emilio Satoshi; Kimura-Ono, Aya; Sonoyama, Wataru; Kuboki, Takuo

    2015-04-01

    The aim of this article was to investigate the accuracy in the reproducibility of full-arch implant provisional restorations to final restorations between a 3D Scan/CAD/CAM technique and the conventional method. We fabricated two final restorations for rehabilitation of maxillary and mandibular complete edentulous area and performed a computer-based comparative analysis of the accuracy in the reproducibility of the provisional restoration to final restoration between a 3D scanning and CAD/CAM (Scan/CAD/CAM) technique and the conventional silicone-mold transfer technique. Final restorations fabricated either by the conventional or Scan/CAD/CAM method were successfully installed in the patient. The total concave/convex volume discrepancy observed with the Scan/CAD/CAM technique was 503.50mm(3) and 338.15 mm(3) for maxillary and mandibular implant-supported prostheses (ISPs), respectively. On the other hand, total concave/convex volume discrepancy observed with the conventional method was markedly high (1106.84 mm(3) and 771.23 mm(3) for maxillary and mandibular ISPs, respectively). The results of the present report suggest that Scan/CAD/CAM method enables a more precise and accurate transfer of provisional restorations to final restorations compared to the conventional method. Copyright © 2014 Japan Prosthodontic Society. Published by Elsevier Ltd. All rights reserved.

  15. 10 CFR 95.43 - Authority to reproduce.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... CSA, Secret and Confidential documents may be reproduced. Reproduced copies of classified documents... material must be conspicuously marked with the same classification markings as the material being...

  16. 10 CFR 95.43 - Authority to reproduce.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... CSA, Secret and Confidential documents may be reproduced. Reproduced copies of classified documents... material must be conspicuously marked with the same classification markings as the material being...

  17. 10 CFR 95.43 - Authority to reproduce.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... CSA, Secret and Confidential documents may be reproduced. Reproduced copies of classified documents... material must be conspicuously marked with the same classification markings as the material being...

  18. 10 CFR 95.43 - Authority to reproduce.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... CSA, Secret and Confidential documents may be reproduced. Reproduced copies of classified documents... material must be conspicuously marked with the same classification markings as the material being...

  19. 10 CFR 95.43 - Authority to reproduce.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... CSA, Secret and Confidential documents may be reproduced. Reproduced copies of classified documents... material must be conspicuously marked with the same classification markings as the material being...

  20. Reproducibility of flow mediated skin fluorescence to assess microvascular function.

    PubMed

    Hellmann, Marcin; Tarnawska, Maria; Dudziak, Maria; Dorniak, Karolina; Roustit, Matthieu; Cracowski, Jean-Luc

    2017-09-01

    Recent technical developments enable skin fluorescence to be quantified in vivo in humans. The present study aimed at determining whether flow mediated skin fluorescence was reproducible, sensitive to changes within an individual, and if it could differ between patients with coronary artery disease and healthy volunteers. First, forearm flow mediated skin fluorescence recorded during and after brachial artery occlusion was assessed following successive forearm occlusion periods (1, 2, 3 and 5min) and expressed as ischemic and hyperemic responses (as % of baseline). Secondly, 3min flow mediated skin fluorescence was assessed before and after 10min local cooling to 15°C. In a third protocol, the inter-day reproducibility of ischemic and hyperemic responses to 3min occlusion was tested at an interval of 7days, and compared between healthy controls and patients with coronary artery disease (CAD). In the first protocol, we observed a time dependent increase in the ischemic and hyperemic responses to occlusion. Next, we observed a lower hyperemic response after local cooling (9.8±4.2 versus 17.8±2.5% respectively, P<0.001), while in contrast, the ischemic response was higher and exhibited greater variability (23±15 versus 11.8±6.4%; P=0.028). In the third protocol, the inter-day reproducibility of flow mediated skin fluorescence for a 3min occlusion period was excellent. The ischemic response was significantly lower in CAD patients than in healthy controls (6.7±4.8% vs 14.7±6.8% respectively, P<0.001). Similarly, the hyperemic response was significantly decreased in the CAD group compared to healthy controls (11.6±3.6% vs 19.5±5.4% respectively, P<0.001). We show that quantifying the ischemic and hyperemic flow mediated skin fluorescence is feasible, reproducible, sensitive to acute changes in skin blood flow, and distinguishes patients populations. However, more data are needed to evaluate the correlation with other methods or specific biochemical endothelial

  1. Respiratory effort correction strategies to improve the reproducibility of lung expansion measurements

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Du, Kaifang; Reinhardt, Joseph M.; Christensen, Gary E.

    2013-12-15

    correlated with respiratory effort difference (R = 0.744 for ELV in the cohort with tidal volume difference greater than 100 cc). In general for all subjects, global normalization, ETV and ELV significantly improved reproducibility compared to no effort correction (p = 0.009, 0.002, 0.005 respectively). When tidal volume difference was small (less than 100 cc), none of the three effort correction strategies improved reproducibility significantly (p = 0.52, 0.46, 0.46 respectively). For the cohort (N = 13) with tidal volume difference greater than 100 cc, the average gamma pass rate improves from 57.3% before correction to 66.3% after global normalization, and 76.3% after ELV. ELV was found to be significantly better than global normalization (p = 0.04 for all subjects, and p = 0.003 for the cohort with tidal volume difference greater than 100 cc).Conclusions: All effort correction strategies improve the reproducibility of the authors' pulmonary ventilation measures, and the improvement of reproducibility is highly correlated with the changes in respiratory effort. ELV gives better results as effort difference increase, followed by ETV, then global. However, based on the spatial and temporal heterogeneity in the lung expansion rate, a single scaling factor (e.g., global normalization) appears to be less accurate to correct the ventilation map when changes in respiratory effort are large.« less

  2. ACCURATE CHARACTERIZATION OF HIGH-DEGREE MODES USING MDI OBSERVATIONS

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Korzennik, S. G.; Rabello-Soares, M. C.; Schou, J.

    2013-08-01

    We present the first accurate characterization of high-degree modes, derived using the best Michelson Doppler Imager (MDI) full-disk full-resolution data set available. A 90 day long time series of full-disk 2 arcsec pixel{sup -1} resolution Dopplergrams was acquired in 2001, thanks to the high rate telemetry provided by the Deep Space Network. These Dopplergrams were spatially decomposed using our best estimate of the image scale and the known components of MDI's image distortion. A multi-taper power spectrum estimator was used to generate power spectra for all degrees and all azimuthal orders, up to l = 1000. We used a largemore » number of tapers to reduce the realization noise, since at high degrees the individual modes blend into ridges and thus there is no reason to preserve a high spectral resolution. These power spectra were fitted for all degrees and all azimuthal orders, between l = 100 and l = 1000, and for all the orders with substantial amplitude. This fitting generated in excess of 5.2 Multiplication-Sign 10{sup 6} individual estimates of ridge frequencies, line widths, amplitudes, and asymmetries (singlets), corresponding to some 5700 multiplets (l, n). Fitting at high degrees generates ridge characteristics, characteristics that do not correspond to the underlying mode characteristics. We used a sophisticated forward modeling to recover the best possible estimate of the underlying mode characteristics (mode frequencies, as well as line widths, amplitudes, and asymmetries). We describe in detail this modeling and its validation. The modeling has been extensively reviewed and refined, by including an iterative process to improve its input parameters to better match the observations. Also, the contribution of the leakage matrix on the accuracy of the procedure has been carefully assessed. We present the derived set of corrected mode characteristics, which includes not only frequencies, but line widths, asymmetries, and amplitudes. We present and

  3. How accurately do force fields represent protein side chain ensembles?

    PubMed

    Petrović, Dušan; Wang, Xue; Strodel, Birgit

    2018-05-23

    Although the protein backbone is the most fundamental part of the structure, the fine-tuning of side-chain conformations is important for protein function, for example, in protein-protein and protein-ligand interactions, and also in enzyme catalysis. While several benchmarks testing the performance of protein force fields for side chain properties have already been published, they often considered only a few force fields and were not tested against the same experimental observables; hence, they are not directly comparable. In this work, we explore the ability of twelve force fields, which are different flavors of AMBER, CHARMM, OPLS, or GROMOS, to reproduce average rotamer angles and rotamer populations obtained from extensive NMR studies of the 3 J and residual dipolar coupling constants for two small proteins: ubiquitin and GB3. Based on a total of 196 μs sampling time, our results reveal that all force fields identify the correct side chain angles, while the AMBER and CHARMM force fields clearly outperform the OPLS and GROMOS force fields in estimating rotamer populations. The three best force fields for representing the protein side chain dynamics are AMBER 14SB, AMBER 99SB*-ILDN, and CHARMM36. Furthermore, we observe that the side chain ensembles of buried amino acid residues are generally more accurately represented than those of the surface exposed residues. This article is protected by copyright. All rights reserved. © 2018 Wiley Periodicals, Inc.

  4. Fourier modeling of the BOLD response to a breath-hold task: Optimization and reproducibility.

    PubMed

    Pinto, Joana; Jorge, João; Sousa, Inês; Vilela, Pedro; Figueiredo, Patrícia

    2016-07-15

    Cerebrovascular reactivity (CVR) reflects the capacity of blood vessels to adjust their caliber in order to maintain a steady supply of brain perfusion, and it may provide a sensitive disease biomarker. Measurement of the blood oxygen level dependent (BOLD) response to a hypercapnia-inducing breath-hold (BH) task has been frequently used to map CVR noninvasively using functional magnetic resonance imaging (fMRI). However, the best modeling approach for the accurate quantification of CVR maps remains an open issue. Here, we compare and optimize Fourier models of the BOLD response to a BH task with a preparatory inspiration, and assess the test-retest reproducibility of the associated CVR measurements, in a group of 10 healthy volunteers studied over two fMRI sessions. Linear combinations of sine-cosine pairs at the BH task frequency and its successive harmonics were added sequentially in a nested models approach, and were compared in terms of the adjusted coefficient of determination and corresponding variance explained (VE) of the BOLD signal, as well as the number of voxels exhibiting significant BOLD responses, the estimated CVR values, and their test-retest reproducibility. The brain average VE increased significantly with the Fourier model order, up to the 3rd order. However, the number of responsive voxels increased significantly only up to the 2nd order, and started to decrease from the 3rd order onwards. Moreover, no significant relative underestimation of CVR values was observed beyond the 2nd order. Hence, the 2nd order model was concluded to be the optimal choice for the studied paradigm. This model also yielded the best test-retest reproducibility results, with intra-subject coefficients of variation of 12 and 16% and an intra-class correlation coefficient of 0.74. In conclusion, our results indicate that a Fourier series set consisting of a sine-cosine pair at the BH task frequency and its two harmonics is a suitable model for BOLD-fMRI CVR measurements

  5. Folding molecular dynamics simulations accurately predict the effect of mutations on the stability and structure of a vammin-derived peptide.

    PubMed

    Koukos, Panagiotis I; Glykos, Nicholas M

    2014-08-28

    Folding molecular dynamics simulations amounting to a grand total of 4 μs of simulation time were performed on two peptides (with native and mutated sequences) derived from loop 3 of the vammin protein and the results compared with the experimentally known peptide stabilities and structures. The simulations faithfully and accurately reproduce the major experimental findings and show that (a) the native peptide is mostly disordered in solution, (b) the mutant peptide has a well-defined and stable structure, and (c) the structure of the mutant is an irregular β-hairpin with a non-glycine β-bulge, in excellent agreement with the peptide's known NMR structure. Additionally, the simulations also predict the presence of a very small β-hairpin-like population for the native peptide but surprisingly indicate that this population is structurally more similar to the structure of the native peptide as observed in the vammin protein than to the NMR structure of the isolated mutant peptide. We conclude that, at least for the given system, force field, and simulation protocol, folding molecular dynamics simulations appear to be successful in reproducing the experimentally accessible physical reality to a satisfactory level of detail and accuracy.

  6. Common Data Models and Efficient Reproducible Workflows for Distributed Ocean Model Skill Assessment

    NASA Astrophysics Data System (ADS)

    Signell, R. P.; Snowden, D. P.; Howlett, E.; Fernandes, F. A.

    2014-12-01

    Model skill assessment requires discovery, access, analysis, and visualization of information from both sensors and models, and traditionally has been possible only by a few experts. The US Integrated Ocean Observing System (US-IOOS) consists of 17 Federal Agencies and 11 Regional Associations that produce data from various sensors and numerical models; exactly the information required for model skill assessment. US-IOOS is seeking to develop documented skill assessment workflows that are standardized, efficient, and reproducible so that a much wider community can participate in the use and assessment of model results. Standardization requires common data models for observational and model data. US-IOOS relies on the CF Conventions for observations and structured grid data, and on the UGRID Conventions for unstructured (e.g. triangular) grid data. This allows applications to obtain only the data they require in a uniform and parsimonious way using web services: OPeNDAP for model output and OGC Sensor Observation Service (SOS) for observed data. Reproducibility is enabled with IPython Notebooks shared on GitHub (http://github.com/ioos). These capture the entire skill assessment workflow, including user input, search, access, analysis, and visualization, ensuring that workflows are self-documenting and reproducible by anyone, using free software. Python packages for common data models are Pyugrid and the British Met Office Iris package. Python packages required to run the workflows (pyugrid, pyoos, and the British Met Office Iris package) are also available on GitHub and on Binstar.org so that users can run scenarios using the free Anaconda Python distribution. Hosted services such as Wakari enable anyone to reproduce these workflows for free, without installing any software locally, using just their web browser. We are also experimenting with Wakari Enterprise, which allows multi-user access from a web browser to an IPython Server running where large quantities of

  7. Research Reproducibility in Geosciences: Current Landscape, Practices and Perspectives

    NASA Astrophysics Data System (ADS)

    Yan, An

    2016-04-01

    Reproducibility of research can gauge the validity of its findings. Yet currently we lack understanding of how much of a problem research reproducibility is in geosciences. We developed an online survey on faculty and graduate students in geosciences, and received 136 responses from research institutions and universities in Americas, Asia, Europe and other parts of the world. This survey examined (1) the current state of research reproducibility in geosciences by asking researchers' experiences with unsuccessful replication work, and what obstacles that lead to their replication failures; (2) the current reproducibility practices in community by asking what efforts researchers made to try to reproduce other's work and make their own work reproducible, and what the underlying factors that contribute to irreproducibility are; (3) the perspectives on reproducibility by collecting researcher's thoughts and opinions on this issue. The survey result indicated that nearly 80% of respondents who had ever reproduced a published study had failed at least one time in reproducing. Only one third of the respondents received helpful feedbacks when they contacted the authors of a published study for data, code, or other information. The primary factors that lead to unsuccessful replication attempts are insufficient details of instructions in published literature, and inaccessibility of data, code and tools needed in the study. Our findings suggest a remarkable lack of research reproducibility in geoscience. Changing the incentive mechanism in academia, as well as developing policies and tools that facilitate open data and code sharing are the promising ways for geosciences community to alleviate this reproducibility problem.

  8. How reproducible are methods to measure the dynamic viscoelastic properties of poroelastic media?

    NASA Astrophysics Data System (ADS)

    Bonfiglio, Paolo; Pompoli, Francesco; Horoshenkov, Kirill V.; Rahim, Mahmud Iskandar B. Seth A.; Jaouen, Luc; Rodenas, Julia; Bécot, François-Xavier; Gourdon, Emmanuel; Jaeger, Dirk; Kursch, Volker; Tarello, Maurizio; Roozen, Nicolaas Bernardus; Glorieux, Christ; Ferrian, Fabrizio; Leroy, Pierre; Vangosa, Francesco Briatico; Dauchez, Nicolas; Foucart, Félix; Lei, Lei; Carillo, Kevin; Doutres, Olivier; Sgard, Franck; Panneton, Raymond; Verdiere, Kévin; Bertolini, Claudio; Bär, Rolf; Groby, Jean-Philippe; Geslain, Alan; Poulain, Nicolas; Rouleau, Lucie; Guinault, Alain; Ahmadi, Hamid; Forge, Charlie

    2018-08-01

    There is a considerable number of research publications on the acoustical properties of porous media with an elastic frame. A simple search through the Web of Science™ (last accessed 21 March 2018) suggests that there are at least 819 publications which deal with the acoustics of poroelastic media. A majority of these researches require accurate knowledge of the elastic properties over a broad frequency range. However, the accuracy of the measurement of the dynamic elastic properties of poroelastic media has been a contentious issue. The novelty of this paper is that it studies the reproducibility of some popular experimental methods which are used routinely to measure the key elastic properties such as the dynamic Young's modulus, loss factor and Poisson ratio of poroelastic media. In this paper, fourteen independent sets of laboratory measurements were performed on specimens of the same porous materials. The results from these measurements suggest that the reproducibility of this type of experimental method is poor. This work can be helpful to suggest improvements which can be developed to harmonize the way the elastic properties of poroelastic media are measured worldwide.

  9. Experimental Procedures for Sensitive and Reproducible In Situ EPR Tooth Dosimetry

    PubMed Central

    Williams, Benjamin B.; Sucheta, Artur; Dong, Ruhong; Sakata, Yasuko; Iwasaki, Akinori; Burke, Gregory; Grinberg, Oleg; Lesniewski, Piotr; Kmiec, Maciej; Swartz, Harold M.

    2007-01-01

    In vivo electron paramagnetic resonance (EPR) tooth dosimetry provides a means for non-invasive retrospective assessment of personal radiation exposure. While there is a clear need for such capabilities following radiation accidents, the most pressing need for the development of this technology is the heightened likelihood of terrorist events or nuclear conflicts. This technique will enable such measurements to be made at the site of an incident, while the subject is present, to assist emergency personnel as they perform triage for the affected population. At Dartmouth Medical School this development is currently being tested with normal volunteers with irradiated teeth placed in their mouths and with patients who have undergone radiation therapy. Here we describe progress in practical procedures to provide accurate and reproducible in vivo dose estimates. PMID:18591989

  10. Interstudy reproducibility of dimensional and functional measurements between cine magnetic resonance studies in the morphologically abnormal left ventricle.

    PubMed

    Semelka, R C; Tomei, E; Wagner, S; Mayo, J; Caputo, G; O'Sullivan, M; Parmley, W W; Chatterjee, K; Wolfe, C; Higgins, C B

    1990-06-01

    The validity of geometric formulas to derive mass and volumes in the morphologically abnormal left ventricle is problematic. Imaging techniques that are tomographic and therefore inherently three-dimensional should be more reliable and reproducible between studies in such ventricles. Determination of reproducibility between studies is essential to define the limits of an imaging technique for evaluating the response to therapy. Sequential cine magnetic resonance (MR) studies were performed on patients with dilated cardiomyopathy (n = 11) and left ventricular hypertrophy (n = 8) within a short interval in order to assess interstudy reproducibility. Left ventricular mass, volumes, ejection fraction, and end-systolic wall stress were determined by two independent observers. Between studies, left ventricular mass was highly reproducible for hypertrophied and dilated ventricles, with percent variability less than 6%. Ejection fraction and end-diastolic volume showed close reproducibility between studies, with percent variability less than 5% End-systolic volume varied by 4.3% and 4.5% in dilated cardiomyopathy and 8.4% and 7.2% in left ventricular hypertrophy for the two observers. End-systolic wall stress, which is derived from multiple measurements, varied the greatest, with percent variability of 17.2% and 15.7% in dilated cardiomyopathy and 14.8% and 13% in left ventricular hypertrophy, respectively. The results of this study demonstrate that mass, volume, and functional measurements are reproducible in morphologically abnormal ventricles.

  11. Accurate atomistic potentials and training sets for boron-nitride nanostructures

    NASA Astrophysics Data System (ADS)

    Tamblyn, Isaac

    Boron nitride nanotubes exhibit exceptional structural, mechanical, and thermal properties. They are optically transparent and have high thermal stability, suggesting a wide range of opportunities for structural reinforcement of materials. Modeling can play an important role in determining the optimal approach to integrating nanotubes into a supporting matrix. Developing accurate, atomistic scale models of such nanoscale interfaces embedded within composites is challenging, however, due to the mismatch of length scales involved. Typical nanotube diameters range from 5-50 nm, with a length as large as a micron (i.e. a relevant length-scale for structural reinforcement). Unlike their carbon-based counterparts, well tested and transferable interatomic force fields are not common for BNNT. In light of this, we have developed an extensive training database of BN rich materials, under conditions relevant for BNNT synthesis and composites based on extensive first principles molecular dynamics simulations. Using this data, we have produced an artificial neural network potential capable of reproducing the accuracy of first principles data at significantly reduced computational cost, allowing for accurate simulation at the much larger length scales needed for composite design.

  12. Interlaboratory Reproducibility of Droplet Digital Polymerase Chain Reaction Using a New DNA Reference Material Format.

    PubMed

    Pinheiro, Leonardo B; O'Brien, Helen; Druce, Julian; Do, Hongdo; Kay, Pippa; Daniels, Marissa; You, Jingjing; Burke, Daniel; Griffiths, Kate; Emslie, Kerry R

    2017-11-07

    Use of droplet digital PCR technology (ddPCR) is expanding rapidly in the diversity of applications and number of users around the world. Access to relatively simple and affordable commercial ddPCR technology has attracted wide interest in use of this technology as a molecular diagnostic tool. For ddPCR to effectively transition to a molecular diagnostic setting requires processes for method validation and verification and demonstration of reproducible instrument performance. In this study, we describe the development and characterization of a DNA reference material (NMI NA008 High GC reference material) comprising a challenging methylated GC-rich DNA template under a novel 96-well microplate format. A scalable process using high precision acoustic dispensing technology was validated to produce the DNA reference material with a certified reference value expressed in amount of DNA molecules per well. An interlaboratory study, conducted using blinded NA008 High GC reference material to assess reproducibility among seven independent laboratories demonstrated less than 4.5% reproducibility relative standard deviation. With the exclusion of one laboratory, laboratories had appropriate technical competency, fully functional instrumentation, and suitable reagents to perform accurate ddPCR based DNA quantification measurements at the time of the study. The study results confirmed that NA008 High GC reference material is fit for the purpose of being used for quality control of ddPCR systems, consumables, instrumentation, and workflow.

  13. Voxel size dependency, reproducibility and sensitivity of an in vivo bone loading estimation algorithm

    PubMed Central

    Christen, Patrik; Schulte, Friederike A.; Zwahlen, Alexander; van Rietbergen, Bert; Boutroy, Stephanie; Melton, L. Joseph; Amin, Shreyasee; Khosla, Sundeep; Goldhahn, Jörg; Müller, Ralph

    2016-01-01

    A bone loading estimation algorithm was previously developed that provides in vivo loading conditions required for in vivo bone remodelling simulations. The algorithm derives a bone's loading history from its microstructure as assessed by high-resolution (HR) computed tomography (CT). This reverse engineering approach showed accurate and realistic results based on micro-CT and HR-peripheral quantitative CT images. However, its voxel size dependency, reproducibility and sensitivity still need to be investigated, which is the purpose of this study. Voxel size dependency was tested on cadaveric distal radii with micro-CT images scanned at 25 µm and downscaled to 50, 61, 75, 82, 100, 125 and 150 µm. Reproducibility was calculated with repeated in vitro as well as in vivo HR-pQCT measurements at 82 µm. Sensitivity was defined using HR-pQCT images from women with fracture versus non-fracture, and low versus high bone volume fraction, expecting similar and different loading histories, respectively. Our results indicate that the algorithm is voxel size independent within an average (maximum) error of 8.2% (32.9%) at 61 µm, but that the dependency increases considerably at voxel sizes bigger than 82 µm. In vitro and in vivo reproducibility are up to 4.5% and 10.2%, respectively, which is comparable to other in vitro studies and slightly higher than in other in vivo studies. Subjects with different bone volume fraction were clearly distinguished but not subjects with and without fracture. This is in agreement with bone adapting to customary loading but not to fall loads. We conclude that the in vivo bone loading estimation algorithm provides reproducible, sensitive and fairly voxel size independent results at up to 82 µm, but that smaller voxel sizes would be advantageous. PMID:26790999

  14. Machine Learning of Accurate Energy-Conserving Molecular Force Fields

    NASA Astrophysics Data System (ADS)

    Chmiela, Stefan; Tkatchenko, Alexandre; Sauceda, Huziel; Poltavsky, Igor; Schütt, Kristof; Müller, Klaus-Robert; GDML Collaboration

    Efficient and accurate access to the Born-Oppenheimer potential energy surface (PES) is essential for long time scale molecular dynamics (MD) simulations. Using conservation of energy - a fundamental property of closed classical and quantum mechanical systems - we develop an efficient gradient-domain machine learning (GDML) approach to construct accurate molecular force fields using a restricted number of samples from ab initio MD trajectories (AIMD). The GDML implementation is able to reproduce global potential-energy surfaces of intermediate-size molecules with an accuracy of 0.3 kcal/mol for energies and 1 kcal/mol/Å for atomic forces using only 1000 conformational geometries for training. We demonstrate this accuracy for AIMD trajectories of molecules, including benzene, toluene, naphthalene, malonaldehyde, ethanol, uracil, and aspirin. The challenge of constructing conservative force fields is accomplished in our work by learning in a Hilbert space of vector-valued functions that obey the law of energy conservation. The GDML approach enables quantitative MD simulations for molecules at a fraction of cost of explicit AIMD calculations, thereby allowing the construction of efficient force fields with the accuracy and transferability of high-level ab initio methods.

  15. Accurate analysis and visualization of cardiac (11)C-PIB uptake in amyloidosis with semiautomatic software.

    PubMed

    Kero, Tanja; Lindsjö, Lars; Sörensen, Jens; Lubberink, Mark

    2016-08-01

    (11)C-PIB PET is a promising non-invasive diagnostic tool for cardiac amyloidosis. Semiautomatic analysis of PET data is now available but it is not known how accurate these methods are for amyloid imaging. The aim of this study was to evaluate the feasibility of one semiautomatic software tool for analysis and visualization of (11)C-PIB left ventricular retention index (RI) in cardiac amyloidosis. Patients with systemic amyloidosis and cardiac involvement (n = 10) and healthy controls (n = 5) were investigated with dynamic (11)C-PIB PET. Two observers analyzed the PET studies with semiautomatic software to calculate the left ventricular RI of (11)C-PIB and to create parametric images. The mean RI at 15-25 min from the semiautomatic analysis was compared with RI based on manual analysis and showed comparable values (0.056 vs 0.054 min(-1) for amyloidosis patients and 0.024 vs 0.025 min(-1) in healthy controls; P = .78) and the correlation was excellent (r = 0.98). Inter-reader reproducibility also was excellent (intraclass correlation coefficient, ICC > 0.98). Parametric polarmaps and histograms made visual separation of amyloidosis patients and healthy controls fast and simple. Accurate semiautomatic analysis of cardiac (11)C-PIB RI in amyloidosis patients is feasible. Parametric polarmaps and histograms make visual interpretation fast and simple.

  16. Bottom-up coarse-grained models that accurately describe the structure, pressure, and compressibility of molecular liquids

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Dunn, Nicholas J. H.; Noid, W. G., E-mail: wnoid@chem.psu.edu

    2015-12-28

    The present work investigates the capability of bottom-up coarse-graining (CG) methods for accurately modeling both structural and thermodynamic properties of all-atom (AA) models for molecular liquids. In particular, we consider 1, 2, and 3-site CG models for heptane, as well as 1 and 3-site CG models for toluene. For each model, we employ the multiscale coarse-graining method to determine interaction potentials that optimally approximate the configuration dependence of the many-body potential of mean force (PMF). We employ a previously developed “pressure-matching” variational principle to determine a volume-dependent contribution to the potential, U{sub V}(V), that approximates the volume-dependence of the PMF.more » We demonstrate that the resulting CG models describe AA density fluctuations with qualitative, but not quantitative, accuracy. Accordingly, we develop a self-consistent approach for further optimizing U{sub V}, such that the CG models accurately reproduce the equilibrium density, compressibility, and average pressure of the AA models, although the CG models still significantly underestimate the atomic pressure fluctuations. Additionally, by comparing this array of models that accurately describe the structure and thermodynamic pressure of heptane and toluene at a range of different resolutions, we investigate the impact of bottom-up coarse-graining upon thermodynamic properties. In particular, we demonstrate that U{sub V} accounts for the reduced cohesion in the CG models. Finally, we observe that bottom-up coarse-graining introduces subtle correlations between the resolution, the cohesive energy density, and the “simplicity” of the model.« less

  17. Robust tissue classification for reproducible wound assessment in telemedicine environments

    NASA Astrophysics Data System (ADS)

    Wannous, Hazem; Treuillet, Sylvie; Lucas, Yves

    2010-04-01

    In telemedicine environments, a standardized and reproducible assessment of wounds, using a simple free-handled digital camera, is an essential requirement. However, to ensure robust tissue classification, particular attention must be paid to the complete design of the color processing chain. We introduce the key steps including color correction, merging of expert labeling, and segmentation-driven classification based on support vector machines. The tool thus developed ensures stability under lighting condition, viewpoint, and camera changes, to achieve accurate and robust classification of skin tissues. Clinical tests demonstrate that such an advanced tool, which forms part of a complete 3-D and color wound assessment system, significantly improves the monitoring of the healing process. It achieves an overlap score of 79.3 against 69.1% for a single expert, after mapping on the medical reference developed from the image labeling by a college of experts.

  18. ROCS: a Reproducibility Index and Confidence Score for Interaction Proteomics Studies

    PubMed Central

    2012-01-01

    published AP-MS experiments, each containing well characterized protein interactions, allowing for systematic benchmarking of ROCS. We show that our method may be used on its own to make accurate identification of specific, biologically relevant protein-protein interactions, or in combination with other AP-MS scoring methods to significantly improve inferences. Conclusions Our method addresses important issues encountered in AP-MS datasets, making ROCS a very promising tool for this purpose, either on its own or in conjunction with other methods. We anticipate that our methodology may be used more generally in proteomics studies and databases, where experimental reproducibility issues arise. The method is implemented in the R language, and is available as an R package called “ROCS”, freely available from the CRAN repository http://cran.r-project.org/. PMID:22682516

  19. T2-mapping of the sacroiliac joints at 1.5 Tesla: a feasibility and reproducibility study.

    PubMed

    Albano, Domenico; Chianca, Vito; Cuocolo, Renato; Bignone, Rodolfo; Ciccia, Francesco; Sconfienza, Luca Maria; Midiri, Massimo; Brunetti, Arturo; Lagalla, Roberto; Galia, Massimo

    2018-04-20

    To evaluate the reproducibility of T2 relaxation time measurements of the sacroiliac joints at 1.5 T. Healthy volunteers underwent an oblique axial multislice multiecho spin-echo sequence of the sacroiliac joints at 1.5 T. Regions of interest were manually drawn using a dedicated software by two musculoskeletal radiologists to include the cartilaginous part of the sacroiliac joints. A senior radiologist performed the measurement twice, while a resident measured once. Intra- and inter-observer reproducibility was tested using the Bland-Altman method. Association between sex and T2 relaxation times was tested using the Mann-Whitney U test. Correlation between T2 relaxation times and body mass index (BMI) was tested using the Spearman's rho. Eighty sacroiliac joints of 40 subjects (mean age: 28 ± 4.8 years, range: 20-43; mean BMI: 23.3 ± 3.1, range: 18.9-30) were imaged. The mean T2 values obtained by the senior radiologist in the first series of measurements were 42 ± 4.4 ms, whereas in the second series were 40.7 ± 4.5 ms. The mean T2 values obtained by the radiology resident were 41.1 ± 4.2 ms. Intra-observer reproducibility was 88% (coefficient of repeatability = 3.8; bias = 1.28; p < .001), while inter-observer reproducibility was 86% (4.7; -.88; p < .001). There was significant association between sex and T2 relaxation times (p = .024) and significant inverse correlation between T2 relaxation times and BMI (r = -.340, p = .002). The assessment of T2 relaxation time measurements of sacroiliac joints seems to be highly reproducible at 1.5 T. Further studies could investigate the potential clinical application of this tool in the sacroiliac joints.

  20. Three Dimensions of Reproducibility in Natural Language Processing.

    PubMed

    Cohen, K Bretonnel; Xia, Jingbo; Zweigenbaum, Pierre; Callahan, Tiffany J; Hargraves, Orin; Goss, Foster; Ide, Nancy; Névéol, Aurélie; Grouin, Cyril; Hunter, Lawrence E

    2018-05-01

    Despite considerable recent attention to problems with reproducibility of scientific research, there is a striking lack of agreement about the definition of the term. That is a problem, because the lack of a consensus definition makes it difficult to compare studies of reproducibility, and thus to have even a broad overview of the state of the issue in natural language processing. This paper proposes an ontology of reproducibility in that field. Its goal is to enhance both future research and communication about the topic, and retrospective meta-analyses. We show that three dimensions of reproducibility, corresponding to three kinds of claims in natural language processing papers, can account for a variety of types of research reports. These dimensions are reproducibility of a conclusion , of a finding , and of a value. Three biomedical natural language processing papers by the authors of this paper are analyzed with respect to these dimensions.

  1. Measuring Age-Dependent Myocardial Stiffness across the Cardiac Cycle using MR Elastography: A Reproducibility Study

    PubMed Central

    Wassenaar, Peter A; Eleswarpu, Chethanya N; Schroeder, Samuel A; Mo, Xiaokui; Raterman, Brian D; White, Richard D; Kolipaka, Arunark

    2015-01-01

    Purpose To assess reproducibility in measuring left ventricular (LV) myocardial stiffness in volunteers throughout the cardiac cycle using magnetic resonance elastography (MRE) and to determine its correlation with age. Methods Cardiac MRE (CMRE) was performed on 29 normal volunteers, with ages ranging from 21 to 73 years. For assessing reproducibility of CMRE-derived stiffness measurements, scans were repeated per volunteer. Wave images were acquired throughout the LV myocardium, and were analyzed to obtain mean stiffness during the cardiac cycle. CMRE-derived stiffness values were correlated to age. Results Concordance correlation coefficient revealed good inter-scan agreement with rc of 0.77, with p-value<0.0001. Significantly higher myocardial stiffness was observed during end-systole (ES) compared to end-diastole (ED) across all subjects. Additionally, increased deviation between ES and ED stiffness was observed with increased age. Conclusion CMRE-derived stiffness is reproducible, with myocardial stiffness changing cyclically across the cardiac cycle. Stiffness is significantly higher during ES compared to ED. With age, ES myocardial stiffness increases more than ED, giving rise to an increased deviation between the two. PMID:26010456

  2. Model-data assimilation of multiple phenological observations to constrain and predict leaf area index.

    PubMed

    Viskari, Toni; Hardiman, Brady; Desai, Ankur R; Dietze, Michael C

    2015-03-01

    Our limited ability to accurately simulate leaf phenology is a leading source of uncertainty in models of ecosystem carbon cycling. We evaluate if continuously updating canopy state variables with observations is beneficial for predicting phenological events. We employed ensemble adjustment Kalman filter (EAKF) to update predictions of leaf area index (LAI) and leaf extension using tower-based photosynthetically active radiation (PAR) and moderate resolution imaging spectrometer (MODIS) data for 2002-2005 at Willow Creek, Wisconsin, USA, a mature, even-aged, northern hardwood, deciduous forest. The ecosystem demography model version 2 (ED2) was used as the prediction model, forced by offline climate data. EAKF successfully incorporated information from both the observations and model predictions weighted by their respective uncertainties. The resulting. estimate reproduced the observed leaf phenological cycle in the spring and the fall better than a parametric model prediction. These results indicate that during spring the observations contribute most in determining the correct bud-burst date, after which the model performs well, but accurately modeling fall leaf senesce requires continuous model updating from observations. While the predicted net ecosystem exchange (NEE) of CO2 precedes tower observations and unassimilated model predictions in the spring, overall the prediction follows observed NEE better than the model alone. Our results show state data assimilation successfully simulates the evolution of plant leaf phenology and improves model predictions of forest NEE.

  3. Rotary head type reproducing apparatus

    DOEpatents

    Takayama, Nobutoshi; Edakubo, Hiroo; Kozuki, Susumu; Takei, Masahiro; Nagasawa, Kenichi

    1986-01-01

    In an apparatus of the kind arranged to reproduce, with a plurality of rotary heads, an information signal from a record bearing medium having many recording tracks which are parallel to each other with the information signal recorded therein and with a plurality of different pilot signals of different frequencies also recorded one by one, one in each of the recording tracks, a plurality of different reference signals of different frequencies are simultaneously generated. A tracking error is detected by using the different reference signals together with the pilot signals which are included in signals reproduced from the plurality of rotary heads.

  4. Reproducibility of precipitation distributions over extratropical continental regions in the CMIP5

    NASA Astrophysics Data System (ADS)

    Hirota, Nagio; Takayabu, Yukari

    2013-04-01

    Reproducibility of precipitation distributions over extratropical continental regions in the CMIP5 Nagio Hirota1,2 and Yukari N. Takayabu2 (1) National Institute of Polar Research (NIPR) (2) Atmosphere and Ocean Research Institute (AORI), the University of Tokyo Reproducibility of precipitation distributions over extratropical continental regions by CMIP5 climate models in their historical runs are evaluated, in comparison with GPCP(V2.2), CMAP(V0911), daily gridded gauge data APHRODITE. Surface temperature, cloud radiative forcing, and atmospheric circulations are also compared with observations of CRU-UEA, CERES, and ERA-interim/ERA40/JRA reanalysis data. It is shown that many CMIP5 models underestimate and overestimate summer precipitation over West and East Eurasia, respectively. These precipitation biases correspond to moisture transport associated with a cyclonic circulation bias over the whole continent of Eurasia. Meanwhile, many models underestimate cloud over the Eurasian continent, and associated shortwave cloud radiative forcing result in a significant warm bias. Evaporation feedback amplify the warm bias over West Eurasia. These processes consistently explain the precipitation biases over the Erasian continent in summer. We also examined reproducibility of winter precipitation, but robust results are not obtained yet due to the large uncertainty in observation associated with the adjustment of snow measurement in windy condition. Better observational data sets are necessary for further model validation. Acknowledgment: This study is supported by the PMM RA of JAXA, Green Network of Excellence (GRENE) Program by the Ministry of Education, Culture, Sports, Science and Technology, Japan, and Environment Research and Technology Development Fund (A-1201) of the Ministry of the Environment, Japan.

  5. Genotypic variability enhances the reproducibility of an ecological study.

    PubMed

    Milcu, Alexandru; Puga-Freitas, Ruben; Ellison, Aaron M; Blouin, Manuel; Scheu, Stefan; Freschet, Grégoire T; Rose, Laura; Barot, Sebastien; Cesarz, Simone; Eisenhauer, Nico; Girin, Thomas; Assandri, Davide; Bonkowski, Michael; Buchmann, Nina; Butenschoen, Olaf; Devidal, Sebastien; Gleixner, Gerd; Gessler, Arthur; Gigon, Agnès; Greiner, Anna; Grignani, Carlo; Hansart, Amandine; Kayler, Zachary; Lange, Markus; Lata, Jean-Christophe; Le Galliard, Jean-François; Lukac, Martin; Mannerheim, Neringa; Müller, Marina E H; Pando, Anne; Rotter, Paula; Scherer-Lorenzen, Michael; Seyhun, Rahme; Urban-Mead, Katherine; Weigelt, Alexandra; Zavattaro, Laura; Roy, Jacques

    2018-02-01

    Many scientific disciplines are currently experiencing a 'reproducibility crisis' because numerous scientific findings cannot be repeated consistently. A novel but controversial hypothesis postulates that stringent levels of environmental and biotic standardization in experimental studies reduce reproducibility by amplifying the impacts of laboratory-specific environmental factors not accounted for in study designs. A corollary to this hypothesis is that a deliberate introduction of controlled systematic variability (CSV) in experimental designs may lead to increased reproducibility. To test this hypothesis, we had 14 European laboratories run a simple microcosm experiment using grass (Brachypodium distachyon L.) monocultures and grass and legume (Medicago truncatula Gaertn.) mixtures. Each laboratory introduced environmental and genotypic CSV within and among replicated microcosms established in either growth chambers (with stringent control of environmental conditions) or glasshouses (with more variable environmental conditions). The introduction of genotypic CSV led to 18% lower among-laboratory variability in growth chambers, indicating increased reproducibility, but had no significant effect in glasshouses where reproducibility was generally lower. Environmental CSV had little effect on reproducibility. Although there are multiple causes for the 'reproducibility crisis', deliberately including genetic variability may be a simple solution for increasing the reproducibility of ecological studies performed under stringently controlled environmental conditions.

  6. Hippocampal Astrocyte Cultures from Adult and Aged Rats Reproduce Changes in Glial Functionality Observed in the Aging Brain.

    PubMed

    Bellaver, Bruna; Souza, Débora Guerini; Souza, Diogo Onofre; Quincozes-Santos, André

    2017-05-01

    Astrocytes are dynamic cells that maintain brain homeostasis, regulate neurotransmitter systems, and process synaptic information, energy metabolism, antioxidant defenses, and inflammatory response. Aging is a biological process that is closely associated with hippocampal astrocyte dysfunction. In this sense, we demonstrated that hippocampal astrocytes from adult and aged Wistar rats reproduce the glial functionality alterations observed in aging by evaluating several senescence, glutamatergic, oxidative and inflammatory parameters commonly associated with the aging process. Here, we show that the p21 senescence-associated gene and classical astrocyte markers, such as glial fibrillary acidic protein (GFAP), vimentin, and actin, changed their expressions in adult and aged astrocytes. Age-dependent changes were also observed in glutamate transporters (glutamate aspartate transporter (GLAST) and glutamate transporter-1 (GLT-1)) and glutamine synthetase immunolabeling and activity. Additionally, according to in vivo aging, astrocytes from adult and aged rats showed an increase in oxidative/nitrosative stress with mitochondrial dysfunction, an increase in RNA oxidation, NADPH oxidase (NOX) activity, superoxide levels, and inducible nitric oxide synthase (iNOS) expression levels. Changes in antioxidant defenses were also observed. Hippocampal astrocytes also displayed age-dependent inflammatory response with augmentation of proinflammatory cytokine levels, such as TNF-α, IL-1β, IL-6, IL-18, and messenger RNA (mRNA) levels of cyclo-oxygenase 2 (COX-2). Furthermore, these cells secrete neurotrophic factors, including glia-derived neurotrophic factor (GDNF), brain-derived neurotrophic factor (BDNF), S100 calcium-binding protein B (S100B) protein, and transforming growth factor-β (TGF-β), which changed in an age-dependent manner. Classical signaling pathways associated with aging, such as nuclear factor erythroid-derived 2-like 2 (Nrf2), nuclear factor kappa B (NFκ

  7. When continuous observations just won't do: developing accurate and efficient sampling strategies for the laying hen.

    PubMed

    Daigle, Courtney L; Siegford, Janice M

    2014-03-01

    Continuous observation is the most accurate way to determine animals' actual time budget and can provide a 'gold standard' representation of resource use, behavior frequency, and duration. Continuous observation is useful for capturing behaviors that are of short duration or occur infrequently. However, collecting continuous data is labor intensive and time consuming, making multiple individual or long-term data collection difficult. Six non-cage laying hens were video recorded for 15 h and behavioral data collected every 2 s were compared with data collected using scan sampling intervals of 5, 10, 15, 30, and 60 min and subsamples of 2 second observations performed for 10 min every 30 min, 15 min every 1 h, 30 min every 1.5 h, and 15 min every 2 h. Three statistical approaches were used to provide a comprehensive analysis to examine the quality of the data obtained via different sampling methods. General linear mixed models identified how the time budget from the sampling techniques differed from continuous observation. Correlation analysis identified how strongly results from the sampling techniques were associated with those from continuous observation. Regression analysis identified how well the results from the sampling techniques were associated with those from continuous observation, changes in magnitude, and whether a sampling technique had bias. Static behaviors were well represented with scan and time sampling techniques, while dynamic behaviors were best represented with time sampling techniques. Methods for identifying an appropriate sampling strategy based upon the type of behavior of interest are outlined and results for non-caged laying hens are presented. Copyright © 2013 Elsevier B.V. All rights reserved.

  8. Reproducibility and validity of the Shanghai Women's Health Study physical activity questionnaire.

    PubMed

    Matthews, Charles E; Shu, Xiao-Ou; Yang, Gong; Jin, Fan; Ainsworth, Barbara E; Liu, Dake; Gao, Yu-Tang; Zheng, Wei

    2003-12-01

    In this investigation, the authors evaluated the reproducibility and validity of the Shanghai Women's Health Study (SWHS) physical activity questionnaire (PAQ), which was administered in a cohort study of approximately 75,000 Chinese women aged 40-70 years. Reproducibility (2-year test-retest) was evaluated using kappa statistics and intraclass correlation coefficients (ICCs). Validity was evaluated by comparing Spearman correlations (r) for the SWHS PAQ with two criterion measures administered over a period of 12 months: four 7-day physical activity logs and up to 28 7-day PAQs. Women were recruited from the SWHS cohort (n = 200). Results indicated that the reproducibility of adolescent and adult exercise participation (kappa = 0.85 and kappa = 0.64, respectively) and years of adolescent exercise and adult exercise energy expenditure (ICC = 0.83 and ICC = 0.70, respectively) was reasonable. Reproducibility values for adult lifestyle activities were lower (ICC = 0.14-0.54). Significant correlations between the PAQ and criterion measures of adult exercise were observed for the first PAQ administration (physical activity log, r = 0.50; 7-day PAQ, r = 0.62) and the second PAQ administration (physical activity log, r = 0.74; 7-day PAQ, r = 0.80). Significant correlations between PAQ lifestyle activities and the 7-day PAQ were also noted (r = 0.33-0.88). These data indicate that the SWHS PAQ is a reproducible and valid measure of exercise behaviors and that it demonstrates utility in stratifying women by levels of important lifestyle activities (e.g., housework, walking, cycling).

  9. Dynamic Contrast-enhanced MR Imaging in Renal Cell Carcinoma: Reproducibility of Histogram Analysis on Pharmacokinetic Parameters

    PubMed Central

    Wang, Hai-yi; Su, Zi-hua; Xu, Xiao; Sun, Zhi-peng; Duan, Fei-xue; Song, Yuan-yuan; Li, Lu; Wang, Ying-wei; Ma, Xin; Guo, Ai-tao; Ma, Lin; Ye, Hui-yi

    2016-01-01

    Pharmacokinetic parameters derived from dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) have been increasingly used to evaluate the permeability of tumor vessel. Histogram metrics are a recognized promising method of quantitative MR imaging that has been recently introduced in analysis of DCE-MRI pharmacokinetic parameters in oncology due to tumor heterogeneity. In this study, 21 patients with renal cell carcinoma (RCC) underwent paired DCE-MRI studies on a 3.0 T MR system. Extended Tofts model and population-based arterial input function were used to calculate kinetic parameters of RCC tumors. Mean value and histogram metrics (Mode, Skewness and Kurtosis) of each pharmacokinetic parameter were generated automatically using ImageJ software. Intra- and inter-observer reproducibility and scan–rescan reproducibility were evaluated using intra-class correlation coefficients (ICCs) and coefficient of variation (CoV). Our results demonstrated that the histogram method (Mode, Skewness and Kurtosis) was not superior to the conventional Mean value method in reproducibility evaluation on DCE-MRI pharmacokinetic parameters (K trans & Ve) in renal cell carcinoma, especially for Skewness and Kurtosis which showed lower intra-, inter-observer and scan-rescan reproducibility than Mean value. Our findings suggest that additional studies are necessary before wide incorporation of histogram metrics in quantitative analysis of DCE-MRI pharmacokinetic parameters. PMID:27380733

  10. Where next for the reproducibility agenda in computational biology?

    PubMed

    Lewis, Joanna; Breeze, Charles E; Charlesworth, Jane; Maclaren, Oliver J; Cooper, Jonathan

    2016-07-15

    The concept of reproducibility is a foundation of the scientific method. With the arrival of fast and powerful computers over the last few decades, there has been an explosion of results based on complex computational analyses and simulations. The reproducibility of these results has been addressed mainly in terms of exact replicability or numerical equivalence, ignoring the wider issue of the reproducibility of conclusions through equivalent, extended or alternative methods. We use case studies from our own research experience to illustrate how concepts of reproducibility might be applied in computational biology. Several fields have developed 'minimum information' checklists to support the full reporting of computational simulations, analyses and results, and standardised data formats and model description languages can facilitate the use of multiple systems to address the same research question. We note the importance of defining the key features of a result to be reproduced, and the expected agreement between original and subsequent results. Dynamic, updatable tools for publishing methods and results are becoming increasingly common, but sometimes come at the cost of clear communication. In general, the reproducibility of computational research is improving but would benefit from additional resources and incentives. We conclude with a series of linked recommendations for improving reproducibility in computational biology through communication, policy, education and research practice. More reproducible research will lead to higher quality conclusions, deeper understanding and more valuable knowledge.

  11. Extreme Rainfall Events Over Southern Africa: Assessment of a Climate Model to Reproduce Daily Extremes

    NASA Astrophysics Data System (ADS)

    Williams, C.; Kniveton, D.; Layberry, R.

    2007-12-01

    It is increasingly accepted that any possible climate change will not only have an influence on mean climate but may also significantly alter climatic variability. This issue is of particular importance for environmentally vulnerable regions such as southern Africa. The subcontinent is considered especially vulnerable extreme events, due to a number of factors including extensive poverty, disease and political instability. Rainfall variability and the identification of rainfall extremes is a function of scale, so high spatial and temporal resolution data are preferred to identify extreme events and accurately predict future variability. The majority of previous climate model verification studies have compared model output with observational data at monthly timescales. In this research, the assessment of a state-of-the-art climate model to simulate climate at daily timescales is carried out using satellite derived rainfall data from the Microwave Infra-Red Algorithm (MIRA). This dataset covers the period from 1993-2002 and the whole of southern Africa at a spatial resolution of 0.1 degree longitude/latitude. Once the model's ability to reproduce extremes has been assessed, idealised regions of SST anomalies are used to force the model, with the overall aim of investigating the ways in which SST anomalies influence rainfall extremes over southern Africa. In this paper, results from sensitivity testing of the UK Meteorological Office Hadley Centre's climate model's domain size are firstly presented. Then simulations of current climate from the model, operating in both regional and global mode, are compared to the MIRA dataset at daily timescales. Thirdly, the ability of the model to reproduce daily rainfall extremes will be assessed, again by a comparison with extremes from the MIRA dataset. Finally, the results from the idealised SST experiments are briefly presented, suggesting associations between rainfall extremes and both local and remote SST anomalies.

  12. Reproducibility of current perception threshold with the Neurometer(®) vs the Stimpod NMS450 peripheral nerve stimulator in healthy volunteers: an observational study.

    PubMed

    Tsui, Ban C H; Shakespeare, Timothy J; Leung, Danika H; Tsui, Jeremy H; Corry, Gareth N

    2013-08-01

    Current methods of assessing nerve blocks, such as loss of perception to cold sensation, are subjective at best. Transcutaneous nerve stimulation is an alternative method that has previously been used to measure the current perception threshold (CPT) in individuals with neuropathic conditions, and various devices to measure CPT are commercially available. Nevertheless, the device must provide reproducible results to be used as an objective tool for assessing nerve blocks. We recruited ten healthy volunteers to examine CPT reproducibility using the Neurometer(®) and the Stimpod NMS450 peripheral nerve stimulator. Each subject's CPT was determined for the median (second digit) and ulnar (fifth digit) nerve sensory distributions on both hands - with the Neurometer at 5 Hz, 250 Hz, and 2000 Hz and with the Stimpod at pulse widths of 0.1 msec, 0.3 msec, 0.5 msec, and 1.0 msec, both at 5 Hz and 2 Hz. Intraclass correlation coefficients (ICC) were also calculated to assess reproducibility; acceptable ICCs were defined as ≥ 0.4. The ICC values for the Stimpod ranged from 0.425-0.79, depending on pulse width, digit, and stimulation; ICCs for the Neurometer were 0.615 and 0.735 at 250 and 2,000 Hz, respectively. These values were considered acceptable; however, the Neurometer performed less efficiently at 5 Hz (ICCs for the second and fifth digits were 0.292 and 0.318, respectively). Overall, the Stimpod device displayed good to excellent reproducibility in measuring CPT in healthy volunteers. The Neurometer displayed poor reproducibility at low frequency (5 Hz). These results suggest that peripheral nerve stimulators may be potential devices for measuring CPT to assess nerve blocks.

  13. A novel methodology to reproduce previously recorded six-degree of freedom kinematics on the same diarthrodial joint.

    PubMed

    Moore, Susan M; Thomas, Maribeth; Woo, Savio L-Y; Gabriel, Mary T; Kilger, Robert; Debski, Richard E

    2006-01-01

    The objective of this study was to develop a novel method to more accurately reproduce previously recorded 6-DOF kinematics of the tibia with respect to the femur using robotic technology. Furthermore, the effect of performing only a single or multiple registrations and the effect of robot joint configuration were investigated. A single registration consisted of registering the tibia and femur with respect to the robot at full extension and reproducing all kinematics while multiple registrations consisted of registering the bones at each flexion angle and reproducing only the kinematics of the corresponding flexion angle. Kinematics of the knee in response to an anterior (134 N) and combined internal/external (+/-10 N m) and varus/valgus (+/-5 N m) loads were collected at 0 degrees , 15 degrees , 30 degrees , 60 degrees , and 90 degrees of flexion. A six axes, serial-articulated robotic manipulator (PUMA Model 762) was calibrated and the working volume was reduced to improve the robot's accuracy. The effect of the robot joint configuration was determined by performing single and multiple registrations for three selected configurations. For each robot joint configuration, the accuracy in position of the reproduced kinematics improved after multiple registrations (0.7+/-0.3, 1.2+/-0.5, and 0.9+/-0.2 mm, respectively) when compared to only a single registration (1.3+/-0.9, 2.0+/-1.0, and 1.5+/-0.7 mm, respectively) (p<0.05). The accuracy in position of each robot joint configuration was unique as significant differences were detected between each of the configurations. These data demonstrate that the number of registrations and the robot joint configuration both affect the accuracy of the reproduced kinematics. Therefore, when using robotic technology to reproduce previously recorded kinematics, it may be necessary to perform these analyses for each individual robotic system and for each diarthrodial joint, as different joints will require the robot to be placed in

  14. Accurate ab initio Quartic Force Fields of Cyclic and Bent HC2N Isomers

    NASA Technical Reports Server (NTRS)

    Inostroza, Natalia; Huang, Xinchuan; Lee, Timothy J.

    2012-01-01

    Highly correlated ab initio quartic force field (QFFs) are used to calculate the equilibrium structures and predict the spectroscopic parameters of three HC2N isomers. Specifically, the ground state quasilinear triplet and the lowest cyclic and bent singlet isomers are included in the present study. Extensive treatment of correlation effects were included using the singles and doubles coupled-cluster method that includes a perturbational estimate of the effects of connected triple excitations, denoted CCSD(T). Dunning s correlation-consistent basis sets cc-pVXZ, X=3,4,5, were used, and a three-point formula for extrapolation to the one-particle basis set limit was used. Core-correlation and scalar relativistic corrections were also included to yield highly accurate QFFs. The QFFs were used together with second-order perturbation theory (with proper treatment of Fermi resonances) and variational methods to solve the nuclear Schr dinger equation. The quasilinear nature of the triplet isomer is problematic, and it is concluded that a QFF is not adequate to describe properly all of the fundamental vibrational frequencies and spectroscopic constants (though some constants not dependent on the bending motion are well reproduced by perturbation theory). On the other hand, this procedure (a QFF together with either perturbation theory or variational methods) leads to highly accurate fundamental vibrational frequencies and spectroscopic constants for the cyclic and bent singlet isomers of HC2N. All three isomers possess significant dipole moments, 3.05D, 3.06D, and 1.71D, for the quasilinear triplet, the cyclic singlet, and the bent singlet isomers, respectively. It is concluded that the spectroscopic constants determined for the cyclic and bent singlet isomers are the most accurate available, and it is hoped that these will be useful in the interpretation of high-resolution astronomical observations or laboratory experiments.

  15. 10 CFR 1016.35 - Authority to reproduce Restricted Data.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 10 Energy 4 2010-01-01 2010-01-01 false Authority to reproduce Restricted Data. 1016.35 Section 1016.35 Energy DEPARTMENT OF ENERGY (GENERAL PROVISIONS) SAFEGUARDING OF RESTRICTED DATA Control of Information § 1016.35 Authority to reproduce Restricted Data. Secret Restricted Data will not be reproduced...

  16. 10 CFR 1016.35 - Authority to reproduce Restricted Data.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 10 Energy 4 2011-01-01 2011-01-01 false Authority to reproduce Restricted Data. 1016.35 Section 1016.35 Energy DEPARTMENT OF ENERGY (GENERAL PROVISIONS) SAFEGUARDING OF RESTRICTED DATA Control of Information § 1016.35 Authority to reproduce Restricted Data. Secret Restricted Data will not be reproduced...

  17. Reproducible research in palaeomagnetism

    NASA Astrophysics Data System (ADS)

    Lurcock, Pontus; Florindo, Fabio

    2015-04-01

    The reproducibility of research findings is attracting increasing attention across all scientific disciplines. In palaeomagnetism as elsewhere, computer-based analysis techniques are becoming more commonplace, complex, and diverse. Analyses can often be difficult to reproduce from scratch, both for the original researchers and for others seeking to build on the work. We present a palaeomagnetic plotting and analysis program designed to make reproducibility easier. Part of the problem is the divide between interactive and scripted (batch) analysis programs. An interactive desktop program with a graphical interface is a powerful tool for exploring data and iteratively refining analyses, but usually cannot operate without human interaction. This makes it impossible to re-run an analysis automatically, or to integrate it into a larger automated scientific workflow - for example, a script to generate figures and tables for a paper. In some cases the parameters of the analysis process itself are not saved explicitly, making it hard to repeat or improve the analysis even with human interaction. Conversely, non-interactive batch tools can be controlled by pre-written scripts and configuration files, allowing an analysis to be 'replayed' automatically from the raw data. However, this advantage comes at the expense of exploratory capability: iteratively improving an analysis entails a time-consuming cycle of editing scripts, running them, and viewing the output. Batch tools also tend to require more computer expertise from their users. PuffinPlot is a palaeomagnetic plotting and analysis program which aims to bridge this gap. First released in 2012, it offers both an interactive, user-friendly desktop interface and a batch scripting interface, both making use of the same core library of palaeomagnetic functions. We present new improvements to the program that help to integrate the interactive and batch approaches, allowing an analysis to be interactively explored and refined

  18. Skill of ship-following large-eddy simulations in reproducing MAGIC observations across the northeast Pacific stratocumulus to cumulus transition region

    DOE PAGES

    McGibbon, J.; Bretherton, C. S.

    2017-03-17

    During the Marine ARM GPCI Investigation of Clouds (MAGIC) in October 2011 to September 2012, a container ship making periodic cruises between Los Angeles, CA, and Honolulu, HI, was instrumented with surface meteorological, aerosol and radiation instruments, a cloud radar and ceilometer, and radiosondes. Here large-eddy simulation (LES) is performed in a ship-following frame of reference for 13 four day transects from the MAGIC field campaign. The goal is to assess if LES can skillfully simulate the broad range of observed cloud characteristics and boundary layer structure across the subtropical stratocumulus to cumulus transition region sampled during different seasons andmore » meteorological conditions. Results from Leg 15A, which sampled a particularly well-defined stratocumulus to cumulus transition, demonstrate the approach. The LES reproduces the observed timing of decoupling and transition from stratocumulus to cumulus and matches the observed evolution of boundary layer structure, cloud fraction, liquid water path, and precipitation statistics remarkably well. Considering the simulations of all 13 cruises, the LES skillfully simulates the mean diurnal variation of key measured quantities, including liquid water path (LWP), cloud fraction, measures of decoupling, and cloud radar-derived precipitation. The daily mean quantities are well represented, and daily mean LWP and cloud fraction show the expected correlation with estimated inversion strength. There is a –0.6 K low bias in LES near-surface air temperature that results in a high bias of 5.6 W m –2 in sensible heat flux (SHF). Altogether, these results build confidence in the ability of LES to represent the northeast Pacific stratocumulus to trade cumulus transition region.« less

  19. Identification and reproducibility of dietary patterns in a Danish cohort: the Inter99 study.

    PubMed

    Lau, Cathrine; Glümer, Charlotte; Toft, Ulla; Tetens, Inge; Carstensen, Bendix; Jørgensen, Torben; Borch-Johnsen, Knut

    2008-05-01

    We aimed to identify dietary patterns in a Danish adult population and assess the reproducibility of the dietary patterns identified. Baseline data of 3,372 women and 3,191 men (30-60 years old) from the population-based survey Inter99 was used. Food intake, assessed by a FFQ, was aggregated into thirty-four separate food groups. Dietary patterns were identified by principal component analysis. Confirmatory factor analysis and Bland Altman plots were used to assess the reproducibility of the dietary patterns identified. The Bland Altman plots were used as an alternative and new method. Two factors were retained for both women and men, which accounted for 15.1-17.4 % of the total variation. The 'Traditional' pattern was characterised by high loadings ( > or = 0.40) on paté or high-fat meat for sandwiches, mayonnaise salads, red meat, potatoes, butter and lard, low-fat fish, low-fat meat for sandwiches, and sauces. The 'Modern' pattern was characterised by high loadings on vegetables, fruit, mixed vegetable dishes, vegetable oil and vinegar dressing, poultry, and pasta, rice and wheat kernels. Small differences were observed between patterns identified for women and men. The root mean square error approximation from the confirmatory factor analysis was 0.08. The variation observed from the Bland Altman plots of factors from explorative v. confirmative analyses and explorative analyses from two sub-samples was between 18.8 and 47.7 %. Pearson's correlation was >0.89 (P < 0.0001). The reproducibility was better for women than for men. We conclude that the 'Traditional' and 'Modern' dietary patterns identified were reproducible.

  20. Can Atmospheric Reanalysis Data Sets Be Used to Reproduce Flooding Over Large Scales?

    NASA Astrophysics Data System (ADS)

    Andreadis, Konstantinos M.; Schumann, Guy J.-P.; Stampoulis, Dimitrios; Bates, Paul D.; Brakenridge, G. Robert; Kettner, Albert J.

    2017-10-01

    Floods are costly to global economies and can be exceptionally lethal. The ability to produce consistent flood hazard maps over large areas could provide a significant contribution to reducing such losses, as the lack of knowledge concerning flood risk is a major factor in the transformation of river floods into flood disasters. In order to accurately reproduce flooding in river channels and floodplains, high spatial resolution hydrodynamic models are needed. Despite being computationally expensive, recent advances have made their continental to global implementation feasible, although inputs for long-term simulations may require the use of reanalysis meteorological products especially in data-poor regions. We employ a coupled hydrologic/hydrodynamic model cascade forced by the 20CRv2 reanalysis data set and evaluate its ability to reproduce flood inundation area and volume for Australia during the 1973-2012 period. Ensemble simulations using the reanalysis data were performed to account for uncertainty in the meteorology and compared with a validated benchmark simulation. Results show that the reanalysis ensemble capture the inundated areas and volumes relatively well, with correlations for the ensemble mean of 0.82 and 0.85 for area and volume, respectively, although the meteorological ensemble spread propagates in large uncertainty of the simulated flood characteristics.

  1. Evaluation of 12 blood glucose monitoring systems for self-testing: system accuracy and measurement reproducibility.

    PubMed

    Freckmann, Guido; Baumstark, Annette; Schmid, Christina; Pleus, Stefan; Link, Manuela; Haug, Cornelia

    2014-02-01

    Systems for self-monitoring of blood glucose (SMBG) have to provide accurate and reproducible blood glucose (BG) values in order to ensure adequate therapeutic decisions by people with diabetes. Twelve SMBG systems were compared in a standardized manner under controlled laboratory conditions: nine systems were available on the German market and were purchased from a local pharmacy, and three systems were obtained from the manufacturer (two systems were available on the U.S. market, and one system was not yet introduced to the German market). System accuracy was evaluated following DIN EN ISO (International Organization for Standardization) 15197:2003. In addition, measurement reproducibility was assessed following a modified TNO (Netherlands Organization for Applied Scientific Research) procedure. Comparison measurements were performed with either the glucose oxidase method (YSI 2300 STAT Plus™ glucose analyzer; YSI Life Sciences, Yellow Springs, OH) or the hexokinase method (cobas(®) c111; Roche Diagnostics GmbH, Mannheim, Germany) according to the manufacturer's measurement procedure. The 12 evaluated systems showed between 71.5% and 100% of the measurement results within the required system accuracy limits. Ten systems fulfilled with the evaluated test strip lot minimum accuracy requirements specified by DIN EN ISO 15197:2003. In addition, accuracy limits of the recently published revision ISO 15197:2013 were applied and showed between 54.5% and 100% of the systems' measurement results within the required accuracy limits. Regarding measurement reproducibility, each of the 12 tested systems met the applied performance criteria. In summary, 83% of the systems fulfilled with the evaluated test strip lot minimum system accuracy requirements of DIN EN ISO 15197:2003. Each of the tested systems showed acceptable measurement reproducibility. In order to ensure sufficient measurement quality of each distributed test strip lot, regular evaluations are required.

  2. Automated selected reaction monitoring software for accurate label-free protein quantification.

    PubMed

    Teleman, Johan; Karlsson, Christofer; Waldemarson, Sofia; Hansson, Karin; James, Peter; Malmström, Johan; Levander, Fredrik

    2012-07-06

    Selected reaction monitoring (SRM) is a mass spectrometry method with documented ability to quantify proteins accurately and reproducibly using labeled reference peptides. However, the use of labeled reference peptides becomes impractical if large numbers of peptides are targeted and when high flexibility is desired when selecting peptides. We have developed a label-free quantitative SRM workflow that relies on a new automated algorithm, Anubis, for accurate peak detection. Anubis efficiently removes interfering signals from contaminating peptides to estimate the true signal of the targeted peptides. We evaluated the algorithm on a published multisite data set and achieved results in line with manual data analysis. In complex peptide mixtures from whole proteome digests of Streptococcus pyogenes we achieved a technical variability across the entire proteome abundance range of 6.5-19.2%, which was considerably below the total variation across biological samples. Our results show that the label-free SRM workflow with automated data analysis is feasible for large-scale biological studies, opening up new possibilities for quantitative proteomics and systems biology.

  3. Making Early Modern Medicine: Reproducing Swedish Bitters.

    PubMed

    Ahnfelt, Nils-Otto; Fors, Hjalmar

    2016-05-01

    Historians of science and medicine have rarely applied themselves to reproducing the experiments and practices of medicine and pharmacy. This paper delineates our efforts to reproduce "Swedish Bitters," an early modern composite medicine in wide European use from the 1730s to the present. In its original formulation, it was made from seven medicinal simples: aloe, rhubarb, saffron, myrrh, gentian, zedoary and agarikon. These were mixed in alcohol together with some theriac, a composite medicine of classical origin. The paper delineates the compositional history of Swedish Bitters and the medical rationale underlying its composition. It also describes how we go about to reproduce the medicine in a laboratory using early modern pharmaceutical methods, and analyse it using contemporary methods of pharmaceutical chemistry. Our aim is twofold: first, to show how reproducing medicines may provide a path towards a deeper understanding of the role of sensual and practical knowledge in the wider context of early modern medical culture; and second, how it may yield interesting results from the point of view of contemporary pharmaceutical science.

  4. Reproducable Paraplegia by Thoracic Aortic Occlusion in a Murine Model of Spinal Cord Ischemia-reperfusion

    PubMed Central

    Bell, Marshall T.; Reece, T. Brett; Smith, Phillip D.; Mares, Joshua; Weyant, Michael J.; Cleveland, Joseph C.; Freeman, Kirsten A.; Fullerton, David A.; Puskas, Ferenc

    2014-01-01

    Background Lower extremity paralysis continues to complicate aortic interventions. The lack of understanding of the underlying pathology has hindered advancements to decrease the occurrence this injury. The current model demonstrates reproducible lower extremity paralysis following thoracic aortic occlusion. Methods Adult male C57BL6 mice were anesthetized with isoflurane. Through a cervicosternal incision the aorta was exposed. The descending thoracic aorta and left subclavian arteries were identified without entrance into pleural space. Skeletonization of these arteries was followed by immediate closure (Sham) or occlusion for 4 min (moderate ischemia) or 8 min (prolonged ischemia). The sternotomy and skin were closed and the mouse was transferred to warming bed for recovery.  Following recovery, functional analysis was obtained at 12 hr intervals until 48 hr. Results Mice that underwent sham surgery showed no observable hind limb deficit. Mice subjected to moderate ischemia for 4 min had minimal functional deficit at 12 hr followed by progression to complete paralysis at 48 hr. Mice subjected to prolonged ischemia had an immediate paralysis with no observable hind-limb movement at any point in the postoperative period. There was no observed intraoperative or post operative mortality. Conclusion Reproducible lower extremity paralysis whether immediate or delayed can be achieved in a murine model. Additionally, by using a median sternotomy and careful dissection, high survival rates, and reproducibility can be achieved. PMID:24637534

  5. Reproducable paraplegia by thoracic aortic occlusion in a murine model of spinal cord ischemia-reperfusion.

    PubMed

    Bell, Marshall T; Reece, T Brett; Smith, Phillip D; Mares, Joshua; Weyant, Michael J; Cleveland, Joseph C; Freeman, Kirsten A; Fullerton, David A; Puskas, Ferenc

    2014-03-03

    Lower extremity paralysis continues to complicate aortic interventions. The lack of understanding of the underlying pathology has hindered advancements to decrease the occurrence this injury. The current model demonstrates reproducible lower extremity paralysis following thoracic aortic occlusion. Adult male C57BL6 mice were anesthetized with isoflurane. Through a cervicosternal incision the aorta was exposed. The descending thoracic aorta and left subclavian arteries were identified without entrance into pleural space. Skeletonization of these arteries was followed by immediate closure (Sham) or occlusion for 4 min (moderate ischemia) or 8 min (prolonged ischemia). The sternotomy and skin were closed and the mouse was transferred to warming bed for recovery. Following recovery, functional analysis was obtained at 12 hr intervals until 48 hr. Mice that underwent sham surgery showed no observable hind limb deficit. Mice subjected to moderate ischemia for 4 min had minimal functional deficit at 12 hr followed by progression to complete paralysis at 48 hr. Mice subjected to prolonged ischemia had an immediate paralysis with no observable hind-limb movement at any point in the postoperative period. There was no observed intraoperative or post operative mortality. Reproducible lower extremity paralysis whether immediate or delayed can be achieved in a murine model. Additionally, by using a median sternotomy and careful dissection, high survival rates, and reproducibility can be achieved.

  6. Reproducibility of blood oxygen level-dependent signal changes with end-tidal carbon dioxide alterations.

    PubMed

    Dengel, Donald R; Evanoff, Nicholas G; Marlatt, Kara L; Geijer, Justin R; Mueller, Bryon A; Lim, Kelvin O

    2017-11-01

    Hypercapnia has been utilized as a stimulus to elicit changes in cerebral blood flow (CBF). However, in many instances it has been delivered in a non-controlled method that is often difficult to reproduce. The purpose of this study was to examine the within- and between-visit reproducibility of blood oxygen level-dependent (BOLD) signal changes to an iso-oxic square wave alteration in end-tidal carbon dioxide partial pressure (P et CO 2 ). Two 3-Tesla (3T) MRI scans were performed on the same visit, with two square wave alterations administered per scan. The protocol was repeated on a separate visit with minimum of 3 days between scanning sessions. P et CO 2 was altered to stimulate changes in cerebral vascular reactivity (CVR), while P et O 2 was held constant. Eleven subjects (six females; mean age 26·5 ± 5·7 years) completed the full testing protocol. Excellent within-visit square wave reproducibility (ICC > 0·75) was observed. Similarly, square waves were reproducible between scanning sessions (ICC > 0·7). This study demonstrates BOLD signal changes in response to alterations in P et CO 2 are reproducible both within- and between-visit MRI scans. © 2016 Scandinavian Society of Clinical Physiology and Nuclear Medicine. Published by John Wiley & Sons Ltd.

  7. Standardization of Sonographic Lung-to-Head Ratio Measurements in Isolated Congenital Diaphragmatic Hernia: Impact on the Reproducibility and Efficacy to Predict Outcomes.

    PubMed

    Britto, Ingrid Schwach Werneck; Sananes, Nicolas; Olutoye, Oluyinka O; Cass, Darrell L; Sangi-Haghpeykar, Haleh; Lee, Timothy C; Cassady, Christopher I; Mehollin-Ray, Amy; Welty, Stephen; Fernandes, Caraciolo; Belfort, Michael A; Lee, Wesley; Ruano, Rodrigo

    2015-10-01

    The purpose of this study was to evaluate the impact of standardization of the lung-to-head ratio measurements in isolated congenital diaphragmatic hernia on prediction of neonatal outcomes and reproducibility. We conducted a retrospective cohort study of 77 cases of isolated congenital diaphragmatic hernia managed in a single center between 2004 and 2012. We compared lung-to-head ratio measurements that were performed prospectively in our institution without standardization to standardized measurements performed according to a defined protocol. The standardized lung-to-head ratio measurements were statistically more accurate than the nonstandardized measurements for predicting neonatal mortality (area under the receiver operating characteristic curve, 0.85 versus 0.732; P = .003). After standardization, there were no statistical differences in accuracy between measurements regardless of whether we considered observed-to-expected values (P > .05). Standardization of the lung-to-head ratio did not improve prediction of the need for extracorporeal membrane oxygenation (P> .05). Both intraoperator and interoperator reproducibility were good for the standardized lung-to-head ratio (intraclass correlation coefficient, 0.98 [95% confidence interval, 0.97-0.99]; bias, 0.02 [limits of agreement, -0.11 to +0.15], respectively). Standardization of lung-to-head ratio measurements improves prediction of neonatal outcomes. Further studies are needed to confirm these results and to assess the utility of standardization of other prognostic parameters.

  8. An effect size filter improves the reproducibility in spectral counting-based comparative proteomics.

    PubMed

    Gregori, Josep; Villarreal, Laura; Sánchez, Alex; Baselga, José; Villanueva, Josep

    2013-12-16

    The microarray community has shown that the low reproducibility observed in gene expression-based biomarker discovery studies is partially due to relying solely on p-values to get the lists of differentially expressed genes. Their conclusions recommended complementing the p-value cutoff with the use of effect-size criteria. The aim of this work was to evaluate the influence of such an effect-size filter on spectral counting-based comparative proteomic analysis. The results proved that the filter increased the number of true positives and decreased the number of false positives and the false discovery rate of the dataset. These results were confirmed by simulation experiments where the effect size filter was used to evaluate systematically variable fractions of differentially expressed proteins. Our results suggest that relaxing the p-value cut-off followed by a post-test filter based on effect size and signal level thresholds can increase the reproducibility of statistical results obtained in comparative proteomic analysis. Based on our work, we recommend using a filter consisting of a minimum absolute log2 fold change of 0.8 and a minimum signal of 2-4 SpC on the most abundant condition for the general practice of comparative proteomics. The implementation of feature filtering approaches could improve proteomic biomarker discovery initiatives by increasing the reproducibility of the results obtained among independent laboratories and MS platforms. Quality control analysis of microarray-based gene expression studies pointed out that the low reproducibility observed in the lists of differentially expressed genes could be partially attributed to the fact that these lists are generated relying solely on p-values. Our study has established that the implementation of an effect size post-test filter improves the statistical results of spectral count-based quantitative proteomics. The results proved that the filter increased the number of true positives whereas decreased

  9. Intra- and inter-radiation therapist reproducibility of daily isocenter verification using prostatic fiducial markers

    PubMed Central

    Ullman, Karen L; Ning, Holly; Susil, Robert C; Ayele, Asna; Jocelyn, Lucresse; Havelos, Jan; Guion, Peter; Xie, Huchen; Li, Guang; Arora, Barbara C; Cannon, Angela; Miller, Robert W; Norman Coleman, C; Camphausen, Kevin; Ménard, Cynthia

    2006-01-01

    Background We sought to determine the intra- and inter-radiation therapist reproducibility of a previously established matching technique for daily verification and correction of isocenter position relative to intraprostatic fiducial markers (FM). Materials and methods With the patient in the treatment position, anterior-posterior and left lateral electronic images are acquired on an amorphous silicon flat panel electronic portal imaging device. After each portal image is acquired, the therapist manually translates and aligns the fiducial markers in the image to the marker contours on the digitally reconstructed radiograph. The distances between the planned and actual isocenter location is displayed. In order to determine the reproducibility of this technique, four therapists repeated and recorded this operation two separate times on 20 previously acquired portal image datasets from two patients. The data were analyzed to obtain the mean variability in the distances measured between and within observers. Results The mean and median intra-observer variability ranged from 0.4 to 0.7 mm and 0.3 to 0.6 mm respectively with a standard deviation of 0.4 to 1.0 mm. Inter-observer results were similar with a mean variability of 0.9 mm, a median of 0.6 mm, and a standard deviation of 0.7 mm. When using a 5 mm threshold, only 0.5% of treatments will undergo a table shift due to intra or inter-observer error, increasing to an error rate of 2.4% if this threshold were reduced to 3 mm. Conclusion We have found high reproducibility with a previously established method for daily verification and correction of isocenter position relative to prostatic fiducial markers using electronic portal imaging. PMID:16722575

  10. Undefined cellulase formulations hinder scientific reproducibility

    DOE PAGES

    Himmel, Michael E.; Abbas, Charles A.; Baker, John O.; ...

    2017-11-28

    In the shadow of a burgeoning biomass-to-fuels industry, biological conversion of lignocellulose to fermentable sugars in a cost-effective manner is key to the success of second-generation and advanced biofuel production. For the effective comparison of one cellulase preparation to another, cellulase assays are typically carried out with one or more engineered cellulase formulations or natural exoproteomes of known performance serving as positive controls. When these formulations have unknown composition, as is the case with several widely used commercial products, it becomes impossible to compare or reproduce work done today to work done in the future, where, for example, such preparationsmore » may not be available. Therefore, being a critical tenet of science publishing, experimental reproducibility is endangered by the continued use of these undisclosed products. We propose the introduction of standard procedures and materials to produce specific and reproducible cellulase formulations. These formulations are to serve as yardsticks to measure improvements and performance of new cellulase formulations.« less

  11. Undefined cellulase formulations hinder scientific reproducibility

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Himmel, Michael E.; Abbas, Charles A.; Baker, John O.

    In the shadow of a burgeoning biomass-to-fuels industry, biological conversion of lignocellulose to fermentable sugars in a cost-effective manner is key to the success of second-generation and advanced biofuel production. For the effective comparison of one cellulase preparation to another, cellulase assays are typically carried out with one or more engineered cellulase formulations or natural exoproteomes of known performance serving as positive controls. When these formulations have unknown composition, as is the case with several widely used commercial products, it becomes impossible to compare or reproduce work done today to work done in the future, where, for example, such preparationsmore » may not be available. Therefore, being a critical tenet of science publishing, experimental reproducibility is endangered by the continued use of these undisclosed products. We propose the introduction of standard procedures and materials to produce specific and reproducible cellulase formulations. These formulations are to serve as yardsticks to measure improvements and performance of new cellulase formulations.« less

  12. Systems-based biological concordance and predictive reproducibility of gene set discovery methods in cardiovascular disease.

    PubMed

    Azuaje, Francisco; Zheng, Huiru; Camargo, Anyela; Wang, Haiying

    2011-08-01

    The discovery of novel disease biomarkers is a crucial challenge for translational bioinformatics. Demonstration of both their classification power and reproducibility across independent datasets are essential requirements to assess their potential clinical relevance. Small datasets and multiplicity of putative biomarker sets may explain lack of predictive reproducibility. Studies based on pathway-driven discovery approaches have suggested that, despite such discrepancies, the resulting putative biomarkers tend to be implicated in common biological processes. Investigations of this problem have been mainly focused on datasets derived from cancer research. We investigated the predictive and functional concordance of five methods for discovering putative biomarkers in four independently-generated datasets from the cardiovascular disease domain. A diversity of biosignatures was identified by the different methods. However, we found strong biological process concordance between them, especially in the case of methods based on gene set analysis. With a few exceptions, we observed lack of classification reproducibility using independent datasets. Partial overlaps between our putative sets of biomarkers and the primary studies exist. Despite the observed limitations, pathway-driven or gene set analysis can predict potentially novel biomarkers and can jointly point to biomedically-relevant underlying molecular mechanisms. Copyright © 2011 Elsevier Inc. All rights reserved.

  13. Towards interoperable and reproducible QSAR analyses: Exchange of datasets.

    PubMed

    Spjuth, Ola; Willighagen, Egon L; Guha, Rajarshi; Eklund, Martin; Wikberg, Jarl Es

    2010-06-30

    QSAR is a widely used method to relate chemical structures to responses or properties based on experimental observations. Much effort has been made to evaluate and validate the statistical modeling in QSAR, but these analyses treat the dataset as fixed. An overlooked but highly important issue is the validation of the setup of the dataset, which comprises addition of chemical structures as well as selection of descriptors and software implementations prior to calculations. This process is hampered by the lack of standards and exchange formats in the field, making it virtually impossible to reproduce and validate analyses and drastically constrain collaborations and re-use of data. We present a step towards standardizing QSAR analyses by defining interoperable and reproducible QSAR datasets, consisting of an open XML format (QSAR-ML) which builds on an open and extensible descriptor ontology. The ontology provides an extensible way of uniquely defining descriptors for use in QSAR experiments, and the exchange format supports multiple versioned implementations of these descriptors. Hence, a dataset described by QSAR-ML makes its setup completely reproducible. We also provide a reference implementation as a set of plugins for Bioclipse which simplifies setup of QSAR datasets, and allows for exporting in QSAR-ML as well as old-fashioned CSV formats. The implementation facilitates addition of new descriptor implementations from locally installed software and remote Web services; the latter is demonstrated with REST and XMPP Web services. Standardized QSAR datasets open up new ways to store, query, and exchange data for subsequent analyses. QSAR-ML supports completely reproducible creation of datasets, solving the problems of defining which software components were used and their versions, and the descriptor ontology eliminates confusions regarding descriptors by defining them crisply. This makes is easy to join, extend, combine datasets and hence work collectively, but

  14. Towards interoperable and reproducible QSAR analyses: Exchange of datasets

    PubMed Central

    2010-01-01

    Background QSAR is a widely used method to relate chemical structures to responses or properties based on experimental observations. Much effort has been made to evaluate and validate the statistical modeling in QSAR, but these analyses treat the dataset as fixed. An overlooked but highly important issue is the validation of the setup of the dataset, which comprises addition of chemical structures as well as selection of descriptors and software implementations prior to calculations. This process is hampered by the lack of standards and exchange formats in the field, making it virtually impossible to reproduce and validate analyses and drastically constrain collaborations and re-use of data. Results We present a step towards standardizing QSAR analyses by defining interoperable and reproducible QSAR datasets, consisting of an open XML format (QSAR-ML) which builds on an open and extensible descriptor ontology. The ontology provides an extensible way of uniquely defining descriptors for use in QSAR experiments, and the exchange format supports multiple versioned implementations of these descriptors. Hence, a dataset described by QSAR-ML makes its setup completely reproducible. We also provide a reference implementation as a set of plugins for Bioclipse which simplifies setup of QSAR datasets, and allows for exporting in QSAR-ML as well as old-fashioned CSV formats. The implementation facilitates addition of new descriptor implementations from locally installed software and remote Web services; the latter is demonstrated with REST and XMPP Web services. Conclusions Standardized QSAR datasets open up new ways to store, query, and exchange data for subsequent analyses. QSAR-ML supports completely reproducible creation of datasets, solving the problems of defining which software components were used and their versions, and the descriptor ontology eliminates confusions regarding descriptors by defining them crisply. This makes is easy to join, extend, combine datasets

  15. Reproducibility and quantitation of amplicon sequencing-based detection

    PubMed Central

    Zhou, Jizhong; Wu, Liyou; Deng, Ye; Zhi, Xiaoyang; Jiang, Yi-Huei; Tu, Qichao; Xie, Jianping; Van Nostrand, Joy D; He, Zhili; Yang, Yunfeng

    2011-01-01

    To determine the reproducibility and quantitation of the amplicon sequencing-based detection approach for analyzing microbial community structure, a total of 24 microbial communities from a long-term global change experimental site were examined. Genomic DNA obtained from each community was used to amplify 16S rRNA genes with two or three barcode tags as technical replicates in the presence of a small quantity (0.1% wt/wt) of genomic DNA from Shewanella oneidensis MR-1 as the control. The technical reproducibility of the amplicon sequencing-based detection approach is quite low, with an average operational taxonomic unit (OTU) overlap of 17.2%±2.3% between two technical replicates, and 8.2%±2.3% among three technical replicates, which is most likely due to problems associated with random sampling processes. Such variations in technical replicates could have substantial effects on estimating β-diversity but less on α-diversity. A high variation was also observed in the control across different samples (for example, 66.7-fold for the forward primer), suggesting that the amplicon sequencing-based detection approach could not be quantitative. In addition, various strategies were examined to improve the comparability of amplicon sequencing data, such as increasing biological replicates, and removing singleton sequences and less-representative OTUs across biological replicates. Finally, as expected, various statistical analyses with preprocessed experimental data revealed clear differences in the composition and structure of microbial communities between warming and non-warming, or between clipping and non-clipping. Taken together, these results suggest that amplicon sequencing-based detection is useful in analyzing microbial community structure even though it is not reproducible and quantitative. However, great caution should be taken in experimental design and data interpretation when the amplicon sequencing-based detection approach is used for quantitative

  16. Towards Reproducibility in Computational Hydrology

    NASA Astrophysics Data System (ADS)

    Hutton, Christopher; Wagener, Thorsten; Freer, Jim; Han, Dawei; Duffy, Chris; Arheimer, Berit

    2017-04-01

    Reproducibility is a foundational principle in scientific research. The ability to independently re-run an experiment helps to verify the legitimacy of individual findings, and evolve (or reject) hypotheses and models of how environmental systems function, and move them from specific circumstances to more general theory. Yet in computational hydrology (and in environmental science more widely) the code and data that produces published results are not regularly made available, and even if they are made available, there remains a multitude of generally unreported choices that an individual scientist may have made that impact the study result. This situation strongly inhibits the ability of our community to reproduce and verify previous findings, as all the information and boundary conditions required to set up a computational experiment simply cannot be reported in an article's text alone. In Hutton et al 2016 [1], we argue that a cultural change is required in the computational hydrological community, in order to advance and make more robust the process of knowledge creation and hypothesis testing. We need to adopt common standards and infrastructures to: (1) make code readable and re-useable; (2) create well-documented workflows that combine re-useable code together with data to enable published scientific findings to be reproduced; (3) make code and workflows available, easy to find, and easy to interpret, using code and code metadata repositories. To create change we argue for improved graduate training in these areas. In this talk we reflect on our progress in achieving reproducible, open science in computational hydrology, which are relevant to the broader computational geoscience community. In particular, we draw on our experience in the Switch-On (EU funded) virtual water science laboratory (http://www.switch-on-vwsl.eu/participate/), which is an open platform for collaboration in hydrological experiments (e.g. [2]). While we use computational hydrology as

  17. Participant Nonnaiveté and the reproducibility of cognitive psychology.

    PubMed

    Zwaan, Rolf A; Pecher, Diane; Paolacci, Gabriele; Bouwmeester, Samantha; Verkoeijen, Peter; Dijkstra, Katinka; Zeelenberg, René

    2017-07-25

    Many argue that there is a reproducibility crisis in psychology. We investigated nine well-known effects from the cognitive psychology literature-three each from the domains of perception/action, memory, and language, respectively-and found that they are highly reproducible. Not only can they be reproduced in online environments, but they also can be reproduced with nonnaïve participants with no reduction of effect size. Apparently, some cognitive tasks are so constraining that they encapsulate behavior from external influences, such as testing situation and prior recent experience with the experiment to yield highly robust effects.

  18. Systematic heterogenization for better reproducibility in animal experimentation.

    PubMed

    Richter, S Helene

    2017-08-31

    The scientific literature is full of articles discussing poor reproducibility of findings from animal experiments as well as failures to translate results from preclinical animal studies to clinical trials in humans. Critics even go so far as to talk about a "reproducibility crisis" in the life sciences, a novel headword that increasingly finds its way into numerous high-impact journals. Viewed from a cynical perspective, Fett's law of the lab "Never replicate a successful experiment" has thus taken on a completely new meaning. So far, poor reproducibility and translational failures in animal experimentation have mostly been attributed to biased animal data, methodological pitfalls, current publication ethics and animal welfare constraints. More recently, the concept of standardization has also been identified as a potential source of these problems. By reducing within-experiment variation, rigorous standardization regimes limit the inference to the specific experimental conditions. In this way, however, individual phenotypic plasticity is largely neglected, resulting in statistically significant but possibly irrelevant findings that are not reproducible under slightly different conditions. By contrast, systematic heterogenization has been proposed as a concept to improve representativeness of study populations, contributing to improved external validity and hence improved reproducibility. While some first heterogenization studies are indeed very promising, it is still not clear how this approach can be transferred into practice in a logistically feasible and effective way. Thus, further research is needed to explore different heterogenization strategies as well as alternative routes toward better reproducibility in animal experimentation.

  19. Are distal radius fracture classifications reproducible? Intra and interobserver agreement.

    PubMed

    Belloti, João Carlos; Tamaoki, Marcel Jun Sugawara; Franciozi, Carlos Eduardo da Silveira; Santos, João Baptista Gomes dos; Balbachevsky, Daniel; Chap Chap, Eduardo; Albertoni, Walter Manna; Faloppa, Flávio

    2008-05-01

    Various classification systems have been proposed for fractures of the distal radius, but the reliability of these classifications is seldom addressed. For a fracture classification to be useful, it must provide prognostic significance, interobserver reliability and intraobserver reproducibility. The aim here was to evaluate the intraobserver and interobserver agreement of distal radius fracture classifications. This was a validation study on interobserver and intraobserver reliability. It was developed in the Department of Orthopedics and Traumatology, Universidade Federal de São Paulo - Escola Paulista de Medicina. X-rays from 98 cases of displaced distal radius fracture were evaluated by five observers: one third-year orthopedic resident (R3), one sixth-year undergraduate medical student (UG6), one radiologist physician (XRP), one orthopedic trauma specialist (OT) and one orthopedic hand surgery specialist (OHS). The radiographs were classified on three different occasions (times T1, T2 and T3) using the Universal (Cooney), Arbeitsgemeinschaft für Osteosynthesefragen/Association for the Study of Internal Fixation (AO/ASIF), Frykman and Fernández classifications. The kappa coefficient (kappa) was applied to assess the degree of agreement. Among the three occasions, the highest mean intraobserver k was observed in the Universal classification (0.61), followed by Fernández (0.59), Frykman (0.55) and AO/ASIF (0.49). The interobserver agreement was unsatisfactory in all classifications. The Fernández classification showed the best agreement (0.44) and the worst was the Frykman classification (0.26). The low agreement levels observed in this study suggest that there is still no classification method with high reproducibility.

  20. The origin of replicators and reproducers

    PubMed Central

    Szathmáry, Eörs

    2006-01-01

    Replicators are fundamental to the origin of life and evolvability. Their survival depends on the accuracy of replication and the efficiency of growth relative to spontaneous decay. Infrabiological systems are built of two coupled autocatalytic systems, in contrast to minimal living systems that must comprise at least a metabolic subsystem, a hereditary subsystem and a boundary, serving respective functions. Some scenarios prefer to unite all these functions into one primordial system, as illustrated in the lipid world scenario, which is considered as a didactic example in detail. Experimentally produced chemical replicators grow parabolically owing to product inhibition. A selection consequence is survival of everybody. The chromatographized replicator model predicts that such replicators spreading on surfaces can be selected for higher replication rate because double strands are washed away slower than single strands from the surface. Analysis of real ribozymes suggests that the error threshold of replication is less severe by about one order of magnitude than thought previously. Surface-bound dynamics is predicted to play a crucial role also for exponential replicators: unlinked genes belonging to the same genome do not displace each other by competition, and efficient and accurate replicases can spread. The most efficient form of such useful population structure is encapsulation by reproducing vesicles. The stochastic corrector model shows how such a bag of genes can survive, and what the role of chromosome formation and intragenic recombination could be. Prebiotic and early evolution cannot be understood without the models of dynamics. PMID:17008217

  1. Response to Comment on "Estimating the reproducibility of psychological science".

    PubMed

    Anderson, Christopher J; Bahník, Štěpán; Barnett-Cowan, Michael; Bosco, Frank A; Chandler, Jesse; Chartier, Christopher R; Cheung, Felix; Christopherson, Cody D; Cordes, Andreas; Cremata, Edward J; Della Penna, Nicolas; Estel, Vivien; Fedor, Anna; Fitneva, Stanka A; Frank, Michael C; Grange, James A; Hartshorne, Joshua K; Hasselman, Fred; Henninger, Felix; van der Hulst, Marije; Jonas, Kai J; Lai, Calvin K; Levitan, Carmel A; Miller, Jeremy K; Moore, Katherine S; Meixner, Johannes M; Munafò, Marcus R; Neijenhuijs, Koen I; Nilsonne, Gustav; Nosek, Brian A; Plessow, Franziska; Prenoveau, Jason M; Ricker, Ashley A; Schmidt, Kathleen; Spies, Jeffrey R; Stieger, Stefan; Strohminger, Nina; Sullivan, Gavin B; van Aert, Robbie C M; van Assen, Marcel A L M; Vanpaemel, Wolf; Vianello, Michelangelo; Voracek, Martin; Zuni, Kellylynn

    2016-03-04

    Gilbert et al. conclude that evidence from the Open Science Collaboration's Reproducibility Project: Psychology indicates high reproducibility, given the study methodology. Their very optimistic assessment is limited by statistical misconceptions and by causal inferences from selectively interpreted, correlational data. Using the Reproducibility Project: Psychology data, both optimistic and pessimistic conclusions about reproducibility are possible, and neither are yet warranted. Copyright © 2016, American Association for the Advancement of Science.

  2. Opening Reproducible Research

    NASA Astrophysics Data System (ADS)

    Nüst, Daniel; Konkol, Markus; Pebesma, Edzer; Kray, Christian; Klötgen, Stephanie; Schutzeichel, Marc; Lorenz, Jörg; Przibytzin, Holger; Kussmann, Dirk

    2016-04-01

    Open access is not only a form of publishing such that research papers become available to the large public free of charge, it also refers to a trend in science that the act of doing research becomes more open and transparent. When science transforms to open access we not only mean access to papers, research data being collected, or data being generated, but also access to the data used and the procedures carried out in the research paper. Increasingly, scientific results are generated by numerical manipulation of data that were already collected, and may involve simulation experiments that are completely carried out computationally. Reproducibility of research findings, the ability to repeat experimental procedures and confirm previously found results, is at the heart of the scientific method (Pebesma, Nüst and Bivand, 2012). As opposed to the collection of experimental data in labs or nature, computational experiments lend themselves very well for reproduction. Some of the reasons why scientists do not publish data and computational procedures that allow reproduction will be hard to change, e.g. privacy concerns in the data, fear for embarrassment or of losing a competitive advantage. Others reasons however involve technical aspects, and include the lack of standard procedures to publish such information and the lack of benefits after publishing them. We aim to resolve these two technical aspects. We propose a system that supports the evolution of scientific publications from static papers into dynamic, executable research documents. The DFG-funded experimental project Opening Reproducible Research (ORR) aims for the main aspects of open access, by improving the exchange of, by facilitating productive access to, and by simplifying reuse of research results that are published over the Internet. Central to the project is a new form for creating and providing research results, the executable research compendium (ERC), which not only enables third parties to

  3. Assessment of Modeling Capability for Reproducing Storm Impacts on TEC

    NASA Astrophysics Data System (ADS)

    Shim, J. S.; Kuznetsova, M. M.; Rastaetter, L.; Bilitza, D.; Codrescu, M.; Coster, A. J.; Emery, B. A.; Foerster, M.; Foster, B.; Fuller-Rowell, T. J.; Huba, J. D.; Goncharenko, L. P.; Mannucci, A. J.; Namgaladze, A. A.; Pi, X.; Prokhorov, B. E.; Ridley, A. J.; Scherliess, L.; Schunk, R. W.; Sojka, J. J.; Zhu, L.

    2014-12-01

    During geomagnetic storm, the energy transfer from solar wind to magnetosphere-ionosphere system adversely affects the communication and navigation systems. Quantifying storm impacts on TEC (Total Electron Content) and assessment of modeling capability of reproducing storm impacts on TEC are of importance to specifying and forecasting space weather. In order to quantify storm impacts on TEC, we considered several parameters: TEC changes compared to quiet time (the day before storm), TEC difference between 24-hour intervals, and maximum increase/decrease during the storm. We investigated the spatial and temporal variations of the parameters during the 2006 AGU storm event (14-15 Dec. 2006) using ground-based GPS TEC measurements in the selected 5 degree eight longitude sectors. The latitudinal variations were also studied in two longitude sectors among the eight sectors where data coverage is relatively better. We obtained modeled TEC from various ionosphere/thermosphere (IT) models. The parameters from the models were compared with each other and with the observed values. We quantified performance of the models in reproducing the TEC variations during the storm using skill scores. This study has been supported by the Community Coordinated Modeling Center (CCMC) at the Goddard Space Flight Center. Model outputs and observational data used for the study will be permanently posted at the CCMC website (http://ccmc.gsfc.nasa.gov) for the space science communities to use.

  4. Repeatability, Reproducibility, Separative Power and Subjectivity of Different Fish Morphometric Analysis Methods

    PubMed Central

    Takács, Péter

    2016-01-01

    We compared the repeatability, reproducibility (intra- and inter-measurer similarity), separative power and subjectivity (measurer effect on results) of four morphometric methods frequently used in ichthyological research, the “traditional” caliper-based (TRA) and truss-network (TRU) distance methods and two geometric methods that compare landmark coordinates on the body (GMB) and scales (GMS). In each case, measurements were performed three times by three measurers on the same specimen of three common cyprinid species (roach Rutilus rutilus (Linnaeus, 1758), bleak Alburnus alburnus (Linnaeus, 1758) and Prussian carp Carassius gibelio (Bloch, 1782)) collected from three closely-situated sites in the Lake Balaton catchment (Hungary) in 2014. TRA measurements were made on conserved specimens using a digital caliper, while TRU, GMB and GMS measurements were undertaken on digital images of the bodies and scales. In most cases, intra-measurer repeatability was similar. While all four methods were able to differentiate the source populations, significant differences were observed in their repeatability, reproducibility and subjectivity. GMB displayed highest overall repeatability and reproducibility and was least burdened by measurer effect. While GMS showed similar repeatability to GMB when fish scales had a characteristic shape, it showed significantly lower reproducability (compared with its repeatability) for each species than the other methods. TRU showed similar repeatability as the GMS. TRA was the least applicable method as measurements were obtained from the fish itself, resulting in poor repeatability and reproducibility. Although all four methods showed some degree of subjectivity, TRA was the only method where population-level detachment was entirely overwritten by measurer effect. Based on these results, we recommend a) avoidance of aggregating different measurer’s datasets when using TRA and GMS methods; and b) use of image-based methods for

  5. Modified method of recording and reproducing natural head position with a multicamera system and a laser level.

    PubMed

    Liu, Xiao-jing; Li, Qian-qian; Pang, Yuan-jie; Tian, Kai-yue; Xie, Zheng; Li, Zi-li

    2015-06-01

    As computer-assisted surgical design becomes increasingly popular in maxillofacial surgery, recording patients' natural head position (NHP) and reproducing it in the virtual environment are vital for preoperative design and postoperative evaluation. Our objective was to test the repeatability and accuracy of recording NHP using a multicamera system and a laser level. A laser level was used to project a horizontal reference line on a physical model, and a 3-dimensional image was obtained using a multicamera system. In surgical simulation software, the recorded NHP was reproduced in the virtual head position by registering the coordinate axes with the horizontal reference on both the frontal and lateral views. The repeatability and accuracy of the method were assessed using a gyroscopic procedure as the gold standard. The interclass correlation coefficients for pitch and roll were 0.982 (0.966, 0.991) and 0.995 (0.992, 0.998), respectively, indicating a high degree of repeatability. Regarding accuracy, the lack of agreement in orientation between the new method and the gold standard was within the ranges for pitch (-0.69°, 1.71°) and for roll (-0.92°, 1.20°); these have no clinical significance. This method of recording and reproducing NHP with a multicamera system and a laser level is repeatable, accurate, and clinically feasible. Copyright © 2015 American Association of Orthodontists. Published by Elsevier Inc. All rights reserved.

  6. Effect of Initial Conditions on Reproducibility of Scientific Research

    PubMed Central

    Djulbegovic, Benjamin; Hozo, Iztok

    2014-01-01

    Background: It is estimated that about half of currently published research cannot be reproduced. Many reasons have been offered as explanations for failure to reproduce scientific research findings- from fraud to the issues related to design, conduct, analysis, or publishing scientific research. We also postulate a sensitive dependency on initial conditions by which small changes can result in the large differences in the research findings when attempted to be reproduced at later times. Methods: We employed a simple logistic regression equation to model the effect of covariates on the initial study findings. We then fed the input from the logistic equation into a logistic map function to model stability of the results in repeated experiments over time. We illustrate the approach by modeling effects of different factors on the choice of correct treatment. Results: We found that reproducibility of the study findings depended both on the initial values of all independent variables and the rate of change in the baseline conditions, the latter being more important. When the changes in the baseline conditions vary by about 3.5 to about 4 in between experiments, no research findings could be reproduced. However, when the rate of change between the experiments is ≤2.5 the results become highly predictable between the experiments. Conclusions: Many results cannot be reproduced because of the changes in the initial conditions between the experiments. Better control of the baseline conditions in-between the experiments may help improve reproducibility of scientific findings. PMID:25132705

  7. Effect of initial conditions on reproducibility of scientific research.

    PubMed

    Djulbegovic, Benjamin; Hozo, Iztok

    2014-06-01

    It is estimated that about half of currently published research cannot be reproduced. Many reasons have been offered as explanations for failure to reproduce scientific research findings- from fraud to the issues related to design, conduct, analysis, or publishing scientific research. We also postulate a sensitive dependency on initial conditions by which small changes can result in the large differences in the research findings when attempted to be reproduced at later times. We employed a simple logistic regression equation to model the effect of covariates on the initial study findings. We then fed the input from the logistic equation into a logistic map function to model stability of the results in repeated experiments over time. We illustrate the approach by modeling effects of different factors on the choice of correct treatment. We found that reproducibility of the study findings depended both on the initial values of all independent variables and the rate of change in the baseline conditions, the latter being more important. When the changes in the baseline conditions vary by about 3.5 to about 4 in between experiments, no research findings could be reproduced. However, when the rate of change between the experiments is ≤2.5 the results become highly predictable between the experiments. Many results cannot be reproduced because of the changes in the initial conditions between the experiments. Better control of the baseline conditions in-between the experiments may help improve reproducibility of scientific findings.

  8. Language-Agnostic Reproducible Data Analysis Using Literate Programming.

    PubMed

    Vassilev, Boris; Louhimo, Riku; Ikonen, Elina; Hautaniemi, Sampsa

    2016-01-01

    A modern biomedical research project can easily contain hundreds of analysis steps and lack of reproducibility of the analyses has been recognized as a severe issue. While thorough documentation enables reproducibility, the number of analysis programs used can be so large that in reality reproducibility cannot be easily achieved. Literate programming is an approach to present computer programs to human readers. The code is rearranged to follow the logic of the program, and to explain that logic in a natural language. The code executed by the computer is extracted from the literate source code. As such, literate programming is an ideal formalism for systematizing analysis steps in biomedical research. We have developed the reproducible computing tool Lir (literate, reproducible computing) that allows a tool-agnostic approach to biomedical data analysis. We demonstrate the utility of Lir by applying it to a case study. Our aim was to investigate the role of endosomal trafficking regulators to the progression of breast cancer. In this analysis, a variety of tools were combined to interpret the available data: a relational database, standard command-line tools, and a statistical computing environment. The analysis revealed that the lipid transport related genes LAPTM4B and NDRG1 are coamplified in breast cancer patients, and identified genes potentially cooperating with LAPTM4B in breast cancer progression. Our case study demonstrates that with Lir, an array of tools can be combined in the same data analysis to improve efficiency, reproducibility, and ease of understanding. Lir is an open-source software available at github.com/borisvassilev/lir.

  9. Language-Agnostic Reproducible Data Analysis Using Literate Programming

    PubMed Central

    Vassilev, Boris; Louhimo, Riku; Ikonen, Elina; Hautaniemi, Sampsa

    2016-01-01

    A modern biomedical research project can easily contain hundreds of analysis steps and lack of reproducibility of the analyses has been recognized as a severe issue. While thorough documentation enables reproducibility, the number of analysis programs used can be so large that in reality reproducibility cannot be easily achieved. Literate programming is an approach to present computer programs to human readers. The code is rearranged to follow the logic of the program, and to explain that logic in a natural language. The code executed by the computer is extracted from the literate source code. As such, literate programming is an ideal formalism for systematizing analysis steps in biomedical research. We have developed the reproducible computing tool Lir (literate, reproducible computing) that allows a tool-agnostic approach to biomedical data analysis. We demonstrate the utility of Lir by applying it to a case study. Our aim was to investigate the role of endosomal trafficking regulators to the progression of breast cancer. In this analysis, a variety of tools were combined to interpret the available data: a relational database, standard command-line tools, and a statistical computing environment. The analysis revealed that the lipid transport related genes LAPTM4B and NDRG1 are coamplified in breast cancer patients, and identified genes potentially cooperating with LAPTM4B in breast cancer progression. Our case study demonstrates that with Lir, an array of tools can be combined in the same data analysis to improve efficiency, reproducibility, and ease of understanding. Lir is an open-source software available at github.com/borisvassilev/lir. PMID:27711123

  10. Reproducibility of ad libitum energy intake with the use of a computerized vending machine system123

    PubMed Central

    Votruba, Susanne B; Franks, Paul W; Krakoff, Jonathan; Salbe, Arline D

    2010-01-01

    Background: Accurate assessment of energy intake is difficult but critical for the evaluation of eating behavior and intervention effects. Consequently, methods to assess ad libitum energy intake under controlled conditions have been developed. Objective: Our objective was to evaluate the reproducibility of ad libitum energy intake with the use of a computerized vending machine system. Design: Twelve individuals (mean ± SD: 36 ± 8 y old; 41 ± 8% body fat) consumed a weight-maintaining diet for 3 d; subsequently, they self-selected all food with the use of a computerized vending machine system for an additional 3 d. Mean daily energy intake was calculated from the actual weight of foods consumed and expressed as a percentage of weight-maintenance energy needs (%WMEN). Subjects repeated the study multiple times during 2 y. The within-person reproducibility of energy intake was determined through the calculation of the intraclass correlation coefficients (ICCs) between visits. Results: Daily energy intake for all subjects was 5020 ± 1753 kcal during visit 1 and 4855 ± 1615 kcal during visit 2. There were no significant associations between energy intake and body weight, body mass index, or percentage body fat while subjects used the vending machines, which indicates that intake was not driven by body size or need. Despite overconsumption (%WMEN = 181 ± 57%), the reproducibility of intake between visits, whether expressed as daily energy intake (ICC = 0.90), %WMEN (ICC = 0.86), weight of food consumed (ICC = 0.87), or fat intake (g/d; ICC = 0.87), was highly significant (P < 0.0001). Conclusion: Although ad libitum energy intake exceeded %WMEN, the within-person reliability of this intake across multiple visits was high, which makes this a reproducible method for the measurement of ad libitum intake in subjects who reside in a research unit. This trial was registered at clinicaltrials.gov as NCT00342732. PMID:19923376

  11. Object strength--an accurate measure for small objects that is insensitive to partial volume effects.

    PubMed

    Tofts, P S; Silver, N C; Barker, G J; Gass, A

    2005-07-01

    There are currently four problems in characterising small nonuniform lesions or other objects in Magnetic Resonance images where partial volume effects are significant. Object size is over- or under-estimated; boundaries are often not reproducible; mean object value cannot be measured; and fuzzy borders cannot be accommodated. A new measure, Object Strength, is proposed. This is the sum of all abnormal intensities, above a uniform background value. For a uniform object, this is simply the product of the increase in intensity and the size of the object. Biologically, this could be at least as relevant as existing measures of size or mean intensity. We hypothesise that Object Strength will perform better than traditional area measurements in characterising small objects. In a pilot study, the reproducibility of object strength measurements was investigated using MR images of small multiple sclerosis (MS) lesions. In addition, accuracy was investigated using artificial lesions of known volume (0.3-6.2 ml) and realistic appearance. Reproducibility approached that of area measurements (in 33/90 lesion reports the difference between repeats was less than for area measurements). Total lesion volume was accurate to 0.2%. In conclusion, Object Strength has potential for improved characterisation of small lesions and objects in imaging and possibly spectroscopy.

  12. Estimating the state of a geophysical system with sparse observations: time delay methods to achieve accurate initial states for prediction

    NASA Astrophysics Data System (ADS)

    An, Zhe; Rey, Daniel; Ye, Jingxin; Abarbanel, Henry D. I.

    2017-01-01

    The problem of forecasting the behavior of a complex dynamical system through analysis of observational time-series data becomes difficult when the system expresses chaotic behavior and the measurements are sparse, in both space and/or time. Despite the fact that this situation is quite typical across many fields, including numerical weather prediction, the issue of whether the available observations are "sufficient" for generating successful forecasts is still not well understood. An analysis by Whartenby et al. (2013) found that in the context of the nonlinear shallow water equations on a β plane, standard nudging techniques require observing approximately 70 % of the full set of state variables. Here we examine the same system using a method introduced by Rey et al. (2014a), which generalizes standard nudging methods to utilize time delayed measurements. We show that in certain circumstances, it provides a sizable reduction in the number of observations required to construct accurate estimates and high-quality predictions. In particular, we find that this estimate of 70 % can be reduced to about 33 % using time delays, and even further if Lagrangian drifter locations are also used as measurements.

  13. REPRODUCIBILITY OF MACULAR PIGMENT OPTICAL DENSITY MEASUREMENT BY TWO-WAVELENGTH AUTOFLUORESCENCE IN A CLINICAL SETTING.

    PubMed

    You, Qi Sheng; Bartsch, Dirk-Uwe G; Espina, Mark; Alam, Mostafa; Camacho, Natalia; Mendoza, Nadia; Freeman, William R

    2016-07-01

    Macular pigment, composed of lutein, zeaxanthin, and meso-zeaxanthin, is postulated to protect against age-related macular degeneration, likely because of filtering blue light and its antioxidant properties. Macular pigment optical density (MPOD) is reported to be associated with macular function evaluated by visual acuity and multifocal electroretinogram. Given the importance of macular pigment, reliable and accurate measurement methods are important. The main purpose of this study is to determine the reproducibility of MPOD measurement by two-wavelength autofluorescence method using scanning laser ophthalmoscopy. Sixty-eight eyes of 39 persons were enrolled in the study, including 11 normal eyes, 16 eyes with wet age-related macular degeneration, 16 eyes with dry age-related macular degeneration, 11 eyes with macular edema due to diabetic mellitus, branch retinal vein occlusion or macular telangiectasia, and 14 eyes with tractional maculopathy, including vitreomacular traction, epiretinal membrane, or macular hole. MPOD was measured with a two-wavelength (488 and 514 nm) autofluorescence method with the Spectralis HRA + OCT after pupil dilation. The measurement was repeated for each eye 10 minutes later. The analysis of variance and Bland-Altman plot were used to assess the reproducibility between the two measurements. The mean MPOD at eccentricities of 1° and 2° was 0.36 ± 0.17 (range: 0.04-0.69) and 0.15 ± 0.08 (range: -0.03 to 0.35) for the first measurement and 0.35 ± 0.17 (range: 0.02-0.68) and 0.15 ± 0.08 (range: -0.01 to 0.33) for the second measurement, respectively. The difference between the 2 measurements was not statistically significant, and the Bland-Altman plot showed 7.4% and 5.9% points outside the 95% limits of agreement, indicating an overall excellent reproducibility. Similarly, there is no significant difference between the first and second measurements of MPOD volume within eccentricities of 1°, 2°, and 6° radius, and the Bland

  14. A Machine Learned Classifier That Uses Gene Expression Data to Accurately Predict Estrogen Receptor Status

    PubMed Central

    Bastani, Meysam; Vos, Larissa; Asgarian, Nasimeh; Deschenes, Jean; Graham, Kathryn; Mackey, John; Greiner, Russell

    2013-01-01

    Background Selecting the appropriate treatment for breast cancer requires accurately determining the estrogen receptor (ER) status of the tumor. However, the standard for determining this status, immunohistochemical analysis of formalin-fixed paraffin embedded samples, suffers from numerous technical and reproducibility issues. Assessment of ER-status based on RNA expression can provide more objective, quantitative and reproducible test results. Methods To learn a parsimonious RNA-based classifier of hormone receptor status, we applied a machine learning tool to a training dataset of gene expression microarray data obtained from 176 frozen breast tumors, whose ER-status was determined by applying ASCO-CAP guidelines to standardized immunohistochemical testing of formalin fixed tumor. Results This produced a three-gene classifier that can predict the ER-status of a novel tumor, with a cross-validation accuracy of 93.17±2.44%. When applied to an independent validation set and to four other public databases, some on different platforms, this classifier obtained over 90% accuracy in each. In addition, we found that this prediction rule separated the patients' recurrence-free survival curves with a hazard ratio lower than the one based on the IHC analysis of ER-status. Conclusions Our efficient and parsimonious classifier lends itself to high throughput, highly accurate and low-cost RNA-based assessments of ER-status, suitable for routine high-throughput clinical use. This analytic method provides a proof-of-principle that may be applicable to developing effective RNA-based tests for other biomarkers and conditions. PMID:24312637

  15. TU-AB-BRC-05: Creation of a Monte Carlo TrueBeam Model by Reproducing Varian Phase Space Data

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    O’Grady, K; Davis, S; Seuntjens, J

    Purpose: To create a Varian TrueBeam 6 MV FFF Monte Carlo model using BEAMnrc/EGSnrc that accurately reproduces the Varian representative dataset, followed by tuning the model’s source parameters to accurately reproduce in-house measurements. Methods: A BEAMnrc TrueBeam model for 6 MV FFF has been created by modifying a validated 6 MV Varian CL21EX model. Geometric dimensions and materials were adjusted in a trial and error approach to match the fluence and spectra of TrueBeam phase spaces output by the Varian VirtuaLinac. Once the model’s phase space matched Varian’s counterpart using the default source parameters, it was validated to match 10more » × 10 cm{sup 2} Varian representative data obtained with the IBA CC13. The source parameters were then tuned to match in-house 5 × 5 cm{sup 2} PTW microDiamond measurements. All dose to water simulations included detector models to include the effects of volume averaging and the non-water equivalence of the chamber materials, allowing for more accurate source parameter selection. Results: The Varian phase space spectra and fluence were matched with excellent agreement. The in-house model’s PDD agreement with CC13 TrueBeam representative data was within 0.9% local percent difference beyond the first 3 mm. Profile agreement at 10 cm depth was within 0.9% local percent difference and 1.3 mm distance-to-agreement in the central axis and penumbra regions, respectively. Once the source parameters were tuned, PDD agreement with microDiamond measurements was within 0.9% local percent difference beyond 2 mm. The microDiamond profile agreement at 10 cm depth was within 0.6% local percent difference and 0.4 mm distance-to-agreement in the central axis and penumbra regions, respectively. Conclusion: An accurate in-house Monte Carlo model of the Varian TrueBeam was achieved independently of the Varian phase space solution and was tuned to in-house measurements. KO acknowledges partial support by the CREATE Medical

  16. Reproducibility in Computational Neuroscience Models and Simulations

    PubMed Central

    McDougal, Robert A.; Bulanova, Anna S.; Lytton, William W.

    2016-01-01

    Objective Like all scientific research, computational neuroscience research must be reproducible. Big data science, including simulation research, cannot depend exclusively on journal articles as the method to provide the sharing and transparency required for reproducibility. Methods Ensuring model reproducibility requires the use of multiple standard software practices and tools, including version control, strong commenting and documentation, and code modularity. Results Building on these standard practices, model sharing sites and tools have been developed that fit into several categories: 1. standardized neural simulators, 2. shared computational resources, 3. declarative model descriptors, ontologies and standardized annotations; 4. model sharing repositories and sharing standards. Conclusion A number of complementary innovations have been proposed to enhance sharing, transparency and reproducibility. The individual user can be encouraged to make use of version control, commenting, documentation and modularity in development of models. The community can help by requiring model sharing as a condition of publication and funding. Significance Model management will become increasingly important as multiscale models become larger, more detailed and correspondingly more difficult to manage by any single investigator or single laboratory. Additional big data management complexity will come as the models become more useful in interpreting experiments, thus increasing the need to ensure clear alignment between modeling data, both parameters and results, and experiment. PMID:27046845

  17. A catalyzing phantom for reproducible dynamic conversion of hyperpolarized [1-¹³C]-pyruvate.

    PubMed

    Walker, Christopher M; Lee, Jaehyuk; Ramirez, Marc S; Schellingerhout, Dawid; Millward, Steven; Bankson, James A

    2013-01-01

    In vivo real time spectroscopic imaging of hyperpolarized ¹³C labeled metabolites shows substantial promise for the assessment of physiological processes that were previously inaccessible. However, reliable and reproducible methods of measurement are necessary to maximize the effectiveness of imaging biomarkers that may one day guide personalized care for diseases such as cancer. Animal models of human disease serve as poor reference standards due to the complexity, heterogeneity, and transient nature of advancing disease. In this study, we describe the reproducible conversion of hyperpolarized [1-¹³C]-pyruvate to [1-¹³C]-lactate using a novel synthetic enzyme phantom system. The rate of reaction can be controlled and tuned to mimic normal or pathologic conditions of varying degree. Variations observed in the use of this phantom compare favorably against within-group variations observed in recent animal studies. This novel phantom system provides crucial capabilities as a reference standard for the optimization, comparison, and certification of quantitative imaging strategies for hyperpolarized tracers.

  18. Size Control of Sessile Microbubbles for Reproducibly Driven Acoustic Streaming

    NASA Astrophysics Data System (ADS)

    Volk, Andreas; Kähler, Christian J.

    2018-05-01

    Acoustically actuated bubbles are receiving growing interest in microfluidic applications, as they induce a streaming field that can be used for particle sorting and fluid mixing. An essential but often unspoken challenge in such applications is to maintain a constant bubble size to achieve reproducible conditions. We present an automatized system for the size control of a cylindrical bubble that is formed at a blind side pit of a polydimethylsiloxane microchannel. Using a pressure control system, we adapt the protrusion depth of the bubble into the microchannel to a precision of approximately 0.5 μ m on a timescale of seconds. By comparing the streaming field generated by bubbles of width 80 μ m with a protrusion depth between -12 and 60 μ m , we find that the mean velocity of the induced streaming fields varies by more than a factor of 4. We also find a qualitative change of the topology of the streaming field. Both observations confirm the importance of the bubble size control system in order to achieve reproducible and reliable bubble-driven streaming experiments.

  19. Visual-Stratigraphic Dating of the GISP2 Ice Core: Basis, Reproducibility, and Application

    NASA Technical Reports Server (NTRS)

    Alley, R. B.; Shuman, C. A.; Meese, D. A.; Gow, A. J.; Taylor, K. C.; Cuffey, K. M.; Fitzpatrick, J. J.; Grootes, P. M.; Zielinski, G. A.; Ram, M.; hide

    1997-01-01

    Annual layers are visible in the Greenland Ice Sheet Project 2 ice core from central Greenland, allowing rapid dating of the core. Changes in bubble and grain structure caused by near-surface, primarily summertime formation of hoar complexes provide the main visible annual marker in the Holocene, and changes in "cloudiness" of the ice correlated with dustiness mark Wisconsinan annual cycles; both markers are evident and have been intercalibrated in early Holocene ice. Layer counts are reproducible between different workers and for one worker at different times, with 1% error over century-length times in the Holocene. Reproducibility is typically 5% in Wisconsinan ice-age ice and decreases with increasing age and depth. Cumulative ages from visible stratigraphy are not significantly different from independent ages of prominent events for ice older than the historical record and younger than approximately 50,000 years. Visible observations are not greatly degraded by "brittle ice" or many other core-quality problems, allowing construction of long, consistently sampled time series. High accuracy requires careful study of the core by dedicated observers.

  20. Visual-stratigraphic dating of the GISP2 ice core: Basis, reproducibility, and application

    NASA Astrophysics Data System (ADS)

    Alley, R. B.; Shuman, C. A.; Meese, D. A.; Gow, A. J.; Taylor, K. C.; Cuffey, K. M.; Fitzpatrick, J. J.; Grootes, P. M.; Zielinski, G. A.; Ram, M.; Spinelli, G.; Elder, B.

    1997-11-01

    Annual layers are visible in the Greenland Ice Sheet Project 2 ice core from central Greenland, allowing rapid dating of the core. Changes in bubble and grain structure caused by near-surface, primarily summertime formation of hoar complexes provide the main visible annual marker in the Holocene, and changes in "cloudiness" of the ice correlated with dustiness mark Wisconsinan annual cycles; both markers are evident and have been intercalibrated in early Holocene ice. Layer counts are reproducible between different workers and for one worker at different times, with 1% error over century-length times in the Holocene. Reproducibility is typically 5% in Wisconsinan ice-age ice and decreases with increasing age and depth. Cumulative ages from visible stratigraphy are not significantly different from independent ages of prominent events for ice older than the historical record and younger than approximately 50,000 years. Visible observations are not greatly degraded by "brittle ice" or many other core-quality problems, allowing construction of long, consistently sampled time series. High accuracy requires careful study of the core by dedicated observers.

  1. Reproducing impact ionization mass spectra of E and F ring ice grains at different impact speeds

    NASA Astrophysics Data System (ADS)

    Klenner, F.; Reviol, R.; Postberg, F.

    2017-09-01

    As impact speeds of E and F ring ice grains impinging onto the target of impact ionization mass spectrometers in space can vary greatly, the resulting cationic or anionic mass spectra can have very different appearances. The mass spectra can be accurately reproduced with an analog experimental setup IR-FL-MALDI-ToF-MS (Infrared Free Liquid Matrix Assisted Laser Desorption and Ionization Time of Flight Mass Spectrometry). We compare mass spectra of E and F ring ice grains taken by the Cosmic Dust Analyzer (CDA) onboard Cassini recorded at different impact speeds with our analog spectra and prove the capability of the analog experiment.

  2. Observer Use of Standardized Observation Protocols in Consequential Observation Systems

    ERIC Educational Resources Information Center

    Bell, Courtney A.; Yi, Qi; Jones, Nathan D.; Lewis, Jennifer M.; McLeod, Monica; Liu, Shuangshuang

    2014-01-01

    Evidence from a handful of large-scale studies suggests that although observers can be trained to score reliably using observation protocols, there are concerns related to initial training and calibration activities designed to keep observers scoring accurately over time (e.g., Bell, et al, 2012; BMGF, 2012). Studies offer little insight into how…

  3. CLARREO Cornerstone of the Earth Observing System: Measuring Decadal Change Through Accurate Emitted Infrared and Reflected Solar Spectra and Radio Occultation

    NASA Technical Reports Server (NTRS)

    Sandford, Stephen P.

    2010-01-01

    The Climate Absolute Radiance and Refractivity Observatory (CLARREO) is one of four Tier 1 missions recommended by the recent NRC Decadal Survey report on Earth Science and Applications from Space (NRC, 2007). The CLARREO mission addresses the need to provide accurate, broadly acknowledged climate records that are used to enable validated long-term climate projections that become the foundation for informed decisions on mitigation and adaptation policies that address the effects of climate change on society. The CLARREO mission accomplishes this critical objective through rigorous SI traceable decadal change observations that are sensitive to many of the key uncertainties in climate radiative forcings, responses, and feedbacks that in turn drive uncertainty in current climate model projections. These same uncertainties also lead to uncertainty in attribution of climate change to anthropogenic forcing. For the first time CLARREO will make highly accurate, global, SI-traceable decadal change observations sensitive to the most critical, but least understood, climate forcings, responses, and feedbacks. The CLARREO breakthrough is to achieve the required levels of accuracy and traceability to SI standards for a set of observations sensitive to a wide range of key decadal change variables. The required accuracy levels are determined so that climate trend signals can be detected against a background of naturally occurring variability. Climate system natural variability therefore determines what level of accuracy is overkill, and what level is critical to obtain. In this sense, the CLARREO mission requirements are considered optimal from a science value perspective. The accuracy for decadal change traceability to SI standards includes uncertainties associated with instrument calibration, satellite orbit sampling, and analysis methods. Unlike most space missions, the CLARREO requirements are driven not by the instantaneous accuracy of the measurements, but by accuracy in

  4. How to Write a Reproducible Paper

    NASA Astrophysics Data System (ADS)

    Irving, D. B.

    2016-12-01

    The geosciences have undergone a computational revolution in recent decades, to the point where almost all modern research relies heavily on software and code. Despite this profound change in the research methods employed by geoscientists, the reporting of computational results has changed very little in academic journals. This lag has led to something of a reproducibility crisis, whereby it is impossible to replicate and verify most of today's published computational results. While it is tempting to decry the slow response of journals and funding agencies in the face of this crisis, there are very few examples of reproducible research upon which to base new communication standards. In an attempt to address this deficiency, this presentation will describe a procedure for reporting computational results that was employed in a recent Journal of Climate paper. The procedure was developed to be consistent with recommended computational best practices and seeks to minimize the time burden on authors, which has been identified as the most important barrier to publishing code. It should provide a starting point for geoscientists looking to publish reproducible research, and could be adopted by journals as a formal minimum communication standard.

  5. Tools and techniques for computational reproducibility.

    PubMed

    Piccolo, Stephen R; Frampton, Michael B

    2016-07-11

    When reporting research findings, scientists document the steps they followed so that others can verify and build upon the research. When those steps have been described in sufficient detail that others can retrace the steps and obtain similar results, the research is said to be reproducible. Computers play a vital role in many research disciplines and present both opportunities and challenges for reproducibility. Computers can be programmed to execute analysis tasks, and those programs can be repeated and shared with others. The deterministic nature of most computer programs means that the same analysis tasks, applied to the same data, will often produce the same outputs. However, in practice, computational findings often cannot be reproduced because of complexities in how software is packaged, installed, and executed-and because of limitations associated with how scientists document analysis steps. Many tools and techniques are available to help overcome these challenges; here we describe seven such strategies. With a broad scientific audience in mind, we describe the strengths and limitations of each approach, as well as the circumstances under which each might be applied. No single strategy is sufficient for every scenario; thus we emphasize that it is often useful to combine approaches.

  6. On the reproducibility of expert-operated and robotic ultrasound acquisitions.

    PubMed

    Kojcev, Risto; Khakzar, Ashkan; Fuerst, Bernhard; Zettinig, Oliver; Fahkry, Carole; DeJong, Robert; Richmon, Jeremy; Taylor, Russell; Sinibaldi, Edoardo; Navab, Nassir

    2017-06-01

    We present the evaluation of the reproducibility of measurements performed using robotic ultrasound imaging in comparison with expert-operated sonography. Robotic imaging for interventional procedures may be a valuable contribution, but requires reproducibility for its acceptance in clinical routine. We study this by comparing repeated measurements based on robotic and expert-operated ultrasound imaging. Robotic ultrasound acquisition is performed in three steps under user guidance: First, the patient is observed using a 3D camera on the robot end effector, and the user selects the region of interest. This allows for automatic planning of the robot trajectory. Next, the robot executes a sweeping motion following the planned trajectory, during which the ultrasound images and tracking data are recorded. As the robot is compliant, deviations from the path are possible, for instance due to patient motion. Finally, the ultrasound slices are compounded to create a volume. Repeated acquisitions can be performed automatically by comparing the previous and current patient surface. After repeated image acquisitions, the measurements based on acquisitions performed by the robotic system and expert are compared. Within our case series, the expert measured the anterior-posterior, longitudinal, transversal lengths of both of the left and right thyroid lobes on each of the 4 healthy volunteers 3 times, providing 72 measurements. Subsequently, the same procedure was performed using the robotic system resulting in a cumulative total of 144 clinically relevant measurements. Our results clearly indicated that robotic ultrasound enables more repeatable measurements. A robotic ultrasound platform leads to more reproducible data, which is of crucial importance for planning and executing interventions.

  7. Characterization and reproducibility of HepG2 hanging drop spheroids toxicology in vitro.

    PubMed

    Hurrell, Tracey; Ellero, Andrea Antonio; Masso, Zelie Flavienne; Cromarty, Allan Duncan

    2018-02-21

    Hepatotoxicity remains a major challenge in drug development despite preclinical toxicity screening using hepatocytes of human origin. To overcome some limitations of reproducing the hepatic phenotype, more structurally and functionally authentic cultures in vitro can be introduced by growing cells in 3D spheroid cultures. Characterisation and reproducibility of HepG2 spheroid cultures using a high-throughput hanging drop technique was performed and features contributing to potential phenotypic variation highlighted. Cultured HepG2 cells were seeded into Perfecta 3D® 96-well hanging drop plates and assessed over time for morphology, viability, cell cycle distribution, protein content and protein-mass profiles. Divergent aspects which were assessed included cell stocks, seeding density, volume of culture medium and use of extracellular matrix additives. Hanging drops are advantageous due to no complex culture matrix being present, enabling background free extractions for downstream experimentation. Varying characteristics were observed across cell stocks and batches, seeding density, culture medium volume and extracellular matrix when using immortalized HepG2 cells. These factors contribute to wide-ranging cellular responses and highlights concerns with respect to generating a reproducible phenotype in HepG2 hanging drop spheroids. Copyright © 2018 Elsevier Ltd. All rights reserved.

  8. Reproducibility of a silicone-based test food to masticatory performance evaluation by different sieve methods.

    PubMed

    Sánchez-Ayala, Alfonso; Vilanova, Larissa Soares Reis; Costa, Marina Abrantes; Farias-Neto, Arcelino

    2014-01-01

    The aim of this study was to evaluate the reproducibility of the condensation silicone Optosil Comfort® as an artificial test food for masticatory performance evaluation. Twenty dentate subjects with mean age of 23.3±0.7 years were selected. Masticatory performance was evaluated using the simple (MPI), the double (IME) and the multiple sieve methods. Trials were carried out five times by three examiners: three times by the first, and once by the second and third examiners. Friedman's test was used to find the differences among time trials. Reproducibility was determined by the intra-class correlation (ICC) test (α=0.05). No differences among time trials were found, except for MPI-4 mm (p=0.022) from the first examiner results. The intra-examiner reproducibility (ICC) of almost all data was high (ICC≥0.92, p<0.001), being moderate only for MPI-0.50 mm (ICC=0.89, p<0.001). The inter-examiner reproducibility was high (ICC>0.93, p<0.001) for all results. For the multiple sieve method, the average mean of absolute difference from repeated measurements were lower than 1 mm. This trend was observed only from MPI-0.50 to MPI-1.4 for the single sieve method, and from IME-0.71/0.50 to IME-1.40/1.00 for the double sieve method. The results suggest that regardless of the method used, the reproducibility of Optosil Comfort® is high.

  9. Reproducibility of Heart Rate Variability Is Parameter and Sleep Stage Dependent.

    PubMed

    Herzig, David; Eser, Prisca; Omlin, Ximena; Riener, Robert; Wilhelm, Matthias; Achermann, Peter

    2017-01-01

    Objective: Measurements of heart rate variability (HRV) during sleep have become increasingly popular as sleep could provide an optimal state for HRV assessments. While sleep stages have been reported to affect HRV, the effect of sleep stages on the variance of HRV parameters were hardly investigated. We aimed to assess the variance of HRV parameters during the different sleep stages. Further, we tested the accuracy of an algorithm using HRV to identify a 5-min segment within an episode of slow wave sleep (SWS, deep sleep). Methods: Polysomnographic (PSG) sleep recordings of 3 nights of 15 healthy young males were analyzed. Sleep was scored according to conventional criteria. HRV parameters of consecutive 5-min segments were analyzed within the different sleep stages. The total variance of HRV parameters was partitioned into between-subjects variance, between-nights variance, and between-segments variance and compared between the different sleep stages. Intra-class correlation coefficients of all HRV parameters were calculated for all sleep stages. To identify an SWS segment based on HRV, Pearson correlation coefficients of consecutive R-R intervals (rRR) of moving 5-min windows (20-s steps). The linear trend was removed from the rRR time series and the first segment with rRR values 0.1 units below the mean rRR for at least 10 min was identified. A 5-min segment was placed in the middle of such an identified segment and the corresponding sleep stage was used to assess the accuracy of the algorithm. Results: Good reproducibility within and across nights was found for heart rate in all sleep stages and for high frequency (HF) power in SWS. Reproducibility of low frequency (LF) power and of LF/HF was poor in all sleep stages. Of all the 5-min segments selected based on HRV data, 87% were accurately located within SWS. Conclusions: SWS, a stable state that, in contrast to waking, is unaffected by internal and external factors, is a reproducible state that allows

  10. Reproducibility of Heart Rate Variability Is Parameter and Sleep Stage Dependent

    PubMed Central

    Herzig, David; Eser, Prisca; Omlin, Ximena; Riener, Robert; Wilhelm, Matthias; Achermann, Peter

    2018-01-01

    Objective: Measurements of heart rate variability (HRV) during sleep have become increasingly popular as sleep could provide an optimal state for HRV assessments. While sleep stages have been reported to affect HRV, the effect of sleep stages on the variance of HRV parameters were hardly investigated. We aimed to assess the variance of HRV parameters during the different sleep stages. Further, we tested the accuracy of an algorithm using HRV to identify a 5-min segment within an episode of slow wave sleep (SWS, deep sleep). Methods: Polysomnographic (PSG) sleep recordings of 3 nights of 15 healthy young males were analyzed. Sleep was scored according to conventional criteria. HRV parameters of consecutive 5-min segments were analyzed within the different sleep stages. The total variance of HRV parameters was partitioned into between-subjects variance, between-nights variance, and between-segments variance and compared between the different sleep stages. Intra-class correlation coefficients of all HRV parameters were calculated for all sleep stages. To identify an SWS segment based on HRV, Pearson correlation coefficients of consecutive R-R intervals (rRR) of moving 5-min windows (20-s steps). The linear trend was removed from the rRR time series and the first segment with rRR values 0.1 units below the mean rRR for at least 10 min was identified. A 5-min segment was placed in the middle of such an identified segment and the corresponding sleep stage was used to assess the accuracy of the algorithm. Results: Good reproducibility within and across nights was found for heart rate in all sleep stages and for high frequency (HF) power in SWS. Reproducibility of low frequency (LF) power and of LF/HF was poor in all sleep stages. Of all the 5-min segments selected based on HRV data, 87% were accurately located within SWS. Conclusions: SWS, a stable state that, in contrast to waking, is unaffected by internal and external factors, is a reproducible state that allows

  11. Reproducible Bioinformatics Research for Biologists

    USDA-ARS?s Scientific Manuscript database

    This book chapter describes the current Big Data problem in Bioinformatics and the resulting issues with performing reproducible computational research. The core of the chapter provides guidelines and summaries of current tools/techniques that a noncomputational researcher would need to learn to pe...

  12. Reproducibility of the Online Food4Me Food-Frequency Questionnaire for Estimating Dietary Intakes across Europe.

    PubMed

    Marshall, Steven J; Livingstone, Katherine M; Celis-Morales, Carlos; Forster, Hannah; Fallaize, Rosalind; O'Donovan, Clare B; Woolhead, Clara; Marsaux, Cyril Fm; Macready, Anna L; Navas-Carretero, Santiago; San-Cristobal, Rodrigo; Kolossa, Silvia; Tsirigoti, Lydia; Lambrinou, Christina P; Moschonis, George; Godlewska, Magdalena; Surwiłło, Agnieszka; Drevon, Christian A; Manios, Yannis; Traczyk, Iwona; Martínez, J Alfredo; Saris, Wim H; Daniel, Hannelore; Gibney, Eileen R; Brennan, Lorraine; Walsh, Marianne C; Lovegrove, Julie A; Gibney, Mike; Mathers, John C

    2016-05-01

    Accurate dietary assessment is key to understanding nutrition-related outcomes and is essential for estimating dietary change in nutrition-based interventions. The objective of this study was to assess the pan-European reproducibility of the Food4Me food-frequency questionnaire (FFQ) in assessing the habitual diet of adults. Participants from the Food4Me study, a 6-mo, Internet-based, randomized controlled trial of personalized nutrition conducted in the United Kingdom, Ireland, Spain, Netherlands, Germany, Greece, and Poland, were included. Screening and baseline data (both collected before commencement of the intervention) were used in the present analyses, and participants were included only if they completed FFQs at screening and at baseline within a 1-mo timeframe before the commencement of the intervention. Sociodemographic (e.g., sex and country) and lifestyle [e.g., body mass index (BMI, in kg/m(2)) and physical activity] characteristics were collected. Linear regression, correlation coefficients, concordance (percentage) in quartile classification, and Bland-Altman plots for daily intakes were used to assess reproducibility. In total, 567 participants (59% female), with a mean ± SD age of 38.7 ± 13.4 y and BMI of 25.4 ± 4.8, completed both FFQs within 1 mo (mean ± SD: 19.2 ± 6.2 d). Exact plus adjacent classification of total energy intake in participants was highest in Ireland (94%) and lowest in Poland (81%). Spearman correlation coefficients (ρ) in total energy intake between FFQs ranged from 0.50 for obese participants to 0.68 and 0.60 in normal-weight and overweight participants, respectively. Bland-Altman plots showed a mean difference between FFQs of 210 kcal/d, with the agreement deteriorating as energy intakes increased. There was little variation in reproducibility of total energy intakes between sex and age groups. The online Food4Me FFQ was shown to be reproducible across 7 European countries when administered within a 1-mo period to a

  13. ACCURATE LOW-MASS STELLAR MODELS OF KOI-126

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Feiden, Gregory A.; Chaboyer, Brian; Dotter, Aaron, E-mail: gregory.a.feiden@dartmouth.edu

    2011-10-10

    The recent discovery of an eclipsing hierarchical triple system with two low-mass stars in a close orbit (KOI-126) by Carter et al. appeared to reinforce the evidence that theoretical stellar evolution models are not able to reproduce the observational mass-radius relation for low-mass stars. We present a set of stellar models for the three stars in the KOI-126 system that show excellent agreement with the observed radii. This agreement appears to be due to the equation of state implemented by our code. A significant dispersion in the observed mass-radius relation for fully convective stars is demonstrated; indicative of the influencemore » of physics currently not incorporated in standard stellar evolution models. We also predict apsidal motion constants for the two M dwarf companions. These values should be observationally determined to within 1% by the end of the Kepler mission.« less

  14. Diagnostic accuracy and reproducibility of pleural and lung ultrasound in discriminating cardiogenic causes of acute dyspnea in the emergency department.

    PubMed

    Cibinel, Gian Alfonso; Casoli, Giovanna; Elia, Fabrizio; Padoan, Monica; Pivetta, Emanuele; Lupia, Enrico; Goffi, Alberto

    2012-02-01

    Dyspnea is a common symptom in patients admitted to the Emergency Department (ED), and discriminating between cardiogenic and non-cardiogenic dyspnea is often a clinical dilemma. The initial diagnostic work-up may be inaccurate in defining the etiology and the underlying pathophysiology. The aim of this study was to evaluate the diagnostic accuracy and reproducibility of pleural and lung ultrasound (PLUS), performed by emergency physicians at the time of a patient's initial evaluation in the ED, in identifying cardiac causes of acute dyspnea. Between February and July 2007, 56 patients presenting to the ED with acute dyspnea were prospectively enrolled in this study. In all patients, PLUS was performed by emergency physicians with the purpose of identifying the presence of diffuse alveolar-interstitial syndrome (AIS) or pleural effusion. All scans were later reviewed by two other emergency physicians, expert in PLUS and blinded to clinical parameters, who were the ultimate judges of positivity for diffuse AIS and pleural effusion. A random set of 80 recorded scannings were also reviewed by two inexperienced observers to assess inter-observer variability. The entire medical record was independently reviewed by two expert physicians (an emergency medicine physician and a cardiologist) blinded to the ultrasound (US) results, in order to determine whether, for each patient, dyspnea was due to heart failure, or not. Sensitivity, specificity, and positive/negative predictive values were obtained; likelihood ratio (LR) test was used. Cohen's kappa was used to assess inter-observer agreement. The presence of diffuse AIS was highly predictive for cardiogenic dyspnea (sensitivity 93.6%, specificity 84%, positive predictive value 87.9%, negative predictive value 91.3%). On the contrary, US detection of pleural effusion was not helpful in the differential diagnosis (sensitivity 83.9%, specificity 52%, positive predictive value 68.4%, negative predictive value 72.2%). Finally

  15. Interpretation of nitric oxide profile observed in January 1992 over Kiruna

    NASA Astrophysics Data System (ADS)

    Kondo, Y.; Kawa, S. R.; Lary, D.; Sugita, T.; Douglass, Anne R.; Lutman, E.; Koike, M.; Deshler, T.

    1996-05-01

    NO mixing ratios measured from Kiruna (68°N, 20°E), Sweden, on January 22, 1992, revealed values much smaller than those observed at midlatitude near equinox and had a sharper vertical gradient around 25 km. Location of the measurements was close to the terminator and near the edge of the polar vortex, which is highly distorted from concentric flow by strong planetary wave activities. These conditions necessitate accurate calculation, properly taking into account the transport and photochemical processes, in order to quantitatively explain the observed NO profile. A three-dimensional chemistry and transport model (CTM) and a trajectory model (TM) were used to interpret the profile observations within their larger spatial, temporal, and chemical context. The NOy profile calculated by the CTM is in good agreement with that observed on January 31, 1992. In addition, model NOy profiles show small variabilities depending on latitudes, and they change little between January 22 and 31. The TM uses the observed NOy values. The NO values calculated by the CTM and TM agree with observations up to 27 km. Between 20 and 27 km the NO values calculated by the trajectory model including only gas phase chemistry are much larger than those including heterogeneous chemistry, indicating that NO mixing ratios were reduced significantly by heterogeneous chemistry on sulfuric acid aerosols. Very little sunlight to generate NOx from HNO3 was available, also causing the very low NO values. The good agreement between the observed and modeled NO profiles indicates that models can reproduce the photochemical and transport processes in the region where NO values have a sharp horizontal gradient. Moreover, CTM and TM model results show that even when the NOy gradients are weak, the model NO depends upon accurate calculation of the transport and insolation for several days.

  16. Observation learning versus physical practice leads to different consolidation outcomes in a movement timing task.

    PubMed

    Trempe, Maxime; Sabourin, Maxime; Rohbanfard, Hassan; Proteau, Luc

    2011-03-01

    Motor learning is a process that extends beyond training sessions. Specifically, physical practice triggers a series of physiological changes in the CNS that are regrouped under the term "consolidation" (Stickgold and Walker 2007). These changes can result in between-session improvement or performance stabilization (Walker 2005). In a series of three experiments, we tested whether consolidation also occurs following observation. In Experiment 1, participants observed an expert model perform a sequence of arm movements. Although we found evidence of observation learning, no significant difference was revealed between participants asked to reproduce the observed sequence either 5 min or 24 h later (no between-session improvement). In Experiment 2, two groups of participants observed an expert model perform two distinct movement sequences (A and B) either 10 min or 8 h apart; participants then physically performed both sequences after a 24-h break. Participants in the 8-h group performed Sequence B less accurately compared to participants in the 5-min group, suggesting that the memory representation of the first sequence had been stabilized and that it interfered with the learning of the second sequence. Finally, in Experiment 3, the initial observation phase was replaced by a physical practice phase. In contrast with the results of Experiment 2, participants in the 8-h group performed Sequence B significantly more accurately compared to participants in the 5-min group. Together, our results suggest that the memory representation of a skill learned through observation undergoes consolidation. However, consolidation of an observed motor skill leads to distinct behavioural outcomes in comparison with physical practice.

  17. [The reproducibility of multifocal ERG recordings].

    PubMed

    Meigen, T; Friedrich, A

    2002-09-01

    Multifocal electroretinogram recordings (mfERG) can be used to detect a local dysfunction of the retina. In this study we tested both the intrasessional and inter-sessional reproducibility of mfERG amplitudes. MfERGs from 6 eyes of 6 normal subjects were recorded on two different days using DTL electrodes. The relative coefficient of variation ( RCV) was used to quantify the amplitude reproducibility. We tested the effect of (a) session (inter- vs. intrasessional), (b) recording duration (7.3 vs. 3.6 min), (c) trace type (hexagon traces vs. ring averages), and (d) amplitude definition (peak-trough analysis vs. scalar product) on RCV. RCV was 6.5+/-0.4% (Mean+/-SEM, n=96) when averaged across all recording conditions and all subjects. The ANOVA showed a significant difference ( p=0.018) between hexagon traces and ring averages. Another significant effect ( p=0.016) occurred for the interaction of (a) and (b). MfERGs can be recorded with a high degree of reproducibility even for short recording durations and single hexagon traces. As the factor (a) did not show a significant effect, the new placement of the DTL electrode in the second session does not necessarily increase the retest variability compared to a second recording within the same session.

  18. Acquisition of reproducible transmission near-infrared (NIR) spectra of solid samples with inconsistent shapes by irradiation with isotropically diffused radiation using polytetrafluoroethylene (PTFE) beads.

    PubMed

    Lee, Jinah; Duy, Pham Khac; Yoon, Jihye; Chung, Hoeil

    2014-06-21

    A bead-incorporated transmission scheme (BITS) has been demonstrated for collecting reproducible transmission near-infrared (NIR) spectra of samples with inconsistent shapes. Isotropically diffused NIR radiation was applied around a sample and the surrounding radiation was allowed to interact homogeneously with the sample for transmission measurement. Samples were packed in 1.40 mm polytetrafluoroethylene (PTFE) beads, ideal diffusers without NIR absorption, and then transmission spectra were collected by illuminating the sample-containing beads using NIR radiation. When collimated radiation was directly applied, a small portion of the non-fully diffused radiation (NFDR) propagated through the void space of the packing and eventually degraded the reproducibility. Pre-diffused radiation was introduced by placing an additional PTFE disk in front of the packing to diminish NFDR, which produced more reproducible spectral features. The proposed scheme was evaluated by analyzing two different solid samples: density determination for individual polyethylene (PE) pellets and identification of mining locality for tourmalines. Because spectral collection was reproducible, the use of the spectrum acquired from one PE pellet was sufficient to accurately determine the density of nine other pellets with different shapes. The differentiation of tourmalines, which are even more dissimilar in appearance, according to their mining locality was also feasible with the help of the scheme.

  19. Reproducibility of blood pressure variation in older ambulatory and bedridden subjects.

    PubMed

    Tsuchihashi, Takuya; Kawakami, Yasunobu; Imamura, Tsuyoshi; Abe, Isao

    2002-06-01

    We investigated the influence of ambulation on the reproducibility of circadian blood pressure variation in older nursing home residents. Ambulatory blood pressure monitoring was performed twice in 37 older nursing home residents. Nursing home in Japan. Subjects included 18 ambulatory nursing home residents who had no limitation on physical activity and 19 bedridden residents who did not participate in physical activity. Twenty-four-hour, daytime, and nighttime blood pressure levels and their variability. The 24-hour and daytime variability of systolic blood pressure (SBP) was significantly greater in ambulatory than in bedridden subjects, whereas nighttime variability was similar. Significant correlations in SBP averaged for the whole day, daytime, and nighttime were observed between the two examinations in ambulatory (r =.80-.83) and bedridden (r =.83-.91) subjects, but the variabilities of SBP for the whole day and during the daytime of the first measurement were correlated with those of the second measurement in bedridden (r =.67 and r =.47, respectively) but not in ambulatory (r =.39 and r =.28, respectively) subjects. Significant correlations were found between the nocturnal SBP changes at two occasions in both ambulatory (r =.50) and bedridden (r =.51) subjects, but the dipper versus nondipper profiles, defined as reduction in SBP of greater than 10% versus not, showed low reproducibility in ambulatory subjects; five ambulatory (28%) and one bedridden (5%) subjects showed divergent profiles between the two examinations. The reproducibility of blood pressure variation in nursing home residents is influenced by ambulation.

  20. Reproducibility of the World Health Organization 2008 criteria for myelodysplastic syndromes

    PubMed Central

    Senent, Leonor; Arenillas, Leonor; Luño, Elisa; Ruiz, Juan C.; Sanz, Guillermo; Florensa, Lourdes

    2013-01-01

    The reproducibility of the World Health Organization 2008 classification for myelodysplastic syndromes is uncertain and its assessment was the major aim of this study. The different peripheral blood and bone marrow variables required for an adequate morphological classification were blindly evaluated by four cytomorphologists in samples from 50 patients with myelodysplastic syndromes. The degree of agreement among observers was calculated using intraclass correlation coefficient and the generalized kappa statistic for multiple raters. The degree of agreement for the percentages of blasts in bone marrow and peripheral blood, ring sideroblasts in bone marrow, and erythroid, granulocytic and megakaryocytic dysplastic cells was strong (P<0.001 in all instances). After stratifying the percentages according to the categories required for the assignment of World Health Organization subtypes, the degree of agreement was not statistically significant for cases with 5-9% blasts in bone marrow (P=0.07), 0.1-1% blasts in peripheral blood (P=0.47), or percentage of erythroid dysplastic cells (P=0.49). Finally, the interobserver concordance for World Health Organization-defined subtypes showed a moderate overall agreement (P<0.001), the reproducibility being lower for cases with refractory anemia with excess of blasts type 1 (P=0.05) and refractory anemia with ring sideroblasts (P=0.09). In conclusion, the reproducibility of the World Health Organization 2008 classification for myelodysplastic syndromes is acceptable but the defining criteria for blast cells and features of erythroid dysplasia need to be refined. PMID:23065505

  1. Reproducibility of the World Health Organization 2008 criteria for myelodysplastic syndromes.

    PubMed

    Senent, Leonor; Arenillas, Leonor; Luño, Elisa; Ruiz, Juan C; Sanz, Guillermo; Florensa, Lourdes

    2013-04-01

    The reproducibility of the World Health Organization 2008 classification for myelodysplastic syndromes is uncertain and its assessment was the major aim of this study. The different peripheral blood and bone marrow variables required for an adequate morphological classification were blindly evaluated by four cytomorphologists in samples from 50 patients with myelodysplastic syndromes. The degree of agreement among observers was calculated using intraclass correlation coefficient and the generalized kappa statistic for multiple raters. The degree of agreement for the percentages of blasts in bone marrow and peripheral blood, ring sideroblasts in bone marrow, and erythroid, granulocytic and megakaryocytic dysplastic cells was strong (P<0.001 in all instances). After stratifying the percentages according to the categories required for the assignment of World Health Organization subtypes, the degree of agreement was not statistically significant for cases with 5-9% blasts in bone marrow (P=0.07), 0.1-1% blasts in peripheral blood (P=0.47), or percentage of erythroid dysplastic cells (P=0.49). Finally, the interobserver concordance for World Health Organization-defined subtypes showed a moderate overall agreement (P<0.001), the reproducibility being lower for cases with refractory anemia with excess of blasts type 1 (P=0.05) and refractory anemia with ring sideroblasts (P=0.09). In conclusion, the reproducibility of the World Health Organization 2008 classification for myelodysplastic syndromes is acceptable but the defining criteria for blast cells and features of erythroid dysplasia need to be refined.

  2. Novel TPLO Alignment Jig/Saw Guide Reproduces Freehand and Ideal Osteotomy Positions

    PubMed Central

    2016-01-01

    Objectives To evaluate the ability of an alignment jig/saw guide to reproduce appropriate osteotomy positions in the tibial plateau leveling osteotomy (TPLO) in the dog. Methods Lateral radiographs of 65 clinical TPLO procedures using an alignment jig and freehand osteotomy performed by experienced TPLO surgeons using a 24 mm radial saw blade between Dec 2005–Dec 2007 and Nov 2013–Nov 2015 were reviewed. The freehand osteotomy position was compared to potential osteotomy positions using the alignment jig/saw guide. The proximal and distal jig pin holes on postoperative radiographs were used to align the jig to the bone; saw guide position was selected to most closely match the osteotomy performed. The guide-to-osteotomy fit was categorized by the distance between the actual osteotomy and proposed saw guide osteotomy at its greatest offset (≤1 mm = excellent; ≤2 mm = good; ≤3 mm = satisfactory; >3 mm = poor). Results Sixty-four of 65 TPLO osteotomies could be matched satisfactorily by the saw guide. Proximal jig pin placement 3–4 mm from the joint surface and pin location in a craniocaudal plane on the proximal tibia were significantly associated with the guide-to-osteotomy fit (P = 0.021 and P = 0.047, respectively). Clinical Significance The alignment jig/saw guide can be used to reproduce appropriate freehand osteotomy position for TPLO. Furthermore, an ideal osteotomy position centered on the tibial intercondylar tubercles also is possible. Accurate placement of the proximal jig pin is a crucial step for correct positioning of the saw guide in either instance. PMID:27556230

  3. Novel TPLO Alignment Jig/Saw Guide Reproduces Freehand and Ideal Osteotomy Positions.

    PubMed

    Mariano, Abigail D; Kowaleski, Michael P; Boudrieau, Randy J

    2016-01-01

    To evaluate the ability of an alignment jig/saw guide to reproduce appropriate osteotomy positions in the tibial plateau leveling osteotomy (TPLO) in the dog. Lateral radiographs of 65 clinical TPLO procedures using an alignment jig and freehand osteotomy performed by experienced TPLO surgeons using a 24 mm radial saw blade between Dec 2005-Dec 2007 and Nov 2013-Nov 2015 were reviewed. The freehand osteotomy position was compared to potential osteotomy positions using the alignment jig/saw guide. The proximal and distal jig pin holes on postoperative radiographs were used to align the jig to the bone; saw guide position was selected to most closely match the osteotomy performed. The guide-to-osteotomy fit was categorized by the distance between the actual osteotomy and proposed saw guide osteotomy at its greatest offset (≤1 mm = excellent; ≤2 mm = good; ≤3 mm = satisfactory; >3 mm = poor). Sixty-four of 65 TPLO osteotomies could be matched satisfactorily by the saw guide. Proximal jig pin placement 3-4 mm from the joint surface and pin location in a craniocaudal plane on the proximal tibia were significantly associated with the guide-to-osteotomy fit (P = 0.021 and P = 0.047, respectively). The alignment jig/saw guide can be used to reproduce appropriate freehand osteotomy position for TPLO. Furthermore, an ideal osteotomy position centered on the tibial intercondylar tubercles also is possible. Accurate placement of the proximal jig pin is a crucial step for correct positioning of the saw guide in either instance.

  4. Modelling soil erosion at European scale: towards harmonization and reproducibility

    NASA Astrophysics Data System (ADS)

    Bosco, C.; de Rigo, D.; Dewitte, O.; Poesen, J.; Panagos, P.

    2015-02-01

    Soil erosion by water is one of the most widespread forms of soil degradation. The loss of soil as a result of erosion can lead to decline in organic matter and nutrient contents, breakdown of soil structure and reduction of the water-holding capacity. Measuring soil loss across the whole landscape is impractical and thus research is needed to improve methods of estimating soil erosion with computational modelling, upon which integrated assessment and mitigation strategies may be based. Despite the efforts, the prediction value of existing models is still limited, especially at regional and continental scale, because a systematic knowledge of local climatological and soil parameters is often unavailable. A new approach for modelling soil erosion at regional scale is here proposed. It is based on the joint use of low-data-demanding models and innovative techniques for better estimating model inputs. The proposed modelling architecture has at its basis the semantic array programming paradigm and a strong effort towards computational reproducibility. An extended version of the Revised Universal Soil Loss Equation (RUSLE) has been implemented merging different empirical rainfall-erosivity equations within a climatic ensemble model and adding a new factor for a better consideration of soil stoniness within the model. Pan-European soil erosion rates by water have been estimated through the use of publicly available data sets and locally reliable empirical relationships. The accuracy of the results is corroborated by a visual plausibility check (63% of a random sample of grid cells are accurate, 83% at least moderately accurate, bootstrap p ≤ 0.05). A comparison with country-level statistics of pre-existing European soil erosion maps is also provided.

  5. Ultrafast laser-induced reproducible nano-gratings on a molybdenum surface

    NASA Astrophysics Data System (ADS)

    Dar, Mudasir H.; Saad, Nabil A.; Sahoo, Chakradhar; Naraharisetty, Sri Ram G.; Rao Desai, Narayana

    2017-02-01

    Wavelength-dependent reproducible nano-gratings were produced on a bulk molybdenum surface upon irradiation with femtosecond laser pulses at near normal incidence in ambient air and water environments. The surface morphology of the irradiated surfaces was characterized by field emission scanning electron microscopy. The ripple spacing was observed to decrease by half when the surface was irradiated with the second harmonic of the fundamental 800 nm radiation. Careful choice of the laser parameters such as fluence, scanning speed, polarization and wavelength were observed to be important for the formation of smooth periodic ripples. The mechanism of formation of polarization-dependent periodic ripples is explained based on the interference model. We also demonstrated the use of a laser direct writing technique for the fabrication of periodic subwavelength structures that have potential applications in photonic devices.

  6. Reliable Mechanochemistry: Protocols for Reproducible Outcomes of Neat and Liquid Assisted Ball-mill Grinding Experiments.

    PubMed

    Belenguer, Ana M; Lampronti, Giulio I; Sanders, Jeremy K M

    2018-01-23

    The equilibrium outcomes of ball mill grinding can dramatically change as a function of even tiny variations in the experimental conditions such as the presence of very small amounts of added solvent. To reproducibly and accurately capture this sensitivity, the experimentalist needs to carefully consider every single factor that can affect the ball mill grinding reaction under investigation, from ensuring the grinding jars are clean and dry before use, to accurately adding the stoichiometry of the starting materials, to validating that the delivery of solvent volume is accurate, to ensuring that the interaction between the solvent and the powder is well understood and, if necessary, a specific soaking time is added to the procedure. Preliminary kinetic studies are essential to determine the necessary milling time to achieve equilibrium. Only then can exquisite phase composition curves be obtained as a function of the solvent concentration under ball mill liquid assisted grinding (LAG). By using strict and careful procedures analogous to the ones here presented, such milling equilibrium curves can be obtained for virtually all milling systems. The system we use to demonstrate these procedures is a disulfide exchange reaction starting from the equimolar mixture of two homodimers to obtain at equilibrium quantitative heterodimer. The latter is formed by ball mill grinding as two different polymorphs, Form A and Form B. The ratio R = [Form B] / ([Form A] + [Form B]) at milling equilibrium depends on the nature and concentration of the solvent in the milling jar.

  7. Reproducible nucleation sites for flux dendrites in MgB 2

    NASA Astrophysics Data System (ADS)

    Johansen, T. H.; Shantsev, D. V.; Olsen, Å. A. F.; Roussel, M.; Pan, A. V.; Dou, S. X.

    2007-12-01

    Magneto-optical imaging was used to study dendritic flux penetration in films of MgB 2. By repeating experiments under the same external conditions, reproducible features were seen in the pattern formation; dendrites tend to nucleate from fixed locations along the edge. However, their detailed structure deeper inside the film is never reproduced. The reproducibility in nucleation sites is explained as a result of edge roughness causing field hot spots.

  8. Can CFMIP2 models reproduce the leading modes of cloud vertical structure in the CALIPSO-GOCCP observations?

    NASA Astrophysics Data System (ADS)

    Wang, Fang; Yang, Song

    2018-02-01

    Using principal component (PC) analysis, three leading modes of cloud vertical structure (CVS) are revealed by the GCM-Oriented CALIPSO Cloud Product (GOCCP), i.e. tropical high, subtropical anticyclonic and extratropical cyclonic cloud modes (THCM, SACM and ECCM, respectively). THCM mainly reflect the contrast between tropical high clouds and clouds in middle/high latitudes. SACM is closely associated with middle-high clouds in tropical convective cores, few-cloud regimes in subtropical anticyclonic clouds and stratocumulus over subtropical eastern oceans. ECCM mainly corresponds to clouds along extratropical cyclonic regions. Models of phase 2 of Cloud Feedback Model Intercomparison Project (CFMIP2) well reproduce the THCM, but SACM and ECCM are generally poorly simulated compared to GOCCP. Standardized PCs corresponding to CVS modes are generally captured, whereas original PCs (OPCs) are consistently underestimated (overestimated) for THCM (SACM and ECCM) by CFMIP2 models. The effects of CVS modes on relative cloud radiative forcing (RSCRF/RLCRF) (RSCRF being calculated at the surface while RLCRF at the top of atmosphere) are studied in terms of principal component regression method. Results show that CFMIP2 models tend to overestimate (underestimated or simulate the opposite sign) RSCRF/RLCRF radiative effects (REs) of ECCM (THCM and SACM) in unit global mean OPC compared to observations. These RE biases may be attributed to two factors, one of which is underestimation (overestimation) of low/middle clouds (high clouds) (also known as stronger (weaker) REs in unit low/middle (high) clouds) in simulated global mean cloud profiles, the other is eigenvector biases in CVS modes (especially for SACM and ECCM). It is suggested that much more attention should be paid on improvement of CVS, especially cloud parameterization associated with particular physical processes (e.g. downwelling regimes with the Hadley circulation, extratropical storm tracks and others), which

  9. Hepatocellular carcinoma: short-term reproducibility of apparent diffusion coefficient and intravoxel incoherent motion parameters at 3.0T.

    PubMed

    Kakite, Suguru; Dyvorne, Hadrien; Besa, Cecilia; Cooper, Nancy; Facciuto, Marcelo; Donnerhack, Claudia; Taouli, Bachir

    2015-01-01

    To evaluate short-term test-retest and interobserver reproducibility of IVIM (intravoxel incoherent motion) diffusion parameters and ADC (apparent diffusion coefficient) of hepatocellular carcinoma (HCC) and liver parenchyma at 3.0T. In this prospective Institutional Review Board (IRB)-approved study, 11 patients were scanned twice using a free-breathing single-shot echo-planar-imaging, diffusion-weighted imaging (DWI) sequence using 4 b values (b = 0, 50, 500, 1000 s/mm(2)) and IVIM DWI using 16 b values (0-800 s/mm(2)) at 3.0T. IVIM parameters (D: true diffusion coefficient, D*: pseudodiffusion coefficient, PF: perfusion fraction) and ADC (using 4 b and 16 b) were calculated. Short-term test-retest and interobserver reproducibility of IVIM parameters and ADC were assessed by measuring correlation coefficient, coefficient of variation (CV), and Bland-Altman limits of agreements (BA-LA). Fifteen HCCs were assessed in 10 patients. Reproducibility of IVIM metrics in HCC was poor for D* and PF (mean CV 60.6% and 37.3%, BA-LA: -161.6% to 135.3% and -66.2% to 101.0%, for D* and PF, respectively), good for D and ADC (CV 19.7% and <16%, BA-LA -57.4% to 36.3% and -38.2 to 34.1%, for D and ADC, respectively). Interobserver reproducibility was on the same order of test-retest reproducibility except for PF in HCC. Reproducibility of diffusion parameters was better in liver parenchyma compared to HCC. Poor reproducibility of D*/PF and good reproducibility for D/ADC were observed in HCC and liver parenchyma. These findings may have implications for trials using DWI in HCC. © 2014 Wiley Periodicals, Inc.

  10. Reproducibility of radiomics for deciphering tumor phenotype with imaging

    NASA Astrophysics Data System (ADS)

    Zhao, Binsheng; Tan, Yongqiang; Tsai, Wei-Yann; Qi, Jing; Xie, Chuanmiao; Lu, Lin; Schwartz, Lawrence H.

    2016-03-01

    Radiomics (radiogenomics) characterizes tumor phenotypes based on quantitative image features derived from routine radiologic imaging to improve cancer diagnosis, prognosis, prediction and response to therapy. Although radiomic features must be reproducible to qualify as biomarkers for clinical care, little is known about how routine imaging acquisition techniques/parameters affect reproducibility. To begin to fill this knowledge gap, we assessed the reproducibility of a comprehensive, commonly-used set of radiomic features using a unique, same-day repeat computed tomography data set from lung cancer patients. Each scan was reconstructed at 6 imaging settings, varying slice thicknesses (1.25 mm, 2.5 mm and 5 mm) and reconstruction algorithms (sharp, smooth). Reproducibility was assessed using the repeat scans reconstructed at identical imaging setting (6 settings in total). In separate analyses, we explored differences in radiomic features due to different imaging parameters by assessing the agreement of these radiomic features extracted from the repeat scans reconstructed at the same slice thickness but different algorithms (3 settings in total). Our data suggest that radiomic features are reproducible over a wide range of imaging settings. However, smooth and sharp reconstruction algorithms should not be used interchangeably. These findings will raise awareness of the importance of properly setting imaging acquisition parameters in radiomics/radiogenomics research.

  11. Metaresearch for Evaluating Reproducibility in Ecology and Evolution.

    PubMed

    Fidler, Fiona; Chee, Yung En; Wintle, Bonnie C; Burgman, Mark A; McCarthy, Michael A; Gordon, Ascelin

    2017-03-01

    Recent replication projects in other disciplines have uncovered disturbingly low levels of reproducibility, suggesting that those research literatures may contain unverifiable claims. The conditions contributing to irreproducibility in other disciplines are also present in ecology. These include a large discrepancy between the proportion of "positive" or "significant" results and the average statistical power of empirical research, incomplete reporting of sampling stopping rules and results, journal policies that discourage replication studies, and a prevailing publish-or-perish research culture that encourages questionable research practices. We argue that these conditions constitute sufficient reason to systematically evaluate the reproducibility of the evidence base in ecology and evolution. In some cases, the direct replication of ecological research is difficult because of strong temporal and spatial dependencies, so here, we propose metaresearch projects that will provide proxy measures of reproducibility.

  12. Fast and Accurate Metadata Authoring Using Ontology-Based Recommendations.

    PubMed

    Martínez-Romero, Marcos; O'Connor, Martin J; Shankar, Ravi D; Panahiazar, Maryam; Willrett, Debra; Egyedi, Attila L; Gevaert, Olivier; Graybeal, John; Musen, Mark A

    2017-01-01

    In biomedicine, high-quality metadata are crucial for finding experimental datasets, for understanding how experiments were performed, and for reproducing those experiments. Despite the recent focus on metadata, the quality of metadata available in public repositories continues to be extremely poor. A key difficulty is that the typical metadata acquisition process is time-consuming and error prone, with weak or nonexistent support for linking metadata to ontologies. There is a pressing need for methods and tools to speed up the metadata acquisition process and to increase the quality of metadata that are entered. In this paper, we describe a methodology and set of associated tools that we developed to address this challenge. A core component of this approach is a value recommendation framework that uses analysis of previously entered metadata and ontology-based metadata specifications to help users rapidly and accurately enter their metadata. We performed an initial evaluation of this approach using metadata from a public metadata repository.

  13. Fast and Accurate Metadata Authoring Using Ontology-Based Recommendations

    PubMed Central

    Martínez-Romero, Marcos; O’Connor, Martin J.; Shankar, Ravi D.; Panahiazar, Maryam; Willrett, Debra; Egyedi, Attila L.; Gevaert, Olivier; Graybeal, John; Musen, Mark A.

    2017-01-01

    In biomedicine, high-quality metadata are crucial for finding experimental datasets, for understanding how experiments were performed, and for reproducing those experiments. Despite the recent focus on metadata, the quality of metadata available in public repositories continues to be extremely poor. A key difficulty is that the typical metadata acquisition process is time-consuming and error prone, with weak or nonexistent support for linking metadata to ontologies. There is a pressing need for methods and tools to speed up the metadata acquisition process and to increase the quality of metadata that are entered. In this paper, we describe a methodology and set of associated tools that we developed to address this challenge. A core component of this approach is a value recommendation framework that uses analysis of previously entered metadata and ontology-based metadata specifications to help users rapidly and accurately enter their metadata. We performed an initial evaluation of this approach using metadata from a public metadata repository. PMID:29854196

  14. Coplanar electrode microfluidic chip enabling accurate sheathless impedance cytometry.

    PubMed

    De Ninno, Adele; Errico, Vito; Bertani, Francesca Romana; Businaro, Luca; Bisegna, Paolo; Caselli, Federica

    2017-03-14

    Microfluidic impedance cytometry offers a simple non-invasive method for single-cell analysis. Coplanar electrode chips are especially attractive due to ease of fabrication, yielding miniaturized, reproducible, and ultimately low-cost devices. However, their accuracy is challenged by the dependence of the measured signal on particle trajectory within the interrogation volume, that manifests itself as an error in the estimated particle size, unless any kind of focusing system is used. In this paper, we present an original five-electrode coplanar chip enabling accurate particle sizing without the need for focusing. The chip layout is designed to provide a peculiar signal shape from which a new metric correlating with particle trajectory can be extracted. This metric is exploited to correct the estimated size of polystyrene beads of 5.2, 6 and 7 μm nominal diameter, reaching coefficient of variations lower than the manufacturers' quoted values. The potential impact of the proposed device in the field of life sciences is demonstrated with an application to Saccharomyces cerevisiae yeast.

  15. Cupping - is it reproducible? Experiments about factors determining the vacuum.

    PubMed

    Huber, R; Emerich, M; Braeunig, M

    2011-04-01

    Cupping is a traditional method for treating pain which is investigated nowadays in clinical studies. Because the methods for producing the vacuum vary considerably we tested their reproducibility. In a first set of experiments (study 1) four methods for producing the vacuum (lighter flame 2 cm (LF1), lighter flame 4 cm (LF2), alcohol flame (AF) and mechanical suction with a balloon (BA)) have been compared in 50 trials each. The cupping glass was prepared with an outlet and stop-cock, the vacuum was measured with a pressure-gauge after the cup was set to a soft rubber pad. In a second series of experiments (study 2) we investigated the stability of pressures in 20 consecutive trials in two experienced cupping practitioners and ten beginners using method AF. In study 1 all four methods yielded consistent pressures. Large differences in magnitude were, however, observed between methods (mean pressures -200±30 hPa with LF1, -310±30 hPa with LF2, -560±30 hPa with AF, and -270±16 hPa with BA). With method BA the standard deviation was reduced by a factor 2 compared to the flame methods. In study 2 beginners had considerably more difficulty obtaining a stable pressure yield than advanced cupping practitioners, showing a distinct learning curve before reaching expertise levels after about 10-20 trials. Cupping is reproducible if the exact method is described in detail. Mechanical suction with a balloon has the best reproducibility. Beginners need at least 10-20 trials to produce stable pressures. Copyright © 2010 Elsevier Ltd. All rights reserved.

  16. Comparing models of star formation simulating observed interacting galaxies

    NASA Astrophysics Data System (ADS)

    Quiroga, L. F.; Muñoz-Cuartas, J. C.; Rodrigues, I.

    2017-07-01

    In this work, we make a comparison between different models of star formation to reproduce observed interacting galaxies. We use observational data to model the evolution of a pair of galaxies undergoing a minor merger. Minor mergers represent situations weakly deviated from the equilibrium configuration but significant changes in star fomation (SF) efficiency can take place, then, minor mergers provide an unique scene to study SF in galaxies in a realistic but yet simple way. Reproducing observed systems also give us the opportunity to compare the results of the simulations with observations, which at the end can be used as probes to characterize the models of SF implemented in the comparison. In this work we compare two different star formation recipes implemented in Gadget3 and GIZMO codes. Both codes share the same numerical background, and differences arise mainly in the star formation recipe they use. We use observations from Pico dos Días and GEMINI telescopes and show how we use observational data of the interacting pair in AM2229-735 to characterize the interacting pair. Later we use this information to simulate the evolution of the system to finally reproduce the observations: Mass distribution, morphology and main features of the merger-induced star formation burst. We show that both methods manage to reproduce roughly the star formation activity. We show, through a careful study, that resolution plays a major role in the reproducibility of the system. In that sense, star formation recipe implemented in GIZMO code has shown a more robust performance. Acknowledgements: This work is supported by Colciencias, Doctorado Nacional - 617 program.

  17. 20180312 - Reproducibility and variance of liver effects in subchronic and chronic repeat dose toxicity studies (SOT)

    EPA Science Inventory

    In vivo studies provide reference data to evaluate alternative methods for predicting toxicity. However, the reproducibility and variance of effects observed across multiple in vivo studies is not well understood. The US EPA’s Toxicity Reference Database (ToxRefDB) stores d...

  18. Reproducing 2D breast mammography images with 3D printed phantoms

    NASA Astrophysics Data System (ADS)

    Clark, Matthew; Ghammraoui, Bahaa; Badal, Andreu

    2016-03-01

    Mammography is currently the standard imaging modality used to screen women for breast abnormalities and, as a result, it is a tool of great importance for the early detection of breast cancer. Physical phantoms are commonly used as surrogates of breast tissue to evaluate some aspects of the performance of mammography systems. However, most phantoms do not reproduce the anatomic heterogeneity of real breasts. New fabrication technologies, such as 3D printing, have created the opportunity to build more complex, anatomically realistic breast phantoms that could potentially assist in the evaluation of mammography systems. The primary objective of this work is to present a simple, easily reproducible methodology to design and print 3D objects that replicate the attenuation profile observed in real 2D mammograms. The secondary objective is to evaluate the capabilities and limitations of the competing 3D printing technologies, and characterize the x-ray properties of the different materials they use. Printable phantoms can be created using the open-source code introduced in this work, which processes a raw mammography image to estimate the amount of x-ray attenuation at each pixel, and outputs a triangle mesh object that encodes the observed attenuation map. The conversion from the observed pixel gray value to a column of printed material with equivalent attenuation requires certain assumptions and knowledge of multiple imaging system parameters, such as x-ray energy spectrum, source-to-object distance, compressed breast thickness, and average breast material attenuation. A detailed description of the new software, a characterization of the printed materials using x-ray spectroscopy, and an evaluation of the realism of the sample printed phantoms are presented.

  19. A Framework for Reproducible Latent Fingerprint Enhancements.

    PubMed

    Carasso, Alfred S

    2014-01-01

    Photoshop processing of latent fingerprints is the preferred methodology among law enforcement forensic experts, but that appproach is not fully reproducible and may lead to questionable enhancements. Alternative, independent, fully reproducible enhancements, using IDL Histogram Equalization and IDL Adaptive Histogram Equalization, can produce better-defined ridge structures, along with considerable background information. Applying a systematic slow motion smoothing procedure to such IDL enhancements, based on the rapid FFT solution of a Lévy stable fractional diffusion equation, can attenuate background detail while preserving ridge information. The resulting smoothed latent print enhancements are comparable to, but distinct from, forensic Photoshop images suitable for input into automated fingerprint identification systems, (AFIS). In addition, this progressive smoothing procedure can be reexamined by displaying the suite of progressively smoother IDL images. That suite can be stored, providing an audit trail that allows monitoring for possible loss of useful information, in transit to the user-selected optimal image. Such independent and fully reproducible enhancements provide a valuable frame of reference that may be helpful in informing, complementing, and possibly validating the forensic Photoshop methodology.

  20. A Framework for Reproducible Latent Fingerprint Enhancements

    PubMed Central

    Carasso, Alfred S.

    2014-01-01

    Photoshop processing1 of latent fingerprints is the preferred methodology among law enforcement forensic experts, but that appproach is not fully reproducible and may lead to questionable enhancements. Alternative, independent, fully reproducible enhancements, using IDL Histogram Equalization and IDL Adaptive Histogram Equalization, can produce better-defined ridge structures, along with considerable background information. Applying a systematic slow motion smoothing procedure to such IDL enhancements, based on the rapid FFT solution of a Lévy stable fractional diffusion equation, can attenuate background detail while preserving ridge information. The resulting smoothed latent print enhancements are comparable to, but distinct from, forensic Photoshop images suitable for input into automated fingerprint identification systems, (AFIS). In addition, this progressive smoothing procedure can be reexamined by displaying the suite of progressively smoother IDL images. That suite can be stored, providing an audit trail that allows monitoring for possible loss of useful information, in transit to the user-selected optimal image. Such independent and fully reproducible enhancements provide a valuable frame of reference that may be helpful in informing, complementing, and possibly validating the forensic Photoshop methodology. PMID:26601028

  1. Assessment of the performance of numerical modeling in reproducing a replenishment of sediments in a water-worked channel

    NASA Astrophysics Data System (ADS)

    Juez, C.; Battisacco, E.; Schleiss, A. J.; Franca, M. J.

    2016-06-01

    The artificial replenishment of sediment is used as a method to re-establish sediment continuity downstream of a dam. However, the impact of this technique on the hydraulics conditions, and resulting bed morphology, is yet to be understood. Several numerical tools have been developed during last years for modeling sediment transport and morphology evolution which can be used for this application. These models range from 1D to 3D approaches: the first being over simplistic for the simulation of such a complex geometry; the latter requires often a prohibitive computational effort. However, 2D models are computationally efficient and in these cases may already provide sufficiently accurate predictions of the morphology evolution caused by the sediment replenishment in a river. Here, the 2D shallow water equations in combination with the Exner equation are solved by means of a weak-coupled strategy. The classical friction approach considered for reproducing the bed channel roughness has been modified to take into account the morphological effect of replenishment which provokes a channel bed fining. Computational outcomes are compared with four sets of experimental data obtained from several replenishment configurations studied in the laboratory. The experiments differ in terms of placement volume and configuration. A set of analysis parameters is proposed for the experimental-numerical comparison, with particular attention to the spreading, covered surface and travel distance of placed replenishment grains. The numerical tool is reliable in reproducing the overall tendency shown by the experimental data. The effect of fining roughness is better reproduced with the approach herein proposed. However, it is also highlighted that the sediment clusters found in the experiment are not well numerically reproduced in the regions of the channel with a limited number of sediment grains.

  2. Reproducibility of three-dimensional cephalometric landmarks in cone-beam and low-dose computed tomography.

    PubMed

    Olszewski, R; Frison, L; Wisniewski, M; Denis, J M; Vynckier, S; Cosnard, G; Zech, F; Reychler, H

    2013-01-01

    The purpose of this study is to compare the reproducibility of three-dimensional cephalometric landmarks on three-dimensional computed tomography (3D-CT) surface rendering using clinical protocols based on low-dose (35-mAs) spiral CT and cone-beam CT (I-CAT). The absorbed dose levels for radiosensitive organs in the maxillofacial region during exposure in both 3D-CT protocols were also assessed. The study population consisted of ten human dry skulls examined with low-dose CT and cone-beam CT. Two independent observers identified 24 cephalometric anatomic landmarks at 13 sites on the 3D-CT surface renderings using both protocols, with each observer repeating the identification 1 month later. A total of 1,920 imaging measurements were performed. Thermoluminescent dosimeters were placed at six sites around the thyroid gland, the submandibular glands, and the eyes in an Alderson phantom to measure the absorbed dose levels. When comparing low-dose CT and cone-beam CT protocols, the cone-beam CT protocol proved to be significantly more reproducible for four of the 13 anatomical sites. There was no significant difference between the protocols for the other nine anatomical sites. Both low-dose and cone-beam CT protocols were equivalent in dose absorption to the eyes and submandibular glands. However, thyroid glands were more irradiated with low-dose CT. Cone-beam CT was more reproducible and procured less irradiation to the thyroid gland than low-dose CT. Cone-beam CT should be preferred over low-dose CT for developing three-dimensional bony cephalometric analyses.

  3. Repeatability and Reproducibility in Proteomic Identifications by Liquid Chromatography—Tandem Mass Spectrometry

    PubMed Central

    Tabb, David L.; Vega-Montoto, Lorenzo; Rudnick, Paul A.; Variyath, Asokan Mulayath; Ham, Amy-Joan L.; Bunk, David M.; Kilpatrick, Lisa E.; Billheimer, Dean D.; Blackman, Ronald K.; Cardasis, Helene L.; Carr, Steven A.; Clauser, Karl R.; Jaffe, Jacob D.; Kowalski, Kevin A.; Neubert, Thomas A.; Regnier, Fred E.; Schilling, Birgit; Tegeler, Tony J.; Wang, Mu; Wang, Pei; Whiteaker, Jeffrey R.; Zimmerman, Lisa J.; Fisher, Susan J.; Gibson, Bradford W.; Kinsinger, Christopher R.; Mesri, Mehdi; Rodriguez, Henry; Stein, Steven E.; Tempst, Paul; Paulovich, Amanda G.; Liebler, Daniel C.; Spiegelman, Cliff

    2009-01-01

    The complexity of proteomic instrumentation for LC-MS/MS introduces many possible sources of variability. Data-dependent sampling of peptides constitutes a stochastic element at the heart of discovery proteomics. Although this variation impacts the identification of peptides, proteomic identifications are far from completely random. In this study, we analyzed interlaboratory data sets from the NCI Clinical Proteomic Technology Assessment for Cancer to examine repeatability and reproducibility in peptide and protein identifications. Included data spanned 144 LC-MS/MS experiments on four Thermo LTQ and four Orbitrap instruments. Samples included yeast lysate, the NCI-20 defined dynamic range protein mix, and the Sigma UPS 1 defined equimolar protein mix. Some of our findings reinforced conventional wisdom, such as repeatability and reproducibility being higher for proteins than for peptides. Most lessons from the data, however, were more subtle. Orbitraps proved capable of higher repeatability and reproducibility, but aberrant performance occasionally erased these gains. Even the simplest protein digestions yielded more peptide ions than LC-MS/MS could identify during a single experiment. We observed that peptide lists from pairs of technical replicates overlapped by 35–60%, giving a range for peptide-level repeatability in these experiments. Sample complexity did not appear to affect peptide identification repeatability, even as numbers of identified spectra changed by an order of magnitude. Statistical analysis of protein spectral counts revealed greater stability across technical replicates for Orbitraps, making them superior to LTQ instruments for biomarker candidate discovery. The most repeatable peptides were those corresponding to conventional tryptic cleavage sites, those that produced intense MS signals, and those that resulted from proteins generating many distinct peptides. Reproducibility among different instruments of the same type lagged behind

  4. Metaresearch for Evaluating Reproducibility in Ecology and Evolution

    PubMed Central

    Fidler, Fiona; Chee, Yung En; Wintle, Bonnie C.; Burgman, Mark A.; McCarthy, Michael A.; Gordon, Ascelin

    2017-01-01

    Abstract Recent replication projects in other disciplines have uncovered disturbingly low levels of reproducibility, suggesting that those research literatures may contain unverifiable claims. The conditions contributing to irreproducibility in other disciplines are also present in ecology. These include a large discrepancy between the proportion of “positive” or “significant” results and the average statistical power of empirical research, incomplete reporting of sampling stopping rules and results, journal policies that discourage replication studies, and a prevailing publish-or-perish research culture that encourages questionable research practices. We argue that these conditions constitute sufficient reason to systematically evaluate the reproducibility of the evidence base in ecology and evolution. In some cases, the direct replication of ecological research is difficult because of strong temporal and spatial dependencies, so here, we propose metaresearch projects that will provide proxy measures of reproducibility. PMID:28596617

  5. Issues on Reproducibility/Reliability of Magnetic NDE Methods

    NASA Technical Reports Server (NTRS)

    Namkung, M.; Fulton, J. P.; Wincheski, B.; Nath, S.

    1994-01-01

    One of the critical elements related to the practicality of any NDE technique is its reproducibility under nominally the same inspection conditions. The results of certain test methodologies, however, are not always repeatable and understanding the origin of the irreproducibility is often as critical as obtaining reproducible results. One example is the characterization of residual stress in structural ferromagnets using the magnetoacoustic (MAC) method. Although it has not been widely publicized, the test results of this method are known to be time-dependent. Two distinct types of time dependencies have been observed during testing. The first type has a clearly definable relaxation time, while no such trend has been observed for the second. The purpose of the present study is to systematically investigate the time dependence of the second type, to find out the range and, if possible, the origin of the variation in the test results. For this, MAC curves were obtained under various stress levels and the tests were repeated over time. Particular attention was given to whether noise in the measuring device or a change in the laboratory environment could have been a contributing factor. The steel samples used for the study were cut from C- and U-class railroad wheels. The MAC behavior of these samples was reported previously. Each steel sample was first machined to be a cylindrical rod of 3.175 cm (1.25 in) in diameter and 26.67 cm (10.5 in) in length. The center portion of the samples were further machined to form a pair of flat and parallel surfaces for the launch and reflection of the ultrasonic pulses. Data acquisition involved two major elements; magnetic and acoustic measurements. Throughout the experiment the net magnetic induction, B, was measured by integrating the induction pickup coil output using an integrating fluxmeter. The acoustic measurements employed the phase-locked technique which will be described in the following.

  6. Clinical signs of early osteoarthritis: reproducibility and relation to x ray changes in 541 women in the general population.

    PubMed Central

    Hart, D J; Spector, T D; Brown, P; Wilson, P; Doyle, D V; Silman, A J

    1991-01-01

    The definition and classification of early clinically apparent osteoarthritis both in clinical situations and in epidemiological surveys remains a problem. Few data exist on the between-observer reproducibility of simple clinical methods of detecting hand and knee osteoarthritis in the population and their sensitivity and specificity as compared with radiography. Two observers first studied the reproducibility of a number of clinical signs in 41 middle aged women. Good rates of agreement were found for most of the clinical signs tested (kappa = 0.54-1.0). The more reproducible signs were then tested on a population of 541 women, aged 45-65, drawn from general practice, screening centres, and patients previously attending hospital for non-rheumatic problems. The major clinical signs used had a high specificity (87-99%) and lower sensitivity (20-49%) when compared with radiographs graded on the Kellgren and Lawrence scale (2+ = positive). When analysis was restricted to symptomatic radiographic osteoarthritis, levels of sensitivity were increased and specificity was lowered. These data show that certain physical signs of osteoarthritis are reproducible and may be used to identify clinical disease. They are not a substitute for radiographs, however, if radiographic change is regarded as the 'gold standard' of diagnosis. As the clinical signs tested seemed specific for osteoarthritis they may be of value in screening populations for clinical disease. PMID:1877852

  7. Accurate Modeling of Dark-Field Scattering Spectra of Plasmonic Nanostructures.

    PubMed

    Jiang, Liyong; Yin, Tingting; Dong, Zhaogang; Liao, Mingyi; Tan, Shawn J; Goh, Xiao Ming; Allioux, David; Hu, Hailong; Li, Xiangyin; Yang, Joel K W; Shen, Zexiang

    2015-10-27

    Dark-field microscopy is a widely used tool for measuring the optical resonance of plasmonic nanostructures. However, current numerical methods for simulating the dark-field scattering spectra were carried out with plane wave illumination either at normal incidence or at an oblique angle from one direction. In actual experiments, light is focused onto the sample through an annular ring within a range of glancing angles. In this paper, we present a theoretical model capable of accurately simulating the dark-field light source with an annular ring. Simulations correctly reproduce a counterintuitive blue shift in the scattering spectra from gold nanodisks with a diameter beyond 140 nm. We believe that our proposed simulation method can be potentially applied as a general tool capable of simulating the dark-field scattering spectra of plasmonic nanostructures as well as other dielectric nanostructures with sizes beyond the quasi-static limit.

  8. 46 CFR 56.80-10 - Forming (reproduces 129.2).

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 46 Shipping 2 2010-10-01 2010-10-01 false Forming (reproduces 129.2). 56.80-10 Section 56.80-10 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) MARINE ENGINEERING PIPING SYSTEMS AND APPURTENANCES Bending and Forming § 56.80-10 Forming (reproduces 129.2). (a) Piping components may be formed...

  9. 46 CFR 56.80-10 - Forming (reproduces 129.2).

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 46 Shipping 2 2011-10-01 2011-10-01 false Forming (reproduces 129.2). 56.80-10 Section 56.80-10 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) MARINE ENGINEERING PIPING SYSTEMS AND APPURTENANCES Bending and Forming § 56.80-10 Forming (reproduces 129.2). (a) Piping components may be formed...

  10. Assessment of a climate model to reproduce rainfall variability and extremes over Southern Africa

    NASA Astrophysics Data System (ADS)

    Williams, C. J. R.; Kniveton, D. R.; Layberry, R.

    2010-01-01

    It is increasingly accepted that any possible climate change will not only have an influence on mean climate but may also significantly alter climatic variability. A change in the distribution and magnitude of extreme rainfall events (associated with changing variability), such as droughts or flooding, may have a far greater impact on human and natural systems than a changing mean. This issue is of particular importance for environmentally vulnerable regions such as southern Africa. The sub-continent is considered especially vulnerable to and ill-equipped (in terms of adaptation) for extreme events, due to a number of factors including extensive poverty, famine, disease and political instability. Rainfall variability and the identification of rainfall extremes is a function of scale, so high spatial and temporal resolution data are preferred to identify extreme events and accurately predict future variability. The majority of previous climate model verification studies have compared model output with observational data at monthly timescales. In this research, the assessment of ability of a state of the art climate model to simulate climate at daily timescales is carried out using satellite-derived rainfall data from the Microwave Infrared Rainfall Algorithm (MIRA). This dataset covers the period from 1993 to 2002 and the whole of southern Africa at a spatial resolution of 0.1° longitude/latitude. This paper concentrates primarily on the ability of the model to simulate the spatial and temporal patterns of present-day rainfall variability over southern Africa and is not intended to discuss possible future changes in climate as these have been documented elsewhere. Simulations of current climate from the UK Meteorological Office Hadley Centre's climate model, in both regional and global mode, are firstly compared to the MIRA dataset at daily timescales. Secondly, the ability of the model to reproduce daily rainfall extremes is assessed, again by a comparison with

  11. Towards the Geometry of Reproducing Kernels

    NASA Astrophysics Data System (ADS)

    Galé, J. E.

    2010-11-01

    It is shown here how one is naturally led to consider a category whose objects are reproducing kernels of Hilbert spaces, and how in this way a differential geometry for such kernels may be settled down.

  12. Reproducibility of cerebrospinal venous blood flow and vessel anatomy with the use of phase contrast-vastly undersampled isotropic projection reconstruction and contrast-enhanced MRA.

    PubMed

    Schrauben, E M; Johnson, K M; Huston, J; Del Rio, A M; Reeder, S B; Field, A; Wieben, O

    2014-05-01

    The chronic cerebrospinal venous insufficiency hypothesis raises interest in cerebrospinal venous blood flow imaging, which is more complex and less established than in arteries. For accurate assessment of venous flow in chronic cerebrospinal venous insufficiency diagnosis and research, we must account for physiologic changes in flow patterns. This study examines day-to-day flow variability in cerebrospinal veins by use of 4D MR flow and contrast-enhanced MRA under typical, uncontrolled conditions in healthy individuals. Ten healthy volunteers were scanned in a test-retest fashion by use of a 4D flow MR imaging technique and contrast-enhanced MRA. Flow parameters obtained from phase contrast-vastly undersampled isotropic projection reconstruction and contrast-enhanced MRA scoring measurements in the head, neck, and chest veins were analyzed for internal consistency and interscan reproducibility. Internal consistency was satisfied at the torcular herophili, with an input-output difference of 2.2%. Percentages of variations in flow were 20.3%, internal jugular vein; 20.4%, azygos vein; 6.8%, transverse sinus; and 5.1%, common carotid artery. Retrograde flow was found in the lower internal jugular vein (4.8%) and azygos vein (7.2%). Contrast-enhanced MRA interscan κ values for the internal jugular vein (left: 0.474, right: 0.366) and azygos vein (-0.053) showed poor interscan agreement. Phase contrast-vastly undersampled isotropic projection reconstruction blood flow measurements are reliable and highly reproducible in intracranial veins and in the common carotid artery but not in veins of the neck (internal jugular vein) and chest (azygos vein) because of normal physiologic variation. Retrograde flow normally may be observed in the lower internal jugular vein and azygos vein. Low interrater agreement in contrast-enhanced MRA scans was observed. These findings have important implications for imaging diagnosis and experimental research of chronic cerebrospinal venous

  13. The puzzling Venusian polar atmospheric structure reproduced by a general circulation model

    PubMed Central

    Ando, Hiroki; Sugimoto, Norihiko; Takagi, Masahiro; Kashimura, Hiroki; Imamura, Takeshi; Matsuda, Yoshihisa

    2016-01-01

    Unlike the polar vortices observed in the Earth, Mars and Titan atmospheres, the observed Venus polar vortex is warmer than the midlatitudes at cloud-top levels (∼65 km). This warm polar vortex is zonally surrounded by a cold latitude band located at ∼60° latitude, which is a unique feature called ‘cold collar' in the Venus atmosphere. Although these structures have been observed in numerous previous observations, the formation mechanism is still unknown. Here we perform numerical simulations of the Venus atmospheric circulation using a general circulation model, and succeed in reproducing these puzzling features in close agreement with the observations. The cold collar and warm polar region are attributed to the residual mean meridional circulation enhanced by the thermal tide. The present results strongly suggest that the thermal tide is crucial for the structure of the Venus upper polar atmosphere at and above cloud levels. PMID:26832195

  14. Comment on "Estimating the reproducibility of psychological science".

    PubMed

    Gilbert, Daniel T; King, Gary; Pettigrew, Stephen; Wilson, Timothy D

    2016-03-04

    A paper from the Open Science Collaboration (Research Articles, 28 August 2015, aac4716) attempting to replicate 100 published studies suggests that the reproducibility of psychological science is surprisingly low. We show that this article contains three statistical errors and provides no support for such a conclusion. Indeed, the data are consistent with the opposite conclusion, namely, that the reproducibility of psychological science is quite high. Copyright © 2016, American Association for the Advancement of Science.

  15. Skill of ship-following large-eddy simulations in reproducing MAGIC observations across the northeast Pacific stratocumulus to cumulus transition region

    NASA Astrophysics Data System (ADS)

    McGibbon, J.; Bretherton, C. S.

    2017-06-01

    During the Marine ARM GPCI Investigation of Clouds (MAGIC) in October 2011 to September 2012, a container ship making periodic cruises between Los Angeles, CA, and Honolulu, HI, was instrumented with surface meteorological, aerosol and radiation instruments, a cloud radar and ceilometer, and radiosondes. Here large-eddy simulation (LES) is performed in a ship-following frame of reference for 13 four day transects from the MAGIC field campaign. The goal is to assess if LES can skillfully simulate the broad range of observed cloud characteristics and boundary layer structure across the subtropical stratocumulus to cumulus transition region sampled during different seasons and meteorological conditions. Results from Leg 15A, which sampled a particularly well-defined stratocumulus to cumulus transition, demonstrate the approach. The LES reproduces the observed timing of decoupling and transition from stratocumulus to cumulus and matches the observed evolution of boundary layer structure, cloud fraction, liquid water path, and precipitation statistics remarkably well. Considering the simulations of all 13 cruises, the LES skillfully simulates the mean diurnal variation of key measured quantities, including liquid water path (LWP), cloud fraction, measures of decoupling, and cloud radar-derived precipitation. The daily mean quantities are well represented, and daily mean LWP and cloud fraction show the expected correlation with estimated inversion strength. There is a -0.6 K low bias in LES near-surface air temperature that results in a high bias of 5.6 W m-2 in sensible heat flux (SHF). Overall, these results build confidence in the ability of LES to represent the northeast Pacific stratocumulus to trade cumulus transition region.Plain Language SummaryDuring the Marine ARM GPCI Investigation of Clouds (MAGIC) field campaign in October 2011 to September 2012, a cargo container ship making regular cruises between Los Angeles</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.osti.gov/biblio/22597660-reproducible-controllable-induction-voltage-adder-scaled-beam-experiments','SCIGOV-STC'); return false;" href="https://www.osti.gov/biblio/22597660-reproducible-controllable-induction-voltage-adder-scaled-beam-experiments"><span><span class="hlt">Reproducible</span> and controllable induction voltage adder for scaled beam experiments</span></a></p> <p><a target="_blank" href="http://www.osti.gov/search">DOE Office of Scientific and Technical Information (OSTI.GOV)</a></p> <p>Sakai, Yasuo; Nakajima, Mitsuo; Horioka, Kazuhiko</p> <p>2016-08-15</p> <p>A <span class="hlt">reproducible</span> and controllable induction adder was developed using solid-state switching devices and Finemet cores for scaled beam compression experiments. A gate controlled MOSFET circuit was developed for the controllable voltage driver. The MOSFET circuit drove the induction adder at low magnetization levels of the cores which enabled us to form <span class="hlt">reproducible</span> modulation voltages with jitter less than 0.3 ns. Preliminary beam compression experiments indicated that the induction adder can improve the <span class="hlt">reproducibility</span> of modulation voltages and advance the beam physics experiments.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.osti.gov/pages/biblio/1366514-estimating-state-geophysical-system-sparse-observations-time-delay-methods-achieve-accurate-initial-nbsp-states-nbsp-prediction','SCIGOV-DOEP'); return false;" href="https://www.osti.gov/pages/biblio/1366514-estimating-state-geophysical-system-sparse-observations-time-delay-methods-achieve-accurate-initial-nbsp-states-nbsp-prediction"><span>Estimating the state of a geophysical system with sparse <span class="hlt">observations</span>: time delay methods to achieve <span class="hlt">accurate</span> initial states for prediction</span></a></p> <p><a target="_blank" href="http://www.osti.gov/pages">DOE PAGES</a></p> <p>An, Zhe; Rey, Daniel; Ye, Jingxin; ...</p> <p>2017-01-16</p> <p>The problem of forecasting the behavior of a complex dynamical system through analysis of <span class="hlt">observational</span> time-series data becomes difficult when the system expresses chaotic behavior and the measurements are sparse, in both space and/or time. Despite the fact that this situation is quite typical across many fields, including numerical weather prediction, the issue of whether the available <span class="hlt">observations</span> are "sufficient" for generating successful forecasts is still not well understood. An analysis by Whartenby et al. (2013) found that in the context of the nonlinear shallow water equations on a β plane, standard nudging techniques require <span class="hlt">observing</span> approximately 70 % of themore » full set of state variables. Here we examine the same system using a method introduced by Rey et al. (2014a), which generalizes standard nudging methods to utilize time delayed measurements. Here, we show that in certain circumstances, it provides a sizable reduction in the number of <span class="hlt">observations</span> required to construct <span class="hlt">accurate</span> estimates and high-quality predictions. In particular, we find that this estimate of 70 % can be reduced to about 33 % using time delays, and even further if Lagrangian drifter locations are also used as measurements.« less</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.osti.gov/servlets/purl/1366514','SCIGOV-STC'); return false;" href="https://www.osti.gov/servlets/purl/1366514"><span>Estimating the state of a geophysical system with sparse <span class="hlt">observations</span>: time delay methods to achieve <span class="hlt">accurate</span> initial states for prediction</span></a></p> <p><a target="_blank" href="http://www.osti.gov/search">DOE Office of Scientific and Technical Information (OSTI.GOV)</a></p> <p>An, Zhe; Rey, Daniel; Ye, Jingxin</p> <p></p> <p>The problem of forecasting the behavior of a complex dynamical system through analysis of <span class="hlt">observational</span> time-series data becomes difficult when the system expresses chaotic behavior and the measurements are sparse, in both space and/or time. Despite the fact that this situation is quite typical across many fields, including numerical weather prediction, the issue of whether the available <span class="hlt">observations</span> are "sufficient" for generating successful forecasts is still not well understood. An analysis by Whartenby et al. (2013) found that in the context of the nonlinear shallow water equations on a β plane, standard nudging techniques require <span class="hlt">observing</span> approximately 70 % of themore » full set of state variables. Here we examine the same system using a method introduced by Rey et al. (2014a), which generalizes standard nudging methods to utilize time delayed measurements. Here, we show that in certain circumstances, it provides a sizable reduction in the number of <span class="hlt">observations</span> required to construct <span class="hlt">accurate</span> estimates and high-quality predictions. In particular, we find that this estimate of 70 % can be reduced to about 33 % using time delays, and even further if Lagrangian drifter locations are also used as measurements.« less</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2011AGUFMIN52A..01T','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2011AGUFMIN52A..01T"><span>Data Identifiers and Citations Enable <span class="hlt">Reproducible</span> Science</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Tilmes, C.</p> <p>2011-12-01</p> <p>Modern science often involves data processing with tremendous volumes of data. Keeping track of that data has been a growing challenge for data center. Researchers who access and use that data don't always reference and cite their data sources adequately for consumers of their research to follow their methodology or <span class="hlt">reproduce</span> their analyses or experiments. Recent research has led to recommendations for good identifiers and citations that can help address this problem. This paper will describe some of the best practices in data identifiers, reference and citation. Using a simplified example scenario based on a long term remote sensing satellite mission, it will explore issues in identifying dynamic data sets and the importance of good data citations for <span class="hlt">reproducibility</span>. It will describe the difference between granule and collection level identifiers, using UUIDs and DOIs to illustrate some recommendations for developing identifiers and assigning them during data processing. As data processors create data products, the provenance of the input products and precise steps that led to their creation are recorded and published for users of the data to see. As researchers access the data from an archive, they can use the provenance to help understand the genesis of the data, which could have effects on their usage of the data. By citing the data on publishing their research, others can retrieve the precise data used in their research and <span class="hlt">reproduce</span> the analyses and experiments to confirm the results. Describing the experiment to a sufficient extent to <span class="hlt">reproduce</span> the research enforces a formal approach that lends credibility to the results, and ultimately, to the policies of decision makers depending on that research.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/27391538','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/27391538"><span>Repeatability and <span class="hlt">Reproducibility</span> of Virtual Subjective Refraction.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Perches, Sara; Collados, M Victoria; Ares, Jorge</p> <p>2016-10-01</p> <p>To establish the repeatability and <span class="hlt">reproducibility</span> of a virtual refraction process using simulated retinal images. With simulation software, aberrated images corresponding with each step of the refraction process were calculated following the typical protocol of conventional subjective refraction. Fifty external examiners judged simulated retinal images until the best sphero-cylindrical refraction and the best visual acuity were achieved starting from the aberrometry data of three patients. Data analyses were performed to assess repeatability and <span class="hlt">reproducibility</span> of the virtual refraction as a function of pupil size and aberrometric profile of different patients. SD values achieved in three components of refraction (M, J0, and J45) are lower than 0.25D in repeatability analysis. Regarding <span class="hlt">reproducibility</span>, we found SD values lower than 0.25D in the most cases. When the results of virtual refraction with different pupil diameters (4 and 6 mm) were compared, the mean of differences (MoD) obtained were not clinically significant (less than 0.25D). Only one of the aberrometry profiles with high uncorrected astigmatism shows poor results for the M component in <span class="hlt">reproducibility</span> and pupil size dependence analysis. In all cases, vision achieved was better than 0 logMAR. A comparison between the compensation obtained with virtual and conventional subjective refraction was made as an example of this application, showing good quality retinal images in both processes. The present study shows that virtual refraction has similar levels of precision as conventional subjective refraction. Moreover, virtual refraction has also shown that when high low order astigmatism is present, the refraction result is less precise and highly dependent on pupil size.</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_12");'>12</a></li> <li><a href="#" onclick='return showDiv("page_13");'>13</a></li> <li class="active"><span>14</span></li> <li><a href="#" onclick='return showDiv("page_15");'>15</a></li> <li><a href="#" onclick='return showDiv("page_16");'>16</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_14 --> <div id="page_15" class="hiddenDiv"> <div class="row"> <div class="col-sm-12"> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_13");'>13</a></li> <li><a href="#" onclick='return showDiv("page_14");'>14</a></li> <li class="active"><span>15</span></li> <li><a href="#" onclick='return showDiv("page_16");'>16</a></li> <li><a href="#" onclick='return showDiv("page_17");'>17</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div> </div> <div class="row"> <div class="col-sm-12"> <ol class="result-class" start="281"> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3916941','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3916941"><span>Maximizing the quantitative accuracy and <span class="hlt">reproducibility</span> of Förster resonance energy transfer measurement for screening by high throughput widefield microscopy</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Schaufele, Fred</p> <p>2013-01-01</p> <p>Förster resonance energy transfer (FRET) between fluorescent proteins (FPs) provides insights into the proximities and orientations of FPs as surrogates of the biochemical interactions and structures of the factors to which the FPs are genetically fused. As powerful as FRET methods are, technical issues have impeded their broad adoption in the biologic sciences. One hurdle to <span class="hlt">accurate</span> and <span class="hlt">reproducible</span> FRET microscopy measurement stems from variable fluorescence backgrounds both within a field and between different fields. Those variations introduce errors into the precise quantification of fluorescence levels on which the quantitative accuracy of FRET measurement is highly dependent. This measurement error is particularly problematic for screening campaigns since minimal well-to-well variation is necessary to faithfully identify wells with altered values. High content screening depends also upon maximizing the numbers of cells imaged, which is best achieved by low magnification high throughput microscopy. But, low magnification introduces flat-field correction issues that degrade the accuracy of background correction to cause poor <span class="hlt">reproducibility</span> in FRET measurement. For live cell imaging, fluorescence of cell culture media in the fluorescence collection channels for the FPs commonly used for FRET analysis is a high source of background error. These signal-to-noise problems are compounded by the desire to express proteins at biologically meaningful levels that may only be marginally above the strong fluorescence background. Here, techniques are presented that correct for background fluctuations. <span class="hlt">Accurate</span> calculation of FRET is realized even from images in which a non-flat background is 10-fold higher than the signal. PMID:23927839</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/26685085','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/26685085"><span>An International Ki67 <span class="hlt">Reproducibility</span> Study in Adrenal Cortical Carcinoma.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Papathomas, Thomas G; Pucci, Eugenio; Giordano, Thomas J; Lu, Hao; Duregon, Eleonora; Volante, Marco; Papotti, Mauro; Lloyd, Ricardo V; Tischler, Arthur S; van Nederveen, Francien H; Nose, Vania; Erickson, Lori; Mete, Ozgur; Asa, Sylvia L; Turchini, John; Gill, Anthony J; Matias-Guiu, Xavier; Skordilis, Kassiani; Stephenson, Timothy J; Tissier, Frédérique; Feelders, Richard A; Smid, Marcel; Nigg, Alex; Korpershoek, Esther; van der Spek, Peter J; Dinjens, Winand N M; Stubbs, Andrew P; de Krijger, Ronald R</p> <p>2016-04-01</p> <p>Despite the established role of Ki67 labeling index in prognostic stratification of adrenocortical carcinomas and its recent integration into treatment flow charts, the <span class="hlt">reproducibility</span> of the assessment method has not been determined. The aim of this study was to investigate interobserver variability among endocrine pathologists using a web-based virtual microscopy approach. Ki67-stained slides of 76 adrenocortical carcinomas were analyzed independently by 14 <span class="hlt">observers</span>, each according to their method of preference including eyeballing, formal manual counting, and digital image analysis. The interobserver variation was statistically significant (P<0.001) in the absence of any correlation between the various methods. Subsequently, 61 static images were distributed among 15 <span class="hlt">observers</span> who were instructed to follow a category-based scoring approach. Low levels of interobserver (F=6.99; Fcrit=1.70; P<0.001) as well as intraobserver concordance (n=11; Cohen κ ranging from -0.057 to 0.361) were detected. To improve harmonization of Ki67 analysis, we tested the utility of an open-source Galaxy virtual machine application, namely Automated Selection of Hotspots, in 61 virtual slides. The software-provided Ki67 values were validated by digital image analysis in identical images, displaying a strong correlation of 0.96 (P<0.0001) and dividing the cases into 3 classes (cutoffs of 0%-15%-30% and/or 0%-10%-20%) with significantly different overall survivals (P<0.05). We conclude that current practices in Ki67 scoring assessment vary greatly, and interobserver variation sets particular limitations to its clinical utility, especially around clinically relevant cutoff values. Novel digital microscopy-enabled methods could provide critical aid in reducing variation, increasing <span class="hlt">reproducibility</span>, and improving reliability in the clinical setting.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2014EGUGA..16.5473C','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2014EGUGA..16.5473C"><span><span class="hlt">Reproducibility</span> of UAV-based earth surface topography based on structure-from-motion algorithms.</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Clapuyt, François; Vanacker, Veerle; Van Oost, Kristof</p> <p>2014-05-01</p> <p>A representation of the earth surface at very high spatial resolution is crucial to <span class="hlt">accurately</span> map small geomorphic landforms with high precision. Very high resolution digital surface models (DSM) can then be used to quantify changes in earth surface topography over time, based on differencing of DSMs taken at various moments in time. However, it is compulsory to have both high accuracy for each topographic representation and consistency between measurements over time, as DSM differencing automatically leads to error propagation. This study investigates the <span class="hlt">reproducibility</span> of reconstructions of earth surface topography based on structure-from-motion (SFM) algorithms. To this end, we equipped an eight-propeller drone with a standard reflex camera. This equipment can easily be deployed in the field, as it is a lightweight, low-cost system in comparison with classic aerial photo surveys and terrestrial or airborne LiDAR scanning. Four sets of aerial photographs were created for one test field. The sets of airphotos differ in focal length, and viewing angles, i.e. nadir view and ground-level view. In addition, the importance of the accuracy of ground control points for the construction of a georeferenced point cloud was assessed using two different GPS devices with horizontal accuracy at resp. the sub-meter and sub-decimeter level. Airphoto datasets were processed with SFM algorithm and the resulting point clouds were georeferenced. Then, the surface representations were compared with each other to assess the <span class="hlt">reproducibility</span> of the earth surface topography. Finally, consistency between independent datasets is discussed.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/24957755','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/24957755"><span>Development and <span class="hlt">reproducibility</span> evaluation of a Monte Carlo-based standard LINAC model for quality assurance of multi-institutional clinical trials.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Usmani, Muhammad Nauman; Takegawa, Hideki; Takashina, Masaaki; Numasaki, Hodaka; Suga, Masaki; Anetai, Yusuke; Kurosu, Keita; Koizumi, Masahiko; Teshima, Teruki</p> <p>2014-11-01</p> <p>Technical developments in radiotherapy (RT) have created a need for systematic quality assurance (QA) to ensure that clinical institutions deliver prescribed radiation doses consistent with the requirements of clinical protocols. For QA, an ideal dose verification system should be independent of the treatment-planning system (TPS). This paper describes the development and <span class="hlt">reproducibility</span> evaluation of a Monte Carlo (MC)-based standard LINAC model as a preliminary requirement for independent verification of dose distributions. The BEAMnrc MC code is used for characterization of the 6-, 10- and 15-MV photon beams for a wide range of field sizes. The modeling of the LINAC head components is based on the specifications provided by the manufacturer. MC dose distributions are tuned to match Varian Golden Beam Data (GBD). For <span class="hlt">reproducibility</span> evaluation, calculated beam data is compared with beam data measured at individual institutions. For all energies and field sizes, the MC and GBD agreed to within 1.0% for percentage depth doses (PDDs), 1.5% for beam profiles and 1.2% for total scatter factors (Scps.). <span class="hlt">Reproducibility</span> evaluation showed that the maximum average local differences were 1.3% and 2.5% for PDDs and beam profiles, respectively. MC and institutions' mean Scps agreed to within 2.0%. An MC-based standard LINAC model developed to independently verify dose distributions for QA of multi-institutional clinical trials and routine clinical practice has proven to be highly <span class="hlt">accurate</span> and <span class="hlt">reproducible</span> and can thus help ensure that prescribed doses delivered are consistent with the requirements of clinical protocols. © The Author 2014. Published by Oxford University Press on behalf of The Japan Radiation Research Society and Japanese Society for Radiation Oncology.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.ars.usda.gov/research/publications/publication/?seqNo115=317922','TEKTRAN'); return false;" href="http://www.ars.usda.gov/research/publications/publication/?seqNo115=317922"><span><span class="hlt">Reproducible</span> research in vadose zone sciences</span></a></p> <p><a target="_blank" href="https://www.ars.usda.gov/research/publications/find-a-publication/">USDA-ARS?s Scientific Manuscript database</a></p> <p></p> <p></p> <p>A significant portion of present-day soil and Earth science research is computational, involving complex data analysis pipelines, advanced mathematical and statistical models, and sophisticated computer codes. Opportunities for scientific progress are greatly diminished if <span class="hlt">reproducing</span> and building o...</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/27979085','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/27979085"><span>Rapid, cost-effective and <span class="hlt">accurate</span> quantification of Yucca schidigera Roezl. steroidal saponins using HPLC-ELSD method.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Tenon, Mathieu; Feuillère, Nicolas; Roller, Marc; Birtić, Simona</p> <p>2017-04-15</p> <p>Yucca GRAS-labelled saponins have been and are increasingly used in food/feed, pharmaceutical or cosmetic industries. Existing techniques presently used for Yucca steroidal saponin quantification remain either inaccurate and misleading or <span class="hlt">accurate</span> but time consuming and cost prohibitive. The method reported here addresses all of the above challenges. HPLC/ELSD technique is an <span class="hlt">accurate</span> and reliable method that yields results of appropriate repeatability and <span class="hlt">reproducibility</span>. This method does not over- or under-estimate levels of steroidal saponins. HPLC/ELSD method does not require each and every pure standard of saponins, to quantify the group of steroidal saponins. The method is a time- and cost-effective technique that is suitable for routine industrial analyses. HPLC/ELSD methods yield a saponin fingerprints specific to the plant species. As the method is capable of distinguishing saponin profiles from taxonomically distant species, it can unravel plant adulteration issues. Copyright © 2016 The Author(s). Published by Elsevier Ltd.. All rights reserved.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2016MNRAS.459.2882M','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2016MNRAS.459.2882M"><span>Radiative transfer of HCN: interpreting <span class="hlt">observations</span> of hyperfine anomalies</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Mullins, A. M.; Loughnane, R. M.; Redman, M. P.; Wiles, B.; Guegan, N.; Barrett, J.; Keto, E. R.</p> <p>2016-07-01</p> <p>Molecules with hyperfine splitting of their rotational line spectra are useful probes of optical depth, via the relative line strengths of their hyperfine components. The hyperfine splitting is particularly advantageous in interpreting the physical conditions of the emitting gas because with a second rotational transition, both gas density and temperature can be derived. For HCN however, the relative strengths of the hyperfine lines are anomalous. They appear in ratios which can vary significantly from source to source, and are inconsistent with local thermodynamic equilibrium (LTE). This is the HCN hyperfine anomaly, and it prevents the use of simple LTE models of HCN emission to derive reliable optical depths. In this paper, we demonstrate how to model HCN hyperfine line emission, and derive <span class="hlt">accurate</span> line ratios, spectral line shapes and optical depths. We show that by carrying out radiative transfer calculations over each hyperfine level individually, as opposed to summing them over each rotational level, the anomalous hyperfine emission emerges naturally. To do this requires not only <span class="hlt">accurate</span> radiative rates between hyperfine states, but also <span class="hlt">accurate</span> collisional rates. We investigate the effects of different sets of hyperfine collisional rates, derived via the proportional method and through direct recoupling calculations. Through an extensive parameter sweep over typical low-mass star-forming conditions, we show the HCN line ratios to be highly variable to optical depth. We also <span class="hlt">reproduce</span> an <span class="hlt">observed</span> effect whereby the red-blue asymmetry of the hyperfine lines (an infall signature) switches sense within a single rotational transition.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://cfpub.epa.gov/si/si_public_record_report.cfm?dirEntryId=308368&keyword=Teaching+AND+Science&actType=&TIMSType=+&TIMSSubTypeID=&DEID=&epaNumber=&ntisID=&archiveStatus=Both&ombCat=Any&dateBeginCreated=&dateEndCreated=&dateBeginPublishedPresented=&dateEndPublishedPresented=&dateBeginUpdated=&dateEndUpdated=&dateBeginCompleted=&dateEndCompleted=&personID=&role=Any&journalID=&publisherID=&sortBy=revisionDate&count=50','EPA-EIMS'); return false;" href="https://cfpub.epa.gov/si/si_public_record_report.cfm?dirEntryId=308368&keyword=Teaching+AND+Science&actType=&TIMSType=+&TIMSSubTypeID=&DEID=&epaNumber=&ntisID=&archiveStatus=Both&ombCat=Any&dateBeginCreated=&dateEndCreated=&dateBeginPublishedPresented=&dateEndPublishedPresented=&dateBeginUpdated=&dateEndUpdated=&dateBeginCompleted=&dateEndCompleted=&personID=&role=Any&journalID=&publisherID=&sortBy=revisionDate&count=50"><span>An Open Science and <span class="hlt">Reproducible</span> Research Primer for Landscape Ecologists</span></a></p> <p><a target="_blank" href="http://oaspub.epa.gov/eims/query.page">EPA Science Inventory</a></p> <p></p> <p></p> <p>In recent years many funding agencies, some publishers, and even the United States government have enacted policies that encourage open science and strive for <span class="hlt">reproducibility</span>; however, the knowledge and skills to implement open science and enable <span class="hlt">reproducible</span> research are not yet...</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.osti.gov/biblio/22493366-multiscale-coarse-graining-method-xi-accurate-interactions-based-centers-charge-coarse-grained-sites','SCIGOV-STC'); return false;" href="https://www.osti.gov/biblio/22493366-multiscale-coarse-graining-method-xi-accurate-interactions-based-centers-charge-coarse-grained-sites"><span>The multiscale coarse-graining method. XI. <span class="hlt">Accurate</span> interactions based on the centers of charge of coarse-grained sites</span></a></p> <p><a target="_blank" href="http://www.osti.gov/search">DOE Office of Scientific and Technical Information (OSTI.GOV)</a></p> <p>Cao, Zhen; Voth, Gregory A., E-mail: gavoth@uchicago.edu</p> <p></p> <p>It is essential to be able to systematically construct coarse-grained (CG) models that can efficiently and <span class="hlt">accurately</span> <span class="hlt">reproduce</span> key properties of higher-resolution models such as all-atom. To fulfill this goal, a mapping operator is needed to transform the higher-resolution configuration to a CG configuration. Certain mapping operators, however, may lose information related to the underlying electrostatic properties. In this paper, a new mapping operator based on the centers of charge of CG sites is proposed to address this issue. Four example systems are chosen to demonstrate this concept. Within the multiscale coarse-graining framework, CG models that use this mapping operatormore » are found to better <span class="hlt">reproduce</span> the structural correlations of atomistic models. The present work also demonstrates the flexibility of the mapping operator and the robustness of the force matching method. For instance, important functional groups can be isolated and emphasized in the CG model.« less</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/16336495','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/16336495"><span>How <span class="hlt">reproducible</span> is cutaneous electrogastrography? An in-depth evidence-based study.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Jonderko, K; Kasicka-Jonderko, A; Krusiec-Swidergoł, B; Dzielicki, M; Strój, L; Doliński, M; Doliński, K; Błońska-Fajfrowska, B</p> <p>2005-12-01</p> <p>To check on <span class="hlt">reproducibility</span> of parameters of the cutaneous electrogastrogram registered at a close or a distant time span. Twenty-two volunteers recruited by an advertisement (11 females and 11 males, median age 25 years, range: 18-35) underwent three surface electrogastrography examinations of which two were taken on consecutive days and the third one was accomplished at least 2 weeks before or after the two other sessions. The examination involved a 30-min fasted recording, followed by a 90-min postprandial registration after intake of a 394-kcal mixed solid-liquid test meal. Parameters of the electrogastrogram pertaining to the frequency of the gastric slow waves exhibited good to moderate <span class="hlt">reproducibility</span>, whereas fair <span class="hlt">reproducibility</span> characterized parameters expected to describe the power of gastric slow waves. With the exception of the difference fed minus fasted power (DeltaDP), in no instance was the medium term <span class="hlt">reproducibility</span> any worse than the short term one. Categorical data analysis revealed that the relative time share of normogastria postprandially exhibited a better <span class="hlt">reproducibility</span> than in the fasted period. The Cohen's kappa-value of 0.459 for the DeltaDP for the medium term <span class="hlt">reproducibility</span> placed this parameter within the range of moderate agreement between repeat examinations. Of the two two-parameter combinations considered, the alliance of the fasted and fed normogastria performed worse than any of those parameters considered alone, whereas a combination of the DeltaDP with the fed-state normogastria revealed a kappa-value amounting to 0.510 for the medium term <span class="hlt">reproducibility</span>. The feasibility of some electrogastrographic parameters to convey clinically useful information may be hampered by their fair <span class="hlt">reproducibility</span>. Recoding of parameters of the cutaneous electrogastrogram from primary continuous to secondary categorical may help achieve a better agreement between repeat examinations.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/12034116','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/12034116"><span>Measures of low back function: a review of <span class="hlt">reproducibility</span> studies.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Essendrop, Morten; Maul, Irina; Läubli, Thomas; Riihimäki, Hilkka; Schibye, Bente</p> <p>2002-05-01</p> <p>The objective of the present study was to make a systematic literature review with preset quality criteria concerning <span class="hlt">reproducibility</span> of the tests of the low back regarding strength, endurance and range of motion. Literature in Medline and local databases was reviewed for articles concerning the <span class="hlt">reproducibility</span> of strength, endurance, and range of motion measurements. Measures of low back function are widely used, and are important for both clinical and research purposes in relation to low back problems. A review of the <span class="hlt">reproducibility</span> of these tests has not previously been made. After extensive discussion among all the authors, general evaluation parameters were defined for the quality assessment. Every study was graded from 0 to 2 for each parameter. Parameters evaluated were: number of subjects, subject description, method description, test/retest interval, description of results, and statistics. The literature search revealed a total of 79 studies. Most studies suffered from methodological weaknesses and only eleven studies received ten or more quality points (maximum 14). The results from the highest graded studies are highlighted. It may be concluded that there is a considerable lack of information about the <span class="hlt">reproducibility</span> of functional measures for the low back, and therefore a recommendation for consensus is difficult. However, most tests performed in the sagittal plane are reliable for use on groups. Measures of low back function are thought to be of great importance for clinicians, and low back researchers in general. A review of <span class="hlt">reproducibility</span> will be helpful both as a survey of tests, and to provide information on the usefulness in relation to the level of <span class="hlt">reproducibility</span>.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2015SPIE.9409E..0EH','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2015SPIE.9409E..0EH"><span>Benchmarking contactless acquisition sensor <span class="hlt">reproducibility</span> for latent fingerprint trace evidence</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Hildebrandt, Mario; Dittmann, Jana</p> <p>2015-03-01</p> <p>Optical, nano-meter range, contactless, non-destructive sensor devices are promising acquisition techniques in crime scene trace forensics, e.g. for digitizing latent fingerprint traces. Before new approaches are introduced in crime investigations, innovations need to be positively tested and quality ensured. In this paper we investigate sensor <span class="hlt">reproducibility</span> by studying different scans from four sensors: two chromatic white light sensors (CWL600/CWL1mm), one confocal laser scanning microscope, and one NIR/VIS/UV reflection spectrometer. Firstly, we perform an intra-sensor <span class="hlt">reproducibility</span> testing for CWL600 with a privacy conform test set of artificial-sweat printed, computer generated fingerprints. We use 24 different fingerprint patterns as original samples (printing samples/templates) for printing with artificial sweat (physical trace samples) and their acquisition with contactless sensory resulting in 96 sensor images, called scan or acquired samples. The second test set for inter-sensor <span class="hlt">reproducibility</span> assessment consists of the first three patterns from the first test set, acquired in two consecutive scans using each device. We suggest using a simple feature space set in spatial and frequency domain known from signal processing and test its suitability for six different classifiers classifying scan data into small differences (<span class="hlt">reproducible</span>) and large differences (non-<span class="hlt">reproducible</span>). Furthermore, we suggest comparing the classification results with biometric verification scores (calculated with NBIS, with threshold of 40) as biometric <span class="hlt">reproducibility</span> score. The Bagging classifier is nearly for all cases the most reliable classifier in our experiments and the results are also confirmed with the biometric matching rates.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/29036464','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/29036464"><span>The MIMIC Code Repository: enabling <span class="hlt">reproducibility</span> in critical care research.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Johnson, Alistair Ew; Stone, David J; Celi, Leo A; Pollard, Tom J</p> <p>2018-01-01</p> <p>Lack of <span class="hlt">reproducibility</span> in medical studies is a barrier to the generation of a robust knowledge base to support clinical decision-making. In this paper we outline the Medical Information Mart for Intensive Care (MIMIC) Code Repository, a centralized code base for generating <span class="hlt">reproducible</span> studies on an openly available critical care dataset. Code is provided to load the data into a relational structure, create extractions of the data, and <span class="hlt">reproduce</span> entire analysis plans including research studies. Concepts extracted include severity of illness scores, comorbid status, administrative definitions of sepsis, physiologic criteria for sepsis, organ failure scores, treatment administration, and more. Executable documents are used for tutorials and <span class="hlt">reproduce</span> published studies end-to-end, providing a template for future researchers to replicate. The repository's issue tracker enables community discussion about the data and concepts, allowing users to collaboratively improve the resource. The centralized repository provides a platform for users of the data to interact directly with the data generators, facilitating greater understanding of the data. It also provides a location for the community to collaborate on necessary concepts for research progress and share them with a larger audience. Consistent application of the same code for underlying concepts is a key step in ensuring that research studies on the MIMIC database are comparable and <span class="hlt">reproducible</span>. By providing open source code alongside the freely accessible MIMIC-III database, we enable end-to-end <span class="hlt">reproducible</span> analysis of electronic health records. © The Author 2017. Published by Oxford University Press on behalf of the American Medical Informatics Association.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2017JChPh.147n4105S','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2017JChPh.147n4105S"><span>A study of <span class="hlt">accurate</span> exchange-correlation functionals through adiabatic connection</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Singh, Rabeet; Harbola, Manoj K.</p> <p>2017-10-01</p> <p>A systematic way of improving exchange-correlation energy functionals of density functional theory has been to make them satisfy more and more exact relations. Starting from the initial generalized gradient approximation (GGA) functionals, this has culminated into the recently proposed SCAN (strongly constrained and appropriately normed) functional that satisfies several known constraints and is appropriately normed. The ultimate test for the functionals developed is the accuracy of energy calculated by employing them. In this paper, we test these exchange-correlation functionals—the GGA hybrid functionals B3LYP and PBE0 and the meta-GGA functional SCAN—from a different perspective. We study how <span class="hlt">accurately</span> these functionals <span class="hlt">reproduce</span> the exchange-correlation energy when electron-electron interaction is scaled as αVee with α varying between 0 and 1. Our study reveals interesting comparison between these functionals and the associated difference Tc between the interacting and the non-interacting kinetic energy for the same density.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/19841401','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/19841401"><span>Reflectance confocal microscopy and features of melanocytic lesions: an internet-based study of the <span class="hlt">reproducibility</span> of terminology.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Pellacani, Giovanni; Vinceti, Marco; Bassoli, Sara; Braun, Ralph; Gonzalez, Salvador; Guitera, Pascale; Longo, Caterina; Marghoob, Ashfaq A; Menzies, Scott W; Puig, Susana; Scope, Alon; Seidenari, Stefania; Malvehy, Josep</p> <p>2009-10-01</p> <p>To test the interobserver and intraobserver <span class="hlt">reproducibility</span> of the standard terminology for description and diagnosis of melanocytic lesions in in vivo confocal microscopy. A dedicated Web platform was developed to train the participants and to allow independent distant evaluations of confocal images via the Internet. Department of Dermatology, University of Modena and Reggio Emilia, Modena, Italy. The study population was composed of 15 melanomas, 30 nevi, and 5 Spitz/Reed nevi. Six expert centers were invited to participate at the study. Intervention Evaluation of 36 features in 345 confocal microscopic images from melanocytic lesions. Interobserved and intraobserved agreement, by calculating the Cohen kappa statistics measure for each descriptor. High overall levels of <span class="hlt">reproducibility</span> were shown for most of the evaluated features. In both the training and test sets there was a parallel trend of decreasing kappa values as deeper anatomic skin levels were evaluated. All of the features, except 1, used for melanoma diagnosis, including roundish pagetoid cells, nonedged papillae, atypical cells in basal layer, cerebriform clusters, and nucleated cells infiltrating dermal papillae, showed high overall levels of <span class="hlt">reproducibility</span>. However, less-than-ideal <span class="hlt">reproducibility</span> was obtained for some descriptors, such as grainy appearance of the epidermis, junctional thickening, mild atypia in basal layer, plump bright cells, small bright cells, and reticulated fibers in the dermis. Conclusion The standard consensus confocal terminology useful for the evaluation of melanocytic lesions was <span class="hlt">reproducibly</span> recognized by independent <span class="hlt">observers</span>.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/28707306','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/28707306"><span>Current reinforcement model <span class="hlt">reproduces</span> center-in-center vein trajectory of Physarum polycephalum.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Akita, Dai; Schenz, Daniel; Kuroda, Shigeru; Sato, Katsuhiko; Ueda, Kei-Ichi; Nakagaki, Toshiyuki</p> <p>2017-06-01</p> <p>Vein networks span the whole body of the amoeboid organism in the plasmodial slime mould Physarum polycephalum, and the network topology is rearranged within an hour in response to spatio-temporal variations of the environment. It has been reported that this tube morphogenesis is capable of solving mazes, and a mathematical model, named the 'current reinforcement rule', was proposed based on the adaptability of the veins. Although it is known that this model works well for <span class="hlt">reproducing</span> some key characters of the organism's maze-solving behaviour, one important issue is still open: In the real organism, the thick veins tend to trace the shortest possible route by cutting the corners at the turn of corridors, following a center-in-center trajectory, but it has not yet been examined whether this feature also appears in the mathematical model, using corridors of finite width. In this report, we confirm that the mathematical model <span class="hlt">reproduces</span> the center-in-center trajectory of veins around corners <span class="hlt">observed</span> in the maze-solving experiment. © 2017 Japanese Society of Developmental Biologists.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/11203625','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/11203625"><span>Materials for interocclusal records and their ability to <span class="hlt">reproduce</span> a 3-dimensional jaw relationship.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Ockert-Eriksson, G; Eriksson, A; Lockowandt, P; Eriksson, O</p> <p>2000-01-01</p> <p>The purpose of this study was to determine if accuracy and dimensional stability of vinyl polysiloxanes and irreversible hydrocolloids stabilized by a tray used for fixed prosthodontics, removable partial, and complete denture cases are comparable to those of waxes and record rims and if storage time (24 hours or 6 days) affects dimensional stability of the tested materials. Two waxes, two record rims, three vinyl polysiloxanes, and one irreversible hydrocolloid (alginate) were examined. Three pairs of master casts with measuring steel rods were mounted on an articulator (initial position). Five records were made of each material, and the upper cast was remounted after 24 hours or 6 days so that deviations from the initial position could be measured. Vinyl polysiloxanes reinforced by a stabilization tray were the most <span class="hlt">accurate</span> materials able to <span class="hlt">reproduce</span> a settled interocclusal position. Mounting casts (fixed prosthodontics cases) without records gave accuracy similar to wax records. Record rims used for removable partial and complete denture cases produced lesser accuracy than vinyl polysiloxanes and irreversible hydrocolloid stabilized by a tray. Accuracy was not significantly affected by storage time. The results show that accuracy of vinyl polysiloxanes and irreversible hydrocolloids reinforced by a tray is superior to that of record rims with regard to the complete denture case and is among the most <span class="hlt">accurate</span> with regard to the removable partial denture case. For fixed prosthodontics, however, reinforcement is unnecessary.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2015AGUFMIN21E..01M','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2015AGUFMIN21E..01M"><span>Personalized, Shareable Geoscience Dataspaces For Simplifying Data Management and Improving <span class="hlt">Reproducibility</span></span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Malik, T.; Foster, I.; Goodall, J. L.; Peckham, S. D.; Baker, J. B. H.; Gurnis, M.</p> <p>2015-12-01</p> <p>Research activities are iterative, collaborative, and now data- and compute-intensive. Such research activities mean that even the many researchers who work in small laboratories must often create, acquire, manage, and manipulate much diverse data and keep track of complex software. They face difficult data and software management challenges, and data sharing and <span class="hlt">reproducibility</span> are neglected. There is signficant federal investment in powerful cyberinfrastructure, in part to lesson the burden associated with modern data- and compute-intensive research. Similarly, geoscience communities are establishing research repositories to facilitate data preservation. Yet we <span class="hlt">observe</span> a large fraction of the geoscience community continues to struggle with data and software management. The reason, studies suggest, is not lack of awareness but rather that tools do not adequately support time-consuming data life cycle activities. Through NSF/EarthCube-funded GeoDataspace project, we are building personalized, shareable dataspaces that help scientists connect their individual or research group efforts with the community at large. The dataspaces provide a light-weight multiplatform research data management system with tools for recording research activities in what we call geounits, so that a geoscientist can at any time snapshot and preserve, both for their own use and to share with the community, all data and code required to understand and <span class="hlt">reproduce</span> a study. A software-as-a-service (SaaS) deployment model enhances usability of core components, and integration with widely used software systems. In this talk we will present the open-source GeoDataspace project and demonstrate how it is enabling <span class="hlt">reproducibility</span> across geoscience domains of hydrology, space science, and modeling toolkits.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/26553988','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/26553988"><span>Using prediction markets to estimate the <span class="hlt">reproducibility</span> of scientific research.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Dreber, Anna; Pfeiffer, Thomas; Almenberg, Johan; Isaksson, Siri; Wilson, Brad; Chen, Yiling; Nosek, Brian A; Johannesson, Magnus</p> <p>2015-12-15</p> <p>Concerns about a lack of <span class="hlt">reproducibility</span> of statistically significant results have recently been raised in many fields, and it has been argued that this lack comes at substantial economic costs. We here report the results from prediction markets set up to quantify the <span class="hlt">reproducibility</span> of 44 studies published in prominent psychology journals and replicated in the <span class="hlt">Reproducibility</span> Project: Psychology. The prediction markets predict the outcomes of the replications well and outperform a survey of market participants' individual forecasts. This shows that prediction markets are a promising tool for assessing the <span class="hlt">reproducibility</span> of published scientific results. The prediction markets also allow us to estimate probabilities for the hypotheses being true at different testing stages, which provides valuable information regarding the temporal dynamics of scientific discovery. We find that the hypotheses being tested in psychology typically have low prior probabilities of being true (median, 9%) and that a "statistically significant" finding needs to be confirmed in a well-powered replication to have a high probability of being true. We argue that prediction markets could be used to obtain speedy information about <span class="hlt">reproducibility</span> at low cost and could potentially even be used to determine which studies to replicate to optimally allocate limited resources into replications.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4687569','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4687569"><span>Using prediction markets to estimate the <span class="hlt">reproducibility</span> of scientific research</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Dreber, Anna; Pfeiffer, Thomas; Almenberg, Johan; Isaksson, Siri; Wilson, Brad; Chen, Yiling; Nosek, Brian A.; Johannesson, Magnus</p> <p>2015-01-01</p> <p>Concerns about a lack of <span class="hlt">reproducibility</span> of statistically significant results have recently been raised in many fields, and it has been argued that this lack comes at substantial economic costs. We here report the results from prediction markets set up to quantify the <span class="hlt">reproducibility</span> of 44 studies published in prominent psychology journals and replicated in the <span class="hlt">Reproducibility</span> Project: Psychology. The prediction markets predict the outcomes of the replications well and outperform a survey of market participants’ individual forecasts. This shows that prediction markets are a promising tool for assessing the <span class="hlt">reproducibility</span> of published scientific results. The prediction markets also allow us to estimate probabilities for the hypotheses being true at different testing stages, which provides valuable information regarding the temporal dynamics of scientific discovery. We find that the hypotheses being tested in psychology typically have low prior probabilities of being true (median, 9%) and that a “statistically significant” finding needs to be confirmed in a well-powered replication to have a high probability of being true. We argue that prediction markets could be used to obtain speedy information about <span class="hlt">reproducibility</span> at low cost and could potentially even be used to determine which studies to replicate to optimally allocate limited resources into replications. PMID:26553988</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_13");'>13</a></li> <li><a href="#" onclick='return showDiv("page_14");'>14</a></li> <li class="active"><span>15</span></li> <li><a href="#" onclick='return showDiv("page_16");'>16</a></li> <li><a href="#" onclick='return showDiv("page_17");'>17</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_15 --> <div id="page_16" class="hiddenDiv"> <div class="row"> <div class="col-sm-12"> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_14");'>14</a></li> <li><a href="#" onclick='return showDiv("page_15");'>15</a></li> <li class="active"><span>16</span></li> <li><a href="#" onclick='return showDiv("page_17");'>17</a></li> <li><a href="#" onclick='return showDiv("page_18");'>18</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div> </div> <div class="row"> <div class="col-sm-12"> <ol class="result-class" start="301"> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2571960','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2571960"><span><span class="hlt">Reproducibility</span> of dynamically represented acoustic lung images from healthy individuals</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Maher, T M; Gat, M; Allen, D; Devaraj, A; Wells, A U; Geddes, D M</p> <p>2008-01-01</p> <p>Background and aim: Acoustic lung imaging offers a unique method for visualising the lung. This study was designed to demonstrate <span class="hlt">reproducibility</span> of acoustic lung images recorded from healthy individuals at different time points and to assess intra- and inter-rater agreement in the assessment of dynamically represented acoustic lung images. Methods: Recordings from 29 healthy volunteers were made on three separate occasions using vibration response imaging. <span class="hlt">Reproducibility</span> was measured using quantitative, computerised assessment of vibration energy. Dynamically represented acoustic lung images were scored by six blinded raters. Results: Quantitative measurement of acoustic recordings was highly <span class="hlt">reproducible</span> with an intraclass correlation score of 0.86 (very good agreement). Intraclass correlations for inter-rater agreement and <span class="hlt">reproducibility</span> were 0.61 (good agreement) and 0.86 (very good agreement), respectively. There was no significant difference found between the six raters at any time point. Raters ranged from 88% to 95% in their ability to identically evaluate the different features of the same image presented to them blinded on two separate occasions. Conclusion: Acoustic lung imaging is <span class="hlt">reproducible</span> in healthy individuals. Graphic representation of lung images can be interpreted with a high degree of accuracy by the same and by different reviewers. PMID:18024534</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3520271','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3520271"><span>The reliability and <span class="hlt">reproducibility</span> of cephalometric measurements: a comparison of conventional and digital methods</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>AlBarakati, SF; Kula, KS; Ghoneima, AA</p> <p>2012-01-01</p> <p>Objective The aim of this study was to assess the reliability and <span class="hlt">reproducibility</span> of angular and linear measurements of conventional and digital cephalometric methods. Methods A total of 13 landmarks and 16 skeletal and dental parameters were defined and measured on pre-treatment cephalometric radiographs of 30 patients. The conventional and digital tracings and measurements were performed twice by the same examiner with a 6 week interval between measurements. The reliability within the method was determined using Pearson's correlation coefficient (r2). The <span class="hlt">reproducibility</span> between methods was calculated by paired t-test. The level of statistical significance was set at p < 0.05. Results All measurements for each method were above 0.90 r2 (strong correlation) except maxillary length, which had a correlation of 0.82 for conventional tracing. Significant differences between the two methods were <span class="hlt">observed</span> in most angular and linear measurements except for ANB angle (p = 0.5), angle of convexity (p = 0.09), anterior cranial base (p = 0.3) and the lower anterior facial height (p = 0.6). Conclusion In general, both methods of conventional and digital cephalometric analysis are highly reliable. Although the <span class="hlt">reproducibility</span> of the two methods showed some statistically significant differences, most differences were not clinically significant. PMID:22184624</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/16336496','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/16336496"><span>Barostat testing of rectal sensation and compliance in humans: comparison of results across two centres and overall <span class="hlt">reproducibility</span>.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Cremonini, F; Houghton, L A; Camilleri, M; Ferber, I; Fell, C; Cox, V; Castillo, E J; Alpers, D H; Dewit, O E; Gray, E; Lea, R; Zinsmeister, A R; Whorwell, P J</p> <p>2005-12-01</p> <p>We assessed <span class="hlt">reproducibility</span> of measurements of rectal compliance and sensation in health in studies conducted at two centres. We estimated samples size necessary to show clinically meaningful changes in future studies. We performed rectal barostat tests three times (day 1, day 1 after 4 h and 14-17 days later) in 34 healthy participants. We measured compliance and pressure thresholds for first sensation, urgency, discomfort and pain using ascending method of limits and symptom ratings for gas, urgency, discomfort and pain during four phasic distensions (12, 24, 36 and 48 mmHg) in random order. Results obtained at the two centres differed minimally. <span class="hlt">Reproducibility</span> of sensory end points varies with type of sensation, pressure level and method of distension. Pressure threshold for pain and sensory ratings for non-painful sensations at 36 and 48 mmHg distension were most <span class="hlt">reproducible</span> in the two centres. Sample size calculations suggested that crossover design is preferable in therapeutic trials: for each dose of medication tested, a sample of 21 should be sufficient to demonstrate 30% changes in all sensory thresholds and almost all sensory ratings. We conclude that <span class="hlt">reproducibility</span> varies with sensation type, pressure level and distension method, but in a two-centre study, differences in <span class="hlt">observed</span> results of sensation are minimal and pressure threshold for pain and sensory ratings at 36-48 mmHg of distension are <span class="hlt">reproducible</span>.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/18709124','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/18709124"><span>In situ <span class="hlt">accurate</span> determination of the zero time delay between two independent ultrashort laser pulses by <span class="hlt">observing</span> the oscillation of an atomic excited wave packet.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Zhang, Qun; Hepburn, John W</p> <p>2008-08-15</p> <p>We propose a novel method that uses the oscillation of an atomic excited wave packet <span class="hlt">observed</span> through a pump-probe technique to <span class="hlt">accurately</span> determine the zero time delay between a pair of ultrashort laser pulses. This physically based approach provides an easy fix for the intractable problem of synchronizing two different femtosecond laser pulses in a practical experimental environment, especially where an in situ time zero measurement with high accuracy is required.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/29804208','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/29804208"><span>Scan-rescan <span class="hlt">reproducibility</span> of segmental aortic wall shear stress as assessed by phase-specific segmentation with 4D flow MRI in healthy volunteers.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>van der Palen, Roel L F; Roest, Arno A W; van den Boogaard, Pieter J; de Roos, Albert; Blom, Nico A; Westenberg, Jos J M</p> <p>2018-05-26</p> <p>The aim was to investigate scan-rescan <span class="hlt">reproducibility</span> and <span class="hlt">observer</span> variability of segmental aortic 3D systolic wall shear stress (WSS) by phase-specific segmentation with 4D flow MRI in healthy volunteers. Ten healthy volunteers (age 26.5 ± 2.6 years) underwent aortic 4D flow MRI twice. Maximum 3D systolic WSS (WSSmax) and mean 3D systolic WSS (WSSmean) for five thoracic aortic segments over five systolic cardiac phases by phase-specific segmentations were calculated. Scan-rescan analysis and <span class="hlt">observer</span> <span class="hlt">reproducibility</span> analysis were performed. Scan-rescan data showed overall good <span class="hlt">reproducibility</span> for WSSmean (coefficient of variation, COV 10-15%) with moderate-to-strong intraclass correlation coefficient (ICC 0.63-0.89). The variability in WSSmax was high (COV 16-31%) with moderate-to-good ICC (0.55-0.79) for different aortic segments. Intra- and interobserver <span class="hlt">reproducibility</span> was good-to-excellent for regional aortic WSSmax (ICC ≥ 0.78; COV ≤ 17%) and strong-to-excellent for WSSmean (ICC ≥ 0.86; COV ≤ 11%). In general, ascending aortic segments showed more WSSmax/WSSmean variability compared to aortic arch or descending aortic segments for scan-rescan, intraobserver and interobserver comparison. Scan-rescan <span class="hlt">reproducibility</span> was good for WSSmean and moderate for WSSmax for all thoracic aortic segments over multiple systolic phases in healthy volunteers. Intra/interobserver <span class="hlt">reproducibility</span> for segmental WSS assessment was good-to-excellent. Variability of WSSmax is higher and should be taken into account in case of individual follow-up or in comparative rest-stress studies to avoid misinterpretation.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4189414','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4189414"><span>Fast and <span class="hlt">Accurate</span> Exhaled Breath Ammonia Measurement</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Solga, Steven F.; Mudalel, Matthew L.; Spacek, Lisa A.; Risby, Terence H.</p> <p>2014-01-01</p> <p>This exhaled breath ammonia method uses a fast and highly sensitive spectroscopic method known as quartz enhanced photoacoustic spectroscopy (QEPAS) that uses a quantum cascade based laser. The monitor is coupled to a sampler that measures mouth pressure and carbon dioxide. The system is temperature controlled and specifically designed to address the reactivity of this compound. The sampler provides immediate feedback to the subject and the technician on the quality of the breath effort. Together with the quick response time of the monitor, this system is capable of <span class="hlt">accurately</span> measuring exhaled breath ammonia representative of deep lung systemic levels. Because the system is easy to use and produces real time results, it has enabled experiments to identify factors that influence measurements. For example, mouth rinse and oral pH <span class="hlt">reproducibly</span> and significantly affect results and therefore must be controlled. Temperature and mode of breathing are other examples. As our understanding of these factors evolves, error is reduced, and clinical studies become more meaningful. This system is very reliable and individual measurements are inexpensive. The sampler is relatively inexpensive and quite portable, but the monitor is neither. This limits options for some clinical studies and provides rational for future innovations. PMID:24962141</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/28508076','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/28508076"><span>Machine learning of <span class="hlt">accurate</span> energy-conserving molecular force fields.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Chmiela, Stefan; Tkatchenko, Alexandre; Sauceda, Huziel E; Poltavsky, Igor; Schütt, Kristof T; Müller, Klaus-Robert</p> <p>2017-05-01</p> <p>Using conservation of energy-a fundamental property of closed classical and quantum mechanical systems-we develop an efficient gradient-domain machine learning (GDML) approach to construct <span class="hlt">accurate</span> molecular force fields using a restricted number of samples from ab initio molecular dynamics (AIMD) trajectories. The GDML implementation is able to <span class="hlt">reproduce</span> global potential energy surfaces of intermediate-sized molecules with an accuracy of 0.3 kcal mol -1 for energies and 1 kcal mol -1 Å̊ -1 for atomic forces using only 1000 conformational geometries for training. We demonstrate this accuracy for AIMD trajectories of molecules, including benzene, toluene, naphthalene, ethanol, uracil, and aspirin. The challenge of constructing conservative force fields is accomplished in our work by learning in a Hilbert space of vector-valued functions that obey the law of energy conservation. The GDML approach enables quantitative molecular dynamics simulations for molecules at a fraction of cost of explicit AIMD calculations, thereby allowing the construction of efficient force fields with the accuracy and transferability of high-level ab initio methods.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=5419702','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=5419702"><span>Machine learning of <span class="hlt">accurate</span> energy-conserving molecular force fields</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Chmiela, Stefan; Tkatchenko, Alexandre; Sauceda, Huziel E.; Poltavsky, Igor; Schütt, Kristof T.; Müller, Klaus-Robert</p> <p>2017-01-01</p> <p>Using conservation of energy—a fundamental property of closed classical and quantum mechanical systems—we develop an efficient gradient-domain machine learning (GDML) approach to construct <span class="hlt">accurate</span> molecular force fields using a restricted number of samples from ab initio molecular dynamics (AIMD) trajectories. The GDML implementation is able to <span class="hlt">reproduce</span> global potential energy surfaces of intermediate-sized molecules with an accuracy of 0.3 kcal mol−1 for energies and 1 kcal mol−1 Å̊−1 for atomic forces using only 1000 conformational geometries for training. We demonstrate this accuracy for AIMD trajectories of molecules, including benzene, toluene, naphthalene, ethanol, uracil, and aspirin. The challenge of constructing conservative force fields is accomplished in our work by learning in a Hilbert space of vector-valued functions that obey the law of energy conservation. The GDML approach enables quantitative molecular dynamics simulations for molecules at a fraction of cost of explicit AIMD calculations, thereby allowing the construction of efficient force fields with the accuracy and transferability of high-level ab initio methods. PMID:28508076</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/27479329','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/27479329"><span>TRIC: an automated alignment strategy for <span class="hlt">reproducible</span> protein quantification in targeted proteomics.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Röst, Hannes L; Liu, Yansheng; D'Agostino, Giuseppe; Zanella, Matteo; Navarro, Pedro; Rosenberger, George; Collins, Ben C; Gillet, Ludovic; Testa, Giuseppe; Malmström, Lars; Aebersold, Ruedi</p> <p>2016-09-01</p> <p>Next-generation mass spectrometric (MS) techniques such as SWATH-MS have substantially increased the throughput and <span class="hlt">reproducibility</span> of proteomic analysis, but ensuring consistent quantification of thousands of peptide analytes across multiple liquid chromatography-tandem MS (LC-MS/MS) runs remains a challenging and laborious manual process. To produce highly consistent and quantitatively <span class="hlt">accurate</span> proteomics data matrices in an automated fashion, we developed TRIC (http://proteomics.ethz.ch/tric/), a software tool that utilizes fragment-ion data to perform cross-run alignment, consistent peak-picking and quantification for high-throughput targeted proteomics. TRIC reduced the identification error compared to a state-of-the-art SWATH-MS analysis without alignment by more than threefold at constant recall while correcting for highly nonlinear chromatographic effects. On a pulsed-SILAC experiment performed on human induced pluripotent stem cells, TRIC was able to automatically align and quantify thousands of light and heavy isotopic peak groups. Thus, TRIC fills a gap in the pipeline for automated analysis of massively parallel targeted proteomics data sets.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/25982348','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/25982348"><span>Quantification of atrial dynamics using cardiovascular magnetic resonance: inter-study <span class="hlt">reproducibility</span>.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Kowallick, Johannes T; Morton, Geraint; Lamata, Pablo; Jogiya, Roy; Kutty, Shelby; Hasenfuß, Gerd; Lotz, Joachim; Nagel, Eike; Chiribiri, Amedeo; Schuster, Andreas</p> <p>2015-05-17</p> <p>Cardiovascular magnetic resonance (CMR) offers quantification of phasic atrial functions based on volumetric assessment and more recently, on CMR feature tracking (CMR-FT) quantitative strain and strain rate (SR) deformation imaging. Inter-study <span class="hlt">reproducibility</span> is a key requirement for longitudinal studies but has not been defined for CMR-based quantification of left atrial (LA) and right atrial (RA) dynamics. Long-axis 2- and 4-chamber cine images were acquired at 9:00 (Exam A), 9:30 (Exam B) and 14:00 (Exam C) in 16 healthy volunteers. LA and RA reservoir, conduit and contractile booster pump functions were quantified by volumetric indexes as derived from fractional volume changes and by strain and SR as derived from CMR-FT. Exam A and B were compared to assess the inter-study <span class="hlt">reproducibility</span>. Morning and afternoon scans were compared to address possible diurnal variation of atrial function. Inter-study <span class="hlt">reproducibility</span> was within acceptable limits for all LA and RA volumetric, strain and SR parameters. Inter-study <span class="hlt">reproducibility</span> was better for volumetric indexes and strain than for SR parameters and better for LA than for RA dynamics. For the LA, reservoir function showed the best <span class="hlt">reproducibility</span> (intraclass correlation coefficient (ICC) 0.94-0.97, coefficient of variation (CoV) 4.5-8.2%), followed by conduit (ICC 0.78-0.97, CoV 8.2-18.5%) and booster pump function (ICC 0.71-0.95, CoV 18.3-22.7). Similarly, for the RA, <span class="hlt">reproducibility</span> was best for reservoir function (ICC 0.76-0.96, CoV 7.5-24.0%) followed by conduit (ICC 0.67-0.91, CoV 13.9-35.9) and booster pump function (ICC 0.73-0.90, CoV 19.4-32.3). Atrial dynamics were not measurably affected by diurnal variation between morning and afternoon scans. Inter-study <span class="hlt">reproducibility</span> for CMR-based derivation of LA and RA functions is acceptable using either volumetric, strain or SR parameters with LA function showing higher <span class="hlt">reproducibility</span> than RA function assessment. Amongst the different functional components</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4764726','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4764726"><span>Advancements in RNASeqGUI towards a <span class="hlt">Reproducible</span> Analysis of RNA-Seq Experiments</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Russo, Francesco; Righelli, Dario</p> <p>2016-01-01</p> <p>We present the advancements and novelties recently introduced in RNASeqGUI, a graphical user interface that helps biologists to handle and analyse large data collected in RNA-Seq experiments. This work focuses on the concept of <span class="hlt">reproducible</span> research and shows how it has been incorporated in RNASeqGUI to provide <span class="hlt">reproducible</span> (computational) results. The novel version of RNASeqGUI combines graphical interfaces with tools for <span class="hlt">reproducible</span> research, such as literate statistical programming, human readable report, parallel executions, caching, and interactive and web-explorable tables of results. These features allow the user to analyse big datasets in a fast, efficient, and <span class="hlt">reproducible</span> way. Moreover, this paper represents a proof of concept, showing a simple way to develop computational tools for Life Science in the spirit of <span class="hlt">reproducible</span> research. PMID:26977414</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.osti.gov/biblio/22494396-repeatability-reproducibility-intracellular-molar-concentration-assessed-synchrotron-based-ray-fluorescence-microscopy','SCIGOV-STC'); return false;" href="https://www.osti.gov/biblio/22494396-repeatability-reproducibility-intracellular-molar-concentration-assessed-synchrotron-based-ray-fluorescence-microscopy"><span>Repeatability and <span class="hlt">reproducibility</span> of intracellular molar concentration assessed by synchrotron-based x-ray fluorescence microscopy</span></a></p> <p><a target="_blank" href="http://www.osti.gov/search">DOE Office of Scientific and Technical Information (OSTI.GOV)</a></p> <p>Merolle, L., E-mail: lucia.merolle@elettra.eu; Gianoncelli, A.; Malucelli, E., E-mail: emil.malucelli@unibo.it</p> <p>2016-01-28</p> <p>Elemental analysis of biological sample can give information about content and distribution of elements essential for human life or trace elements whose absence is the cause of abnormal biological function or development. However, biological systems contain an ensemble of cells with heterogeneous chemistry and elemental content; therefore, <span class="hlt">accurate</span> characterization of samples with high cellular heterogeneity may only be achieved by analyzing single cells. Powerful methods in molecular biology are abundant, among them X-Ray microscopy based on synchrotron light source has gaining increasing attention thanks to its extremely sensitivity. However, <span class="hlt">reproducibility</span> and repeatability of these measurements is one of the majormore » obstacles in achieving a statistical significance in single cells population analysis. In this study, we compared the elemental content of human colon adenocarcinoma cells obtained by three distinct accesses to synchrotron radiation light.« less</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4905645','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4905645"><span>Excellent Intra and Inter-<span class="hlt">Observer</span> <span class="hlt">Reproducibility</span> of Wrist Circumference Measurements in Obese Children and Adolescents</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Campagna, Giuseppe; Zampetti, Simona; Gallozzi, Alessia; Giansanti, Sara; Chiesa, Claudio; Pacifico, Lucia; Buzzetti, Raffaella</p> <p>2016-01-01</p> <p>In a previous study, we found that wrist circumference, in particular its bone component, was associated with insulin resistance in a population of overweight/obese children. The aim of the present study was to evaluate the intra- and inter-operator variability in wrist circumference measurement in a population of obese children and adolescents. One hundred and two (54 male and 48 female) obese children and adolescents were consecutively enrolled. In all subjects wrist circumferences were measured by two different operators two times to assess intra- and inter-operator variability. Statistical analysis was performed using SAS v.9.4 and JMP v.12. Measurements of wrist circumference showed excellent inter-operator reliability with Intra class Correlation Coefficients (ICC) of 0.96 and ICC of 0.97 for the first and the second measurement, respectively. The intra-operator reliability was, also, very strong with a Concordance Correlation Coefficient (CCC) of 0.98 for both operators. The high <span class="hlt">reproducibility</span> demonstrated in our results suggests that wrist circumference measurement, being safe, non-invasive and repeatable can be easily used in out-patient settings to identify youths with increased risk of insulin-resistance. This can avoid testing the entire population of overweight/obese children for insulin resistance parameters. PMID:27294398</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/28000258','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/28000258"><span>Introduction to the special issue on recentering science: Replication, robustness, and <span class="hlt">reproducibility</span> in psychophysiology.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Kappenman, Emily S; Keil, Andreas</p> <p>2017-01-01</p> <p>In recent years, the psychological and behavioral sciences have increased efforts to strengthen methodological practices and publication standards, with the ultimate goal of enhancing the value and <span class="hlt">reproducibility</span> of published reports. These issues are especially important in the multidisciplinary field of psychophysiology, which yields rich and complex data sets with a large number of <span class="hlt">observations</span>. In addition, the technological tools and analysis methods available in the field of psychophysiology are continually evolving, widening the array of techniques and approaches available to researchers. This special issue presents articles detailing rigorous and systematic evaluations of tasks, measures, materials, analysis approaches, and statistical practices in a variety of subdisciplines of psychophysiology. These articles highlight challenges in conducting and interpreting psychophysiological research and provide data-driven, evidence-based recommendations for overcoming those challenges to produce robust, <span class="hlt">reproducible</span> results in the field of psychophysiology. © 2016 Society for Psychophysiological Research.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4223662','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4223662"><span>Planar heterojunction perovskite solar cells with superior <span class="hlt">reproducibility</span></span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Jeon, Ye-Jin; Lee, Sehyun; Kang, Rira; Kim, Jueng-Eun; Yeo, Jun-Seok; Lee, Seung-Hoon; Kim, Seok-Soon; Yun, Jin-Mun; Kim, Dong-Yu</p> <p>2014-01-01</p> <p>Perovskite solar cells (PeSCs) have been considered one of the competitive next generation power sources. To date, light-to-electric conversion efficiencies have rapidly increased to over 10%, and further improvements are expected. However, the poor device <span class="hlt">reproducibility</span> of PeSCs ascribed to their inhomogeneously covered film morphology has hindered their practical application. Here, we demonstrate high-performance PeSCs with superior <span class="hlt">reproducibility</span> by introducing small amounts of N-cyclohexyl-2-pyrrolidone (CHP) as a morphology controller into N,N-dimethylformamide (DMF). As a result, highly homogeneous film morphology, similar to that achieved by vacuum-deposition methods, as well as a high PCE of 10% and an extremely small performance deviation within 0.14% were achieved. This study represents a method for realizing efficient and <span class="hlt">reproducible</span> planar heterojunction (PHJ) PeSCs through morphology control, taking a major step forward in the low-cost and rapid production of PeSCs by solving one of the biggest problems of PHJ perovskite photovoltaic technology through a facile method. PMID:25377945</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=5224496','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=5224496"><span>Methods to increase <span class="hlt">reproducibility</span> in differential gene expression via meta-analysis</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Sweeney, Timothy E.; Haynes, Winston A.; Vallania, Francesco; Ioannidis, John P.; Khatri, Purvesh</p> <p>2017-01-01</p> <p>Findings from clinical and biological studies are often not <span class="hlt">reproducible</span> when tested in independent cohorts. Due to the testing of a large number of hypotheses and relatively small sample sizes, results from whole-genome expression studies in particular are often not <span class="hlt">reproducible</span>. Compared to single-study analysis, gene expression meta-analysis can improve <span class="hlt">reproducibility</span> by integrating data from multiple studies. However, there are multiple choices in designing and carrying out a meta-analysis. Yet, clear guidelines on best practices are scarce. Here, we hypothesized that studying subsets of very large meta-analyses would allow for systematic identification of best practices to improve <span class="hlt">reproducibility</span>. We therefore constructed three very large gene expression meta-analyses from clinical samples, and then examined meta-analyses of subsets of the datasets (all combinations of datasets with up to N/2 samples and K/2 datasets) compared to a ‘silver standard’ of differentially expressed genes found in the entire cohort. We tested three random-effects meta-analysis models using this procedure. We showed relatively greater <span class="hlt">reproducibility</span> with more-stringent effect size thresholds with relaxed significance thresholds; relatively lower <span class="hlt">reproducibility</span> when imposing extraneous constraints on residual heterogeneity; and an underestimation of actual false positive rate by Benjamini–Hochberg correction. In addition, multivariate regression showed that the accuracy of a meta-analysis increased significantly with more included datasets even when controlling for sample size. PMID:27634930</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/28476308','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/28476308"><span>Magnetic resonance elastography of the pancreas: Measurement <span class="hlt">reproducibility</span> and relationship with age.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Kolipaka, Arunark; Schroeder, Samuel; Mo, Xiaokui; Shah, Zarine; Hart, Phil A; Conwell, Darwin L</p> <p>2017-10-01</p> <p>To determine magnetic resonance elastography (MRE)-derived stiffness of pancreas in healthy volunteers with emphasis on: 1) short term and midterm repeatability; and 2) variance as a function of age. Pancreatic MRE was performed on 22 healthy volunteers (age range:20-64years) in a 3T-scanner. For evaluation of <span class="hlt">reproducibility</span> of stiffness estimates, the scans were repeated per volunteer on the same day (short term) and one month apart (midterm). MRE wave images were analyzed using 3D inversion to estimate the stiffness of overall pancreas and different anatomic regions (i.e., head, neck, body, and tail). Concordance and Spearman correlation tests were performed to determine <span class="hlt">reproducibility</span> of stiffness measurements and relationship to age. A strong concordance correlation (ρ c =0.99; p-value<0.001) was found between short term and midterm repeatability pancreatic stiffness measurements. Additionally, the pancreatic stiffness significantly increased with age with good Spearman correlation coefficient (all ρ>0.81; p<0.001). The older age group (>45yrs) had significantly higher stiffness compared to the younger group (≤45yrs) (p<0.001). No significant difference (p>0.05) in stiffness measurements was <span class="hlt">observed</span> between different anatomical regions of pancreas, except neck stiffness was slightly lower (p<0.012) compared to head and overall pancreas at month 1. MRE-derived pancreatic stiffness measurements are highly <span class="hlt">reproducible</span> in the short and midterm and increase linearly with age in healthy volunteers. Further studies are needed to examine these effects in patients with various pancreatic diseases to understand potential clinical applications. Copyright © 2017 Elsevier Inc. All rights reserved.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.gpo.gov/fdsys/pkg/CFR-2010-title36-vol3/pdf/CFR-2010-title36-vol3-sec903-12.pdf','CFR'); return false;" href="https://www.gpo.gov/fdsys/pkg/CFR-2010-title36-vol3/pdf/CFR-2010-title36-vol3-sec903-12.pdf"><span>36 CFR 903.12 - Fees for furnishing and <span class="hlt">reproducing</span> records.</span></a></p> <p><a target="_blank" href="http://www.gpo.gov/fdsys/browse/collectionCfr.action?selectedYearFrom=2010&page.go=Go">Code of Federal Regulations, 2010 CFR</a></p> <p></p> <p>2010-07-01</p> <p>... 36 Parks, Forests, and Public Property 3 2010-07-01 2010-07-01 false Fees for furnishing and <span class="hlt">reproducing</span> records. 903.12 Section 903.12 Parks, Forests, and Public Property PENNSYLVANIA AVENUE DEVELOPMENT CORPORATION PRIVACY ACT § 903.12 Fees for furnishing and <span class="hlt">reproducing</span> records. (a) Individuals will not be...</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4903092','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4903092"><span><span class="hlt">Reproducibility</span> of Macular Pigment Optical Density Measurement by Two-wave Length Auto-fluorescence in a Clinical Setting</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>You, Qi-Sheng; Bartsch, Dirk-Uwe G.; Espina, Mark; Alam, Mostafa; Camacho, Natalia; Mendoza, Nadia; Freeman, William</p> <p>2015-01-01</p> <p>Purpose Macular pigment, composed of lutein, zeaxanthin, and meso-zeaxanthin, is postulated to protect against age-related macular degeneration (AMD), likely due to filtering blue light and its antioxidant properties. Macular pigment optical density (MPOD) is reported to be associated with macular function evaluated by visual acuity and multifocal electroretinogram. Given the importance of macular pigment, reliable and <span class="hlt">accurate</span> measurement methods are important. The main purpose of current study is to determine the <span class="hlt">reproducibility</span> of MPOD measurement by two-wave length auto-fluorescence method using scanning laser ophthalmoscopy. Methods Sixty eight eyes of 39 persons were enrolled in the study, including 11 normal eyes, 16 eyes with wet AMD, 16 eyes with dry AMD, 11 eyes with macular edema due to diabetic mellitus, branch retinal vein occlusion or macular telangiectasia and 14 eyes with tractional maculopathy including vitreomacular traction, epiretinal membrane or macular hole. MPOD was measured with a two-wavelength (488 and 514 nm) auto-fluorescence method with the Spectralis HRA+OCT after pupil dilation. The measurement was repeated for each eye 10 minutes later. The Analysis of variance (ANOVA) and Bland-Altman plot were used to assess the <span class="hlt">reproducibility</span> between the two measurements. Results The mean MPOD at eccentricities of 1° and 2° was 0.36±0.17 (range: 0.04–0.69) and 0.15±0.08(range: −0.03, 0.35) for the first measurement and 0.35±0.17 (range: 0.02, 0.68) and 0.15±0.08 (range: −0.01, 0.33) for the second measurement respectively. The difference between the two measurements was not statistically significant, and the Bland-Altman plot showed 7.4% and 5.9% points outside the 95% limits of agreement, indicating an overall excellent <span class="hlt">reproducibility</span>. Similarly, there is no significant difference between the first and second measurements of MPOD volume within eccentricities of 1°, 2° and 6° radius, and the Bland-Altman plot showed 8.8%, 2.9% and</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/26159429','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/26159429"><span>Histopathological grading of breast ductal carcinoma in situ: validation of a web-based survey through intra-<span class="hlt">observer</span> <span class="hlt">reproducibility</span> analysis.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Schuh, Fernando; Biazús, Jorge Villanova; Resetkova, Erika; Benfica, Camila Zanella; Ventura, Alessandra de Freitas; Uchoa, Diego; Graudenz, Márcia; Edelweiss, Maria Isabel Albano</p> <p>2015-07-10</p> <p>Histopathological grading diagnosis of ductal carcinoma in situ (DCIS) of the breast may be very difficult even for experts, and it is important for therapeutic decisions. The challenge may be due to the inaccurate and/or subjective application of the diagnosis criteria. The aim of this study was to investigate the intra-<span class="hlt">observer</span> agreement between a traditional method and a developed web-based questionnaire for scoring breast DCIS. A cross-sectional study was carried out to evaluate the diagnostic agreement of an electronic questionnaire and its point scoring system with the subjective reading of digital images for 3 different DCIS grading systems: Holland, Van Nuys and modified Black nuclear grade system. Three pathologists analyzed the same set of digitized images from 43 DCIS cases using two different web-based programs. In the first phase, they accessed a website with a newly created questionnaire and scoring system developed to allow the determination of the histological grade of the cases. After at least 6 months, the pathologists read again the same images, but without the help of the questionnaire, indicating subjectively the diagnoses. The intra-<span class="hlt">observer</span> agreement analysis was employed to validate this innovative web-based survey. Overall, diagnostic <span class="hlt">reproducibility</span> was similar for all histologic grading classification systems, with kappa values of 0.57 ± 0.10, 0.67 ± 0.09 and 0.67 ± 0.09 for Holland, Van Nuys classification and modified Black nuclear grade system respectively. Only two 2-step diagnostic disagreements were found, one for Holland and another for Van Nuys. Both cases were superestimated by the web-based survey. The diagnostic agreement between the web-based questionnaire and a traditional method, both using digital images, is moderate to good for Holland, Van Nuys and modified Black nuclear grade system. The use of a scoring point system does not appear to pose a major risk of presenting large (2-step) diagnostic</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_14");'>14</a></li> <li><a href="#" onclick='return showDiv("page_15");'>15</a></li> <li class="active"><span>16</span></li> <li><a href="#" onclick='return showDiv("page_17");'>17</a></li> <li><a href="#" onclick='return showDiv("page_18");'>18</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_16 --> <div id="page_17" class="hiddenDiv"> <div class="row"> <div class="col-sm-12"> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_15");'>15</a></li> <li><a href="#" onclick='return showDiv("page_16");'>16</a></li> <li class="active"><span>17</span></li> <li><a href="#" onclick='return showDiv("page_18");'>18</a></li> <li><a href="#" onclick='return showDiv("page_19");'>19</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div> </div> <div class="row"> <div class="col-sm-12"> <ol class="result-class" start="321"> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/7871359','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/7871359"><span>Microbiologic tests in epidemiologic studies: are they <span class="hlt">reproducible</span>?</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Aass, A M; Preus, H R; Zambon, J J; Gjermo, P</p> <p>1994-12-01</p> <p>Microbiologic assessments are often included in longitudinal studies to elucidate the significance of the association of certain Gram-negative bacteria and the development of periodontal diseases. In such studies, the reliability of methods is crucial. There are several methods to identify putative pathogens, and some of them are commercially available. The purpose of the present study was to compare the <span class="hlt">reproducibility</span> of four different methods for detecting Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis, and Prevotella intermedia in order to evaluate their usefulness in epidemiologic studies. The test panel consisted of 10 young subjects and 10 adult periodontitis patients. Subgingival plaque was sampled from sites showing bone loss and "healthy" control sites. The four different methods for detecting the target bacteria were 1) cultivation, 2) Evalusite (a chair-side kit based on ELISA), 3) OmniGene, Inc, based on DNA probes, and 4) indirect immunofluorescence (IIF). The test procedure was repeated after a 1-wk interval and was performed by one examiner. Sites reported to be positive for a microorganism by any of the four methods at one or both examinations were considered to be positive for that organism and included in the analysis. The <span class="hlt">reproducibility</span> of the four methods was low. The IIF and the cultivation methods showed somewhat higher <span class="hlt">reproducibility</span> than did the commercial systems. A second test was done for Evalusite, three paper points for sampling being used instead of one as described in the manual. The <span class="hlt">reproducibility</span> of the second test was improved, indicating that the detection level of the system may influence the reliability.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2017HESS...21.3597F','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2017HESS...21.3597F"><span><span class="hlt">Reproducing</span> an extreme flood with uncertain post-event information</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Fuentes-Andino, Diana; Beven, Keith; Halldin, Sven; Xu, Chong-Yu; Reynolds, José Eduardo; Di Baldassarre, Giuliano</p> <p>2017-07-01</p> <p>Studies for the prevention and mitigation of floods require information on discharge and extent of inundation, commonly unavailable or uncertain, especially during extreme events. This study was initiated by the devastating flood in Tegucigalpa, the capital of Honduras, when Hurricane Mitch struck the city. In this study we hypothesized that it is possible to estimate, in a trustworthy way considering large data uncertainties, this extreme 1998 flood discharge and the extent of the inundations that followed from a combination of models and post-event measured data. Post-event data collected in 2000 and 2001 were used to estimate discharge peaks, times of peak, and high-water marks. These data were used in combination with rain data from two gauges to drive and constrain a combination of well-known modelling tools: TOPMODEL, Muskingum-Cunge-Todini routing, and the LISFLOOD-FP hydraulic model. Simulations were performed within the generalized likelihood uncertainty estimation (GLUE) uncertainty-analysis framework. The model combination predicted peak discharge, times of peaks, and more than 90 % of the <span class="hlt">observed</span> high-water marks within the uncertainty bounds of the evaluation data. This allowed an inundation likelihood map to be produced. <span class="hlt">Observed</span> high-water marks could not be <span class="hlt">reproduced</span> at a few locations on the floodplain. Identifications of these locations are useful to improve model set-up, model structure, or post-event data-estimation methods. Rainfall data were of central importance in simulating the times of peak and results would be improved by a better spatial assessment of rainfall, e.g. from radar data or a denser rain-gauge network. Our study demonstrated that it was possible, considering the uncertainty in the post-event data, to reasonably <span class="hlt">reproduce</span> the extreme Mitch flood in Tegucigalpa in spite of no hydrometric gauging during the event. The method proposed here can be part of a Bayesian framework in which more events can be added into the analysis as</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3707959','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3707959"><span>Dermoscopic patterns of Melanoma Metastases: inter-<span class="hlt">observer</span> consistency and accuracy for metastases recognition</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Costa, J.; Ortiz-Ibañez, K.; Salerni, G.; Borges, V.; Carrera, C.; Puig, S.; Malvehy, J.</p> <p>2013-01-01</p> <p>Background Cutaneous metastases of malignant melanoma (CMMM) can be confused with other skin lesions. Dermoscopy could be helpful in the differential diagnosis. Objective To describe distinctive dermoscopic patterns that are <span class="hlt">reproducible</span> and <span class="hlt">accurate</span> in the identification of CMMM Methods A retrospective study of 146 dermoscopic images of CMMM from 42 patients attending a Melanoma Unit between 2002 and 2009 was performed. Firstly, two investigators established six dermoscopic patterns for CMMM. The correlation of 73 dermoscopic images with their distinctive patterns was assessed by four independent dermatologists to evaluate the <span class="hlt">reproducibility</span> in the identification of the patterns. Finally, 163 dermoscopic images, including CMMM and non-metastatic lesions, were evaluated by the same four dermatologists to calculate the accuracy of the patterns in the recognition of CMMM. Results Five CMMM dermoscopic patterns had a good inter-<span class="hlt">observer</span> agreement (blue nevus-like, nevus-like, angioma like, vascular and unspecific). When CMMM were classified according to these patterns, correlation between the investigators and the four dermatologists ranged from κ = 0.56 to 0.7. 71 CMMM, 16 angiomas, 22 blue nevus, 15 malignant melanoma, 11 seborrheic keratosis, 15 melanocytic nevus with globular pattern and 13 pink lesions with vascular pattern were evaluated according to the previously described CMMM dermoscopy patterns, showing an overall sensitivity of 68% (between 54.9–76%) and a specificity of 81% (between 68.6–93.5) for the diagnosis of CMMM. Conclusion Five dermoscopic patterns of CMMM with good inter-<span class="hlt">observer</span> agreement obtained a high sensitivity and specificity in the diagnosis of metastasis, the accuracy varying according to the experience of the <span class="hlt">observer</span>. PMID:23495915</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/26703300','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/26703300"><span>Repeatability and <span class="hlt">reproducibility</span> of ocular biometry using a new noncontact optical low-coherence interferometer.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Huang, Jinhai; Savini, Giacomo; Wu, Fan; Yu, Xinxin; Yang, Jing; Yu, Ayong; Yu, Ye; Wang, Qinmei</p> <p>2015-10-01</p> <p>To assess the precision of ocular biometry with a new noncontact optical low-coherence interferometer (Aladdin) in healthy subjects and patients with cataracts. Eye Hospital of Wenzhou Medical University, Wenzhou, China. <span class="hlt">Observational</span> cross-sectional study. Eyes from healthy subjects and eyes from patients with cataracts were examined with the new interferometer. Axial length (AL), anterior chamber depth (ACD), keratometry (K), and white-to-white (WTW) values were measured by 2 operators. The test-retest repeatability, coefficient of variation (CoV), and intraclass correlation coefficient (ICC) were calculated to evaluate intraoperator repeatability. Different-operator comparison was analyzed with paired t tests and Bland-Altman plots to assess interoperator <span class="hlt">reproducibility</span>. Ninety-eight people were enrolled for this study, of which 52 eyes were from healthy subjects and 46 eyes were from patients with cataracts. The AL was the most repeatable and <span class="hlt">reproducible</span> parameter. The ACD, K values, and WTW measurements were highly repeatable in healthy subjects with CoV less than 0.89% and ICC more than 0.94. However, in patients with cataracts, high repeatability could only be <span class="hlt">observed</span> for AL, ACD, and K values, whereas WTW measurement had test-retest repeatability of 0.80 mm and an ICC of 0.795. Bland-Altman analysis also showed good agreement between the 2 operators for ocular component measurements, except that the WTW in patients with cataracts had wider 95% limits of agreement (range -0.88 to 0.95 mm). The new biometer showed excellent intraoperator repeatability and interoperator <span class="hlt">reproducibility</span> for AL, ACD, and K values measurements in both groups. The precision of WTW measurements was lower in patients with cataracts. No author has a financial or proprietary interest in any material or method mentioned. Copyright © 2015 ASCRS and ESCRS. Published by Elsevier Inc. All rights reserved.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/23326504','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/23326504"><span>Learning by <span class="hlt">observation</span>: insights from Williams syndrome.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Foti, Francesca; Menghini, Deny; Mandolesi, Laura; Federico, Francesca; Vicari, Stefano; Petrosini, Laura</p> <p>2013-01-01</p> <p><span class="hlt">Observing</span> another person performing a complex action accelerates the <span class="hlt">observer</span>'s acquisition of the same action and limits the time-consuming process of learning by trial and error. <span class="hlt">Observational</span> learning makes an interesting and potentially important topic in the developmental domain, especially when disorders are considered. The implications of studies aimed at clarifying whether and how this form of learning is spared by pathology are manifold. We focused on a specific population with learning and intellectual disabilities, the individuals with Williams syndrome. The performance of twenty-eight individuals with Williams syndrome was compared with that of mental age- and gender-matched thirty-two typically developing children on tasks of learning of a visuo-motor sequence by <span class="hlt">observation</span> or by trial and error. Regardless of the learning modality, acquiring the correct sequence involved three main phases: a detection phase, in which participants discovered the correct sequence and learned how to perform the task; an exercise phase, in which they <span class="hlt">reproduced</span> the sequence until performance was error-free; an automatization phase, in which by repeating the error-free sequence they became <span class="hlt">accurate</span> and speedy. Participants with Williams syndrome beneficiated of <span class="hlt">observational</span> training (in which they <span class="hlt">observed</span> an actor detecting the visuo-motor sequence) in the detection phase, while they performed worse than typically developing children in the exercise and automatization phases. Thus, by exploiting competencies learned by <span class="hlt">observation</span>, individuals with Williams syndrome detected the visuo-motor sequence, putting into action the appropriate procedural strategies. Conversely, their impaired performances in the exercise phases appeared linked to impaired spatial working memory, while their deficits in automatization phases to deficits in processes increasing efficiency and speed of the response. Overall, <span class="hlt">observational</span> experience was advantageous for acquiring competencies</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2001SPIE.4322..158L','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2001SPIE.4322..158L"><span>Automatic, <span class="hlt">accurate</span>, and <span class="hlt">reproducible</span> segmentation of the brain and cerebro-spinal fluid in T1-weighted volume MRI scans and its application to serial cerebral and intracranial volumetry</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Lemieux, Louis</p> <p>2001-07-01</p> <p>A new fully automatic algorithm for the segmentation of the brain and cerebro-spinal fluid (CSF) from T1-weighted volume MRI scans of the head was specifically developed in the context of serial intra-cranial volumetry. The method is an extension of a previously published brain extraction algorithm. The brain mask is used as a basis for CSF segmentation based on morphological operations, automatic histogram analysis and thresholding. Brain segmentation is then obtained by iterative tracking of the brain-CSF interface. Grey matter (GM), white matter (WM) and CSF volumes are calculated based on a model of intensity probability distribution that includes partial volume effects. Accuracy was assessed using a digital phantom scan. <span class="hlt">Reproducibility</span> was assessed by segmenting pairs of scans from 20 normal subjects scanned 8 months apart and 11 patients with epilepsy scanned 3.5 years apart. Segmentation accuracy as measured by overlap was 98% for the brain and 96% for the intra-cranial tissues. The volume errors were: total brain (TBV): -1.0%, intra-cranial (ICV):0.1%, CSF: +4.8%. For repeated scans, matching resulted in improved <span class="hlt">reproducibility</span>. In the controls, the coefficient of reliability (CR) was 1.5% for the TVB and 1.0% for the ICV. In the patients, the Cr for the ICV was 1.2%.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/12390670','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/12390670"><span>Testing high SPF sunscreens: a demonstration of the accuracy and <span class="hlt">reproducibility</span> of the results of testing high SPF formulations by two methods and at different testing sites.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Agin, Patricia Poh; Edmonds, Susan H</p> <p>2002-08-01</p> <p>The goals of this study were (i) to demonstrate that existing and widely used sun protection factor (SPF) test methodologies can produce <span class="hlt">accurate</span> and <span class="hlt">reproducible</span> results for high SPF formulations and (ii) to provide data on the number of test-subjects needed, the variability of the data, and the appropriate exposure increments needed for testing high SPF formulations. Three high SPF formulations were tested, according to the Food and Drug Administration's (FDA) 1993 tentative final monograph (TFM) 'very water resistant' test method and/or the 1978 proposed monograph 'waterproof' test method, within one laboratory. A fourth high SPF formulation was tested at four independent SPF testing laboratories, using the 1978 waterproof SPF test method. All laboratories utilized xenon arc solar simulators. The data illustrate that the testing conducted within one laboratory, following either the 1978 proposed or the 1993 TFM SPF test method, was able to <span class="hlt">reproducibly</span> determine the SPFs of the formulations tested, using either the statistical analysis method in the proposed monograph or the statistical method described in the TFM. When one formulation was tested at four different laboratories, the anticipated variation in the data owing to the equipment and other operational differences was minimized through the use of the statistical method described in the 1993 monograph. The data illustrate that either the 1978 proposed monograph SPF test method or the 1993 TFM SPF test method can provide <span class="hlt">accurate</span> and <span class="hlt">reproducible</span> results for high SPF formulations. Further, these results can be achieved with panels of 20-25 subjects with an acceptable level of variability. Utilization of the statistical controls from the 1993 sunscreen monograph can help to minimize lab-to-lab variability for well-formulated products.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=505311','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=505311"><span><span class="hlt">Reproducibility</span> of corneal astigmatism measurements with a hand held keratometer in preschool children.</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Harvey, E M; Miller, J M; Dobson, V</p> <p>1995-01-01</p> <p>AIMS--To evaluate the overall accuracy and <span class="hlt">reproducibility</span> of the Alcon portable autokeratometer (PAK) measurements in infants and young children. METHODS--The accuracy of the Alcon PAK in measuring toric reference surfaces (1, 3, 5, and 7 D) under various suboptimal measurement conditions was assessed, and the <span class="hlt">reproducibility</span> of PAK measurements of corneal astigmatism in newborn infants (n = 5), children (n = 19, age 3-5 years), and adults (n = 14) was evaluated. RESULTS--Measurements of toric reference surfaces indicated (a) no significant effect of distance (17-30 mm) on accuracy of measurements, (b) no systematic relation between amount of toricity and accuracy of measurements, (c) no systematic relation between angle of measurement and accuracy, (d) no difference in accuracy of measurements when the PAK is hand held in comparison with when it is mounted, (e) no difference in accuracy of measurements when axis of toricity is oriented obliquely than when it is oriented horizontally, with respect to the PAK, and (f) a small positive bias (+0.16 D) in measurement of spherical equivalent. The PAK did not prove useful for screening newborns. However, measurements were successfully obtained from 18/19 children and 14/14 adults. There was no significant difference in median measurement deviation (deviation of a subject's five measurements from his/her mean) between children (0.21 D) and adults (0.13 D). CONCLUSIONS--The PAK produces <span class="hlt">accurate</span> measurements of surface curvature under a variety of suboptimal conditions. Variability of PAK measurements in preschool children is small enough to suggest that it would be useful for screening for corneal astigmatism in young children. PMID:8534668</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/21302997','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/21302997"><span>A synthesis approach for <span class="hlt">reproducing</span> the response of aircraft panels to a turbulent boundary layer excitation.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Bravo, Teresa; Maury, Cédric</p> <p>2011-01-01</p> <p>Random wall-pressure fluctuations due to the turbulent boundary layer (TBL) are a feature of the air flow over an aircraft fuselage under cruise conditions, creating undesirable effects such as cabin noise annoyance. In order to test potential solutions to reduce the TBL-induced noise, a cost-efficient alternative to in-flight or wind-tunnel measurements involves the laboratory simulation of the response of aircraft sidewalls to high-speed subsonic TBL excitation. Previously published work has shown that TBL simulation using a near-field array of loudspeakers is only feasible in the low frequency range due to the rapid decay of the spanwise correlation length with frequency. This paper demonstrates through theoretical criteria how the wavenumber filtering capabilities of the radiating panel reduces the number of sources required, thus dramatically enlarging the frequency range over which the response of the TBL-excited panel is <span class="hlt">accurately</span> <span class="hlt">reproduced</span>. Experimental synthesis of the panel response to high-speed TBL excitation is found to be feasible over the hydrodynamic coincidence frequency range using a reduced set of near-field loudspeakers driven by optimal signals. Effective methodologies are proposed for an <span class="hlt">accurate</span> reproduction of the TBL-induced sound power radiated by the panel into a free-field and when coupled to a cavity.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://ntrs.nasa.gov/search.jsp?R=19890026705&hterms=platinum&qs=Ntx%3Dmode%2Bmatchall%26Ntk%3DAll%26N%3D0%26No%3D40%26Ntt%3Dplatinum','NASA-TRS'); return false;" href="https://ntrs.nasa.gov/search.jsp?R=19890026705&hterms=platinum&qs=Ntx%3Dmode%2Bmatchall%26Ntk%3DAll%26N%3D0%26No%3D40%26Ntt%3Dplatinum"><span><span class="hlt">Accurate</span> energy levels for singly ionized platinum (Pt II)</span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Reader, Joseph; Acquista, Nicolo; Sansonetti, Craig J.; Engleman, Rolf, Jr.</p> <p>1988-01-01</p> <p>New <span class="hlt">observations</span> of the spectrum of Pt II have been made with hollow-cathode lamps. The region from 1032 to 4101 A was <span class="hlt">observed</span> photographically with a 10.7-m normal-incidence spectrograph. The region from 2245 to 5223 A was <span class="hlt">observed</span> with a Fourier-transform spectrometer. Wavelength measurements were made for 558 lines. The uncertainties vary from 0.0005 to 0.004 A. From these measurements and three parity-forbidden transitions in the infrared, <span class="hlt">accurate</span> values were determined for 28 even and 72 odd energy levels of Pt II.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/25824529','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/25824529"><span>Local cooling and warming effects of forests based on satellite <span class="hlt">observations</span>.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Li, Yan; Zhao, Maosheng; Motesharrei, Safa; Mu, Qiaozhen; Kalnay, Eugenia; Li, Shuangcheng</p> <p>2015-03-31</p> <p>The biophysical effects of forests on climate have been extensively studied with climate models. However, models cannot <span class="hlt">accurately</span> <span class="hlt">reproduce</span> local climate effects due to their coarse spatial resolution and uncertainties, and field <span class="hlt">observations</span> are valuable but often insufficient due to their limited coverage. Here we present new evidence acquired from global satellite data to analyse the biophysical effects of forests on local climate. Results show that tropical forests have a strong cooling effect throughout the year; temperate forests show moderate cooling in summer and moderate warming in winter with net cooling annually; and boreal forests have strong warming in winter and moderate cooling in summer with net warming annually. The spatiotemporal cooling or warming effects are mainly driven by the two competing biophysical effects, evapotranspiration and albedo, which in turn are strongly influenced by rainfall and snow. Implications of our satellite-based study could be useful for informing local forestry policies.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2015PEPS....2...42S','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2015PEPS....2...42S"><span>Ensemble experiments using a nested LETKF system to <span class="hlt">reproduce</span> intense vortices associated with tornadoes of 6 May 2012 in Japan</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Seko, Hiromu; Kunii, Masaru; Yokota, Sho; Tsuyuki, Tadashi; Miyoshi, Takemasa</p> <p>2015-12-01</p> <p>Experiments simulating intense vortices associated with tornadoes that occurred on 6 May 2012 on the Kanto Plain, Japan, were performed with a nested local ensemble transform Kalman filter (LETKF) system. Intense vortices were <span class="hlt">reproduced</span> by downscale experiments with a 12-member ensemble in which the initial conditions were obtained from the nested LETKF system analyses. The downscale experiments successfully generated intense vortices in three regions similar to the <span class="hlt">observed</span> vortices, whereas only one tornado was <span class="hlt">reproduced</span> by a deterministic forecast. The intense vorticity of the strongest tornado, which was <span class="hlt">observed</span> in the southernmost region, was successfully <span class="hlt">reproduced</span> by 10 of the 12 ensemble members. An examination of the results of the ensemble downscale experiments showed that the duration of intense vorticities tended to be longer when the vertical shear of the horizontal wind was larger and the lower airflow was more humid. Overall, the study results show that ensemble forecasts have the following merits: (1) probabilistic forecasts of the outbreak of intense vortices associated with tornadoes are possible; (2) the miss rate of outbreaks should decrease; and (3) environmental factors favoring outbreaks can be obtained by comparing the multiple possible scenarios of the ensemble forecasts.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2017EGUGA..19.9484S','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2017EGUGA..19.9484S"><span><span class="hlt">Reproducibility</span> in cyclostratigraphy: initiating an intercomparison project</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Sinnesael, Matthias; De Vleeschouwer, David; Zeeden, Christian; Claeys, Philippe</p> <p>2017-04-01</p> <p>The study of astronomical climate forcing and the application of cyclostratigraphy have experienced a spectacular growth over the last decades. In the field of cyclostratigraphy a broad range in methodological approaches exist. However, comparative study between the different approaches is lacking. Different cases demand different approaches, but with the growing importance of the field, questions arise about <span class="hlt">reproducibility</span>, uncertainties and standardization of results. The radioisotopic dating community, in particular, has done far-reaching efforts to improve <span class="hlt">reproducibility</span> and intercomparison of radioisotopic dates and their errors. To satisfy this need in cyclostratigraphy, we initiate a comparable framework for the community. The aims are to investigate and quantify <span class="hlt">reproducibility</span> of, and uncertainties related to cyclostratigraphic studies and to provide a platform to discuss the merits and pitfalls of different methodologies, and their applicabilities. With this poster, we ask the feedback from the community on how to design this comparative framework in a useful, meaningful and productive manner. In parallel, we would like to discuss how <span class="hlt">reproducibility</span> should be tested and what uncertainties should stand for in cyclostratigraphy. On the other hand, we intend to trigger interest for a cyclostratigraphic intercomparison project. This intercomparison project would imply the analysis of artificial and genuine geological records by individual researchers. All participants would be free to determine their method of choice. However, a handful of criterions will be required for an outcome to be comparable. The different results would be compared (e.g. during a workshop or a special session), and the lessons learned from the comparison could potentially be reported in a review paper. The aim of an intercomparison project is not to rank the different methods according to their merits, but to get insight into which specific methods are most suitable for which</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/28464561','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/28464561"><span>Progress toward openness, transparency, and <span class="hlt">reproducibility</span> in cognitive neuroscience.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Gilmore, Rick O; Diaz, Michele T; Wyble, Brad A; Yarkoni, Tal</p> <p>2017-05-01</p> <p>Accumulating evidence suggests that many findings in psychological science and cognitive neuroscience may prove difficult to <span class="hlt">reproduce</span>; statistical power in brain imaging studies is low and has not improved recently; software errors in analysis tools are common and can go undetected for many years; and, a few large-scale studies notwithstanding, open sharing of data, code, and materials remain the rare exception. At the same time, there is a renewed focus on <span class="hlt">reproducibility</span>, transparency, and openness as essential core values in cognitive neuroscience. The emergence and rapid growth of data archives, meta-analytic tools, software pipelines, and research groups devoted to improved methodology reflect this new sensibility. We review evidence that the field has begun to embrace new open research practices and illustrate how these can begin to address problems of <span class="hlt">reproducibility</span>, statistical power, and transparency in ways that will ultimately accelerate discovery. © 2017 New York Academy of Sciences.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/27420733','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/27420733"><span>The quest for improved <span class="hlt">reproducibility</span> in MALDI mass spectrometry.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>O'Rourke, Matthew B; Djordjevic, Steven P; Padula, Matthew P</p> <p>2018-03-01</p> <p><span class="hlt">Reproducibility</span> has been one of the biggest hurdles faced when attempting to develop quantitative protocols for MALDI mass spectrometry. The heterogeneous nature of sample recrystallization has made automated sample acquisition somewhat "hit and miss" with manual intervention needed to ensure that all sample spots have been analyzed. In this review, we explore the last 30 years of literature and anecdotal evidence that has attempted to address and improve <span class="hlt">reproducibility</span> in MALDI MS. Though many methods have been attempted, we have discovered a significant publication history surrounding the use of nitrocellulose as a substrate to improve homogeneity of crystal formation and therefore <span class="hlt">reproducibility</span>. We therefore propose that this is the most promising avenue of research for developing a comprehensive and universal preparation protocol for quantitative MALDI MS analysis. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 37:217-228, 2018. © 2016 Wiley Periodicals, Inc.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/26168127','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/26168127"><span>An Open, Large-Scale, Collaborative Effort to Estimate the <span class="hlt">Reproducibility</span> of Psychological Science.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p></p> <p>2012-11-01</p> <p><span class="hlt">Reproducibility</span> is a defining feature of science. However, because of strong incentives for innovation and weak incentives for confirmation, direct replication is rarely practiced or published. The <span class="hlt">Reproducibility</span> Project is an open, large-scale, collaborative effort to systematically examine the rate and predictors of <span class="hlt">reproducibility</span> in psychological science. So far, 72 volunteer researchers from 41 institutions have organized to openly and transparently replicate studies published in three prominent psychological journals in 2008. Multiple methods will be used to evaluate the findings, calculate an empirical rate of replication, and investigate factors that predict <span class="hlt">reproducibility</span>. Whatever the result, a better understanding of <span class="hlt">reproducibility</span> will ultimately improve confidence in scientific methodology and findings. © The Author(s) 2012.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/27255286','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/27255286"><span>The Road to <span class="hlt">Reproducibility</span> in Animal Research.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Jilka, Robert L</p> <p>2016-07-01</p> <p><span class="hlt">Reproducibility</span> of research findings is the hallmark of scientific advance. However, the recently noted lack of <span class="hlt">reproducibility</span> and transparency of published research using animal models of human biology and disease has alarmed funders, scientists, and the public. Improved reporting of methodology and better use of statistical tools are needed to enhance the quality and utility of published research. Reporting guidelines like Animal Research: Reporting In Vivo Experiments (ARRIVE) have been devised to achieve these goals, but most biomedical research journals, including the JBMR, have not been able to obtain high compliance. Cooperative efforts among authors, reviewers and editors-empowered by increased awareness of their responsibilities, and enabled by user-friendly guidelines-are needed to solve this problem. © 2016 American Society for Bone and Mineral Research. © 2016 American Society for Bone and Mineral Research.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/18372415','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/18372415"><span><span class="hlt">Reproducibility</span>, interrater agreement, and age-related changes of fractional anisotropy measures at 3T in healthy subjects: effect of the applied b-value.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Bisdas, S; Bohning, D E; Besenski, N; Nicholas, J S; Rumboldt, Z</p> <p>2008-06-01</p> <p>There is no <span class="hlt">reproducibility</span> study of fractional anisotropy (FA) measurements at 3T using regions of interest (ROIs). Our purpose was to establish the extent and statistical significance of the interrater variability, the variability <span class="hlt">observed</span> with 2 different b-values, and in 2 separate scanning sessions. Twelve healthy volunteers underwent MR imaging twice. MR imaging was performed on a 3T unit, and FA maps were analyzed independently by 2 <span class="hlt">observers</span> using ROIs positioned in the corpus callosum, internal capsules, corticospinal tracts, and right thalamus. Changes in FA values (x10(3)) measured with 2 b-values (700 and 1000 s/mm(2)), age-related differences, interobserver agreement, and measurement <span class="hlt">reproducibility</span> were assessed. In the right internal capsule genu (FA = 702/728; b = 1000/700 s/mm(2)) and the left anterior limb of the internal capsule (AIC; FA = 617/745; b = 1000/700 s/mm(2)), the FA values were significantly different between the 2 b-values (P = .02 and .05, respectively). Significant age-related differences in FA were <span class="hlt">observed</span> in the genu of the corpus callosum and in the left AIC. Interrater measurements showed fair-to-moderate agreement for most anatomic structures. The lowest significant change for a single subject regarding any FA values between the 2 sessions was in the corpus callosum (4%), whereas the highest one was in the corticospinal tracts (27%). The Bland-Altman plot analysis showed that the 1000-s/mm(2) b-value gave satisfactorily <span class="hlt">reproducible</span> measurements equally good or better than the 700-s/mm(2) b-value. The <span class="hlt">reproducibility</span> of FA estimates using ROIs was satisfactory. Measurements with a b-value at 1000 s/mm(2) showed superior <span class="hlt">reproducibility</span> in most anatomic locations.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://hdl.handle.net/2060/19790003985','NASA-TRS'); return false;" href="http://hdl.handle.net/2060/19790003985"><span><span class="hlt">Reproducibility</span> of structural strength and stiffness for graphite-epoxy aircraft spoilers</span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Howell, W. E.; Reese, C. D.</p> <p>1978-01-01</p> <p>Structural strength <span class="hlt">reproducibility</span> of graphite epoxy composite spoilers for the Boeing 737 aircraft was evaluated by statically loading fifteen spoilers to failure at conditions simulating aerodynamic loads. Spoiler strength and stiffness data were statistically modeled using a two parameter Weibull distribution function. Shape parameter values calculated for the composite spoiler strength and stiffness were within the range of corresponding shape parameter values calculated for material property data of composite laminates. This agreement showed that <span class="hlt">reproducibility</span> of full scale component structural properties was within the <span class="hlt">reproducibility</span> range of data from material property tests.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/26338484','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/26338484"><span><span class="hlt">Reproducibility</span> Between Brain Uptake Ratio Using Anatomic Standardization and Patlak-Plot Methods.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Shibutani, Takayuki; Onoguchi, Masahisa; Noguchi, Atsushi; Yamada, Tomoki; Tsuchihashi, Hiroko; Nakajima, Tadashi; Kinuya, Seigo</p> <p>2015-12-01</p> <p>The Patlak-plot and conventional methods of determining brain uptake ratio (BUR) have some problems with <span class="hlt">reproducibility</span>. We formulated a method of determining BUR using anatomic standardization (BUR-AS) in a statistical parametric mapping algorithm to improve <span class="hlt">reproducibility</span>. The objective of this study was to demonstrate the inter- and intraoperator <span class="hlt">reproducibility</span> of mean cerebral blood flow as determined using BUR-AS in comparison to the conventional-BUR (BUR-C) and Patlak-plot methods. The images of 30 patients who underwent brain perfusion SPECT were retrospectively used in this study. The images were reconstructed using ordered-subset expectation maximization and processed using an automatic quantitative analysis for cerebral blood flow of ECD tool. The mean SPECT count was calculated from axial basal ganglia slices of the normal side (slices 31-40) drawn using a 3-dimensional stereotactic region-of-interest template after anatomic standardization. The mean cerebral blood flow was calculated from the mean SPECT count. <span class="hlt">Reproducibility</span> was evaluated using coefficient of variation and Bland-Altman plotting. For both inter- and intraoperator <span class="hlt">reproducibility</span>, the BUR-AS method had the lowest coefficient of variation and smallest error range about the Bland-Altman plot. Mean CBF obtained using the BUR-AS method had the highest <span class="hlt">reproducibility</span>. Compared with the Patlak-plot and BUR-C methods, the BUR-AS method provides greater inter- and intraoperator <span class="hlt">reproducibility</span> of cerebral blood flow measurement. © 2015 by the Society of Nuclear Medicine and Molecular Imaging, Inc.</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_15");'>15</a></li> <li><a href="#" onclick='return showDiv("page_16");'>16</a></li> <li class="active"><span>17</span></li> <li><a href="#" onclick='return showDiv("page_18");'>18</a></li> <li><a href="#" onclick='return showDiv("page_19");'>19</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_17 --> <div id="page_18" class="hiddenDiv"> <div class="row"> <div class="col-sm-12"> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_16");'>16</a></li> <li><a href="#" onclick='return showDiv("page_17");'>17</a></li> <li class="active"><span>18</span></li> <li><a href="#" onclick='return showDiv("page_19");'>19</a></li> <li><a href="#" onclick='return showDiv("page_20");'>20</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div> </div> <div class="row"> <div class="col-sm-12"> <ol class="result-class" start="341"> <li> <p><a target="_blank" onclick="trackOutboundLink('http://files.eric.ed.gov/fulltext/ED269377.pdf','ERIC'); return false;" href="http://files.eric.ed.gov/fulltext/ED269377.pdf"><span><span class="hlt">Reproducing</span> Domestic Laborers through Office Education.</span></a></p> <p><a target="_blank" href="http://www.eric.ed.gov/ERICWebPortal/search/extended.jsp?_pageLabel=advanced">ERIC Educational Resources Information Center</a></p> <p>Valli, Linda R.</p> <p></p> <p>Scholars have long acknowledged the role schools have in <span class="hlt">reproducing</span> a sexual division of labor. Despite the reemergence of a feminist movement and anti-sex-discrimination legislation, schools are still places where boys and girls tend to study different curricula and where traditional sex roles are perpetuated. Physics, calculus, and shop classes…</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2015JAP...118g5703A','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2015JAP...118g5703A"><span>Spatial mapping and statistical <span class="hlt">reproducibility</span> of an array of 256 one-dimensional quantum wires</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Al-Taie, H.; Smith, L. W.; Lesage, A. A. J.; See, P.; Griffiths, J. P.; Beere, H. E.; Jones, G. A. C.; Ritchie, D. A.; Kelly, M. J.; Smith, C. G.</p> <p>2015-08-01</p> <p>We utilize a multiplexing architecture to measure the conductance properties of an array of 256 split gates. We investigate the <span class="hlt">reproducibility</span> of the pinch off and one-dimensional definition voltage as a function of spatial location on two different cooldowns, and after illuminating the device. The <span class="hlt">reproducibility</span> of both these properties on the two cooldowns is high, the result of the density of the two-dimensional electron gas returning to a similar state after thermal cycling. The spatial variation of the pinch-off voltage reduces after illumination; however, the variation of the one-dimensional definition voltage increases due to an anomalous feature in the center of the array. A technique which quantifies the homogeneity of split-gate properties across the array is developed which captures the experimentally <span class="hlt">observed</span> trends. In addition, the one-dimensional definition voltage is used to probe the density of the wafer at each split gate in the array on a micron scale using a capacitive model.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/29607086','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/29607086"><span>Actinic cheilitis: proposition and <span class="hlt">reproducibility</span> of a clinical criterion.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Poitevin, Nádia Antunes; Rodrigues, Mariana Sudati; Weigert, Karen Loureiro; Macedo, Carmen Lúcia Rodrigues; Dos Santos, Rubem Beraldo</p> <p>2017-01-01</p> <p>The actinic cheilitis (AC) is a precancerous lip lesion seen as a consequence of chronic sun exposure. Clinically, the border between the lip's skin and the semimucosa could be blurred; in the more aggressive cases, leucoplakia and ulcers also represent its clinical feature. It seems that no clinical criterion is universally accepted for this disease yet. Therefore, this study was carried out to make a proposition of a clinical score to actinic cheilitis (Grade I starting from dryness of vermilion to endured ulcers representing Grade IV) and to assess its <span class="hlt">reproducibility</span>. Fifty subjects were assessed, most of whom were male, Caucasian farmers, with an average age of 46.12 (18-74) years. The obtained data were analysed by means of descriptive statistics and by Kappa test to assess the inter-examiners and the clinical Golden-Pattern concordance (95% CI). During calibration, 15 patients were examined three times a week by each examiner (4) until Kappa test <span class="hlt">observed</span> k =0.8 or more. In the main experiment, the inter-examiner concordance was classified between good ( k =0.779; P <0.05) and very good ( k =0.925; P <0.05) from the 35 examined subjects. With the Golden-Pattern, it was considered very good ( k =0.812; P <0.05 to k =0.925; P <0.05). Four examiners with different experiences could strongly suggest that after adequate calibration, it could be well applied by examiners with as much experience as a dental student. The authors concluded that the proposed classification was easily applied and had a very good <span class="hlt">reproducibility</span>.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2018ClDy..tmp...92D','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2018ClDy..tmp...92D"><span>Breakdown of NAO <span class="hlt">reproducibility</span> into internal versus externally-forced components: a two-tier pilot study</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Douville, Hervé; Ribes, A.; Tyteca, S.</p> <p>2018-03-01</p> <p>Assessing the ability of atmospheric models to capture <span class="hlt">observed</span> climate variations when driven by <span class="hlt">observed</span> sea surface temperature (SST), sea ice concentration (SIC) and radiative forcings is a prerequisite for the feasibility of near term climate predictions. Here we achieve ensembles of global atmospheric simulations to assess and attribute the <span class="hlt">reproducibility</span> of the boreal winter atmospheric circulation against the European Centre for Medium Range Forecasts (ECMWF) twentieth century reanalysis (ERA20C). Our control experiment is driven by the <span class="hlt">observed</span> SST/SIC from the Atmospheric Model Intercomparison Project. It is compared to a similar ensemble performed with the ECMWF model as a first step toward ERA20C. Moreover, a two-tier methodology is used to disentangle externally-forced versus internal variations in the <span class="hlt">observed</span> SST/SIC boundary conditions and run additional ensembles allowing us to attribute the <span class="hlt">observed</span> atmospheric variability. The focus is mainly on the North Atlantic Oscillation (NAO) variability which is more <span class="hlt">reproducible</span> in our model than in the ECMWF model. This result is partly due to the simulation of a positive NAO trend across the full 1920-2014 integration period. In line with former studies, this trend might be mediated by a circumglobal teleconnection mechanism triggered by increasing precipitation over the tropical Indian Ocean (TIO). Surprisingly, this response is mainly related to the internal SST variability and is not found in the ECMWF model driven by an alternative SST dataset showing a weaker TIO warming in the first half of the twentieth century. Our results may reconcile the twentieth century <span class="hlt">observations</span> with the twenty-first century projections of the NAO. They should be however considered with caution given the limited size of our ensembles, the possible influence of other sources of NAO variability, and the uncertainties in the tropical SST trend and breakdown between internal versus externally-forced variability.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/11592012','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/11592012"><span>[The Autocad system for planimetric study of the optic disc in glaucoma: technique and <span class="hlt">reproducibility</span> study].</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Sánchez Pérez, A; Honrubia López, F M; Larrosa Poves, J M; Polo Llorens, V; Melcon Sánchez-Frieras, B</p> <p>2001-09-01</p> <p>To develop a lens planimetry technique for the optic disc using AutoCAD. To determine variability magnitude of the optic disc morphological measurements. We employed AutoCAD R.14.0 Autodesk: image acquisition, contour delimitation by multiple lines fitting or ellipse adjustment, image sectorialization and measurements quantification (optic disc and excavation, vertical diameters, optic disc area, excavation area, neuroretinal sector area and Beta atrophy area). Intraimage or operator and interimage o total <span class="hlt">reproducibility</span> was studied by coefficient of variability (CV) (n=10) in normal and myopic optic discs. This technique allows to obtain optic disc measurement in 5 to 10 minutes time. Total or interimage variability of measurements introduced by one <span class="hlt">observer</span> presents CV range from 1.18-4.42. Operator or intraimage measurement presents CV range from 0.30-4.21. Optic disc contour delimitation by ellipse adjustment achieved better <span class="hlt">reproducibility</span> results than multiple lines adjustment in all measurements. Computer assisted AutoCAD planimetry is an interactive method to analyse the optic disc, feasible to incorporate to clinical practice. <span class="hlt">Reproducibility</span> results are comparable to other analyzers in quantification optic disc morphology. Ellipse adjustment improves results in optic disc contours delimitation.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://ntrs.nasa.gov/search.jsp?R=19740034360&hterms=801&qs=Ntx%3Dmode%2Bmatchall%26Ntk%3DAll%26N%3D0%26No%3D90%26Ntt%3D801','NASA-TRS'); return false;" href="https://ntrs.nasa.gov/search.jsp?R=19740034360&hterms=801&qs=Ntx%3Dmode%2Bmatchall%26Ntk%3DAll%26N%3D0%26No%3D90%26Ntt%3D801"><span>Extragalactic radio sources - <span class="hlt">Accurate</span> positions from very-long-baseline interferometry <span class="hlt">observations</span></span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Rogers, A. E. E.; Counselman, C. C., III; Hinteregger, H. F.; Knight, C. A.; Robertson, D. S.; Shapiro, I. I.; Whitney, A. R.; Clark, T. A.</p> <p>1973-01-01</p> <p>Relative positions for 12 extragalactic radio sources have been determined via wide-band very-long-baseline interferometry (wavelength of about 3.8 cm). The standard error, based on consistency between results from widely separated periods of <span class="hlt">observation</span>, appears to be no more than 0.1 sec for each coordinate of the seven sources that were well <span class="hlt">observed</span> during two or more periods. The uncertainties in the coordinates determined for the other five sources are larger, but in no case exceed 0.5 sec.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.osti.gov/biblio/22600142-reproducibility-cutoff-probe-measurement-electron-density','SCIGOV-STC'); return false;" href="https://www.osti.gov/biblio/22600142-reproducibility-cutoff-probe-measurement-electron-density"><span><span class="hlt">Reproducibility</span> of the cutoff probe for the measurement of electron density</span></a></p> <p><a target="_blank" href="http://www.osti.gov/search">DOE Office of Scientific and Technical Information (OSTI.GOV)</a></p> <p>Kim, D. W.; Oh, W. Y.; You, S. J., E-mail: sjyou@cnu.ac.kr</p> <p>2016-06-15</p> <p>Since a plasma processing control based on plasma diagnostics attracted considerable attention in industry, the <span class="hlt">reproducibility</span> of the diagnostics using in this application has become a great interest. Because the cutoff probe is one of the potential candidates for this application, knowing the <span class="hlt">reproducibility</span> of the cutoff probe measurement becomes quit important in the cutoff probe application research. To test the <span class="hlt">reproducibility</span> of the cutoff probe measurement, in this paper, a comparative study among the different cutoff probe measurements was performed. The comparative study revealed remarkable result: the cutoff probe has a great <span class="hlt">reproducibility</span> for the electron density measurement, i.e.,more » there are little differences among measurements by different probes made by different experimenters. The discussion including the reason for the result was addressed via this paper by using a basic measurement principle of cutoff probe and a comparative experiment with Langmuir probe.« less</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/28533373','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/28533373"><span>Mental models <span class="hlt">accurately</span> predict emotion transitions.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Thornton, Mark A; Tamir, Diana I</p> <p>2017-06-06</p> <p>Successful social interactions depend on people's ability to predict others' future actions and emotions. People possess many mechanisms for perceiving others' current emotional states, but how might they use this information to predict others' future states? We hypothesized that people might capitalize on an overlooked aspect of affective experience: current emotions predict future emotions. By attending to regularities in emotion transitions, perceivers might develop <span class="hlt">accurate</span> mental models of others' emotional dynamics. People could then use these mental models of emotion transitions to predict others' future emotions from currently <span class="hlt">observable</span> emotions. To test this hypothesis, studies 1-3 used data from three extant experience-sampling datasets to establish the actual rates of emotional transitions. We then collected three parallel datasets in which participants rated the transition likelihoods between the same set of emotions. Participants' ratings of emotion transitions predicted others' experienced transitional likelihoods with high accuracy. Study 4 demonstrated that four conceptual dimensions of mental state representation-valence, social impact, rationality, and human mind-inform participants' mental models. Study 5 used 2 million emotion reports on the Experience Project to replicate both of these findings: again people reported <span class="hlt">accurate</span> models of emotion transitions, and these models were informed by the same four conceptual dimensions. Importantly, neither these conceptual dimensions nor holistic similarity could fully explain participants' accuracy, suggesting that their mental models contain <span class="hlt">accurate</span> information about emotion dynamics above and beyond what might be predicted by static emotion knowledge alone.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=5468631','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=5468631"><span>Mental models <span class="hlt">accurately</span> predict emotion transitions</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Thornton, Mark A.; Tamir, Diana I.</p> <p>2017-01-01</p> <p>Successful social interactions depend on people’s ability to predict others’ future actions and emotions. People possess many mechanisms for perceiving others’ current emotional states, but how might they use this information to predict others’ future states? We hypothesized that people might capitalize on an overlooked aspect of affective experience: current emotions predict future emotions. By attending to regularities in emotion transitions, perceivers might develop <span class="hlt">accurate</span> mental models of others’ emotional dynamics. People could then use these mental models of emotion transitions to predict others’ future emotions from currently <span class="hlt">observable</span> emotions. To test this hypothesis, studies 1–3 used data from three extant experience-sampling datasets to establish the actual rates of emotional transitions. We then collected three parallel datasets in which participants rated the transition likelihoods between the same set of emotions. Participants’ ratings of emotion transitions predicted others’ experienced transitional likelihoods with high accuracy. Study 4 demonstrated that four conceptual dimensions of mental state representation—valence, social impact, rationality, and human mind—inform participants’ mental models. Study 5 used 2 million emotion reports on the Experience Project to replicate both of these findings: again people reported <span class="hlt">accurate</span> models of emotion transitions, and these models were informed by the same four conceptual dimensions. Importantly, neither these conceptual dimensions nor holistic similarity could fully explain participants’ accuracy, suggesting that their mental models contain <span class="hlt">accurate</span> information about emotion dynamics above and beyond what might be predicted by static emotion knowledge alone. PMID:28533373</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/25634767','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/25634767"><span>Modest validity and fair <span class="hlt">reproducibility</span> of dietary patterns derived by cluster analysis.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Funtikova, Anna N; Benítez-Arciniega, Alejandra A; Fitó, Montserrat; Schröder, Helmut</p> <p>2015-03-01</p> <p>Cluster analysis is widely used to analyze dietary patterns. We aimed to analyze the validity and <span class="hlt">reproducibility</span> of the dietary patterns defined by cluster analysis derived from a food frequency questionnaire (FFQ). We hypothesized that the dietary patterns derived by cluster analysis have fair to modest <span class="hlt">reproducibility</span> and validity. Dietary data were collected from 107 individuals from population-based survey, by an FFQ at baseline (FFQ1) and after 1 year (FFQ2), and by twelve 24-hour dietary recalls (24-HDR). Repeatability and validity were measured by comparing clusters obtained by the FFQ1 and FFQ2 and by the FFQ2 and 24-HDR (reference method), respectively. Cluster analysis identified a "fruits & vegetables" and a "meat" pattern in each dietary data source. Cluster membership was concordant for 66.7% of participants in FFQ1 and FFQ2 (<span class="hlt">reproducibility</span>), and for 67.0% in FFQ2 and 24-HDR (validity). Spearman correlation analysis showed reasonable <span class="hlt">reproducibility</span>, especially in the "fruits & vegetables" pattern, and lower validity also especially in the "fruits & vegetables" pattern. κ statistic revealed a fair validity and <span class="hlt">reproducibility</span> of clusters. Our findings indicate a reasonable <span class="hlt">reproducibility</span> and fair to modest validity of dietary patterns derived by cluster analysis. Copyright © 2015 Elsevier Inc. All rights reserved.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/28636642','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/28636642"><span>In vivo evaluation of inter-operator <span class="hlt">reproducibility</span> of digital dental and conventional impression techniques.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Kamimura, Emi; Tanaka, Shinpei; Takaba, Masayuki; Tachi, Keita; Baba, Kazuyoshi</p> <p>2017-01-01</p> <p>The aim of this study was to evaluate and compare the inter-operator <span class="hlt">reproducibility</span> of three-dimensional (3D) images of teeth captured by a digital impression technique to a conventional impression technique in vivo. Twelve participants with complete natural dentition were included in this study. A digital impression of the mandibular molars of these participants was made by two operators with different levels of clinical experience, 3 or 16 years, using an intra-oral scanner (Lava COS, 3M ESPE). A silicone impression also was made by the same operators using the double mix impression technique (Imprint3, 3M ESPE). Stereolithography (STL) data were directly exported from the Lava COS system, while STL data of a plaster model made from silicone impression were captured by a three-dimensional (3D) laboratory scanner (D810, 3shape). The STL datasets recorded by two different operators were compared using 3D evaluation software and superimposed using the best-fit-algorithm method (least-squares method, PolyWorks, InnovMetric Software) for each impression technique. Inter-operator <span class="hlt">reproducibility</span> as evaluated by average discrepancies of corresponding 3D data was compared between the two techniques (Wilcoxon signed-rank test). The visual inspection of superimposed datasets revealed that discrepancies between repeated digital impression were smaller than <span class="hlt">observed</span> with silicone impression. Confirmation was forthcoming from statistical analysis revealing significantly smaller average inter-operator <span class="hlt">reproducibility</span> using a digital impression technique (0.014± 0.02 mm) than when using a conventional impression technique (0.023 ± 0.01 mm). The results of this in vivo study suggest that inter-operator <span class="hlt">reproducibility</span> with a digital impression technique may be better than that of a conventional impression technique and is independent of the clinical experience of the operator.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=5479543','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=5479543"><span>In vivo evaluation of inter-operator <span class="hlt">reproducibility</span> of digital dental and conventional impression techniques</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Kamimura, Emi; Tanaka, Shinpei; Takaba, Masayuki; Tachi, Keita; Baba, Kazuyoshi</p> <p>2017-01-01</p> <p>Purpose The aim of this study was to evaluate and compare the inter-operator <span class="hlt">reproducibility</span> of three-dimensional (3D) images of teeth captured by a digital impression technique to a conventional impression technique in vivo. Materials and methods Twelve participants with complete natural dentition were included in this study. A digital impression of the mandibular molars of these participants was made by two operators with different levels of clinical experience, 3 or 16 years, using an intra-oral scanner (Lava COS, 3M ESPE). A silicone impression also was made by the same operators using the double mix impression technique (Imprint3, 3M ESPE). Stereolithography (STL) data were directly exported from the Lava COS system, while STL data of a plaster model made from silicone impression were captured by a three-dimensional (3D) laboratory scanner (D810, 3shape). The STL datasets recorded by two different operators were compared using 3D evaluation software and superimposed using the best-fit-algorithm method (least-squares method, PolyWorks, InnovMetric Software) for each impression technique. Inter-operator <span class="hlt">reproducibility</span> as evaluated by average discrepancies of corresponding 3D data was compared between the two techniques (Wilcoxon signed-rank test). Results The visual inspection of superimposed datasets revealed that discrepancies between repeated digital impression were smaller than <span class="hlt">observed</span> with silicone impression. Confirmation was forthcoming from statistical analysis revealing significantly smaller average inter-operator <span class="hlt">reproducibility</span> using a digital impression technique (0.014± 0.02 mm) than when using a conventional impression technique (0.023 ± 0.01 mm). Conclusion The results of this in vivo study suggest that inter-operator <span class="hlt">reproducibility</span> with a digital impression technique may be better than that of a conventional impression technique and is independent of the clinical experience of the operator. PMID:28636642</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/27038897','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/27038897"><span><span class="hlt">Reproducibility</span> of Illumina platform deep sequencing errors allows <span class="hlt">accurate</span> determination of DNA barcodes in cells.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Beltman, Joost B; Urbanus, Jos; Velds, Arno; van Rooij, Nienke; Rohr, Jan C; Naik, Shalin H; Schumacher, Ton N</p> <p>2016-04-02</p> <p>Next generation sequencing (NGS) of amplified DNA is a powerful tool to describe genetic heterogeneity within cell populations that can both be used to investigate the clonal structure of cell populations and to perform genetic lineage tracing. For applications in which both abundant and rare sequences are biologically relevant, the relatively high error rate of NGS techniques complicates data analysis, as it is difficult to distinguish rare true sequences from spurious sequences that are generated by PCR or sequencing errors. This issue, for instance, applies to cellular barcoding strategies that aim to follow the amount and type of offspring of single cells, by supplying these with unique heritable DNA tags. Here, we use genetic barcoding data from the Illumina HiSeq platform to show that straightforward read threshold-based filtering of data is typically insufficient to filter out spurious barcodes. Importantly, we demonstrate that specific sequencing errors occur at an approximately constant rate across different samples that are sequenced in parallel. We exploit this <span class="hlt">observation</span> by developing a novel approach to filter out spurious sequences. Application of our new method demonstrates its value in the identification of true sequences amongst spurious sequences in biological data sets.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.osti.gov/servlets/purl/863093','DOE-PATENT-XML'); return false;" href="https://www.osti.gov/servlets/purl/863093"><span>Method for <span class="hlt">reproducibly</span> preparing a low-melting high-carbon yield precursor</span></a></p> <p><a target="_blank" href="http://www.osti.gov/doepatents">DOEpatents</a></p> <p>Smith, Wesley E.; Napier, Jr., Bradley</p> <p>1978-01-01</p> <p>The present invention is directed to a method for preparing a <span class="hlt">reproducible</span> synthetic carbon precursor by the autoclave polymerization of indene (C.sub.9 H.sub.8) at a temperature in the range of 470.degree.-485.degree. C, and at a pressure in the range of about 1000 to about 4300 psi. Volatiles in the resulting liquid indene polymer are removed by vacuum outgassing to form a solid carbon precursor characterized by having a relatively low melting temperature, high-carbon yield, and high <span class="hlt">reproducibility</span> which provide for the fabrication of carbon and graphite composites having strict requirements for <span class="hlt">reproducible</span> properties.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/28670024','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/28670024"><span><span class="hlt">Reproducibility</span> of abdominal fat assessment by ultrasound and computed tomography.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Mauad, Fernando Marum; Chagas-Neto, Francisco Abaeté; Benedeti, Augusto César Garcia Saab; Nogueira-Barbosa, Marcello Henrique; Muglia, Valdair Francisco; Carneiro, Antonio Adilton Oliveira; Muller, Enrico Mattana; Elias Junior, Jorge</p> <p>2017-01-01</p> <p>To test the accuracy and <span class="hlt">reproducibility</span> of ultrasound and computed tomography (CT) for the quantification of abdominal fat in correlation with the anthropometric, clinical, and biochemical assessments. Using ultrasound and CT, we determined the thickness of subcutaneous and intra-abdominal fat in 101 subjects-of whom 39 (38.6%) were men and 62 (61.4%) were women-with a mean age of 66.3 years (60-80 years). The ultrasound data were correlated with the anthropometric, clinical, and biochemical parameters, as well as with the areas measured by abdominal CT. Intra-abdominal thickness was the variable for which the correlation with the areas of abdominal fat was strongest (i.e., the correlation coefficient was highest). We also tested the <span class="hlt">reproducibility</span> of ultrasound and CT for the assessment of abdominal fat and found that CT measurements of abdominal fat showed greater <span class="hlt">reproducibility</span>, having higher intraobserver and interobserver reliability than had the ultrasound measurements. There was a significant correlation between ultrasound and CT, with a correlation coefficient of 0.71. In the assessment of abdominal fat, the intraobserver and interobserver reliability were greater for CT than for ultrasound, although both methods showed high accuracy and good <span class="hlt">reproducibility</span>.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/29531050','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/29531050"><span>An empirical analysis of journal policy effectiveness for computational <span class="hlt">reproducibility</span>.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Stodden, Victoria; Seiler, Jennifer; Ma, Zhaokun</p> <p>2018-03-13</p> <p>A key component of scientific communication is sufficient information for other researchers in the field to <span class="hlt">reproduce</span> published findings. For computational and data-enabled research, this has often been interpreted to mean making available the raw data from which results were generated, the computer code that generated the findings, and any additional information needed such as workflows and input parameters. Many journals are revising author guidelines to include data and code availability. This work evaluates the effectiveness of journal policy that requires the data and code necessary for <span class="hlt">reproducibility</span> be made available postpublication by the authors upon request. We assess the effectiveness of such a policy by ( i ) requesting data and code from authors and ( ii ) attempting replication of the published findings. We chose a random sample of 204 scientific papers published in the journal Science after the implementation of their policy in February 2011. We found that we were able to obtain artifacts from 44% of our sample and were able to <span class="hlt">reproduce</span> the findings for 26%. We find this policy-author remission of data and code postpublication upon request-an improvement over no policy, but currently insufficient for <span class="hlt">reproducibility</span>.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=5856507','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=5856507"><span>An empirical analysis of journal policy effectiveness for computational <span class="hlt">reproducibility</span></span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Seiler, Jennifer; Ma, Zhaokun</p> <p>2018-01-01</p> <p>A key component of scientific communication is sufficient information for other researchers in the field to <span class="hlt">reproduce</span> published findings. For computational and data-enabled research, this has often been interpreted to mean making available the raw data from which results were generated, the computer code that generated the findings, and any additional information needed such as workflows and input parameters. Many journals are revising author guidelines to include data and code availability. This work evaluates the effectiveness of journal policy that requires the data and code necessary for <span class="hlt">reproducibility</span> be made available postpublication by the authors upon request. We assess the effectiveness of such a policy by (i) requesting data and code from authors and (ii) attempting replication of the published findings. We chose a random sample of 204 scientific papers published in the journal Science after the implementation of their policy in February 2011. We found that we were able to obtain artifacts from 44% of our sample and were able to <span class="hlt">reproduce</span> the findings for 26%. We find this policy—author remission of data and code postpublication upon request—an improvement over no policy, but currently insufficient for <span class="hlt">reproducibility</span>. PMID:29531050</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/27908190','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/27908190"><span>Accuracy, <span class="hlt">reproducibility</span>, and uncertainty analysis of thyroid-probe-based activity measurements for determination of dose calibrator settings.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Esquinas, Pedro L; Tanguay, Jesse; Gonzalez, Marjorie; Vuckovic, Milan; Rodríguez-Rodríguez, Cristina; Häfeli, Urs O; Celler, Anna</p> <p>2016-12-01</p> <p>In the nuclear medicine department, the activity of radiopharmaceuticals is measured using dose calibrators (DCs) prior to patient injection. The DC consists of an ionization chamber that measures current generated by ionizing radiation (emitted from the radiotracer). In order to obtain an activity reading, the current is converted into units of activity by applying an appropriate calibration factor (also referred to as DC dial setting). <span class="hlt">Accurate</span> determination of DC dial settings is crucial to ensure that patients receive the appropriate dose in diagnostic scans or radionuclide therapies. The goals of this study were (1) to describe a practical method to experimentally determine dose calibrator settings using a thyroid-probe (TP) and (2) to investigate the accuracy, <span class="hlt">reproducibility</span>, and uncertainties of the method. As an illustration, the TP method was applied to determine 188 Re dial settings for two dose calibrator models: Atomlab 100plus and Capintec CRC-55tR. Using the TP to determine dose calibrator settings involved three measurements. First, the energy-dependent efficiency of the TP was determined from energy spectra measurements of two calibration sources ( 152 Eu and 22 Na). Second, the gamma emissions from the investigated isotope ( 188 Re) were measured using the TP and its activity was determined using γ-ray spectroscopy methods. Ambient background, scatter, and source-geometry corrections were applied during the efficiency and activity determination steps. Third, the TP-based 188 Re activity was used to determine the dose calibrator settings following the calibration curve method [B. E. Zimmerman et al., J. Nucl. Med. 40, 1508-1516 (1999)]. The interobserver <span class="hlt">reproducibility</span> of TP measurements was determined by the coefficient of variation (COV) and uncertainties associated to each step of the measuring process were estimated. The accuracy of activity measurements using the proposed method was evaluated by comparing the TP activity estimates of 99m Tc</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2005SPIE.5655...41R','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2005SPIE.5655...41R"><span>Highly <span class="hlt">accurate</span> FTIR <span class="hlt">observations</span> from the scanning HIS aircraft instrument</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Revercomb, Henry E.; Tobin, David C.; Knuteson, Robert O.; Best, Fred A.; Smith, William L., Sr.; van Delst, Paul F. W.; LaPorte, Daniel D.; Ellington, Scott D.; Werner, Mark W.; Dedecker, Ralph G.; Garcia, Raymond K.; Ciganovich, Nick N.; Howell, Hugh B.; Olson, Erik R.; Dutcher, Steven B.; Taylor, Joseph K.</p> <p>2005-01-01</p> <p>Development in the mid 80s of the High-resolution Interferometer Sounder (HIS) instrument for the high altitude NASA ER2 aircraft demonstrated the capability for advanced atmospheric temperature and water vapor sounding and set the stage for new satellite instruments that are now becoming a reality [AIRS(2002), CrIS(2006), IASI(2006), GIFTS(200?), HES(2013)]. Follow-on developments at the University of Wisconsin that employ Fourier Transform Infrared (FTIR) for Earth <span class="hlt">observations</span> include the ground-based Atmospheric Emitted Radiance Interferometer (AERI) and the new Scanning HIS aircraft instrument. The Scanning HIS is a smaller version of the original HIS that uses cross-track scanning to enhance spatial coverage. Scanning HIS and its close cousin, the NPOESS Airborne Sounder Testbed (NAST), are being used for satellite instrument validation and for atmospheric research. A novel detector configuration on Scanning HIS allows the incorporation of a single focal plane and cooler with three or four spectral bands that view the same spot on the ground. The calibration accuracy of the S-HIS and results from recent field campaigns are presented, including validation comparisons with the NASA EOS infrared <span class="hlt">observations</span> (AIRS and MODIS). Aircraft comparisons of this type provide a mechanism for periodically testing the absolute calibration of spacecraft instruments with instrumentation for which the calibration can be carefully maintained on the ground. This capability is especially valuable for assuring the long-term consistency and accuracy of climate <span class="hlt">observations</span>, including those from the NASA EOS spacecrafts (Terra, Aqua and Aura) and the new complement of NPOESS operational instruments. It is expected that aircraft flights of the S-HIS and the NAST will be used to check the long-term stability of AIRS and the NPOESS operational follow-on sounder, the Cross-track Infrared Sounder (CrIS), over the life of the mission.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://eric.ed.gov/?q=volcanoes&pg=7&id=ED400206','ERIC'); return false;" href="https://eric.ed.gov/?q=volcanoes&pg=7&id=ED400206"><span>Natural Disasters: Earth Science Readings. <span class="hlt">Reproducibles</span>.</span></a></p> <p><a target="_blank" href="http://www.eric.ed.gov/ERICWebPortal/search/extended.jsp?_pageLabel=advanced">ERIC Educational Resources Information Center</a></p> <p>Lobb, Nancy</p> <p></p> <p>Natural Disasters is a <span class="hlt">reproducible</span> teacher book that explains what scientists believe to be the causes of a variety of natural disasters and suggests steps that teachers and students can take to be better prepared in the event of a natural disaster. It contains both student and teacher sections. Teacher sections include vocabulary, an answer key,…</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_16");'>16</a></li> <li><a href="#" onclick='return showDiv("page_17");'>17</a></li> <li class="active"><span>18</span></li> <li><a href="#" onclick='return showDiv("page_19");'>19</a></li> <li><a href="#" onclick='return showDiv("page_20");'>20</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_18 --> <div id="page_19" class="hiddenDiv"> <div class="row"> <div class="col-sm-12"> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_17");'>17</a></li> <li><a href="#" onclick='return showDiv("page_18");'>18</a></li> <li class="active"><span>19</span></li> <li><a href="#" onclick='return showDiv("page_20");'>20</a></li> <li><a href="#" onclick='return showDiv("page_21");'>21</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div> </div> <div class="row"> <div class="col-sm-12"> <ol class="result-class" start="361"> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/29463308','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/29463308"><span><span class="hlt">Reproducibility</span> of clinical research in critical care: a scoping review.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Niven, Daniel J; McCormick, T Jared; Straus, Sharon E; Hemmelgarn, Brenda R; Jeffs, Lianne; Barnes, Tavish R M; Stelfox, Henry T</p> <p>2018-02-21</p> <p>The ability to <span class="hlt">reproduce</span> experiments is a defining principle of science. <span class="hlt">Reproducibility</span> of clinical research has received relatively little scientific attention. However, it is important as it may inform clinical practice, research agendas, and the design of future studies. We used scoping review methods to examine <span class="hlt">reproducibility</span> within a cohort of randomized trials examining clinical critical care research and published in the top general medical and critical care journals. To identify relevant clinical practices, we searched the New England Journal of Medicine, The Lancet, and JAMA for randomized trials published up to April 2016. To identify a comprehensive set of studies for these practices, included articles informed secondary searches within other high-impact medical and specialty journals. We included late-phase randomized controlled trials examining therapeutic clinical practices in adults admitted to general medical-surgical or specialty intensive care units (ICUs). Included articles were classified using a <span class="hlt">reproducibility</span> framework. An original study was the first to evaluate a clinical practice. A reproduction attempt re-evaluated that practice in a new set of participants. Overall, 158 practices were examined in 275 included articles. A reproduction attempt was identified for 66 practices (42%, 95% CI 33-50%). Original studies reported larger effects than reproduction attempts (primary endpoint, risk difference 16.0%, 95% CI 11.6-20.5% vs. 8.4%, 95% CI 6.0-10.8%, P = 0.003). More than half of clinical practices with a reproduction attempt demonstrated effects that were inconsistent with the original study (56%, 95% CI 42-68%), among which a large number were reported to be efficacious in the original study and to lack efficacy in the reproduction attempt (34%, 95% CI 19-52%). Two practices reported to be efficacious in the original study were found to be harmful in the reproduction attempt. A minority of critical care practices with research published</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/27634258','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/27634258"><span>A highly <span class="hlt">accurate</span> ab initio potential energy surface for methane.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Owens, Alec; Yurchenko, Sergei N; Yachmenev, Andrey; Tennyson, Jonathan; Thiel, Walter</p> <p>2016-09-14</p> <p>A new nine-dimensional potential energy surface (PES) for methane has been generated using state-of-the-art ab initio theory. The PES is based on explicitly correlated coupled cluster calculations with extrapolation to the complete basis set limit and incorporates a range of higher-level additive energy corrections. These include core-valence electron correlation, higher-order coupled cluster terms beyond perturbative triples, scalar relativistic effects, and the diagonal Born-Oppenheimer correction. Sub-wavenumber accuracy is achieved for the majority of experimentally known vibrational energy levels with the four fundamentals of (12)CH4 <span class="hlt">reproduced</span> with a root-mean-square error of 0.70 cm(-1). The computed ab initio equilibrium C-H bond length is in excellent agreement with previous values despite pure rotational energies displaying minor systematic errors as J (rotational excitation) increases. It is shown that these errors can be significantly reduced by adjusting the equilibrium geometry. The PES represents the most <span class="hlt">accurate</span> ab initio surface to date and will serve as a good starting point for empirical refinement.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/29725015','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/29725015"><span><span class="hlt">Observation</span> of the thermal influenced quantum behaviour of water near a solid interface.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Yoon, Hongkee; Yoon, Byoung Jip</p> <p>2018-05-03</p> <p>Water is essential for life. However, the structure and properties of water are still not well understood. It has been introduced that anomalies are in vicinal water near solid interfaces. We performed capillary flow experiments on water with a silica colloid sample using a high-performance liquid chromatography (HPLC) system by <span class="hlt">accurately</span> varying the temperature and analysed the peak shape rigorously. We obtained a novel anomalous temperature spectrum from the peak-shape analysis. Here we report the <span class="hlt">observed</span> distinct specific anomalous temperature (SAT) behaviour in vicinal water at silica interface. The anomaly appeared in the viscous force that was derived from a relationship between the shape of the HPLC peak and the velocity profile for the capillary flow. The <span class="hlt">observations</span> were highly <span class="hlt">reproducible</span>, and we conclude that the SAT is related to the quantum mechanical behaviour of water, in agreement of the characteristic acceptance of thermal displacement according to the Franck-Condon principle. We performed the same experiments using heavy water and water mixed with a small amount of methanol, and the results support the quantum phenomenological origin.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4491554','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4491554"><span>Repeatability and <span class="hlt">Reproducibility</span> of Retinal Nerve Fiber Layer Parameters Measured by Scanning Laser Polarimetry with Enhanced Corneal Compensation in Normal and Glaucomatous Eyes</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Ara, Mirian; Pajarin, Ana B.</p> <p>2015-01-01</p> <p>Objective. To assess the intrasession repeatability and intersession <span class="hlt">reproducibility</span> of peripapillary retinal nerve fiber layer (RNFL) thickness parameters measured by scanning laser polarimetry (SLP) with enhanced corneal compensation (ECC) in healthy and glaucomatous eyes. Methods. One randomly selected eye of 82 healthy individuals and 60 glaucoma subjects was evaluated. Three scans were acquired during the first visit to evaluate intravisit repeatability. A different operator obtained two additional scans within 2 months after the first session to determine intervisit <span class="hlt">reproducibility</span>. The intraclass correlation coefficient (ICC), coefficient of variation (COV), and test-retest variability (TRT) were calculated for all SLP parameters in both groups. Results. ICCs ranged from 0.920 to 0.982 for intravisit measurements and from 0.910 to 0.978 for intervisit measurements. The temporal-superior-nasal-inferior-temporal (TSNIT) average was the highest (0.967 and 0.946) in normal eyes, while nerve fiber indicator (NFI; 0.982) and inferior average (0.978) yielded the best ICC in glaucomatous eyes for intravisit and intervisit measurements, respectively. All COVs were under 10% in both groups, except NFI. TSNIT average had the lowest COV (2.43%) in either type of measurement. Intervisit TRT ranged from 6.48 to 12.84. Conclusions. The <span class="hlt">reproducibility</span> of peripapillary RNFL measurements obtained with SLP-ECC was excellent, indicating that SLP-ECC is sufficiently <span class="hlt">accurate</span> for monitoring glaucoma progression. PMID:26185762</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/26185762','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/26185762"><span>Repeatability and <span class="hlt">Reproducibility</span> of Retinal Nerve Fiber Layer Parameters Measured by Scanning Laser Polarimetry with Enhanced Corneal Compensation in Normal and Glaucomatous Eyes.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Ara, Mirian; Ferreras, Antonio; Pajarin, Ana B; Calvo, Pilar; Figus, Michele; Frezzotti, Paolo</p> <p>2015-01-01</p> <p>To assess the intrasession repeatability and intersession <span class="hlt">reproducibility</span> of peripapillary retinal nerve fiber layer (RNFL) thickness parameters measured by scanning laser polarimetry (SLP) with enhanced corneal compensation (ECC) in healthy and glaucomatous eyes. One randomly selected eye of 82 healthy individuals and 60 glaucoma subjects was evaluated. Three scans were acquired during the first visit to evaluate intravisit repeatability. A different operator obtained two additional scans within 2 months after the first session to determine intervisit <span class="hlt">reproducibility</span>. The intraclass correlation coefficient (ICC), coefficient of variation (COV), and test-retest variability (TRT) were calculated for all SLP parameters in both groups. ICCs ranged from 0.920 to 0.982 for intravisit measurements and from 0.910 to 0.978 for intervisit measurements. The temporal-superior-nasal-inferior-temporal (TSNIT) average was the highest (0.967 and 0.946) in normal eyes, while nerve fiber indicator (NFI; 0.982) and inferior average (0.978) yielded the best ICC in glaucomatous eyes for intravisit and intervisit measurements, respectively. All COVs were under 10% in both groups, except NFI. TSNIT average had the lowest COV (2.43%) in either type of measurement. Intervisit TRT ranged from 6.48 to 12.84. The <span class="hlt">reproducibility</span> of peripapillary RNFL measurements obtained with SLP-ECC was excellent, indicating that SLP-ECC is sufficiently <span class="hlt">accurate</span> for monitoring glaucoma progression.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=5409056','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=5409056"><span>Evaluation of the <span class="hlt">reproducibility</span> of amplicon sequencing with Illumina MiSeq platform</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Van Nostrand, Joy D.; Ning, Daliang; Sun, Bo; Xue, Kai; Liu, Feifei; Deng, Ye; Liang, Yuting; Zhou, Jizhong</p> <p>2017-01-01</p> <p>Illumina’s MiSeq has become the dominant platform for gene amplicon sequencing in microbial ecology studies; however, various technical concerns, such as <span class="hlt">reproducibility</span>, still exist. To assess <span class="hlt">reproducibility</span>, 16S rRNA gene amplicons from 18 soil samples of a reciprocal transplantation experiment were sequenced on an Illumina MiSeq. The V4 region of 16S rRNA gene from each sample was sequenced in triplicate with each replicate having a unique barcode. The average OTU overlap, without considering sequence abundance, at a rarefaction level of 10,323 sequences was 33.4±2.1% and 20.2±1.7% between two and among three technical replicates, respectively. When OTU sequence abundance was considered, the average sequence abundance weighted OTU overlap was 85.6±1.6% and 81.2±2.1% for two and three replicates, respectively. Removing singletons significantly increased the overlap for both (~1–3%, p<0.001). Increasing the sequencing depth to 160,000 reads by deep sequencing increased OTU overlap both when sequence abundance was considered (95%) and when not (44%). However, if singletons were not removed the overlap between two technical replicates (not considering sequence abundance) plateaus at 39% with 30,000 sequences. Diversity measures were not affected by the low overlap as α-diversities were similar among technical replicates while β-diversities (Bray-Curtis) were much smaller among technical replicates than among treatment replicates (e.g., 0.269 vs. 0.374). Higher diversity coverage, but lower OTU overlap, was <span class="hlt">observed</span> when replicates were sequenced in separate runs. Detrended correspondence analysis indicated that while there was considerable variation among technical replicates, the <span class="hlt">reproducibility</span> was sufficient for detecting treatment effects for the samples examined. These results suggest that although there is variation among technical replicates, amplicon sequencing on MiSeq is useful for analyzing microbial community structure if used appropriately</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/28453559','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/28453559"><span>Evaluation of the <span class="hlt">reproducibility</span> of amplicon sequencing with Illumina MiSeq platform.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Wen, Chongqing; Wu, Liyou; Qin, Yujia; Van Nostrand, Joy D; Ning, Daliang; Sun, Bo; Xue, Kai; Liu, Feifei; Deng, Ye; Liang, Yuting; Zhou, Jizhong</p> <p>2017-01-01</p> <p>Illumina's MiSeq has become the dominant platform for gene amplicon sequencing in microbial ecology studies; however, various technical concerns, such as <span class="hlt">reproducibility</span>, still exist. To assess <span class="hlt">reproducibility</span>, 16S rRNA gene amplicons from 18 soil samples of a reciprocal transplantation experiment were sequenced on an Illumina MiSeq. The V4 region of 16S rRNA gene from each sample was sequenced in triplicate with each replicate having a unique barcode. The average OTU overlap, without considering sequence abundance, at a rarefaction level of 10,323 sequences was 33.4±2.1% and 20.2±1.7% between two and among three technical replicates, respectively. When OTU sequence abundance was considered, the average sequence abundance weighted OTU overlap was 85.6±1.6% and 81.2±2.1% for two and three replicates, respectively. Removing singletons significantly increased the overlap for both (~1-3%, p<0.001). Increasing the sequencing depth to 160,000 reads by deep sequencing increased OTU overlap both when sequence abundance was considered (95%) and when not (44%). However, if singletons were not removed the overlap between two technical replicates (not considering sequence abundance) plateaus at 39% with 30,000 sequences. Diversity measures were not affected by the low overlap as α-diversities were similar among technical replicates while β-diversities (Bray-Curtis) were much smaller among technical replicates than among treatment replicates (e.g., 0.269 vs. 0.374). Higher diversity coverage, but lower OTU overlap, was <span class="hlt">observed</span> when replicates were sequenced in separate runs. Detrended correspondence analysis indicated that while there was considerable variation among technical replicates, the <span class="hlt">reproducibility</span> was sufficient for detecting treatment effects for the samples examined. These results suggest that although there is variation among technical replicates, amplicon sequencing on MiSeq is useful for analyzing microbial community structure if used appropriately and</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/28882498','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/28882498"><span><span class="hlt">Reproducibility</span> of the dynamics of facial expressions in unilateral facial palsy.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Alagha, M A; Ju, X; Morley, S; Ayoub, A</p> <p>2018-02-01</p> <p>The aim of this study was to assess the <span class="hlt">reproducibility</span> of non-verbal facial expressions in unilateral facial paralysis using dynamic four-dimensional (4D) imaging. The Di4D system was used to record five facial expressions of 20 adult patients. The system captured 60 three-dimensional (3D) images per second; each facial expression took 3-4seconds which was recorded in real time. Thus a set of 180 3D facial images was generated for each expression. The procedure was repeated after 30min to assess the <span class="hlt">reproducibility</span> of the expressions. A mathematical facial mesh consisting of thousands of quasi-point 'vertices' was conformed to the face in order to determine the morphological characteristics in a comprehensive manner. The vertices were tracked throughout the sequence of the 180 images. Five key 3D facial frames from each sequence of images were analyzed. Comparisons were made between the first and second capture of each facial expression to assess the <span class="hlt">reproducibility</span> of facial movements. Corresponding images were aligned using partial Procrustes analysis, and the root mean square distance between them was calculated and analyzed statistically (paired Student t-test, P<0.05). Facial expressions of lip purse, cheek puff, and raising of eyebrows were <span class="hlt">reproducible</span>. Facial expressions of maximum smile and forceful eye closure were not <span class="hlt">reproducible</span>. The limited coordination of various groups of facial muscles contributed to the lack of <span class="hlt">reproducibility</span> of these facial expressions. 4D imaging is a useful clinical tool for the assessment of facial expressions. Copyright © 2017 International Association of Oral and Maxillofacial Surgeons. Published by Elsevier Ltd. All rights reserved.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3292844','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3292844"><span><span class="hlt">Reproducible</span> computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p></p> <p>2011-01-01</p> <p>Background The increasing use of computational simulation experiments to inform modern biological research creates new challenges to annotate, archive, share and <span class="hlt">reproduce</span> such experiments. The recently published Minimum Information About a Simulation Experiment (MIASE) proposes a minimal set of information that should be provided to allow the reproduction of simulation experiments among users and software tools. Results In this article, we present the Simulation Experiment Description Markup Language (SED-ML). SED-ML encodes in a computer-readable exchange format the information required by MIASE to enable reproduction of simulation experiments. It has been developed as a community project and it is defined in a detailed technical specification and additionally provides an XML schema. The version of SED-ML described in this publication is Level 1 Version 1. It covers the description of the most frequent type of simulation experiments in the area, namely time course simulations. SED-ML documents specify which models to use in an experiment, modifications to apply on the models before using them, which simulation procedures to run on each model, what analysis results to output, and how the results should be presented. These descriptions are independent of the underlying model implementation. SED-ML is a software-independent format for encoding the description of simulation experiments; it is not specific to particular simulation tools. Here, we demonstrate that with the growing software support for SED-ML we can effectively exchange executable simulation descriptions. Conclusions With SED-ML, software can exchange simulation experiment descriptions, enabling the validation and reuse of simulation experiments in different tools. Authors of papers reporting simulation experiments can make their simulation protocols available for other scientists to <span class="hlt">reproduce</span> the results. Because SED-ML is agnostic about exact modeling language(s) used, experiments covering models from</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/22172142','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/22172142"><span><span class="hlt">Reproducible</span> computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Waltemath, Dagmar; Adams, Richard; Bergmann, Frank T; Hucka, Michael; Kolpakov, Fedor; Miller, Andrew K; Moraru, Ion I; Nickerson, David; Sahle, Sven; Snoep, Jacky L; Le Novère, Nicolas</p> <p>2011-12-15</p> <p>The increasing use of computational simulation experiments to inform modern biological research creates new challenges to annotate, archive, share and <span class="hlt">reproduce</span> such experiments. The recently published Minimum Information About a Simulation Experiment (MIASE) proposes a minimal set of information that should be provided to allow the reproduction of simulation experiments among users and software tools. In this article, we present the Simulation Experiment Description Markup Language (SED-ML). SED-ML encodes in a computer-readable exchange format the information required by MIASE to enable reproduction of simulation experiments. It has been developed as a community project and it is defined in a detailed technical specification and additionally provides an XML schema. The version of SED-ML described in this publication is Level 1 Version 1. It covers the description of the most frequent type of simulation experiments in the area, namely time course simulations. SED-ML documents specify which models to use in an experiment, modifications to apply on the models before using them, which simulation procedures to run on each model, what analysis results to output, and how the results should be presented. These descriptions are independent of the underlying model implementation. SED-ML is a software-independent format for encoding the description of simulation experiments; it is not specific to particular simulation tools. Here, we demonstrate that with the growing software support for SED-ML we can effectively exchange executable simulation descriptions. With SED-ML, software can exchange simulation experiment descriptions, enabling the validation and reuse of simulation experiments in different tools. Authors of papers reporting simulation experiments can make their simulation protocols available for other scientists to <span class="hlt">reproduce</span> the results. Because SED-ML is agnostic about exact modeling language(s) used, experiments covering models from different fields of research</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3812573','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3812573"><span>Electrical Detection of C-Reactive Protein Using a Single Free-Standing, Thermally Controlled Piezoresistive Microcantilever for Highly <span class="hlt">Reproducible</span> and <span class="hlt">Accurate</span> Measurements</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Yen, Yi-Kuang; Lai, Yu-Cheng; Hong, Wei-Ting; Pheanpanitporn, Yotsapoom; Chen, Chuin-Shan; Huang, Long-Sun</p> <p>2013-01-01</p> <p>This study demonstrates a novel method for electrical detection of C-reactive protein (CRP) as a means of identifying an infection in the body, or as a cardiovascular disease risk assay. The method uses a single free-standing, thermally controlled piezoresistive microcantilever biosensor. In a commonly used sensing arrangement of conventional dual cantilevers in the Wheatstone bridge circuit, reference and gold-coated sensing cantilevers that inherently have heterogeneous surface materials and different multilayer structures may yield independent responses to the liquid environmental changes of chemical substances, flow field and temperature, leading to unwanted signal disturbance for biosensing targets. In this study, the single free-standing microcantilever for biosensing applications is employed to resolve the dual-beam problem of individual responses in chemical solutions and, in a thermally controlled system, to maintain its sensor performance due to the sensitive temperature effect. With this type of single temperature-controlled microcantilever sensor, the electrical detection of various CRP concentrations from 1 μg/mL to 200 μg/mL was performed, which covers the clinically relevant range. Induced surface stresses were measured at between 0.25 N/m and 3.4 N/m with high <span class="hlt">reproducibility</span>. Moreover, the binding affinity (KD) of CRP and anti-CRP interaction was found to be 18.83 ± 2.99 μg/mL, which agreed with results in previous reported studies. This biosensing technique thus proves valuable in detecting inflammation, and in cardiovascular disease risk assays. PMID:23899933</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/23009734','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/23009734"><span><span class="hlt">Reproducibility</span> of intraocular pressure peak and fluctuation of the water-drinking test.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Hatanaka, Marcelo; Alencar, Luciana M; De Moraes, Carlos G; Susanna, Remo</p> <p>2013-01-01</p> <p>The water-drinking test has been used as a stress test to evaluate the drainage system of the eye. However, in order to be clinically applicable,a test must provide <span class="hlt">reproducible</span> results with consistent measurements. This study was performed to verify the <span class="hlt">reproducibility</span> of intraocular pressure peaks and fluctuation detected during the water-drinking test in patients with ocular hypertension and open-angle glaucoma. A prospective analysis of patients in a tertiary care unit for glaucoma treatment. Twenty-four ocular hypertension and 64 open-angle glaucoma patients not under treatment. The water-drinking test was performed in 2 consecutive days by the same examiners in patients not under treatment. <span class="hlt">Reproducibility</span> was assessed using the intraclass correlation coefficient. Peak and fluctuation of intraocular pressure obtained with the water-drinking test were analysed for <span class="hlt">reproducibility</span>. Eighty-eight eyes from 24 ocular hypertension and 64 open-angle glaucoma patients not under treatment were evaluated. Test and retest intraocular pressure peak values were 28.38 ± 4.64 and 28.38 ± 4.56 mmHg, respectively (P = 1.00). Test and retest intraocular pressure fluctuation values were 5.75 ± 3.9 and 4.99 ± 2.7 mmHg, respectively (P = 0.06). Based on intraclass coefficient, <span class="hlt">reproducibility</span> was excellent for peak intraocular pressure (intraclass correlation coefficient = 0.79) and fair for intraocular pressure fluctuation (intraclass correlation coefficient = 0.37). Intraocular pressure peaks detected during the water-drinking test presented excellent <span class="hlt">reproducibility</span>, whereas the <span class="hlt">reproducibility</span> of fluctuation was considered fair. © 2012 The Authors. Clinical and Experimental Ophthalmology © 2012 Royal Australian and New Zealand College of Ophthalmologists.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2006cmns...11...60N','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2006cmns...11...60N"><span><span class="hlt">Reproducibility</span>, Controllability, and Optimization of Lenr Experiments</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Nagel, David J.</p> <p>2006-02-01</p> <p>Low-energy nuclear reaction (LENR) measurements are significantly and increasingly <span class="hlt">reproducible</span>. Practical control of the production of energy or materials by LENR has yet to be demonstrated. Minimization of costly inputs and maximization of desired outputs of LENR remain for future developments.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/25892714','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/25892714"><span>A nondestructive, <span class="hlt">reproducible</span> method of measuring joint reaction force at the distal radioulnar joint.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Canham, Colin D; Schreck, Michael J; Maqsoodi, Noorullah; Doolittle, Madison; Olles, Mark; Elfar, John C</p> <p>2015-06-01</p> <p>To develop a nondestructive method of measuring distal radioulnar joint (DRUJ) joint reaction force (JRF) that preserves all periarticular soft tissues and more <span class="hlt">accurately</span> reflects in vivo conditions. Eight fresh-frozen human cadaveric limbs were obtained. A threaded Steinmann pin was placed in the middle of the lateral side of the distal radius transverse to the DRUJ. A second pin was placed into the middle of the medial side of the distal ulna colinear to the distal radial pin. Specimens were mounted onto a tensile testing machine using a custom fixture. A uniaxial distracting force was applied across the DRUJ while force and displacement were simultaneously measured. Force-displacement curves were generated and a best-fit polynomial was solved to determine JRF. All force-displacement curves demonstrated an initial high slope where relatively large forces were required to distract the joint. This ended with an inflection point followed by a linear area with a low slope, where small increases in force generated larger amounts of distraction. Each sample was measured 3 times and there was high <span class="hlt">reproducibility</span> between repeated measurements. The average baseline DRUJ JRF was 7.5 N (n = 8). This study describes a <span class="hlt">reproducible</span> method of measuring DRUJ reaction forces that preserves all periarticular stabilizing structures. This technique of JRF measurement may also be suited for applications in the small joints of the wrist and hand. Changes in JRF can alter native joint mechanics and lead to pathology. Reliable methods of measuring these forces are important for determining how pathology and surgical interventions affect joint biomechanics. Copyright © 2015 American Society for Surgery of the Hand. Published by Elsevier Inc. All rights reserved.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/21803255','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/21803255"><span>Cervical vertebrae maturation method morphologic criteria: poor <span class="hlt">reproducibility</span>.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Nestman, Trenton S; Marshall, Steven D; Qian, Fang; Holton, Nathan; Franciscus, Robert G; Southard, Thomas E</p> <p>2011-08-01</p> <p>The cervical vertebrae maturation (CVM) method has been advocated as a predictor of peak mandibular growth. A careful review of the literature showed potential methodologic errors that might influence the high reported <span class="hlt">reproducibility</span> of the CVM method, and we recently established that the <span class="hlt">reproducibility</span> of the CVM method was poor when these potential errors were eliminated. The purpose of this study was to further investigate the <span class="hlt">reproducibility</span> of the individual vertebral patterns. In other words, the purpose was to determine which of the individual CVM vertebral patterns could be classified reliably and which could not. Ten practicing orthodontists, trained in the CVM method, evaluated the morphology of cervical vertebrae C2 through C4 from 30 cephalometric radiographs using questions based on the CVM method. The Fleiss kappa statistic was used to assess interobserver agreement when evaluating each cervical vertebrae morphology question for each subject. The Kendall coefficient of concordance was used to assess the level of interobserver agreement when determining a "derived CVM stage" for each subject. Interobserver agreement was high for assessment of the lower borders of C2, C3, and C4 that were either flat or curved in the CVM method, but interobserver agreement was low for assessment of the vertebral bodies of C3 and C4 when they were either trapezoidal, rectangular horizontal, square, or rectangular vertical; this led to the overall poor <span class="hlt">reproducibility</span> of the CVM method. These findings were reflected in the Fleiss kappa statistic. Furthermore, nearly 30% of the time, individual morphologic criteria could not be combined to generate a final CVM stage because of incompatible responses to the 5 questions. Intraobserver agreement in this study was only 62%, on average, when the inconclusive stagings were excluded as disagreements. Intraobserver agreement was worse (44%) when the inconclusive stagings were included as disagreements. For the group of subjects</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/16166438','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/16166438"><span>Diagnostic evaluation of HER-2 as a molecular target: an assessment of accuracy and <span class="hlt">reproducibility</span> of laboratory testing in large, prospective, randomized clinical trials.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Press, Michael F; Sauter, Guido; Bernstein, Leslie; Villalobos, Ivonne E; Mirlacher, Martina; Zhou, Jian-Yuan; Wardeh, Rooba; Li, Yong-Tian; Guzman, Roberta; Ma, Yanling; Sullivan-Halley, Jane; Santiago, Angela; Park, Jinha M; Riva, Alessandro; Slamon, Dennis J</p> <p>2005-09-15</p> <p>To critically assess the accuracy and <span class="hlt">reproducibility</span> of human epidermal growth factor receptor type 2 (HER-2) testing in outside/local community-based hospitals versus two centralized reference laboratories and its effect on selection of women for trastuzumab (Herceptin)-based clinical trials. Breast cancer specimens from 2,600 women were prospectively evaluated by fluorescence in situ hybridization (FISH) for entry into Breast Cancer International Research Group (BCIRG) clinical trials for HER-2-directed therapies. HER-2 gene amplification by FISH was <span class="hlt">observed</span> in 657 of the 2,502 (26%) breast cancers successfully analyzed. Among 2,243 breast cancers with central laboratory immunohistochemistry (10H8-IHC) analysis, 504 (22.54%) showed overexpression (2+ or 3+). Outside/local laboratories assessed HER-2 status by immunohistochemistry in 1,536 of these cases and by FISH in 131 cases. Overall, the HER-2 alteration status determined by outside/local immunohistochemistry showed a 79% agreement rate [kappa statistic, 0.56; 95% confidence interval (95% CI), 0.52-0.60], with FISH done by the central laboratories. The agreement rate comparing BCIRG central laboratory 10H8-IHC and outside/local laboratory immunohistochemistry was 77.5% (kappa statistic, 0.51; 95% CI, 0.46-0.55). Finally, HER-2 status, determined by unspecified FISH assay methods at outside/local laboratories, showed a 92% agreement rate (kappa statistic, 0.83; 95% CI, 0.73-0.93), with FISH done at the BCIRG central laboratories. Compared with the HER-2 status determined at centralized BCIRG reference laboratories, these results indicate superiority of FISH to <span class="hlt">accurately</span> and <span class="hlt">reproducibly</span> assess tumors for the HER-2 alteration at outside/local laboratories for entry to clinical trials.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4389237','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4389237"><span>Local cooling and warming effects of forests based on satellite <span class="hlt">observations</span></span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Li, Yan; Zhao, Maosheng; Motesharrei, Safa; Mu, Qiaozhen; Kalnay, Eugenia; Li, Shuangcheng</p> <p>2015-01-01</p> <p>The biophysical effects of forests on climate have been extensively studied with climate models. However, models cannot <span class="hlt">accurately</span> <span class="hlt">reproduce</span> local climate effects due to their coarse spatial resolution and uncertainties, and field <span class="hlt">observations</span> are valuable but often insufficient due to their limited coverage. Here we present new evidence acquired from global satellite data to analyse the biophysical effects of forests on local climate. Results show that tropical forests have a strong cooling effect throughout the year; temperate forests show moderate cooling in summer and moderate warming in winter with net cooling annually; and boreal forests have strong warming in winter and moderate cooling in summer with net warming annually. The spatiotemporal cooling or warming effects are mainly driven by the two competing biophysical effects, evapotranspiration and albedo, which in turn are strongly influenced by rainfall and snow. Implications of our satellite-based study could be useful for informing local forestry policies. PMID:25824529</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/18976308','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/18976308"><span>Twelve-hour <span class="hlt">reproducibility</span> of retinal and optic nerve blood flow parameters in healthy individuals.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Luksch, Alexandra; Lasta, Michael; Polak, Kaija; Fuchsjäger-Mayrl, Gabriele; Polska, Elzbieta; Garhöfer, Gerhard; Schmetterer, Leopold</p> <p>2009-11-01</p> <p>The aim of the present study was to investigate the <span class="hlt">reproducibility</span> and potential diurnal variation of optic nerve head and retinal blood flow parameters in healthy individuals over a period of 12 hr. We measured optic nerve head and retinal blood flow parameters in 16 healthy male non-smoking individuals at five time-points during the day (08:00, 11:00, 14:00, 17:00 and 20:00 hr). Outcome parameters were perimacular white blood cell flux (as assessed with the blue field entoptic technique), blood velocities in retinal veins (as assessed with bi-directional laser Doppler velocimetry), retinal arterial and venous diameters (as assessed with the retinal vessel analyser), optic nerve head blood flow, volume and velocity (as assessed with single point and scanning laser Doppler flowmetry) and blood velocities in the central retinal artery (as assessed with colour Doppler imaging). The coefficient of variation and the maximum change from baseline in an individual were calculated for each outcome parameter. No diurnal variation in optic nerve head or retinal blood flow was <span class="hlt">observed</span> with any of the techniques employed. Coefficients of variation were between 1.6% and 18.5% for all outcome parameters. The maximum change from baseline in an individual was much higher, ranging from 3.7% to 78.2%. Our data indicate that in healthy individuals the selected techniques provide adequate <span class="hlt">reproducibility</span> to be used in clinical studies. However, in patients with eye diseases and reduced vision the <span class="hlt">reproducibility</span> may be considerably worse.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/20398067','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/20398067"><span>Natural progression of blood-induced joint damage in patients with haemophilia: clinical relevance and <span class="hlt">reproducibility</span> of three-dimensional gait analysis.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Lobet, S; Detrembleur, C; Francq, B; Hermans, C</p> <p>2010-09-01</p> <p>A major complication in haemophilia is the destruction of joint cartilage because of recurrent intraarticular and intramuscular bleeds. Therefore, joint assessment is critical to quantify the extent of joint damage, which has traditionally been evaluated using both radiological and clinical joint scores. Our study aimed to evaluate the natural progression of haemophilic arthopathy using three-dimensional gait analysis (3DGA) and to assess the <span class="hlt">reproducibility</span> of this technique. We hypothesized that the musculoskeletal function was relatively stable in patients with haemophilia. Eighteen adults with established haemophilic arthropathies were evaluated twice by 3DGA (mean follow-up: 18 +/- 5 weeks). Unexpectedly, our findings revealed infraclinical deterioration of gait pattern, characterized by a 3.2% decrease in the recovery index, which is indicative of the subject's ability to save energy while walking. A tendency towards modification of segmental joint function was also <span class="hlt">observed</span>. Gait analysis was sufficiently <span class="hlt">reproducible</span> with regards to spatiotemporal parameters as well as kinetic, mechanical and energetic gait variables. The kinematic variables were <span class="hlt">reproducible</span> in both the sagittal and frontal planes. In conclusion, 3DGA is a <span class="hlt">reproducible</span> tool to assess abnormal gait patterns and monitor natural disease progression in haemophilic patients.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=5842833','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=5842833"><span>Actinic cheilitis: proposition and <span class="hlt">reproducibility</span> of a clinical criterion</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Poitevin, Nádia Antunes; Rodrigues, Mariana Sudati; Weigert, Karen Loureiro; Macedo, Carmen Lúcia Rodrigues; dos Santos, Rubem Beraldo</p> <p>2017-01-01</p> <p>Objectives/Aims: The actinic cheilitis (AC) is a precancerous lip lesion seen as a consequence of chronic sun exposure. Clinically, the border between the lip’s skin and the semimucosa could be blurred; in the more aggressive cases, leucoplakia and ulcers also represent its clinical feature. It seems that no clinical criterion is universally accepted for this disease yet. Therefore, this study was carried out to make a proposition of a clinical score to actinic cheilitis (Grade I starting from dryness of vermilion to endured ulcers representing Grade IV) and to assess its <span class="hlt">reproducibility</span>. Materials and Methods: Fifty subjects were assessed, most of whom were male, Caucasian farmers, with an average age of 46.12 (18–74) years. The obtained data were analysed by means of descriptive statistics and by Kappa test to assess the inter-examiners and the clinical Golden-Pattern concordance (95% CI). Results: During calibration, 15 patients were examined three times a week by each examiner (4) until Kappa test <span class="hlt">observed</span> k=0.8 or more. In the main experiment, the inter-examiner concordance was classified between good (k=0.779; P<0.05) and very good (k=0.925; P<0.05) from the 35 examined subjects. With the Golden-Pattern, it was considered very good (k=0.812; P<0.05 to k=0.925; P<0.05). Discussion: Four examiners with different experiences could strongly suggest that after adequate calibration, it could be well applied by examiners with as much experience as a dental student. Conclusions: The authors concluded that the proposed classification was easily applied and had a very good <span class="hlt">reproducibility</span>. PMID:29607086</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_17");'>17</a></li> <li><a href="#" onclick='return showDiv("page_18");'>18</a></li> <li class="active"><span>19</span></li> <li><a href="#" onclick='return showDiv("page_20");'>20</a></li> <li><a href="#" onclick='return showDiv("page_21");'>21</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_19 --> <div id="page_20" class="hiddenDiv"> <div class="row"> <div class="col-sm-12"> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_18");'>18</a></li> <li><a href="#" onclick='return showDiv("page_19");'>19</a></li> <li class="active"><span>20</span></li> <li><a href="#" onclick='return showDiv("page_21");'>21</a></li> <li><a href="#" onclick='return showDiv("page_22");'>22</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div> </div> <div class="row"> <div class="col-sm-12"> <ol class="result-class" start="381"> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2015AGUFMGC33G..06M','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2015AGUFMGC33G..06M"><span>Evaluation of Statistical Downscaling Skill at <span class="hlt">Reproducing</span> Extreme Events</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>McGinnis, S. A.; Tye, M. R.; Nychka, D. W.; Mearns, L. O.</p> <p>2015-12-01</p> <p>Climate model outputs usually have much coarser spatial resolution than is needed by impacts models. Although higher resolution can be achieved using regional climate models for dynamical downscaling, further downscaling is often required. The final resolution gap is often closed with a combination of spatial interpolation and bias correction, which constitutes a form of statistical downscaling. We use this technique to downscale regional climate model data and evaluate its skill in <span class="hlt">reproducing</span> extreme events. We downscale output from the North American Regional Climate Change Assessment Program (NARCCAP) dataset from its native 50-km spatial resolution to the 4-km resolution of University of Idaho's METDATA gridded surface meterological dataset, which derives from the PRISM and NLDAS-2 <span class="hlt">observational</span> datasets. We operate on the major variables used in impacts analysis at a daily timescale: daily minimum and maximum temperature, precipitation, humidity, pressure, solar radiation, and winds. To interpolate the data, we use the patch recovery method from the Earth System Modeling Framework (ESMF) regridding package. We then bias correct the data using Kernel Density Distribution Mapping (KDDM), which has been shown to exhibit superior overall performance across multiple metrics. Finally, we evaluate the skill of this technique in <span class="hlt">reproducing</span> extreme events by comparing raw and downscaled output with meterological station data in different bioclimatic regions according to the the skill scores defined by Perkins et al in 2013 for evaluation of AR4 climate models. We also investigate techniques for improving bias correction of values in the tails of the distributions. These techniques include binned kernel density estimation, logspline kernel density estimation, and transfer functions constructed by fitting the tails with a generalized pareto distribution.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=5487227','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=5487227"><span><span class="hlt">Reproducibility</span> of abdominal fat assessment by ultrasound and computed tomography</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Mauad, Fernando Marum; Chagas-Neto, Francisco Abaeté; Benedeti, Augusto César Garcia Saab; Nogueira-Barbosa, Marcello Henrique; Muglia, Valdair Francisco; Carneiro, Antonio Adilton Oliveira; Muller, Enrico Mattana; Elias Junior, Jorge</p> <p>2017-01-01</p> <p>Objective: To test the accuracy and <span class="hlt">reproducibility</span> of ultrasound and computed tomography (CT) for the quantification of abdominal fat in correlation with the anthropometric, clinical, and biochemical assessments. Materials and Methods: Using ultrasound and CT, we determined the thickness of subcutaneous and intra-abdominal fat in 101 subjects-of whom 39 (38.6%) were men and 62 (61.4%) were women-with a mean age of 66.3 years (60-80 years). The ultrasound data were correlated with the anthropometric, clinical, and biochemical parameters, as well as with the areas measured by abdominal CT. Results: Intra-abdominal thickness was the variable for which the correlation with the areas of abdominal fat was strongest (i.e., the correlation coefficient was highest). We also tested the <span class="hlt">reproducibility</span> of ultrasound and CT for the assessment of abdominal fat and found that CT measurements of abdominal fat showed greater <span class="hlt">reproducibility</span>, having higher intraobserver and interobserver reliability than had the ultrasound measurements. There was a significant correlation between ultrasound and CT, with a correlation coefficient of 0.71. Conclusion: In the assessment of abdominal fat, the intraobserver and interobserver reliability were greater for CT than for ultrasound, although both methods showed high accuracy and good <span class="hlt">reproducibility</span>. PMID:28670024</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/27538512','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/27538512"><span><span class="hlt">Reproducible</span> detection of disease-associated markers from gene expression data.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Omae, Katsuhiro; Komori, Osamu; Eguchi, Shinto</p> <p>2016-08-18</p> <p>Detection of disease-associated markers plays a crucial role in gene screening for biological studies. Two-sample test statistics, such as the t-statistic, are widely used to rank genes based on gene expression data. However, the resultant gene ranking is often not <span class="hlt">reproducible</span> among different data sets. Such irreproducibility may be caused by disease heterogeneity. When we divided data into two subsets, we found that the signs of the two t-statistics were often reversed. Focusing on such instability, we proposed a sign-sum statistic that counts the signs of the t-statistics for all possible subsets. The proposed method excludes genes affected by heterogeneity, thereby improving the <span class="hlt">reproducibility</span> of gene ranking. We compared the sign-sum statistic with the t-statistic by a theoretical evaluation of the upper confidence limit. Through simulations and applications to real data sets, we show that the sign-sum statistic exhibits superior performance. We derive the sign-sum statistic for getting a robust gene ranking. The sign-sum statistic gives more <span class="hlt">reproducible</span> ranking than the t-statistic. Using simulated data sets we show that the sign-sum statistic excludes hetero-type genes well. Also for the real data sets, the sign-sum statistic performs well in a viewpoint of ranking <span class="hlt">reproducibility</span>.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/29494624','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/29494624"><span>Selection and testing of reference genes for <span class="hlt">accurate</span> RT-qPCR in rice seedlings under iron toxicity.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Santos, Fabiane Igansi de Castro Dos; Marini, Naciele; Santos, Railson Schreinert Dos; Hoffman, Bianca Silva Fernandes; Alves-Ferreira, Marcio; de Oliveira, Antonio Costa</p> <p>2018-01-01</p> <p>Reverse Transcription quantitative PCR (RT-qPCR) is a technique for gene expression profiling with high sensibility and <span class="hlt">reproducibility</span>. However, to obtain <span class="hlt">accurate</span> results, it depends on data normalization by using endogenous reference genes whose expression is constitutive or invariable. Although the technique is widely used in plant stress analyzes, the stability of reference genes for iron toxicity in rice (Oryza sativa L.) has not been thoroughly investigated. Here, we tested a set of candidate reference genes for use in rice under this stressful condition. The test was performed using four distinct methods: NormFinder, BestKeeper, geNorm and the comparative ΔCt. To achieve <span class="hlt">reproducible</span> and reliable results, Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines were followed. Valid reference genes were found for shoot (P2, OsGAPDH and OsNABP), root (OsEF-1a, P8 and OsGAPDH) and root+shoot (OsNABP, OsGAPDH and P8) enabling us to perform further reliable studies for iron toxicity in both indica and japonica subspecies. The importance of the study of other than the traditional endogenous genes for use as normalizers is also shown here.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=5832244','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=5832244"><span>Selection and testing of reference genes for <span class="hlt">accurate</span> RT-qPCR in rice seedlings under iron toxicity</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>dos Santos, Fabiane Igansi de Castro; Marini, Naciele; dos Santos, Railson Schreinert; Hoffman, Bianca Silva Fernandes; Alves-Ferreira, Marcio</p> <p>2018-01-01</p> <p>Reverse Transcription quantitative PCR (RT-qPCR) is a technique for gene expression profiling with high sensibility and <span class="hlt">reproducibility</span>. However, to obtain <span class="hlt">accurate</span> results, it depends on data normalization by using endogenous reference genes whose expression is constitutive or invariable. Although the technique is widely used in plant stress analyzes, the stability of reference genes for iron toxicity in rice (Oryza sativa L.) has not been thoroughly investigated. Here, we tested a set of candidate reference genes for use in rice under this stressful condition. The test was performed using four distinct methods: NormFinder, BestKeeper, geNorm and the comparative ΔCt. To achieve <span class="hlt">reproducible</span> and reliable results, Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines were followed. Valid reference genes were found for shoot (P2, OsGAPDH and OsNABP), root (OsEF-1a, P8 and OsGAPDH) and root+shoot (OsNABP, OsGAPDH and P8) enabling us to perform further reliable studies for iron toxicity in both indica and japonica subspecies. The importance of the study of other than the traditional endogenous genes for use as normalizers is also shown here. PMID:29494624</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/24685835','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/24685835"><span><span class="hlt">Reproducibility</span> studies for experimental epitope detection in macrophages (EDIM).</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Japink, Dennis; Nap, Marius; Sosef, Meindert N; Nelemans, Patty J; Coy, Johannes F; Beets, Geerard; von Meyenfeldt, Maarten F; Leers, Math P G</p> <p>2014-05-01</p> <p>We have recently described epitope detection in macrophages (EDIM) by flow cytometry. This is a promising tool for the diagnosis and follow-up of malignancies. However, biological and technical validation is warranted before clinical applicability can be explored. The pre-analytic and analytic phases were investigated. Five different aspects were assessed: blood sample stability, intra-individual variability in healthy persons, intra-assay variation, inter-assay variation and assay transferability. The post-analytic phase was already partly standardized and described in an earlier study. The outcomes in the pre-analytic phase showed that samples are stable for 24h after venipuncture. Biological variation over time was similar to that of serum tumor marker assays; each patient has a baseline value. Intra-assay variation showed good <span class="hlt">reproducibility</span>, while inter-assay variation showed <span class="hlt">reproducibility</span> similar to that of to established serum tumor marker assays. Furthermore, the assay showed excellent transferability between analyzers. Under optimal analytic conditions the EDIM method is technically stable, <span class="hlt">reproducible</span> and transferable. Biological variation over time needs further assessment in future work. Copyright © 2014 Elsevier B.V. All rights reserved.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/25256068','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/25256068"><span><span class="hlt">Reproducibility</span> of retinal nerve fiber layer thickness measures using eye tracking in children with nonglaucomatous optic neuropathy.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Rajjoub, Raneem D; Trimboli-Heidler, Carmelina; Packer, Roger J; Avery, Robert A</p> <p>2015-01-01</p> <p>To determine the intra- and intervisit <span class="hlt">reproducibility</span> of circumpapillary retinal nerve fiber layer (RNFL) thickness measures using eye tracking-assisted spectral-domain optical coherence tomography (SD OCT) in children with nonglaucomatous optic neuropathy. Prospective longitudinal study. Circumpapillary RNFL thickness measures were acquired with SD OCT using the eye-tracking feature at 2 separate study visits. Children with normal and abnormal vision (visual acuity ≥ 0.2 logMAR above normal and/or visual field loss) who demonstrated clinical and radiographic stability were enrolled. Intra- and intervisit <span class="hlt">reproducibility</span> was calculated for the global average and 9 anatomic sectors by calculating the coefficient of variation and intraclass correlation coefficient. Forty-two subjects (median age 8.6 years, range 3.9-18.2 years) met inclusion criteria and contributed 62 study eyes. Both the abnormal and normal vision cohort demonstrated the lowest intravisit coefficient of variation for the global RNFL thickness. Intervisit <span class="hlt">reproducibility</span> remained good for those with normal and abnormal vision, although small but statistically significant increases in the coefficient of variation were <span class="hlt">observed</span> for multiple anatomic sectors in both cohorts. The magnitude of visual acuity loss was significantly associated with the global (ß = 0.026, P < .01) and temporal sector coefficient of variation (ß = 0.099, P < .01). SD OCT with eye tracking demonstrates highly <span class="hlt">reproducible</span> RNFL thickness measures. Subjects with vision loss demonstrate greater intra- and intervisit variability than those with normal vision. Copyright © 2015 Elsevier Inc. All rights reserved.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2018SPIE10575E..0BC','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2018SPIE10575E..0BC"><span>Empirical evaluation of cross-site <span class="hlt">reproducibility</span> in radiomic features for characterizing prostate MRI</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Chirra, Prathyush; Leo, Patrick; Yim, Michael; Bloch, B. Nicolas; Rastinehad, Ardeshir R.; Purysko, Andrei; Rosen, Mark; Madabhushi, Anant; Viswanath, Satish</p> <p>2018-02-01</p> <p>The recent advent of radiomics has enabled the development of prognostic and predictive tools which use routine imaging, but a key question that still remains is how <span class="hlt">reproducible</span> these features may be across multiple sites and scanners. This is especially relevant in the context of MRI data, where signal intensity values lack tissue specific, quantitative meaning, as well as being dependent on acquisition parameters (magnetic field strength, image resolution, type of receiver coil). In this paper we present the first empirical study of the <span class="hlt">reproducibility</span> of 5 different radiomic feature families in a multi-site setting; specifically, for characterizing prostate MRI appearance. Our cohort comprised 147 patient T2w MRI datasets from 4 different sites, all of which were first pre-processed to correct acquisition-related for artifacts such as bias field, differing voxel resolutions, as well as intensity drift (non-standardness). 406 3D voxel wise radiomic features were extracted and evaluated in a cross-site setting to determine how <span class="hlt">reproducible</span> they were within a relatively homogeneous non-tumor tissue region; using 2 different measures of <span class="hlt">reproducibility</span>: Multivariate Coefficient of Variation and Instability Score. Our results demonstrated that Haralick features were most <span class="hlt">reproducible</span> between all 4 sites. By comparison, Laws features were among the least <span class="hlt">reproducible</span> between sites, as well as performing highly variably across their entire parameter space. Similarly, the Gabor feature family demonstrated good cross-site <span class="hlt">reproducibility</span>, but for certain parameter combinations alone. These trends indicate that despite extensive pre-processing, only a subset of radiomic features and associated parameters may be <span class="hlt">reproducible</span> enough for use within radiomics-based machine learning classifier schemes.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/26803369','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/26803369"><span>Novel burn device for rapid, <span class="hlt">reproducible</span> burn wound generation.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Kim, J Y; Dunham, D M; Supp, D M; Sen, C K; Powell, H M</p> <p>2016-03-01</p> <p>Scarring following full thickness burns leads to significant reductions in range of motion and quality of life for burn patients. To effectively study scar development and the efficacy of anti-scarring treatments in a large animal model (female red Duroc pigs), <span class="hlt">reproducible</span>, uniform, full-thickness, burn wounds are needed to reduce variability in <span class="hlt">observed</span> results that occur with burn depth. Prior studies have proposed that initial temperature of the burner, contact time with skin, thermal capacity of burner material, and the amount of pressure applied to the skin need to be strictly controlled to ensure <span class="hlt">reproducibility</span>. The purpose of this study was to develop a new burner that enables temperature and pressure to be digitally controlled and monitored in real-time throughout burn wound creation and compare it to a standard burn device. A custom burn device was manufactured with an electrically heated burn stylus and a temperature control feedback loop via an electronic microstat. Pressure monitoring was controlled by incorporation of a digital scale into the device, which measured downward force. The standard device was comprised of a heat resistant handle with a long rod connected to the burn stylus, which was heated using a hot plate. To quantify skin surface temperature and internal stylus temperature as a function of contact time, the burners were heated to the target temperature (200±5°C) and pressed into the skin for 40s to create the thermal injuries. Time to reach target temperature and elapsed time between burns were recorded. In addition, each unit was evaluated for <span class="hlt">reproducibility</span> within and across three independent users by generating burn wounds at contact times spanning from 5 to 40s at a constant pressure and at pressures of 1 or 3lbs with a constant contact time of 40s. Biopsies were collected for histological analysis and burn depth quantification using digital image analysis (ImageJ). The custom burn device maintained both its internal</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=5207794','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=5207794"><span>Novel burn device for rapid, <span class="hlt">reproducible</span> burn wound generation</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Kim, J.Y.; Dunham, D.M.; Supp, D.M.; Sen, C.K.; Powell, H.M.</p> <p>2016-01-01</p> <p>Introduction Scarring following full thickness burns leads to significant reductions in range of motion and quality of life for burn patients. To effectively study scar development and the efficacy of anti-scarring treatments in a large animal model (female red Duroc pigs), <span class="hlt">reproducible</span>, uniform, full-thickness, burn wounds are needed to reduce variability in <span class="hlt">observed</span> results that occur with burn depth. Prior studies have proposed that initial temperature of the burner, contact time with skin, thermal capacity of burner material, and the amount of pressure applied to the skin need to be strictly controlled to ensure <span class="hlt">reproducibility</span>. The purpose of this study was to develop a new burner that enables temperature and pressure to be digitally controlled and monitored in real-time throughout burn wound creation and compare it to a standard burn device. Methods A custom burn device was manufactured with an electrically heated burn stylus and a temperature control feedback loop via an electronic microstat. Pressure monitoring was controlled by incorporation of a digital scale into the device, which measured downward force. The standard device was comprised of a heat resistant handle with a long rod connected to the burn stylus, which was heated using a hot plate. To quantify skin surface temperature and internal stylus temperature as a function of contact time, the burners were heated to the target temperature (200 ± 5 °C) and pressed into the skin for 40 s to create the thermal injuries. Time to reach target temperature and elapsed time between burns were recorded. In addition, each unit was evaluated for <span class="hlt">reproducibility</span> within and across three independent users by generating burn wounds at contact times spanning from 5 to 40 s at a constant pressure and at pressures of 1 or 3 lbs with a constant contact time of 40 s. Biopsies were collected for histological analysis and burn depth quantification using digital image analysis (ImageJ). Results The custom burn device</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.osti.gov/biblio/1003724-graded-interface-models-more-accurate-determination-van-der-waals-london-dispersion-interactions-across-grain-boundaries','SCIGOV-STC'); return false;" href="https://www.osti.gov/biblio/1003724-graded-interface-models-more-accurate-determination-van-der-waals-london-dispersion-interactions-across-grain-boundaries"><span>Graded Interface Models for more <span class="hlt">accurate</span> Determination of van der Waals-London Dispersion Interactions across Grain Boundaries</span></a></p> <p><a target="_blank" href="http://www.osti.gov/search">DOE Office of Scientific and Technical Information (OSTI.GOV)</a></p> <p>van Benthem, Klaus; Tan, Guolong; French, Roger H</p> <p>2006-01-01</p> <p>Attractive van der Waals V London dispersion interactions between two half crystals arise from local physical property gradients within the interface layer separating the crystals. Hamaker coefficients and London dispersion energies were quantitatively determined for 5 and near- 13 grain boundaries in SrTiO3 by analysis of spatially resolved valence electron energy-loss spectroscopy (VEELS) data. From the experimental data, local complex dielectric functions were determined, from which optical properties can be locally analysed. Both local electronic structures and optical properties revealed gradients within the grain boundary cores of both investigated interfaces. The obtained results show that even in the presence ofmore » atomically structured grain boundary cores with widths of less than 1 nm, optical properties have to be represented with gradual changes across the grain boundary structures to quantitatively <span class="hlt">reproduce</span> <span class="hlt">accurate</span> van der Waals V London dispersion interactions. London dispersion energies of the order of 10% of the apparent interface energies of SrTiO3 were <span class="hlt">observed</span>, demonstrating their significance in the grain boundary formation process. The application of different models to represent optical property gradients shows that long-range van der Waals V London dispersion interactions scale significantly with local, i.e atomic length scale property variations.« less</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/29481544','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/29481544"><span>Examining the <span class="hlt">Reproducibility</span> of 6 Published Studies in Public Health Services and Systems Research.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Harris, Jenine K; B Wondmeneh, Sarah; Zhao, Yiqiang; Leider, Jonathon P</p> <p>2018-02-23</p> <p>Research replication, or repeating a study de novo, is the scientific standard for building evidence and identifying spurious results. While replication is ideal, it is often expensive and time consuming. <span class="hlt">Reproducibility</span>, or reanalysis of data to verify published findings, is one proposed minimum alternative standard. While a lack of research <span class="hlt">reproducibility</span> has been identified as a serious and prevalent problem in biomedical research and a few other fields, little work has been done to examine the <span class="hlt">reproducibility</span> of public health research. We examined <span class="hlt">reproducibility</span> in 6 studies from the public health services and systems research subfield of public health research. Following the methods described in each of the 6 papers, we computed the descriptive and inferential statistics for each study. We compared our results with the original study results and examined the percentage differences in descriptive statistics and differences in effect size, significance, and precision of inferential statistics. All project work was completed in 2017. We found consistency between original and <span class="hlt">reproduced</span> results for each paper in at least 1 of the 4 areas examined. However, we also found some inconsistency. We identified incorrect transcription of results and omitting detail about data management and analyses as the primary contributors to the inconsistencies. Increasing <span class="hlt">reproducibility</span>, or reanalysis of data to verify published results, can improve the quality of science. Researchers, journals, employers, and funders can all play a role in improving the <span class="hlt">reproducibility</span> of science through several strategies including publishing data and statistical code, using guidelines to write clear and complete methods sections, conducting <span class="hlt">reproducibility</span> reviews, and incentivizing <span class="hlt">reproducible</span> science.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/18840068','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/18840068"><span><span class="hlt">Reproducibility</span> of electronic tooth colour measurements.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Ratzmann, Anja; Klinke, Thomas; Schwahn, Christian; Treichel, Anja; Gedrange, Tomasz</p> <p>2008-10-01</p> <p>Clinical methods of investigation, such as tooth colour determination, should be simple, quick and <span class="hlt">reproducible</span>. The determination of tooth colours usually relies upon manual comparison of a patient's tooth colour with a colour ring. After some days, however, measurement results frequently lack unequivocal <span class="hlt">reproducibility</span>. This study aimed to examine an electronic method for reliable colour measurement. The colours of the teeth 14 to 24 were determined by three different examiners in 10 subjects using the colour measuring device Shade Inspector. In total, 12 measurements per tooth were taken. Two measurement time points were scheduled to be taken, namely at study onset (T(1)) and after 6 months (T(2)). At either time point, two measurement series per subject were taken by the different examiners at 2-week intervals. The inter-examiner and intra-examiner agreement of the measurement results was assessed. The concordance for lightness and colour intensity (saturation) was represented by the intra-class correlation coefficient. The categorical variable colour shade (hue) was assessed using the kappa statistic. The study results show that tooth colour can be measured independently of the examiner. Good agreement was found between the examiners.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/27542906','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/27542906"><span><span class="hlt">Reproducibility</span> assessment of brain responses to visual food stimuli in adults with overweight and obesity.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Drew Sayer, R; Tamer, Gregory G; Chen, Ningning; Tregellas, Jason R; Cornier, Marc-Andre; Kareken, David A; Talavage, Thomas M; McCrory, Megan A; Campbell, Wayne W</p> <p>2016-10-01</p> <p>The brain's reward system influences ingestive behavior and subsequently obesity risk. Functional magnetic resonance imaging (fMRI) is a common method for investigating brain reward function. This study sought to assess the <span class="hlt">reproducibility</span> of fasting-state brain responses to visual food stimuli using BOLD fMRI. A priori brain regions of interest included bilateral insula, amygdala, orbitofrontal cortex, caudate, and putamen. Fasting-state fMRI and appetite assessments were completed by 28 women (n = 16) and men (n = 12) with overweight or obesity on 2 days. <span class="hlt">Reproducibility</span> was assessed by comparing mean fasting-state brain responses and measuring test-retest reliability of these responses on the two testing days. Mean fasting-state brain responses on day 2 were reduced compared with day 1 in the left insula and right amygdala, but mean day 1 and day 2 responses were not different in the other regions of interest. With the exception of the left orbitofrontal cortex response (fair reliability), test-retest reliabilities of brain responses were poor or unreliable. fMRI-measured responses to visual food cues in adults with overweight or obesity show relatively good mean-level <span class="hlt">reproducibility</span> but considerable within-subject variability. Poor test-retest reliability reduces the likelihood of <span class="hlt">observing</span> true correlations and increases the necessary sample sizes for studies. © 2016 The Obesity Society.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=5039059','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=5039059"><span><span class="hlt">Reproducibility</span> assessment of brain responses to visual food stimuli in adults with overweight and obesity</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Sayer, R Drew; Tamer, Gregory G; Chen, Ningning; Tregellas, Jason R; Cornier, Marc-Andre; Kareken, David A; Talavage, Thomas M; McCrory, Megan A; Campbell, Wayne W</p> <p>2016-01-01</p> <p>Objective The brain’s reward system influences ingestive behavior and subsequently, obesity risk. Functional magnetic resonance imaging (fMRI) is a common method for investigating brain reward function. We sought to assess the <span class="hlt">reproducibility</span> of fasting-state brain responses to visual food stimuli using BOLD fMRI. Methods A priori brain regions of interest included bilateral insula, amygdala, orbitofrontal cortex, caudate, and putamen. Fasting-state fMRI and appetite assessments were completed by 28 women (n=16) and men (n=12) with overweight or obesity on 2 days. <span class="hlt">Reproducibility</span> was assessed by comparing mean fasting-state brain responses and measuring test-retest reliability of these responses on the 2 testing days. Results Mean fasting-state brain responses on Day 2 were reduced compared to Day 1 in the left insula and right amygdala, but mean Day 1 and Day 2 responses were not different in the other regions of interest. With the exception of the left orbitofrontal cortex response (fair reliability), test-retest reliabilities of brain responses were poor or unreliable. Conclusion fMRI-measured responses to visual food cues in adults with overweight or obesity show relatively good mean-level <span class="hlt">reproducibility</span>, but considerable within-subject variability. Poor test-retest reliability reduces the likelihood of <span class="hlt">observing</span> true correlations and increases the necessary sample sizes for studies. PMID:27542906</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.osti.gov/servlets/purl/1426894','SCIGOV-STC'); return false;" href="https://www.osti.gov/servlets/purl/1426894"><span>Spectral neighbor analysis method for automated generation of quantum-<span class="hlt">accurate</span> interatomic potentials</span></a></p> <p><a target="_blank" href="http://www.osti.gov/search">DOE Office of Scientific and Technical Information (OSTI.GOV)</a></p> <p>Thompson, Aidan P.; Swiler, Laura P.; Trott, Christian R.</p> <p>2015-03-15</p> <p>Here, we present a new interatomic potential for solids and liquids called Spectral Neighbor Analysis Potential (SNAP). The SNAP potential has a very general form and uses machine-learning techniques to <span class="hlt">reproduce</span> the energies, forces, and stress tensors of a large set of small configurations of atoms, which are obtained using high-accuracy quantum electronic structure (QM) calculations. The local environment of each atom is characterized by a set of bispectrum components of the local neighbor density projected onto a basis of hyperspherical harmonics in four dimensions. The bispectrum components are the same bond-orientational order parameters employed by the GAP potential [1].more » The SNAP potential, unlike GAP, assumes a linear relationship between atom energy and bispectrum components. The linear SNAP coefficients are determined using weighted least-squares linear regression against the full QM training set. This allows the SNAP potential to be fit in a robust, automated manner to large QM data sets using many bispectrum components. The calculation of the bispectrum components and the SNAP potential are implemented in the LAMMPS parallel molecular dynamics code. We demonstrate that a previously unnoticed symmetry property can be exploited to reduce the computational cost of the force calculations by more than one order of magnitude. We present results for a SNAP potential for tantalum, showing that it <span class="hlt">accurately</span> <span class="hlt">reproduces</span> a range of commonly calculated properties of both the crystalline solid and the liquid phases. In addition, unlike simpler existing potentials, SNAP correctly predicts the energy barrier for screw dislocation migration in BCC tantalum.« less</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.osti.gov/biblio/22465612-spectral-neighbor-analysis-method-automated-generation-quantum-accurate-interatomic-potentials','SCIGOV-STC'); return false;" href="https://www.osti.gov/biblio/22465612-spectral-neighbor-analysis-method-automated-generation-quantum-accurate-interatomic-potentials"><span>Spectral neighbor analysis method for automated generation of quantum-<span class="hlt">accurate</span> interatomic potentials</span></a></p> <p><a target="_blank" href="http://www.osti.gov/search">DOE Office of Scientific and Technical Information (OSTI.GOV)</a></p> <p>Thompson, A.P., E-mail: athomps@sandia.gov; Swiler, L.P., E-mail: lpswile@sandia.gov; Trott, C.R., E-mail: crtrott@sandia.gov</p> <p>2015-03-15</p> <p>We present a new interatomic potential for solids and liquids called Spectral Neighbor Analysis Potential (SNAP). The SNAP potential has a very general form and uses machine-learning techniques to <span class="hlt">reproduce</span> the energies, forces, and stress tensors of a large set of small configurations of atoms, which are obtained using high-accuracy quantum electronic structure (QM) calculations. The local environment of each atom is characterized by a set of bispectrum components of the local neighbor density projected onto a basis of hyperspherical harmonics in four dimensions. The bispectrum components are the same bond-orientational order parameters employed by the GAP potential [1]. Themore » SNAP potential, unlike GAP, assumes a linear relationship between atom energy and bispectrum components. The linear SNAP coefficients are determined using weighted least-squares linear regression against the full QM training set. This allows the SNAP potential to be fit in a robust, automated manner to large QM data sets using many bispectrum components. The calculation of the bispectrum components and the SNAP potential are implemented in the LAMMPS parallel molecular dynamics code. We demonstrate that a previously unnoticed symmetry property can be exploited to reduce the computational cost of the force calculations by more than one order of magnitude. We present results for a SNAP potential for tantalum, showing that it <span class="hlt">accurately</span> <span class="hlt">reproduces</span> a range of commonly calculated properties of both the crystalline solid and the liquid phases. In addition, unlike simpler existing potentials, SNAP correctly predicts the energy barrier for screw dislocation migration in BCC tantalum.« less</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2015JCoPh.285..316T','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2015JCoPh.285..316T"><span>Spectral neighbor analysis method for automated generation of quantum-<span class="hlt">accurate</span> interatomic potentials</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Thompson, A. P.; Swiler, L. P.; Trott, C. R.; Foiles, S. M.; Tucker, G. J.</p> <p>2015-03-01</p> <p>We present a new interatomic potential for solids and liquids called Spectral Neighbor Analysis Potential (SNAP). The SNAP potential has a very general form and uses machine-learning techniques to <span class="hlt">reproduce</span> the energies, forces, and stress tensors of a large set of small configurations of atoms, which are obtained using high-accuracy quantum electronic structure (QM) calculations. The local environment of each atom is characterized by a set of bispectrum components of the local neighbor density projected onto a basis of hyperspherical harmonics in four dimensions. The bispectrum components are the same bond-orientational order parameters employed by the GAP potential [1]. The SNAP potential, unlike GAP, assumes a linear relationship between atom energy and bispectrum components. The linear SNAP coefficients are determined using weighted least-squares linear regression against the full QM training set. This allows the SNAP potential to be fit in a robust, automated manner to large QM data sets using many bispectrum components. The calculation of the bispectrum components and the SNAP potential are implemented in the LAMMPS parallel molecular dynamics code. We demonstrate that a previously unnoticed symmetry property can be exploited to reduce the computational cost of the force calculations by more than one order of magnitude. We present results for a SNAP potential for tantalum, showing that it <span class="hlt">accurately</span> <span class="hlt">reproduces</span> a range of commonly calculated properties of both the crystalline solid and the liquid phases. In addition, unlike simpler existing potentials, SNAP correctly predicts the energy barrier for screw dislocation migration in BCC tantalum.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/24847245','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/24847245"><span><span class="hlt">Reproducibility</span> of graph metrics of human brain structural networks.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Duda, Jeffrey T; Cook, Philip A; Gee, James C</p> <p>2014-01-01</p> <p>Recent interest in human brain connectivity has led to the application of graph theoretical analysis to human brain structural networks, in particular white matter connectivity inferred from diffusion imaging and fiber tractography. While these methods have been used to study a variety of patient populations, there has been less examination of the <span class="hlt">reproducibility</span> of these methods. A number of tractography algorithms exist and many of these are known to be sensitive to user-selected parameters. The methods used to derive a connectivity matrix from fiber tractography output may also influence the resulting graph metrics. Here we examine how these algorithm and parameter choices influence the <span class="hlt">reproducibility</span> of proposed graph metrics on a publicly available test-retest dataset consisting of 21 healthy adults. The dice coefficient is used to examine topological similarity of constant density subgraphs both within and between subjects. Seven graph metrics are examined here: mean clustering coefficient, characteristic path length, largest connected component size, assortativity, global efficiency, local efficiency, and rich club coefficient. The <span class="hlt">reproducibility</span> of these network summary measures is examined using the intraclass correlation coefficient (ICC). Graph curves are created by treating the graph metrics as functions of a parameter such as graph density. Functional data analysis techniques are used to examine differences in graph measures that result from the choice of fiber tracking algorithm. The graph metrics consistently showed good levels of <span class="hlt">reproducibility</span> as measured with ICC, with the exception of some instability at low graph density levels. The global and local efficiency measures were the most robust to the choice of fiber tracking algorithm.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2018JASMS..29..405M','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2018JASMS..29..405M"><span>On the <span class="hlt">Reproducibility</span> of Label-Free Quantitative Cross-Linking/Mass Spectrometry</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Müller, Fränze; Fischer, Lutz; Chen, Zhuo Angel; Auchynnikava, Tania; Rappsilber, Juri</p> <p>2018-02-01</p> <p>Quantitative cross-linking/mass spectrometry (QCLMS) is an emerging approach to study conformational changes of proteins and multi-subunit complexes. Distinguishing protein conformations requires <span class="hlt">reproducibly</span> identifying and quantifying cross-linked peptides. Here we analyzed the variation between multiple cross-linking reactions using bis[sulfosuccinimidyl] suberate (BS3)-cross-linked human serum albumin (HSA) and evaluated how <span class="hlt">reproducible</span> cross-linked peptides can be identified and quantified by LC-MS analysis. To make QCLMS accessible to a broader research community, we developed a workflow that integrates the established software tools MaxQuant for spectra preprocessing, Xi for cross-linked peptide identification, and finally Skyline for quantification (MS1 filtering). Out of the 221 unique residue pairs identified in our sample, 124 were subsequently quantified across 10 analyses with coefficient of variation (CV) values of 14% (injection replica) and 32% (reaction replica). Thus our results demonstrate that the <span class="hlt">reproducibility</span> of QCLMS is in line with the <span class="hlt">reproducibility</span> of general quantitative proteomics and we establish a robust workflow for MS1-based quantitation of cross-linked peptides.</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_18");'>18</a></li> <li><a href="#" onclick='return showDiv("page_19");'>19</a></li> <li class="active"><span>20</span></li> <li><a href="#" onclick='return showDiv("page_21");'>21</a></li> <li><a href="#" onclick='return showDiv("page_22");'>22</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_20 --> <div id="page_21" class="hiddenDiv"> <div class="row"> <div class="col-sm-12"> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_19");'>19</a></li> <li><a href="#" onclick='return showDiv("page_20");'>20</a></li> <li class="active"><span>21</span></li> <li><a href="#" onclick='return showDiv("page_22");'>22</a></li> <li><a href="#" onclick='return showDiv("page_23");'>23</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div> </div> <div class="row"> <div class="col-sm-12"> <ol class="result-class" start="401"> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4937183','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4937183"><span>High- and <span class="hlt">Reproducible</span>-Performance Graphene/II-VI Semiconductor Film Hybrid Photodetectors</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Huang, Fan; Jia, Feixiang; Cai, Caoyuan; Xu, Zhihao; Wu, Congjun; Ma, Yang; Fei, Guangtao; Wang, Min</p> <p>2016-01-01</p> <p>High- and <span class="hlt">reproducible</span>-performance photodetectors are critical to the development of many technologies, which mainly include one-dimensional (1D) nanostructure based and film based photodetectors. The former suffer from a huge performance variation because the performance is quite sensitive to the synthesis microenvironment of 1D nanostructure. Herein, we show that the graphene/semiconductor film hybrid photodetectors not only possess a high performance but also have a <span class="hlt">reproducible</span> performance. As a demo, the as-produced graphene/ZnS film hybrid photodetector shows a high responsivity of 1.7 × 107 A/W and a fast response speed of 50 ms, and shows a highly <span class="hlt">reproducible</span> performance, in terms of narrow distribution of photocurrent (38–65 μA) and response speed (40–60 ms) for 20 devices. Graphene/ZnSe film and graphene/CdSe film hybrid photodetectors fabricated by this method also show a high and <span class="hlt">reproducible</span> performance. The general method is compatible with the conventional planar process, and would be easily standardized and thus pay a way for the photodetector applications. PMID:27349692</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/15649545','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/15649545"><span><span class="hlt">Reproducibility</span> of the spectral components of the electroencephalogram during driver fatigue.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Lal, Saroj K L; Craig, Ashley</p> <p>2005-02-01</p> <p>To date, no study has tested the <span class="hlt">reproducibility</span> of EEG changes that occur during driver fatigue. For the EEG changes to be useful in the development of a fatigue countermeasure device the EEG response during each onset period of fatigue in individuals needs to be <span class="hlt">reproducible</span>. It should be noted that fatigue during driving is not a continuous process but consists of successive episodes of 'microsleeps' where the subject may go in and out of a fatigue state. The aim of the present study was to investigate the <span class="hlt">reproducibility</span> of fatigue during driving in both professional and non-professional drivers. Thirty five non-professional drivers and twenty professional drivers were tested during two separate sessions of a driver simulator task. EEG, EOG and behavioural measurements of fatigue were obtained during the driving task. The results showed high <span class="hlt">reproducibility</span> for the delta and theta bands (r>0.95) in both groups of drivers. The results are discussed in light of implications for future studies and for the development of an EEG based fatigue countermeasure device.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/23905679','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/23905679"><span>The repeatability and <span class="hlt">reproducibility</span> of the BioRID IIg in a repeatable laboratory seat based on a production car seat.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Hynd, David; Depinet, Paul; Lorenz, Bernd</p> <p>2013-01-01</p> <p>The United Nations Economic Commission for Europe Informal Group on GTR No. 7 Phase 2 are working to define a build level for the BioRID II rear impact (whiplash) crash test dummy that ensures repeatable and <span class="hlt">reproducible</span> performance in a test procedure that has been proposed for future legislation. This includes the specification of dummy hardware, as well as the development of comprehensive certification procedures for the dummy. This study evaluated whether the dummy build level and certification procedures deliver the desired level of repeatability and <span class="hlt">reproducibility</span>. A custom-designed laboratory seat was made using the seat base, back, and head restraint from a production car seat to ensure a representative interface with the dummy. The seat back was reinforced for use in multiple tests and the recliner mechanism was replaced by an external spring-damper mechanism. A total of 65 tests were performed with 6 BioRID IIg dummies using the draft GTR No.7 sled pulse and seating procedure. All dummies were subject to the build, maintenance, and certification procedures defined by the Informal Group. The test condition was highly repeatable, with a very repeatable pulse, a well-controlled seat back response, and minimal <span class="hlt">observed</span> degradation of seat foams. The results showed qualitatively reasonable repeatability and <span class="hlt">reproducibility</span> for the upper torso and head accelerations, as well as for T1 Fx and upper neck Fx . However, <span class="hlt">reproducibility</span> was not acceptable for T1 and upper neck Fz or for T1 and upper neck My . The Informal Group has not selected injury or seat assessment criteria for use with BioRID II, so it is not known whether these channels would be used in the regulation. However, the ramping-up behavior of the dummy showed poor <span class="hlt">reproducibility</span>, which would be expected to affect the <span class="hlt">reproducibility</span> of dummy measurements in general. Pelvis and spine characteristics were found to significantly influence the dummy measurements for which poor <span class="hlt">reproducibility</span> was</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/28705995','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/28705995"><span><span class="hlt">Reproducibility</span> of airway luminal size in asthma measured by HRCT.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Brown, Robert H; Henderson, Robert J; Sugar, Elizabeth A; Holbrook, Janet T; Wise, Robert A</p> <p>2017-10-01</p> <p>Brown RH, Henderson RJ, Sugar EA, Holbrook JT, Wise RA, on behalf of the American Lung Association Airways Clinical Research Centers. <span class="hlt">Reproducibility</span> of airway luminal size in asthma measured by HRCT. J Appl Physiol 123: 876-883, 2017. First published July 13, 2017; doi:10.1152/japplphysiol.00307.2017.-High-resolution CT (HRCT) is a well-established imaging technology used to measure lung and airway morphology in vivo. However, there is a surprising lack of studies examining HRCT <span class="hlt">reproducibility</span>. The CPAP Trial was a multicenter, randomized, three-parallel-arm, sham-controlled 12-wk clinical trial to assess the use of a nocturnal continuous positive airway pressure (CPAP) device on airway reactivity to methacholine. The lack of a treatment effect of CPAP on clinical or HRCT measures provided an opportunity for the current analysis. We assessed the <span class="hlt">reproducibility</span> of HRCT imaging over 12 wk. Intraclass correlation coefficients (ICCs) were calculated for individual airway segments, individual lung lobes, both lungs, and air trapping. The ICC [95% confidence interval (CI)] for airway luminal size at total lung capacity ranged from 0.95 (0.91, 0.97) to 0.47 (0.27, 0.69). The ICC (95% CI) for airway luminal size at functional residual capacity ranged from 0.91 (0.85, 0.95) to 0.32 (0.11, 0.65). The ICC measurements for airway distensibility index and wall thickness were lower, ranging from poor (0.08) to moderate (0.63) agreement. The ICC for air trapping at functional residual capacity was 0.89 (0.81, 0.94) and varied only modestly by lobe from 0.76 (0.61, 0.87) to 0.95 (0.92, 0.97). In stable well-controlled asthmatic subjects, it is possible to <span class="hlt">reproducibly</span> image unstimulated airway luminal areas over time, by region, and by size at total lung capacity throughout the lungs. Therefore, any changes in luminal size on repeat CT imaging are more likely due to changes in disease state and less likely due to normal variability. NEW & NOTEWORTHY There is a surprising lack</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.osti.gov/servlets/purl/902922','DOE-PATENT-XML'); return false;" href="https://www.osti.gov/servlets/purl/902922"><span><span class="hlt">Reproducible</span>, high performance patch antenna array apparatus and method of fabrication</span></a></p> <p><a target="_blank" href="http://www.osti.gov/doepatents">DOEpatents</a></p> <p>Strassner, II, Bernd H.</p> <p>2007-01-23</p> <p>A <span class="hlt">reproducible</span>, high-performance patch antenna array apparatus includes a patch antenna array provided on a unitary dielectric substrate, and a feed network provided on the same unitary substrate and proximity coupled to the patch antenna array. The <span class="hlt">reproducibility</span> is enhanced by using photolithographic patterning and etching to produce both the patch antenna array and the feed network.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/27977067','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/27977067"><span>Morphology Engineering: A Route to Highly <span class="hlt">Reproducible</span> and High Efficiency Perovskite Solar Cells.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Bi, Dongqin; Luo, Jingshan; Zhang, Fei; Magrez, Arnaud; Athanasopoulou, Evangelia Nefeli; Hagfeldt, Anders; Grätzel, Michael</p> <p>2017-04-10</p> <p>Despite the rapid increase in the performance of perovskite solar cells (PSC), they still suffer from low lab-to-lab or people-to-people <span class="hlt">reproducibility</span>. Aiming for a universal condition to high-performance devices, we investigated the morphology evolution of a composite perovskite by tuning annealing temperature and precursor concentration of the perovskite film. Here, we introduce thermal annealing as a powerful tool to generate a well-controlled excess of PbI 2 in the perovskite formulation and show that this benefits the photovoltaic performance. We demonstrated the correlation between the film microstructure and electronic property and device performance. An optimized average grain size/thickness aspect ratio of the perovskite crystallite is identified, which brings about a highly <span class="hlt">reproducible</span> power conversion efficiency (PCE) of 19.5 %, with a certified value of 19.08 %. Negligible hysteresis and outstanding morphology stability are <span class="hlt">observed</span> with these devices. These findings lay the foundation for further boosting the PCE of PSC and can be very instructive for fabrication of high-quality perovskite films for a variety of applications, such as light-emitting diodes, field-effect transistors, and photodetectors. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2000ITNS...47.1567B','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2000ITNS...47.1567B"><span>Covariance approximation for fast and <span class="hlt">accurate</span> computation of channelized Hotelling <span class="hlt">observer</span> statistics</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Bonetto, P.; Qi, Jinyi; Leahy, R. M.</p> <p>2000-08-01</p> <p>Describes a method for computing linear <span class="hlt">observer</span> statistics for maximum a posteriori (MAP) reconstructions of PET images. The method is based on a theoretical approximation for the mean and covariance of MAP reconstructions. In particular, the authors derive here a closed form for the channelized Hotelling <span class="hlt">observer</span> (CHO) statistic applied to 2D MAP images. The theoretical analysis models both the Poission statistics of PET data and the inhomogeneity of tracer uptake. The authors show reasonably good correspondence between these theoretical results and Monte Carlo studies. The accuracy and low computational cost of the approximation allow the authors to analyze the <span class="hlt">observer</span> performance over a wide range of operating conditions and parameter settings for the MAP reconstruction algorithm.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.osti.gov/pages/biblio/1326029-time-dependent-mhd-simulations-solar-wind-outflow-using-interplanetary-scintillation-observations','SCIGOV-DOEP'); return false;" href="https://www.osti.gov/pages/biblio/1326029-time-dependent-mhd-simulations-solar-wind-outflow-using-interplanetary-scintillation-observations"><span>Time-dependent MHD simulations of the solar wind outflow using interplanetary scintillation <span class="hlt">observations</span></span></a></p> <p><a target="_blank" href="http://www.osti.gov/pages">DOE PAGES</a></p> <p>Kim, Tae K.; Pogorelov, Nikolai V.; Borovikov, Sergey N.; ...</p> <p>2012-11-20</p> <p>Numerical modeling of the heliosphere is a critical component of space weather forecasting. The accuracy of heliospheric models can be improved by using realistic boundary conditions and confirming the results with in situ spacecraft measurements. To <span class="hlt">accurately</span> <span class="hlt">reproduce</span> the solar wind (SW) plasma flow near Earth, we need realistic, time-dependent boundary conditions at a fixed distance from the Sun. We may prepare such boundary conditions using SW speed and density determined from interplanetary scintillation (IPS) <span class="hlt">observations</span>, magnetic field derived from photospheric magnetograms, and temperature estimated from its correlation with SW speed. In conclusion, we present here the time-dependent MHD simulationmore » results obtained by using the 2011 IPS data from the Solar-Terrestrial Environment Laboratory as time-varying inner boundary conditions and compare the simulated data at Earth with OMNI data (spacecraft-interspersed, near-Earth solar wind data).« less</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/28229336','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/28229336"><span>Relevant principal factors affecting the <span class="hlt">reproducibility</span> of insect primary culture.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Ogata, Norichika; Iwabuchi, Kikuo</p> <p>2017-06-01</p> <p>The primary culture of insect cells often suffers from problems with poor <span class="hlt">reproducibility</span> in the quality of the final cell preparations. The cellular composition of the explants (cell number and cell types), surgical methods (surgical duration and surgical isolation), and physiological and genetic differences between donors may be critical factors affecting the <span class="hlt">reproducibility</span> of culture. However, little is known about where biological variation (interindividual differences between donors) ends and technical variation (variance in replication of culture conditions) begins. In this study, we cultured larval fat bodies from the Japanese rhinoceros beetle, Allomyrina dichotoma, and evaluated, using linear mixed models, the effect of interindividual variation between donors on the <span class="hlt">reproducibility</span> of the culture. We also performed transcriptome analysis of the hemocyte-like cells mainly seen in the cultures using RNA sequencing and ultrastructural analyses of hemocytes using a transmission electron microscope, revealing that the cultured cells have many characteristics of insect hemocytes.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.osti.gov/servlets/purl/1177498','DOE-PATENT-XML'); return false;" href="https://www.osti.gov/servlets/purl/1177498"><span>Wire like link for cycle <span class="hlt">reproducible</span> and cycle <span class="hlt">accurate</span> hardware accelerator</span></a></p> <p><a target="_blank" href="http://www.osti.gov/doepatents">DOEpatents</a></p> <p>Asaad, Sameh; Kapur, Mohit; Parker, Benjamin D</p> <p>2015-04-07</p> <p>First and second field programmable gate arrays are provided which implement first and second blocks of a circuit design to be simulated. The field programmable gate arrays are operated at a first clock frequency and a wire like link is provided to send a plurality of signals between them. The wire like link includes a serializer, on the first field programmable gate array, to serialize the plurality of signals; a deserializer on the second field programmable gate array, to deserialize the plurality of signals; and a connection between the serializer and the deserializer. The serializer and the deserializer are operated at a second clock frequency, greater than the first clock frequency, and the second clock frequency is selected such that latency of transmission and reception of the plurality of signals is less than the period corresponding to the first clock frequency.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2017ApJ...841...39Y','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2017ApJ...841...39Y"><span>Disk Masses around Solar-mass Stars are Underestimated by CO <span class="hlt">Observations</span></span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Yu, Mo; Evans, Neal J., II; Dodson-Robinson, Sarah E.; Willacy, Karen; Turner, Neal J.</p> <p>2017-05-01</p> <p>Gas in protostellar disks provides the raw material for giant planet formation and controls the dynamics of the planetesimal-building dust grains. <span class="hlt">Accurate</span> gas mass measurements help map the <span class="hlt">observed</span> properties of planet-forming disks onto the formation environments of known exoplanets. Rare isotopologues of carbon monoxide (CO) have been used as gas mass tracers for disks in the Lupus star-forming region, with an assumed interstellar CO/H2 abundance ratio. Unfortunately, <span class="hlt">observations</span> of T-Tauri disks show that CO abundance is not interstellar, a finding <span class="hlt">reproduced</span> by models that show CO abundance decreasing both with distance from the star and as a function of time. Here, we present radiative transfer simulations that assess the accuracy of CO-based disk mass measurements. We find that the combination of CO chemical depletion in the outer disk and optically thick emission from the inner disk leads <span class="hlt">observers</span> to underestimate gas mass by more than an order of magnitude if they use the standard assumptions of interstellar CO/H2 ratio and optically thin emission. Furthermore, CO abundance changes on million-year timescales, introducing an age/mass degeneracy into <span class="hlt">observations</span>. To reach a factor of a few accuracy for CO-based disk mass measurements, we suggest that <span class="hlt">observers</span> and modelers adopt the following strategies: (1) select low-J transitions; (2) <span class="hlt">observe</span> multiple CO isotopologues and use either intensity ratios or normalized line profiles to diagnose CO chemical depletion; and (3) use spatially resolved <span class="hlt">observations</span> to measure the CO-abundance distribution.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2016AGUFMIN43A1680Y','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2016AGUFMIN43A1680Y"><span>Exploring the Role of Information Professionals in Improving Research <span class="hlt">Reproducibility</span>:A Case Study in Geosciences</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Yan, A.; West, J.</p> <p>2016-12-01</p> <p>The validity of Geosciences research is of great significance to general public and policy-makers. In an earlier study, we surveyed 136 faculty and graduate students in geosciences. The result indicated that nearly 80% of respondents who had ever <span class="hlt">reproduced</span> a published study had failed at least one time in <span class="hlt">reproducing</span>, suggesting a general lack of research <span class="hlt">reproducibility</span> in geosciences. Although there is much enthusiasm for creation of technologies such as workflow system, literate programming, and cloud-based system to facilitate <span class="hlt">reproducibility</span>, much less emphasis has been placed on the information services essential for meaningful use of these tools. Library and Information Science (LIS) has a rich tradition of providing customized service for research communities. LIS professionals such as academic librarians have made strong contribution to resources locating, software recommending, data curation, metadata guidance, project management, submission review and author training. In particular, university libraries have been actively developing tools and offering guidelines, consultations, and trainings on Data Management Plan (DMP) required by National Science Foundation (NSF). And effective data management is a significant first step towards <span class="hlt">reproducible</span> research. Hereby we argue that LIS professionals may be well-positioned to assist researchers to make their research <span class="hlt">reproducible</span>. In this study, we aim to answer the question: how can LIS professionals assist geoscience researchers in making their research capable of being <span class="hlt">reproduced</span>? We first synthesize different definitions of "<span class="hlt">reproducibility</span>" and provide a conceptual framework of "<span class="hlt">reproducibility</span>" in geosciences to resolve some of the misunderstandings around related terminology. Using a case study approach, we then examine 1) university librarians' technical skills, domain knowledge, professional activities, together with their awareness of, readiness for, and attitudes towards research <span class="hlt">reproducibility</span> and</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2003EAEJA.....3381L','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2003EAEJA.....3381L"><span><span class="hlt">Accurate</span> determination of the geoid undulation N</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Lambrou, E.; Pantazis, G.; Balodimos, D. D.</p> <p>2003-04-01</p> <p>This work is related to the activities of the CERGOP Study Group Geodynamics of the Balkan Peninsula, presents a method for the determination of the variation ΔN and, indirectly, of the geoid undulation N with an accuracy of a few millimeters. It is based on the determination of the components xi, eta of the deflection of the vertical using modern geodetic instruments (digital total station and GPS receiver). An analysis of the method is given. Accuracy of the order of 0.01arcsec in the estimated values of the astronomical coordinates Φ and Δ is achieved. The result of applying the proposed method in an area around Athens is presented. In this test application, a system is used which takes advantage of the capabilities of modern geodetic instruments. The GPS receiver permits the determination of the geodetic coordinates at a chosen reference system and, in addition, provides <span class="hlt">accurate</span> timing information. The astronomical <span class="hlt">observations</span> are performed through a digital total station with electronic registering of angles and time. The required accuracy of the values of the coordinates is achieved in about four hours of fieldwork. In addition, the instrumentation is lightweight, easily transportable and can be setup in the field very quickly. Combined with a stream-lined data reduction procedure and the use of up-to-date astrometric data, the values of the components xi, eta of the deflection of the vertical and, eventually, the changes ΔN of the geoid undulation are determined easily and <span class="hlt">accurately</span>. In conclusion, this work demonstrates that it is quite feasible to create an <span class="hlt">accurate</span> map of the geoid undulation, especially in areas that present large geoid variations and other methods are not capable to give <span class="hlt">accurate</span> and reliable results.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/25345402','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/25345402"><span>Influence of parameter settings in voxel-based morphometry 8. Using DARTEL and region-of-interest on <span class="hlt">reproducibility</span> in gray matter volumetry.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Goto, M; Abe, O; Aoki, S; Hayashi, N; Miyati, T; Takao, H; Matsuda, H; Yamashita, F; Iwatsubo, T; Mori, H; Kunimatsu, A; Ino, K; Yano, K; Ohtomo, K</p> <p>2015-01-01</p> <p>To investigate whether <span class="hlt">reproducibility</span> of gray matter volumetry is influenced by parameter settings for VBM 8 using Diffeomorphic Anatomical Registration Through Exponentiated Lie Algebra (DARTEL) with region-of-interest (ROI) analyses. We prepared three-dimensional T1-weighted magnetic resonance images (3D-T1WIs) of 21 healthy subjects. All subjects were imaged with each of five MRI systems. Voxel-based morphometry 8 (VBM 8) and WFU PickAtlas software were used for gray matter volumetry. The bilateral ROI labels used were those provided as default settings with the software: Frontal Lobe, Hippocampus, Occipital Lobe, Orbital Gyrus, Parietal Lobe, Putamen, and Temporal Lobe. All 3D-T1WIs were segmented to gray matter with six parameters of VBM 8, with each parameter having between three and eight selectable levels. <span class="hlt">Reproducibility</span> was evaluated as the standard deviation (mm³) of measured values for the five MRI systems. <span class="hlt">Reproducibility</span> was influenced by 'Bias regularization (BiasR)', 'Bias FWHM', and 'De-noising filter' settings, but not by 'MRF weighting', 'Sampling distance', or 'Warping regularization' settings. <span class="hlt">Reproducibility</span> in BiasR was influenced by ROI. Superior <span class="hlt">reproducibility</span> was <span class="hlt">observed</span> in Frontal Lobe with the BiasR1 setting, and in Hippocampus, Parietal Lobe, and Putamen with the BiasR3*, BiasR1, and BiasR5 settings, respectively. <span class="hlt">Reproducibility</span> of gray matter volumetry was influenced by parameter settings in VBM 8 using DARTEL and ROI. In multi-center studies, the use of appropriate settings in VBM 8 with DARTEL results in reduced scanner effect.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/26008923','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/26008923"><span><span class="hlt">Reproducibility</span> of the water drinking test.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Muñoz, C R; Macias, J H; Hartleben, C</p> <p>2015-11-01</p> <p>To investigate the <span class="hlt">reproducibility</span> of the water drinking test in determining intraocular pressure peaks and fluctuation. It has been suggested that there is limited agreement between the water drinking test and diurnal tension curve. This may be because it has only been compared with a 10-hour modified diurnal tension curve, missing 70% of IOP peaks that occurred during night. This was a prospective, analytical and comparative study that assesses the correlation, agreement, sensitivity and specificity of the water drinking test. The correlation between the water drinking test and diurnal tension curve was significant and strong (r=0.93, Confidence interval 95% between 0.79 and 0.96, p<01). A moderate agreement was <span class="hlt">observed</span> between these measurements (pc=0.93, Confidence interval 95% between 0.87 and 0.95, p<.01). The agreement was within±2mmHg in 89% of the tests. Our study found a moderate agreement between the water drinking test and diurnal tension curve, in contrast with the poor agreement found in other studies, possibly due to the absence of nocturnal IOP peaks. These findings suggest that the water drinking test could be used to determine IOP peaks, as well as for determining baseline IOP. Copyright © 2014 Sociedad Española de Oftalmología. Published by Elsevier España, S.L.U. All rights reserved.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/28267238','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/28267238"><span>Ultrahigh b-values MRI in normal human prostate: Initial research on <span class="hlt">reproducibility</span> and age-related differences.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Shi, Changzheng; Zhang, Dong; Xiao, Zeyu; Wang, Li; Ma, Rong; Chen, Hanwei; Luo, Liangping</p> <p>2017-09-01</p> <p>To investigate the <span class="hlt">reproducibility</span> of diffusion-weighted imaging (DWI) with ultrahigh b-values, and analyze the age-related differences in normal prostates. In all, 67 healthy participants were divided into three age groups (group A, 15-30 years; group B, 31-50 years; group C, ≥51 years), and underwent DWI scanning twice with 15 b-factors from 0 to 3000 at 3.0T. Triexponential fits were applied to calculate the molecular diffusion coefficient (D), the pseudo-diffusion coefficient (D*), the ultrahigh apparent diffusion coefficient (ADC uh ), and perfusion fraction (f). The interobserver and short-term interscan <span class="hlt">reproducibility</span> were evaluated, and the change in these parameters with age were assessed. The D, ADC uh , and f values presented good to excellent <span class="hlt">reproducibility</span>. With increasing age, a trend of increasing D values was <span class="hlt">observed</span>, with significant difference in both peripheral zone (PZ, P = 0.01) and central gland (CG, P = 0.01) of normal prostate tissue. The f value increased in the CG beginning at 50 years of age while the ADC uh value decreased in the PZ after 50 years of age; all of them showed significant differences between groups A and C and groups B and C (P = 0.01/0.01). The D, ADC uh , and f values have good to excellent <span class="hlt">reproducibility</span> in the normal prostate, and these values change with age. The ultrahigh b-values magnetic resonance imaging (MRI) can provide additional information (ADC uh ), which is different from the IVIM (intravoxel incoherent motion)-derived parameters. 1 Technical Efficacy: Stage 2 J. MAGN. RESON. IMAGING 2017;46:801-812. © 2017 International Society for Magnetic Resonance in Medicine.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/24654705','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/24654705"><span>Exhaled breath temperature in children: <span class="hlt">reproducibility</span> and influencing factors.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Vermeulen, S; Barreto, M; La Penna, F; Prete, A; Martella, S; Biagiarelli, F; Villa, M P</p> <p>2014-09-01</p> <p>This study will investigate the <span class="hlt">reproducibility</span> and influencing factors of exhaled breath temperature measured with the tidal breathing technique in asthmatic patients and healthy children. Exhaled breath temperature, fractional exhaled nitric oxide, and spirometry were assessed in 124 children (63 healthy and 61 asthmatic), aged 11.2 ± 2.5 year, M/F 73/51. A modified version of the American Thoracic Society questionnaire on the child's present and past respiratory history was obtained from parents. Parents were also asked to provide detailed information on their child's medication use during the previous 4 weeks. Ear temperature, ambient temperature, and relative-ambient humidity were also recorded. Exhaled breath temperature measurements were highly <span class="hlt">reproducible</span>; the second measurement was higher than the first measurement, consistent with a test-retest situation. In 13 subjects, between-session within-day <span class="hlt">reproducibility</span> of exhaled breath temperature was still high. Exhaled breath temperature increased with age and relative-ambient humidity. Exhaled breath temperature was comparable in healthy and asthmatic children; when adjusted for potential confounders (i.e. ambient conditions and subject characteristics), thermal values of asthmatic patients exceeded those of the healthy children by 1.1 °C. Normalized exhaled breath temperature, by subtracting ambient temperature, was lower in asthmatic patients treated with inhaled corticosteroids than in those who were corticosteroid-naive. Measurements of exhaled breath temperature are highly <span class="hlt">reproducible</span>, yet influenced by several factors. Corrected values, i.e. normalized exhaled breath temperature, could help us to assess the effect of therapy with inhaled corticosteroids. More studies are needed to improve the usefulness of the exhaled breath temperature measured with the tidal breathing technique in children.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/29703675','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/29703675"><span>Accuracy and <span class="hlt">reproducibility</span> of virtual edentulous casts created by laboratory impression scan protocols.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Peng, Lingyan; Chen, Li; Harris, Bryan T; Bhandari, Bikash; Morton, Dean; Lin, Wei-Shao</p> <p>2018-04-24</p> <p> significantly different (P=.968), and the percentage of measurement data points within 1 SD of mean RMS values (90.1 ±1.1% versus 89.5 ±0.8%) were also not significantly different (P=.662). The numeric distance differences across 5 regions were affected by the scanning protocols (P<.001). The laboratory scanner and laboratory scanner-spray groups had significantly higher numeric distance differences at the apex of the denture border and crest of the ridge regions (P<.001). The CBCT scanner created more <span class="hlt">accurate</span> and <span class="hlt">reproducible</span> virtual edentulous casts, and the antiglare spray only significantly improved the accuracy and <span class="hlt">reproducibility</span> of virtual edentulous casts created by the dental laboratory laser scanner. The accuracy of the virtual edentulous casts was different across 5 regions and was affected by the scanning protocols. Copyright © 2018 Editorial Council for the Journal of Prosthetic Dentistry. Published by Elsevier Inc. All rights reserved.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4327429','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4327429"><span>EVALUATION OF THE <span class="hlt">REPRODUCIBILITY</span> OF TWO TECHNIQUES USED TO DETERMINE AND RECORD CENTRIC RELATION IN ANGLE’S CLASS I PATIENTS</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Paixão, Fernanda; Silva, Wilkens Aurélio Buarque e; Silva, Frederico Andrade e; Ramos, Guilherme da Gama; Cruz, Mônica Vieira de Jesus</p> <p>2007-01-01</p> <p>The centric relation is a mandibular position that determines a balance relation among the temporomandibular joints, the chew muscles and the occlusion. This position makes possible to the dentist to plan and to execute oral rehabilitation respecting the physiological principles of the stomatognathic system. The aim of this study was to investigate the <span class="hlt">reproducibility</span> of centric relation records obtained using two techniques: Dawson’s Bilateral Manipulation and Gysi’s Gothic Arch Tracing. Twenty volunteers (14 females and 6 males) with no dental loss, presenting occlusal contacts according to those described in Angle’s I classification and without signs and symptoms of temporomandibular disorders were selected. All volunteers were submitted five times with a 1-week interval, always in the same schedule, to the Dawson’s Bilateral Manipulation and to the Gysi’s Gothic Arch Tracing with aid of an intraoral apparatus. The average standard error of each technique was calculated (Bilateral Manipulation 0.94 and Gothic Arch Tracing 0.27). Shapiro-Wilk test was applied and the results allowed application of Student’s t-test (sampling error of 5%). The techniques showed different degrees of variability. The Gysi’s Gothic Arch Tracing was found to be more <span class="hlt">accurate</span> than the Bilateral Manipulation in <span class="hlt">reproducing</span> the centric relation records. PMID:19089144</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/19539979','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/19539979"><span><span class="hlt">Reproducing</span> ten years of road ageing--accelerated carbonation and leaching of EAF steel slag.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Suer, Pascal; Lindqvist, Jan-Erik; Arm, Maria; Frogner-Kockum, Paul</p> <p>2009-09-01</p> <p>Reuse of industrial aggregates is still hindered by concern for their long-term properties. This paper proposes a laboratory method for accelerated ageing of steel slag, to predict environmental and technical properties, starting from fresh slag. Ageing processes in a 10-year old asphalt road with steel slag of electric arc furnace (EAF) type in the subbase were identified by scanning electron microscopy (SEM) and leaching tests. Samples from the road centre and the pavement edge were compared with each other and with samples of fresh slag. It was found that slag from the pavement edge showed traces of carbonation and leaching processes, whereas the road centre material was nearly identical to fresh slag, in spite of an accessible particle structure. Batches of moisturized road centre material exposed to oxygen, nitrogen or carbon dioxide (CO2) were used for accelerated ageing. Time (7-14 days), temperature (20-40 degrees C) and initial slag moisture content (8-20%) were varied to achieve the carbonation (decrease in pH) and leaching that was <span class="hlt">observed</span> in the pavement edge material. After ageing, water was added to assess leaching of metals and macroelements. 12% moisture, CO2 and seven days at 40 degrees C gave the lowest pH value. This also <span class="hlt">reproduced</span> the <span class="hlt">observed</span> ageing effect for Ca, Cu, Ba, Fe, Mn, Pb, Ca (decreased leaching) and for V, Si, and Al (increased leaching). However, ageing effects on SO4, DOC and Cr were not <span class="hlt">reproduced</span>.</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_19");'>19</a></li> <li><a href="#" onclick='return showDiv("page_20");'>20</a></li> <li class="active"><span>21</span></li> <li><a href="#" onclick='return showDiv("page_22");'>22</a></li> <li><a href="#" onclick='return showDiv("page_23");'>23</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_21 --> <div id="page_22" class="hiddenDiv"> <div class="row"> <div class="col-sm-12"> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_20");'>20</a></li> <li><a href="#" onclick='return showDiv("page_21");'>21</a></li> <li class="active"><span>22</span></li> <li><a href="#" onclick='return showDiv("page_23");'>23</a></li> <li><a href="#" onclick='return showDiv("page_24");'>24</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div> </div> <div class="row"> <div class="col-sm-12"> <ol class="result-class" start="421"> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/18973458','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/18973458"><span><span class="hlt">Accurate</span> assessment and identification of naturally occurring cellular cobalamins.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Hannibal, Luciana; Axhemi, Armend; Glushchenko, Alla V; Moreira, Edward S; Brasch, Nicola E; Jacobsen, Donald W</p> <p>2008-01-01</p> <p><span class="hlt">Accurate</span> assessment of cobalamin profiles in human serum, cells, and tissues may have clinical diagnostic value. However, non-alkyl forms of cobalamin undergo beta-axial ligand exchange reactions during extraction, which leads to inaccurate profiles having little or no diagnostic value. Experiments were designed to: 1) assess beta-axial ligand exchange chemistry during the extraction and isolation of cobalamins from cultured bovine aortic endothelial cells, human foreskin fibroblasts, and human hepatoma HepG2 cells, and 2) to establish extraction conditions that would provide a more <span class="hlt">accurate</span> assessment of endogenous forms containing both exchangeable and non-exchangeable beta-axial ligands. The cobalamin profile of cells grown in the presence of [ 57Co]-cyanocobalamin as a source of vitamin B12 shows that the following derivatives are present: [ 57Co]-aquacobalamin, [ 57Co]-glutathionylcobalamin, [ 57Co]-sulfitocobalamin, [ 57Co]-cyanocobalamin, [ 57Co]-adenosylcobalamin, [ 57Co]-methylcobalamin, as well as other yet unidentified corrinoids. When the extraction is performed in the presence of excess cold aquacobalaminacting as a scavenger cobalamin (i.e. "cold trapping"), the recovery of both [ 57Co]-glutathionylcobalamin and [ 57Co]-sulfitocobalamin decreases to low but consistent levels. In contrasts, the [ 57Co]-nitrocobalamin <span class="hlt">observed</span> in the extracts prepared without excess aquacobalamin is undetected in extracts prepared with cold trapping. This demonstrates that beta-ligand exchange occur with non-covalently bound beta-ligands. The exception to this <span class="hlt">observation</span> is cyanocobalamin with a non-exchangeable CN- group. It is now possible to obtain <span class="hlt">accurate</span> profiles of cellular cobalamin.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2756674','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2756674"><span><span class="hlt">Accurate</span> assessment and identification of naturally occurring cellular cobalamins</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Hannibal, Luciana; Axhemi, Armend; Glushchenko, Alla V.; Moreira, Edward S.; Brasch, Nicola E.; Jacobsen, Donald W.</p> <p>2009-01-01</p> <p>Background <span class="hlt">Accurate</span> assessment of cobalamin profiles in human serum, cells, and tissues may have clinical diagnostic value. However, non-alkyl forms of cobalamin undergo β-axial ligand exchange reactions during extraction, which leads to inaccurate profiles having little or no diagnostic value. Methods Experiments were designed to: 1) assess β-axial ligand exchange chemistry during the extraction and isolation of cobalamins from cultured bovine aortic endothelial cells, human foreskin fibroblasts, and human hepatoma HepG2 cells, and 2) to establish extraction conditions that would provide a more <span class="hlt">accurate</span> assessment of endogenous forms containing both exchangeable and non-exchangeable β-axial ligands. Results The cobalamin profile of cells grown in the presence of [57Co]-cyanocobalamin as a source of vitamin B12 shows that the following derivatives are present: [57Co]-aquacobalamin, [57Co]-glutathionylcobalamin, [57Co]-sulfitocobalamin, [57Co]-cyanocobalamin, [57Co]-adenosylcobalamin, [57Co]-methylcobalamin, as well as other yet unidentified corrinoids. When the extraction is performed in the presence of excess cold aquacobalamin acting as a scavenger cobalamin (i.e., “cold trapping”), the recovery of both [57Co]-glutathionylcobalamin and [57Co]-sulfitocobalamin decreases to low but consistent levels. In contrast, the [57Co]-nitrocobalamin <span class="hlt">observed</span> in extracts prepared without excess aquacobalamin is undetectable in extracts prepared with cold trapping. Conclusions This demonstrates that β-ligand exchange occurs with non-covalently bound β-ligands. The exception to this <span class="hlt">observation</span> is cyanocobalamin with a non-covalent but non-exchangeable− CNT group. It is now possible to obtain <span class="hlt">accurate</span> profiles of cellular cobalamins. PMID:18973458</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2008ApSS..255.1427G','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2008ApSS..255.1427G"><span>Long-term <span class="hlt">reproducibility</span> of relative sensitivity factors obtained with CAMECA Wf</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Gui, D.; Xing, Z. X.; Huang, Y. H.; Mo, Z. Q.; Hua, Y. N.; Zhao, S. P.; Cha, L. Z.</p> <p>2008-12-01</p> <p>As the wafer size continues to increase and the feature size of the integrated circuits (IC) continues to shrink, process control of IC manufacturing becomes ever more important to reduce the cost of failures caused by the drift of processes or equipments. Characterization tools with high precision and <span class="hlt">reproducibility</span> are required to capture any abnormality of the process. Although Secondary ion mass spectrometry (SIMS) has been widely used in dopant profile control, it was reported that magnetic sector SIMS, compared to quadrupole SIMS, has lower short-term repeatability and long-term <span class="hlt">reproducibility</span> due to the high extraction field applied between sample and extraction lens. In this paper, we demonstrate that CAMECA Wf can deliver high long-term <span class="hlt">reproducibility</span> because of its high-level automation and improved design of immersion lens. The relative standard deviation (R.S.D.) of the relative sensitivity factors (RSF) of three typical elements, i.e., boron (B), phosphorous (P) and nitrogen (N), over 3 years are 3.7%, 5.5% and 4.1%, respectively. The high <span class="hlt">reproducibility</span> results have a practical implication that deviation can be estimated without testing the standards.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/23063535','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/23063535"><span>Accessing the <span class="hlt">reproducibility</span> and specificity of pepsin and other aspartic proteases.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Ahn, Joomi; Cao, Min-Jie; Yu, Ying Qing; Engen, John R</p> <p>2013-06-01</p> <p>The aspartic protease pepsin is less specific than other endoproteinases. Because aspartic proteases like pepsin are active at low pH, they are utilized in hydrogen deuterium exchange mass spectrometry (HDX MS) experiments for digestion under hydrogen exchange quench conditions. We investigated the <span class="hlt">reproducibility</span>, both qualitatively and quantitatively, of online and offline pepsin digestion to understand the compliment of <span class="hlt">reproducible</span> pepsin fragments that can be expected during a typical pepsin digestion. The collection of <span class="hlt">reproducible</span> peptides was identified from >30 replicate digestions of the same protein and it was found that the number of <span class="hlt">reproducible</span> peptides produced during pepsin digestion becomes constant above 5-6 replicate digestions. We also investigated a new aspartic protease from the stomach of the rice field eel (Monopterus albus Zuiew) and compared digestion efficiency and specificity to porcine pepsin and aspergillopepsin. Unique cleavage specificity was found for rice field eel pepsin at arginine, asparagine, and glycine. Different peptides produced by the various proteases can enhance protein sequence coverage and improve the spatial resolution of HDX MS data. This article is part of a Special Issue entitled: Mass spectrometry in structural biology. Copyright © 2012 Elsevier B.V. All rights reserved.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/12688786','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/12688786"><span>Pauling's electronegativity equation and a new corollary <span class="hlt">accurately</span> predict bond dissociation enthalpies and enhance current understanding of the nature of the chemical bond.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Matsunaga, Nikita; Rogers, Donald W; Zavitsas, Andreas A</p> <p>2003-04-18</p> <p>Contrary to other recent reports, Pauling's original electronegativity equation, applied as Pauling specified, describes quite <span class="hlt">accurately</span> homolytic bond dissociation enthalpies of common covalent bonds, including highly polar ones, with an average deviation of +/-1.5 kcal mol(-1) from literature values for 117 such bonds. Dissociation enthalpies are presented for more than 250 bonds, including 79 for which experimental values are not available. Some previous evaluations of accuracy gave misleadingly poor results by applying the equation to cases for which it was not derived and for which it should not <span class="hlt">reproduce</span> experimental values. Properly interpreted, the results of the equation provide new and quantitative insights into many facets of chemistry such as radical stabilities, factors influencing reactivity in electrophilic aromatic substitutions, the magnitude of steric effects, conjugative stabilization in unsaturated systems, rotational barriers, molecular and electronic structure, and aspects of autoxidation. A new corollary of the original equation expands its applicability and provides a rationale for previously <span class="hlt">observed</span> empirical correlations. The equation raises doubts about a new bonding theory. Hydrogen is unique in that its electronegativity is not constant.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/25611611','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/25611611"><span>Controlling the <span class="hlt">reproducibility</span> of Coulomb blockade phenomena for gold nanoparticles on an organic monolayer/silicon system.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Caillard, L; Sattayaporn, S; Lamic-Humblot, A-F; Casale, S; Campbell, P; Chabal, Y J; Pluchery, O</p> <p>2015-02-13</p> <p>Two types of highly ordered organic layers were prepared on silicon modified with an amine termination for binding gold nanoparticles (AuNPs). These two grafted organic monolayers (GOMs), consisting of alkyl chains with seven or 11 carbon atoms, were grafted on oxide-free Si(111) surfaces as tunnel barriers between the silicon electrode and the AuNPs. Three kinds of colloidal AuNPs were prepared by reducing HAuCl4 with three different reactants: citrate (Turkevich synthesis, diameter ∼16 nm), ascorbic acid (diameter ∼9 nm), or NaBH4 (Natan synthesis, diameter ∼7 nm). Scanning tunnel spectroscopy (STS) was performed in a UHV STM at 40 K, and Coulomb blockade behaviour was <span class="hlt">observed</span>. The <span class="hlt">reproducibility</span> of the Coulomb behavior was analysed as a function of several chemical and physical parameters: size, crystallinity of the AuNPs, influence of surrounding surfactant molecules, and quality of the GOM/Si interface (degree of oxidation after the full processing). Samples were characterized with scanning tunneling microscope, STS, atomic force microscope, Fourier transform infrared spectroscopy, x-ray photoelectron spectroscopy (XPS), and high resolution transmission electronic microscope. We show that the <span class="hlt">reproducibility</span> in <span class="hlt">observing</span> Coulomb behavior can be as high as ∼80% with the Natan synthesis of AuNPs and GOMs with short alkyl chains.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/28574941','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/28574941"><span>An <span class="hlt">Accurate</span> Full-flexion Anterolateral Portal for Needle Placement in the Knee Joint With Dry Osteoarthritis.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Hussein, Mohamed</p> <p>2017-07-01</p> <p><span class="hlt">Accurate</span> delivery of an injection into the intra-articular space of the knee is achieved in only two thirds of knees when using the standard anterolateral portal. The use of a modified full-flexion anterolateral portal provides a highly <span class="hlt">accurate</span>, less painful, and more effective method for <span class="hlt">reproducible</span> intra-articular injection without the need for ultrasonographic or fluoroscopic guidance in patients with dry osteoarthritis of the knee. The accuracy of needle placement was assessed in a prospective series of 140 consecutive injections in patients with symptomatic degenerative knee arthritis without clinical knee effusion. Procedural pain was determined using the Numerical Rating Scale. The accuracy rates of needle placement were confirmed with fluoroscopic imaging to document the dispersion pattern of injected contrast material. Using the standard anterolateral portal, 52 of 70 injections were confirmed to have been placed in the intra-articular space on the first attempt (accuracy rate, 74.2%). Using the modified full-flexion anterolateral portal, 68 of 70 injections were placed in the intra-articular space on the first attempt (accuracy rate, 97.1%; P = 0.000). This study revealed that using the modified full-flexion anterolateral portal for injections into the knee joint resulted in more <span class="hlt">accurate</span> and less painful injections than those performed by the same orthopaedic surgeon using the standard anterolateral portal. In addition, the technique offered therapeutic delivery into the joint without the need for fluoroscopic confirmation. Therapeutic Level II.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2008JChPh.128a4302V','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2008JChPh.128a4302V"><span>Water trimer torsional spectrum from <span class="hlt">accurate</span> ab initio and semiempirical potentials</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>van der Avoird, Ad; Szalewicz, Krzysztof</p> <p>2008-01-01</p> <p>The torsional levels of (H2O)3 and (D2O)3 were calculated in a restricted dimensionality (three-dimensional) model with several recently proposed water potentials. Comparison with the experimental data provides a critical test, not only of the pair interactions that have already been probed on the water dimer spectra, but also of the nonadditive three-body contributions to the potential. The purely ab initio CC-pol and HBB potentials that were previously shown to yield very <span class="hlt">accurate</span> water dimer levels, also <span class="hlt">reproduce</span> the trimer levels well when supplemented with an appropriate three-body interaction potential. The TTM2.1 potential gives considerably less good agreement with experiment. Also the semiempirical VRT(ASP-W)III potential, fitted to the water dimer vibration-rotation-tunneling levels, gives substantial disagreement with the measured water trimer levels, which shows that the latter probe the potential for geometries other than those probed by the dimer spectrum. Although the three-body nonadditive interactions significantly increase the stability of the water trimer, their effect on the torsional energy barriers and vibration-tunneling frequencies is less significant.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1343553','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1343553"><span><span class="hlt">Reproducibility</span> of cervical range of motion in patients with neck pain</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Hoving, Jan Lucas; Pool, Jan JM; van Mameren, Henk; Devillé, Walter JLM; Assendelft, Willem JJ; de Vet, Henrica CW; de Winter, Andrea F; Koes, Bart W; Bouter, Lex M</p> <p>2005-01-01</p> <p>Background <span class="hlt">Reproducibility</span> measurements of the range of motion are an important prerequisite for the interpretation of study results. The aim of the study is to assess the intra-rater and inter-rater <span class="hlt">reproducibility</span> of the measurement of active Range of Motion (ROM) in patients with neck pain using the Cybex Electronic Digital Inclinometer-320 (EDI-320). Methods In an outpatient clinic in a primary care setting 32 patients with at least 2 weeks of pain and/or stiffness in the neck were randomly assessed, in a test- retest design with blinded raters using a standardized measurement protocol. Cervical flexion-extension, lateral flexion and rotation were assessed. Results Reliability expressed by the Intraclass Correlation Coefficient (ICC) was 0.93 (lateral flexion) or higher for intra-rater reliability and 0.89 (lateral flexion) or higher for inter-rater reliability. The 95% limits of agreement for intra-rater agreement, expressing the range of the differences between two ratings were -2.5 ± 11.1° for flexion-extension, -0.1 ± 10.4° for lateral flexion and -5.9 ± 13.5° for rotation. For inter-rater agreement the limits of agreement were 3.3 ± 17.0° for flexion-extension, 0.5 ± 17.0° for lateral flexion and -1.3 ± 24.6° for rotation. Conclusion In general, the intra-rater <span class="hlt">reproducibility</span> and the inter-rater <span class="hlt">reproducibility</span> were good. We recommend to compare the <span class="hlt">reproducibility</span> and clinical applicability of the EDI-320 inclinometer with other cervical ROM measures in symptomatic patients. PMID:16351719</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.osti.gov/biblio/1352231-accurate-optimization-amino-acid-form-factors-computing-small-angle-ray-scattering-intensity-atomistic-protein-structures','SCIGOV-STC'); return false;" href="https://www.osti.gov/biblio/1352231-accurate-optimization-amino-acid-form-factors-computing-small-angle-ray-scattering-intensity-atomistic-protein-structures"><span><span class="hlt">Accurate</span> optimization of amino acid form factors for computing small-angle X-ray scattering intensity of atomistic protein structures</span></a></p> <p><a target="_blank" href="http://www.osti.gov/search">DOE Office of Scientific and Technical Information (OSTI.GOV)</a></p> <p>Tong, Dudu; Yang, Sichun; Lu, Lanyuan</p> <p>2016-06-20</p> <p>Structure modellingviasmall-angle X-ray scattering (SAXS) data generally requires intensive computations of scattering intensity from any given biomolecular structure, where the <span class="hlt">accurate</span> evaluation of SAXS profiles using coarse-grained (CG) methods is vital to improve computational efficiency. To date, most CG SAXS computing methods have been based on a single-bead-per-residue approximation but have neglected structural correlations between amino acids. To improve the accuracy of scattering calculations, <span class="hlt">accurate</span> CG form factors of amino acids are now derived using a rigorous optimization strategy, termed electron-density matching (EDM), to best fit electron-density distributions of protein structures. This EDM method is compared with and tested againstmore » other CG SAXS computing methods, and the resulting CG SAXS profiles from EDM agree better with all-atom theoretical SAXS data. By including the protein hydration shell represented by explicit CG water molecules and the correction of protein excluded volume, the developed CG form factors also <span class="hlt">reproduce</span> the selected experimental SAXS profiles with very small deviations. Taken together, these EDM-derived CG form factors present an <span class="hlt">accurate</span> and efficient computational approach for SAXS computing, especially when higher molecular details (represented by theqrange of the SAXS data) become necessary for effective structure modelling.« less</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.osti.gov/biblio/1353514-evaluation-reproducibility-amplicon-sequencing-illumina-miseq-platform','SCIGOV-STC'); return false;" href="https://www.osti.gov/biblio/1353514-evaluation-reproducibility-amplicon-sequencing-illumina-miseq-platform"><span>Evaluation of the <span class="hlt">reproducibility</span> of amplicon sequencing with Illumina MiSeq platform</span></a></p> <p><a target="_blank" href="http://www.osti.gov/search">DOE Office of Scientific and Technical Information (OSTI.GOV)</a></p> <p>Wen, Chongqing; Wu, Liyou; Qin, Yujia</p> <p></p> <p>Illumina's MiSeq has become the dominant platform for gene amplicon sequencing in microbial ecology studies; however, various technical concerns, such as <span class="hlt">reproducibility</span>, still exist. To assess <span class="hlt">reproducibility</span>, 16S rRNA gene amplicons from 18 soil samples of a reciprocal transplantation experiment were sequenced on an Illumina MiSeq. The V4 region of 16S rRNA gene from each sample was sequenced in triplicate with each replicate having a unique barcode. The average OTU overlap, without considering sequence abundance, at a rarefaction level of 10,323 sequences was 33.4±2.1% and 20.2±1.7% between two and among three technical replicates, respectively. When OTU sequence abundance was considered,more » the average sequence abundance weighted OTU overlap was 85.6±1.6% and 81.2±2.1% for two and three replicates, respectively. Removing singletons significantly increased the overlap for both (~1-3%, p<0.001). Increasing the sequencing depth to 160,000 reads by deep sequencing increased OTU overlap both when sequence abundance was considered (95%) and when not (44%). However, if singletons were not removed the overlap between two technical replicates (not considering sequence abundance) plateaus at 39% with 30,000 sequences. Diversity measures were not affected by the low overlap as α-diversities were similar among technical replicates while β-diversities (Bray-Curtis) were much smaller among technical replicates than among treatment replicates (e.g., 0.269 vs. 0.374). Higher diversity coverage, but lower OTU overlap, was <span class="hlt">observed</span> when replicates were sequenced in separate runs. Detrended correspondence analysis indicated that while there was considerable variation among technical replicates, the <span class="hlt">reproducibility</span> was sufficient for detecting treatment effects for the samples examined. These results suggest that although there is variation among technical replicates, amplicon sequencing on MiSeq is useful for analyzing microbial community structure if used</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.osti.gov/pages/biblio/1353514-evaluation-reproducibility-amplicon-sequencing-illumina-miseq-platform','SCIGOV-DOEP'); return false;" href="https://www.osti.gov/pages/biblio/1353514-evaluation-reproducibility-amplicon-sequencing-illumina-miseq-platform"><span>Evaluation of the <span class="hlt">reproducibility</span> of amplicon sequencing with Illumina MiSeq platform</span></a></p> <p><a target="_blank" href="http://www.osti.gov/pages">DOE PAGES</a></p> <p>Wen, Chongqing; Wu, Liyou; Qin, Yujia; ...</p> <p>2017-04-28</p> <p>Illumina's MiSeq has become the dominant platform for gene amplicon sequencing in microbial ecology studies; however, various technical concerns, such as <span class="hlt">reproducibility</span>, still exist. To assess <span class="hlt">reproducibility</span>, 16S rRNA gene amplicons from 18 soil samples of a reciprocal transplantation experiment were sequenced on an Illumina MiSeq. The V4 region of 16S rRNA gene from each sample was sequenced in triplicate with each replicate having a unique barcode. The average OTU overlap, without considering sequence abundance, at a rarefaction level of 10,323 sequences was 33.4±2.1% and 20.2±1.7% between two and among three technical replicates, respectively. When OTU sequence abundance was considered,more » the average sequence abundance weighted OTU overlap was 85.6±1.6% and 81.2±2.1% for two and three replicates, respectively. Removing singletons significantly increased the overlap for both (~1-3%, p<0.001). Increasing the sequencing depth to 160,000 reads by deep sequencing increased OTU overlap both when sequence abundance was considered (95%) and when not (44%). However, if singletons were not removed the overlap between two technical replicates (not considering sequence abundance) plateaus at 39% with 30,000 sequences. Diversity measures were not affected by the low overlap as α-diversities were similar among technical replicates while β-diversities (Bray-Curtis) were much smaller among technical replicates than among treatment replicates (e.g., 0.269 vs. 0.374). Higher diversity coverage, but lower OTU overlap, was <span class="hlt">observed</span> when replicates were sequenced in separate runs. Detrended correspondence analysis indicated that while there was considerable variation among technical replicates, the <span class="hlt">reproducibility</span> was sufficient for detecting treatment effects for the samples examined. These results suggest that although there is variation among technical replicates, amplicon sequencing on MiSeq is useful for analyzing microbial community structure if used</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2017EGUGA..19.3737H','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2017EGUGA..19.3737H"><span><span class="hlt">Observations</span> and Simulations of the Impact of Wave-Current Interaction on Wave Direction in the Surf Zone</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Hopkins, Julia; Elgar, Steve; Raubenheimer, Britt</p> <p>2017-04-01</p> <p><span class="hlt">Accurately</span> characterizing the interaction of waves and currents can improve predictions of wave propagation and subsequent sediment transport in the nearshore. Along the southern shoreline of Martha's Vineyard, MA, waves propagate across strong tidal currents as they shoal, providing an ideal environment for investigating wave-current interaction. Wave directions and mean currents <span class="hlt">observed</span> for two 1-month-long periods in 7- and 2-m water depths along 11 km of the Martha's Vineyard shoreline have strong tidal modulations. Wave directions shift by as much as 70 degrees over a tidal cycle in 7 m depth, and by as much as 25 degrees in 2 m depth. The magnitude of the tidal modulations in the wave field decreases alongshore to the west, consistent with the <span class="hlt">observed</span> decrease in tidal currents from 2.1 to 0.2 m/s. The <span class="hlt">observations</span> are <span class="hlt">reproduced</span> <span class="hlt">accurately</span> by a numerical model (SWAN and Deflt3D-FLOW) that simulates waves and currents over the <span class="hlt">observed</span> bathymetry. Model simulations with and without wave-current interaction and tidal depth changes demonstrate that the <span class="hlt">observed</span> tidal modulations of the wave field primarily are caused by wave-current interaction and not by tidal changes to water depths over the nearby complex shoals. Sediment transport estimates from simulated wave conditions using a range of tidal currents and offshore wave fields indicate that the modulation of the wave field at Martha's Vineyard can impact the direction of wave-induced alongshore sediment transport, sometimes driving transport opposing the direction of the offshore incident wave field. As such, the <span class="hlt">observations</span> and model simulations suggest the importance of wave-current interaction to tidally averaged transport in mixed-energy wave-and-current nearshore environments. Supported by ASD(R&E), NSF, NOAA (Sea Grant), and ONR.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2006NIMPB.247..381B','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2006NIMPB.247..381B"><span><span class="hlt">Accurate</span> simulation of backscattering spectra in the presence of sharp resonances</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Barradas, N. P.; Alves, E.; Jeynes, C.; Tosaki, M.</p> <p>2006-06-01</p> <p>In elastic backscattering spectrometry, the shape of the <span class="hlt">observed</span> spectrum due to resonances in the nuclear scattering cross-section is influenced by many factors. If the energy spread of the beam before interaction is larger than the resonance width, then a simple convolution with the energy spread on exit and with the detection system resolution will lead to a calculated spectrum with a resonance much sharper than the <span class="hlt">observed</span> signal. Also, the yield from a thin layer will not be calculated <span class="hlt">accurately</span>. We have developed an algorithm for the <span class="hlt">accurate</span> simulation of backscattering spectra in the presence of sharp resonances. Albeit approximate, the algorithm leads to dramatic improvements in the quality and accuracy of the simulations. It is simple to implement and leads to only small increases of the calculation time, being thus suitable for routine data analysis. We show different experimental examples, including samples with roughness and porosity.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2015AGUFMIN53B1834H','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2015AGUFMIN53B1834H"><span><span class="hlt">Reproducibility</span> and Transparency in Ocean-Climate Modeling</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Hannah, N.; Adcroft, A.; Hallberg, R.; Griffies, S. M.</p> <p>2015-12-01</p> <p><span class="hlt">Reproducibility</span> is a cornerstone of the scientific method. Within geophysical modeling and simulation achieving <span class="hlt">reproducibility</span> can be difficult, especially given the complexity of numerical codes, enormous and disparate data sets, and variety of supercomputing technology. We have made progress on this problem in the context of a large project - the development of new ocean and sea ice models, MOM6 and SIS2. Here we present useful techniques and experience.We use version control not only for code but the entire experiment working directory, including configuration (run-time parameters, component versions), input data and checksums on experiment output. This allows us to document when the solutions to experiments change, whether due to code updates or changes in input data. To avoid distributing large input datasets we provide the tools for generating these from the sources, rather than provide raw input data.Bugs can be a source of non-determinism and hence irreproducibility, e.g. reading from or branching on uninitialized memory. To expose these we routinely run system tests, using a memory debugger, multiple compilers and different machines. Additional confidence in the code comes from specialised tests, for example automated dimensional analysis and domain transformations. This has entailed adopting a code style where we deliberately restrict what a compiler can do when re-arranging mathematical expressions.In the spirit of open science, all development is in the public domain. This leads to a positive feedback, where increased transparency and <span class="hlt">reproducibility</span> makes using the model easier for external collaborators, who in turn provide valuable contributions. To facilitate users installing and running the model we provide (version controlled) digital notebooks that illustrate and record analysis of output. This has the dual role of providing a gross, platform-independent, testing capability and a means to documents model output and analysis.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://hdl.handle.net/2060/19950009774','NASA-TRS'); return false;" href="http://hdl.handle.net/2060/19950009774"><span>Mars Pathfinder meteorological <span class="hlt">observations</span> on the basis of results of an atmospheric global circulation model</span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Forget, Francois; Hourdin, F.; Talagrand, O.</p> <p>1994-01-01</p> <p>The Mars Pathfinder Meteorological Package (ASI/MET) will measure the local pressure, temperature, and winds at its future landing site, somewhere between the latitudes 0 deg N and 30 deg N. Comparable measurements have already been obtained at the surface of Mars by the Viking Landers at 22 deg N (VL1) and 48 deg N (VL2), providing much useful information on the martian atmosphere. In particular the pressure measurements contain very instructive information on the global atmospheric circulation. At the Laboratoire de Meteorologie Dynamique (LMD), we have analyzed and simulated these measurements with a martian atmospheric global circulation model (GCM), which was the first to simulate the martian atmospheric circulation over more than 1 year. The model is able to <span class="hlt">reproduce</span> rather <span class="hlt">accurately</span> many <span class="hlt">observed</span> features of the martian atmosphere, including the long- and short-period oscillations of the surface pressure <span class="hlt">observed</span> by the Viking landers. From a meteorological point of view, we think that a landing site located near or at the equator would be an interesting choice.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/28063033','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/28063033"><span><span class="hlt">Reproducibility</span> Issues: Avoiding Pitfalls in Animal Inflammation Models.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Laman, Jon D; Kooistra, Susanne M; Clausen, Björn E</p> <p>2017-01-01</p> <p>In light of an enhanced awareness of ethical questions and ever increasing costs when working with animals in biomedical research, there is a dedicated and sometimes fierce debate concerning the (lack of) <span class="hlt">reproducibility</span> of animal models and their relevance for human inflammatory diseases. Despite evident advancements in searching for alternatives, that is, replacing, reducing, and refining animal experiments-the three R's of Russel and Burch (1959)-understanding the complex interactions of the cells of the immune system, the nervous system and the affected tissue/organ during inflammation critically relies on in vivo models. Consequently, scientific advancement and ultimately novel therapeutic interventions depend on improving the <span class="hlt">reproducibility</span> of animal inflammation models. As a prelude to the remaining hands-on protocols described in this volume, here, we summarize potential pitfalls of preclinical animal research and provide resources and background reading on how to avoid them.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.osti.gov/servlets/purl/949042','SCIGOV-STC'); return false;" href="https://www.osti.gov/servlets/purl/949042"><span>ChIP-seq <span class="hlt">Accurately</span> Predicts Tissue-Specific Activity of Enhancers</span></a></p> <p><a target="_blank" href="http://www.osti.gov/search">DOE Office of Scientific and Technical Information (OSTI.GOV)</a></p> <p>Visel, Axel; Blow, Matthew J.; Li, Zirong</p> <p>2009-02-01</p> <p>A major yet unresolved quest in decoding the human genome is the identification of the regulatory sequences that control the spatial and temporal expression of genes. Distant-acting transcriptional enhancers are particularly challenging to uncover since they are scattered amongst the vast non-coding portion of the genome. Evolutionary sequence constraint can facilitate the discovery of enhancers, but fails to predict when and where they are active in vivo. Here, we performed chromatin immunoprecipitation with the enhancer-associated protein p300, followed by massively-parallel sequencing, to map several thousand in vivo binding sites of p300 in mouse embryonic forebrain, midbrain, and limb tissue. Wemore » tested 86 of these sequences in a transgenic mouse assay, which in nearly all cases revealed <span class="hlt">reproducible</span> enhancer activity in those tissues predicted by p300 binding. Our results indicate that in vivo mapping of p300 binding is a highly <span class="hlt">accurate</span> means for identifying enhancers and their associated activities and suggest that such datasets will be useful to study the role of tissue-specific enhancers in human biology and disease on a genome-wide scale.« less</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2010AIPC.1215..311M','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2010AIPC.1215..311M"><span>Regulating Ultrasound Cavitation in order to Induce <span class="hlt">Reproducible</span> Sonoporation</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Mestas, J.-L.; Alberti, L.; El Maalouf, J.; Béra, J.-C.; Gilles, B.</p> <p>2010-03-01</p> <p>Sonoporation would be linked to cavitation, which generally appears to be a non <span class="hlt">reproducible</span> and unstationary phenomenon. In order to obtain an acceptable trade-off between cell mortality and transfection, a regulated cavitation generator based on an acoustical cavitation measurement was developed and tested. The medium to be sonicated is placed in a sample tray. This tray is immersed in in degassed water and positioned above the face of a flat ultrasonic transducer (frequency: 445 kHz; intensity range: 0.08-1.09 W/cm2). This technical configuration was admitted to be conducive to standing-wave generation through reflection at the air/medium interface in the well thus enhancing the cavitation phenomenon. Laterally to the transducer, a homemade hydrophone was oriented to receive the acoustical signal from the bubbles. From this spectral signal recorded at intervals of 5 ms, a cavitation index was calculated as the mean of the cavitation spectrum integration in a logarithmic scale, and the excitation power is automatically corrected. The device generates stable and <span class="hlt">reproducible</span> cavitation level for a wide range of cavitation setpoint from stable cavitation condition up to full-developed inertial cavitation. For the ultrasound intensity range used, the time delay of the response is lower than 200 ms. The cavitation regulation device was evaluated in terms of chemical bubble collapse effect. Hydroxyl radical production was measured on terephthalic acid solutions. In open loop, the results present a great variability whatever the excitation power. On the contrary the closed loop allows a great <span class="hlt">reproducibility</span>. This device was implemented for study of sonodynamic effect. The regulation provides more <span class="hlt">reproducible</span> results independent of cell medium and experimental conditions (temperature, pressure). Other applications of this regulated cavitation device concern internalization of different particles (Quantum Dot) molecules (SiRNA) or plasmids (GFP, DsRed) into different</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/26074626','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/26074626"><span>Contrasting response to nutrient manipulation in Arctic mesocosms are <span class="hlt">reproduced</span> by a minimum microbial food web model.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Larsen, Aud; Egge, Jorun K; Nejstgaard, Jens C; Di Capua, Iole; Thyrhaug, Runar; Bratbak, Gunnar; Thingstad, T Frede</p> <p>2015-03-01</p> <p>A minimum mathematical model of the marine pelagic microbial food web has previously shown to be able to <span class="hlt">reproduce</span> central aspects of <span class="hlt">observed</span> system response to different bottom-up manipulations in a mesocosm experiment Microbial Ecosystem Dynamics (MEDEA) in Danish waters. In this study, we apply this model to two mesocosm experiments (Polar Aquatic Microbial Ecology (PAME)-I and PAME-II) conducted at the Arctic location Kongsfjorden, Svalbard. The different responses of the microbial community to similar nutrient manipulation in the three mesocosm experiments may be described as diatom-dominated (MEDEA), bacteria-dominated (PAME-I), and flagellated-dominated (PAME-II). When allowing ciliates to be able to feed on small diatoms, the model describing the diatom-dominated MEDEA experiment give a bacteria-dominated response as <span class="hlt">observed</span> in PAME I in which the diatom community comprised almost exclusively small-sized cells. Introducing a high initial mesozooplankton stock as <span class="hlt">observed</span> in PAME-II, the model gives a flagellate-dominated response in accordance with the <span class="hlt">observed</span> response also of this experiment. The ability of the model originally developed for temperate waters to <span class="hlt">reproduce</span> population dynamics in a 10°C colder Arctic fjord, does not support the existence of important shifts in population balances over this temperature range. Rather, it suggests a quite resilient microbial food web when adapted to in situ temperature. The sensitivity of the model response to its mesozooplankton component suggests, however, that the seasonal vertical migration of Arctic copepods may be a strong forcing factor on Arctic microbial food webs.</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_20");'>20</a></li> <li><a href="#" onclick='return showDiv("page_21");'>21</a></li> <li class="active"><span>22</span></li> <li><a href="#" onclick='return showDiv("page_23");'>23</a></li> <li><a href="#" onclick='return showDiv("page_24");'>24</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_22 --> <div id="page_23" class="hiddenDiv"> <div class="row"> <div class="col-sm-12"> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_21");'>21</a></li> <li><a href="#" onclick='return showDiv("page_22");'>22</a></li> <li class="active"><span>23</span></li> <li><a href="#" onclick='return showDiv("page_24");'>24</a></li> <li><a href="#" onclick='return showDiv("page_25");'>25</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div> </div> <div class="row"> <div class="col-sm-12"> <ol class="result-class" start="441"> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4459036','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4459036"><span>Contrasting response to nutrient manipulation in Arctic mesocosms are <span class="hlt">reproduced</span> by a minimum microbial food web model</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Larsen, Aud; Egge, Jorun K; Nejstgaard, Jens C; Di Capua, Iole; Thyrhaug, Runar; Bratbak, Gunnar; Thingstad, T Frede</p> <p>2015-01-01</p> <p>A minimum mathematical model of the marine pelagic microbial food web has previously shown to be able to <span class="hlt">reproduce</span> central aspects of <span class="hlt">observed</span> system response to different bottom-up manipulations in a mesocosm experiment Microbial Ecosystem Dynamics (MEDEA) in Danish waters. In this study, we apply this model to two mesocosm experiments (Polar Aquatic Microbial Ecology (PAME)-I and PAME-II) conducted at the Arctic location Kongsfjorden, Svalbard. The different responses of the microbial community to similar nutrient manipulation in the three mesocosm experiments may be described as diatom-dominated (MEDEA), bacteria-dominated (PAME-I), and flagellated-dominated (PAME-II). When allowing ciliates to be able to feed on small diatoms, the model describing the diatom-dominated MEDEA experiment give a bacteria-dominated response as <span class="hlt">observed</span> in PAME I in which the diatom community comprised almost exclusively small-sized cells. Introducing a high initial mesozooplankton stock as <span class="hlt">observed</span> in PAME-II, the model gives a flagellate-dominated response in accordance with the <span class="hlt">observed</span> response also of this experiment. The ability of the model originally developed for temperate waters to <span class="hlt">reproduce</span> population dynamics in a 10°C colder Arctic fjord, does not support the existence of important shifts in population balances over this temperature range. Rather, it suggests a quite resilient microbial food web when adapted to in situ temperature. The sensitivity of the model response to its mesozooplankton component suggests, however, that the seasonal vertical migration of Arctic copepods may be a strong forcing factor on Arctic microbial food webs. PMID:26074626</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2013PhRvL.111i1302F','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2013PhRvL.111i1302F"><span>Can All Cosmological <span class="hlt">Observations</span> Be <span class="hlt">Accurately</span> Interpreted with a Unique Geometry?</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Fleury, Pierre; Dupuy, Hélène; Uzan, Jean-Philippe</p> <p>2013-08-01</p> <p>The recent analysis of the Planck results reveals a tension between the best fits for (Ωm0, H0) derived from the cosmic microwave background or baryonic acoustic oscillations on the one hand, and the Hubble diagram on the other hand. These <span class="hlt">observations</span> probe the Universe on very different scales since they involve light beams of very different angular sizes; hence, the tension between them may indicate that they should not be interpreted the same way. More precisely, this Letter questions the accuracy of using only the (perturbed) Friedmann-Lemaître geometry to interpret all the cosmological <span class="hlt">observations</span>, regardless of their angular or spatial resolution. We show that using an inhomogeneous “Swiss-cheese” model to interpret the Hubble diagram allows us to reconcile the inferred value of Ωm0 with the Planck results. Such an approach does not require us to invoke new physics nor to violate the Copernican principle.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.osti.gov/biblio/22661373-reproducing-correlations-type-low-frequency-quasi-periodic-oscillation-parameters-xte-j1550564-spiral-structure','SCIGOV-STC'); return false;" href="https://www.osti.gov/biblio/22661373-reproducing-correlations-type-low-frequency-quasi-periodic-oscillation-parameters-xte-j1550564-spiral-structure"><span><span class="hlt">REPRODUCING</span> THE CORRELATIONS OF TYPE C LOW-FREQUENCY QUASI-PERIODIC OSCILLATION PARAMETERS IN XTE J1550–564 WITH A SPIRAL STRUCTURE</span></a></p> <p><a target="_blank" href="http://www.osti.gov/search">DOE Office of Scientific and Technical Information (OSTI.GOV)</a></p> <p>Varniere, Peggy; Vincent, Frederic H., E-mail: varniere@apc.univ-paris7.fr</p> <p></p> <p>While it has been <span class="hlt">observed</span> that the parameters intrinsic to the type C low-frequency quasi-periodic oscillations are related in a nonlinear manner among themselves, there has been, up to now, no model to explain or <span class="hlt">reproduce</span> how the frequency, the FWHM, and the rms amplitude of the type C low-frequency quasi-periodic oscillations behave with respect to one another. Here we are using a simple toy model representing the emission from a standard disk and a spiral such as that caused by the accretion–ejection instability to <span class="hlt">reproduce</span> the overall <span class="hlt">observed</span> behavior and shed some light on its origin. This allows usmore » to prove the ability of such a spiral structure to be at the origin of flux modulation over more than an order of magnitude in frequency.« less</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/9246080','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/9246080"><span><span class="hlt">Reproducibility</span> of the kinematics and kinetics of the lower extremity during normal stair-climbing.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Yu, B; Kienbacher, T; Growney, E S; Johnson, M E; An, K N</p> <p>1997-05-01</p> <p>The purpose of this study was to examine the intrasubject <span class="hlt">reproducibility</span> of the kinematic and kinetic measures of the lower extremity during normal stair-climbing. Three-dimensional video and force-plate data were collected for three trials per subject during each of three conditions: ascending, descending, and level walking. Three-dimensional angles and moments of the ankle, knee, and hip joints were calculated. The coefficient of multiple correlation was used to determine the intrasubject <span class="hlt">reproducibility</span> of joint angles and resultant moments. Analysis of variance with repeated measures was conducted to compare the magnitudes of the coefficients between different steps, different joints, and different joint functions. The results showed that (a) generally, the kinematic and kinetic measures of normal subjects climbing stairs were <span class="hlt">reproducible</span>; (b) the kinetic measures during the transition steps from level walking to ascending and from descending to level walking were significantly less <span class="hlt">reproducible</span> than those during the other steps; (c) the data from the sagittal plane were more <span class="hlt">reproducible</span> than those from the other two planes; and (d) the kinetic measures were more <span class="hlt">reproducible</span> than the kinematic measures, especially for abduction-adduction and internal-external rotation.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.osti.gov/biblio/20951642-reproducibility-abdominal-chest-wall-position-voluntary-breath-hold-technique-using-laser-based-monitoring-visual-feedback-system','SCIGOV-STC'); return false;" href="https://www.osti.gov/biblio/20951642-reproducibility-abdominal-chest-wall-position-voluntary-breath-hold-technique-using-laser-based-monitoring-visual-feedback-system"><span><span class="hlt">Reproducibility</span> of The Abdominal and Chest Wall Position by Voluntary Breath-Hold Technique Using a Laser-Based Monitoring and Visual Feedback System</span></a></p> <p><a target="_blank" href="http://www.osti.gov/search">DOE Office of Scientific and Technical Information (OSTI.GOV)</a></p> <p>Nakamura, Katsumasa; Shioyama, Yoshiyuki; Nomoto, Satoru</p> <p>2007-05-01</p> <p>Purpose: The voluntary breath-hold (BH) technique is a simple method to control the respiration-related motion of a tumor during irradiation. However, the abdominal and chest wall position may not be <span class="hlt">accurately</span> <span class="hlt">reproduced</span> using the BH technique. The purpose of this study was to examine whether visual feedback can reduce the fluctuation in wall motion during BH using a new respiratory monitoring device. Methods and Materials: We developed a laser-based BH monitoring and visual feedback system. For this study, five healthy volunteers were enrolled. The volunteers, practicing abdominal breathing, performed shallow end-expiration BH (SEBH), shallow end-inspiration BH (SIBH), and deep end-inspirationmore » BH (DIBH) with or without visual feedback. The abdominal and chest wall positions were measured at 80-ms intervals during BHs. Results: The fluctuation in the chest wall position was smaller than that of the abdominal wall position. The <span class="hlt">reproducibility</span> of the wall position was improved by visual feedback. With a monitoring device, visual feedback reduced the mean deviation of the abdominal wall from 2.1 {+-} 1.3 mm to 1.5 {+-} 0.5 mm, 2.5 {+-} 1.9 mm to 1.1 {+-} 0.4 mm, and 6.6 {+-} 2.4 mm to 2.6 {+-} 1.4 mm in SEBH, SIBH, and DIBH, respectively. Conclusions: Volunteers can perform the BH maneuver in a highly <span class="hlt">reproducible</span> fashion when informed about the position of the wall, although in the case of DIBH, the deviation in the wall position remained substantial.« less</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://hdl.handle.net/2060/20130003182','NASA-TRS'); return false;" href="http://hdl.handle.net/2060/20130003182"><span><span class="hlt">Reproducing</span> the Photospheric Magnetic Field Evolution during the Rise of Cycle 24 with Flux Transport by Supergranules</span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Hathaway, David; Upton, Lisa</p> <p>2012-01-01</p> <p>We simulate the transport of magnetic flux in the Sun s photosphere by an evolving pattern of cellular horizontal flows (supergranules). Characteristics of the simulated flow pattern can match <span class="hlt">observed</span> characteristics including the velocity power spectrum, cell lifetimes, and cell motions in longitude and latitude. Simulations using an average, and north-south symmetric, meridional motion of the cellular pattern produce polar magnetic fields that are too weak in the North and too strong in the South. Simulations using cellular patterns with meridional motions that evolve with the <span class="hlt">observed</span> changes in strength and north-south asymmetry will be analyzed to see if they <span class="hlt">reproduce</span> the polar field evolution <span class="hlt">observed</span> during the rise of Cycle 24.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://hdl.handle.net/2060/20130003202','NASA-TRS'); return false;" href="http://hdl.handle.net/2060/20130003202"><span><span class="hlt">Reproducing</span> the Photospheric Magnetic Field Evolution During the Rise of Cycle 24 with Flux Transport by Supergranules</span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Hathaway, David H.; Upton, Lisa</p> <p>2012-01-01</p> <p>We simulate the transport of magnetic flux in the Sun s photosphere by an evolving pattern of cellular horizontal flows (supergranules). Characteristics of the simulated flow pattern match <span class="hlt">observed</span> characteristics including the velocity power spectrum, cell lifetimes, and cell pattern motion in longitude and latitude. Simulations using an average, and north-south symmetric, meridional motion of the cellular pattern produce polar magnetic fields that are too weak in the North and too strong in the South. Simulations using cellular patterns with meridional motions that evolve with the <span class="hlt">observed</span> changes in strength and north-south asymmetry will be analyzed to see if they <span class="hlt">reproduce</span> the polar field evolution <span class="hlt">observed</span> during the rise of Cycle 24.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4121318','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4121318"><span>Inter-Vendor <span class="hlt">Reproducibility</span> of Pseudo-Continuous Arterial Spin Labeling at 3 Tesla</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Mutsaerts, Henri J. M. M.; Steketee, Rebecca M. E.; Heijtel, Dennis F. R.; Kuijer, Joost P. A.; van Osch, Matthias J. P.; Majoie, Charles B. L. M.; Smits, Marion; Nederveen, Aart J.</p> <p>2014-01-01</p> <p>Purpose Prior to the implementation of arterial spin labeling (ASL) in clinical multi-center studies, it is important to establish its status quo inter-vendor <span class="hlt">reproducibility</span>. This study evaluates and compares the intra- and inter-vendor <span class="hlt">reproducibility</span> of pseudo-continuous ASL (pCASL) as clinically implemented by GE and Philips. Material and Methods 22 healthy volunteers were scanned twice on both a 3T GE and a 3T Philips scanner. The main difference in implementation between the vendors was the readout module: spiral 3D fast spin echo vs. 2D gradient-echo echo-planar imaging respectively. Mean and variation of cerebral blood flow (CBF) were compared for the total gray matter (GM) and white matter (WM), and on a voxel-level. Results Whereas the mean GM CBF of both vendors was almost equal (p = 1.0), the mean WM CBF was significantly different (p<0.01). The inter-vendor GM variation did not differ from the intra-vendor GM variation (p = 0.3 and p = 0.5 for GE and Philips respectively). Spatial inter-vendor CBF and variation differences were <span class="hlt">observed</span> in several GM regions and in the WM. Conclusion These results show that total GM CBF-values can be exchanged between vendors. For the inter-vendor comparison of GM regions or WM, these results encourage further standardization of ASL implementation among vendors. PMID:25090654</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/25090654','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/25090654"><span>Inter-vendor <span class="hlt">reproducibility</span> of pseudo-continuous arterial spin labeling at 3 Tesla.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Mutsaerts, Henri J M M; Steketee, Rebecca M E; Heijtel, Dennis F R; Kuijer, Joost P A; van Osch, Matthias J P; Majoie, Charles B L M; Smits, Marion; Nederveen, Aart J</p> <p>2014-01-01</p> <p>Prior to the implementation of arterial spin labeling (ASL) in clinical multi-center studies, it is important to establish its status quo inter-vendor <span class="hlt">reproducibility</span>. This study evaluates and compares the intra- and inter-vendor <span class="hlt">reproducibility</span> of pseudo-continuous ASL (pCASL) as clinically implemented by GE and Philips. 22 healthy volunteers were scanned twice on both a 3T GE and a 3T Philips scanner. The main difference in implementation between the vendors was the readout module: spiral 3D fast spin echo vs. 2D gradient-echo echo-planar imaging respectively. Mean and variation of cerebral blood flow (CBF) were compared for the total gray matter (GM) and white matter (WM), and on a voxel-level. Whereas the mean GM CBF of both vendors was almost equal (p = 1.0), the mean WM CBF was significantly different (p<0.01). The inter-vendor GM variation did not differ from the intra-vendor GM variation (p = 0.3 and p = 0.5 for GE and Philips respectively). Spatial inter-vendor CBF and variation differences were <span class="hlt">observed</span> in several GM regions and in the WM. These results show that total GM CBF-values can be exchanged between vendors. For the inter-vendor comparison of GM regions or WM, these results encourage further standardization of ASL implementation among vendors.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/7885721','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/7885721"><span><span class="hlt">Reproducibility</span> of Nordic Sleep Questionnaire in spinal cord injured.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Biering-Sørensen, F; Biering-Sørensen, M; Hilden, J</p> <p>1994-11-01</p> <p>A recently proposed Nordic Sleep Questionnaire (NSQ) comprises 26 questions concerning qualitative and quantitative aspects of the respondent's sleep habits. Its <span class="hlt">reproducibility</span> was evaluated in 32 spinal cord injured individuals (SCI), 24 men and eight women (23-72 years), and 79 normal subjects, 23 men and 56 women (19-77 years). They completed the NSQ twice at a median interval of 15 days (range 10-26) and 27 days (range 4-103) respectively. The group of normal subjects were evenly divided into group 26, i.e. those who completed the two NSQs within 26 days, and group 27 with 27 days or more between their replies. Generally, group 27 showed no worse test-retest agreement than group 26. In addition, the respondents' answers, with a few exceptions, were reasonably stable in terms of test-retest agreement or standard deviation. The SCI group exhibited the same level of <span class="hlt">reproducibility</span>, although they had more 'pathology' to report and thus more scope for contradicting themselves. The questions in the NSQ generally were satisfactorily <span class="hlt">reproducible</span>. However, answers to the ordered five-point questions about sleepiness in the morning and during the daytime ought to be interpreted with caution. The same may be said about the number of minutes required to fall asleep, and the duration of daytime naps.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/18632747','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/18632747"><span>Apparently low <span class="hlt">reproducibility</span> of true differential expression discoveries in microarray studies.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Zhang, Min; Yao, Chen; Guo, Zheng; Zou, Jinfeng; Zhang, Lin; Xiao, Hui; Wang, Dong; Yang, Da; Gong, Xue; Zhu, Jing; Li, Yanhui; Li, Xia</p> <p>2008-09-15</p> <p>Differentially expressed gene (DEG) lists detected from different microarray studies for a same disease are often highly inconsistent. Even in technical replicate tests using identical samples, DEG detection still shows very low <span class="hlt">reproducibility</span>. It is often believed that current small microarray studies will largely introduce false discoveries. Based on a statistical model, we show that even in technical replicate tests using identical samples, it is highly likely that the selected DEG lists will be very inconsistent in the presence of small measurement variations. Therefore, the apparently low <span class="hlt">reproducibility</span> of DEG detection from current technical replicate tests does not indicate low quality of microarray technology. We also demonstrate that heterogeneous biological variations existing in real cancer data will further reduce the overall <span class="hlt">reproducibility</span> of DEG detection. Nevertheless, in small subsamples from both simulated and real data, the actual false discovery rate (FDR) for each DEG list tends to be low, suggesting that each separately determined list may comprise mostly true DEGs. Rather than simply counting the overlaps of the discovery lists from different studies for a complex disease, novel metrics are needed for evaluating the <span class="hlt">reproducibility</span> of discoveries characterized with correlated molecular changes. Supplementaty information: Supplementary data are available at Bioinformatics online.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3667053','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3667053"><span>Inter-study <span class="hlt">reproducibility</span> of cardiovascular magnetic resonance tagging</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p></p> <p>2013-01-01</p> <p>Background The aim of this study is to determine the test-retest reliability of the measurement of regional myocardial function by cardiovascular magnetic resonance (CMR) tagging using spatial modulation of magnetization. Methods Twenty-five participants underwent CMR tagging twice over 12 ± 7 days. To assess the role of slice orientation on strain measurement, two healthy volunteers had a first exam, followed by image acquisition repeated with slices rotated ±15 degrees out of true short axis, followed by a second exam in the true short axis plane. To assess the role of slice location, two healthy volunteers had whole heart tagging. The harmonic phase (HARP) method was used to analyze the tagged images. Peak midwall circumferential strain (Ecc), radial strain (Err), Lambda 1, Lambda 2, and Angle α were determined in basal, mid and apical slices. LV torsion, systolic and early diastolic circumferential strain and torsion rates were also determined. Results LV Ecc and torsion had excellent intra-, interobserver, and inter-study intra-class correlation coefficients (ICC range, 0.7 to 0.9). Err, Lambda 1, Lambda 2 and angle had excellent intra- and interobserver ICC than inter-study ICC. Angle had least inter-study <span class="hlt">reproducibility</span>. Torsion rates had superior intra-, interobserver, and inter-study <span class="hlt">reproducibility</span> to strain rates. The measurements of LV Ecc were comparable in all three slices with different short axis orientations (standard deviation of mean Ecc was 0.09, 0.18 and 0.16 at basal, mid and apical slices, respectively). The mean difference in LV Ecc between slices was more pronounced in most of the basal slices compared to the rest of the heart. Conclusions Intraobserver and interobserver <span class="hlt">reproducibility</span> of all strain and torsion parameters was excellent. Inter-study <span class="hlt">reproducibility</span> of CMR tagging by SPAMM varied between different parameters as described in the results above and was superior for Ecc and LV torsion. The variation in LV Ecc</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.gpo.gov/fdsys/pkg/CFR-2010-title46-vol2/pdf/CFR-2010-title46-vol2-sec56-97-38.pdf','CFR'); return false;" href="https://www.gpo.gov/fdsys/pkg/CFR-2010-title46-vol2/pdf/CFR-2010-title46-vol2-sec56-97-38.pdf"><span>46 CFR 56.97-38 - Initial service leak test (<span class="hlt">reproduces</span> 137.7).</span></a></p> <p><a target="_blank" href="http://www.gpo.gov/fdsys/browse/collectionCfr.action?selectedYearFrom=2010&page.go=Go">Code of Federal Regulations, 2010 CFR</a></p> <p></p> <p>2010-10-01</p> <p>... 46 Shipping 2 2010-10-01 2010-10-01 false Initial service leak test (<span class="hlt">reproduces</span> 137.7). 56.97-38... PIPING SYSTEMS AND APPURTENANCES Pressure Tests § 56.97-38 Initial service leak test (<span class="hlt">reproduces</span> 137.7). (a) An initial service leak test and inspection is acceptable when other types of test are not...</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.gpo.gov/fdsys/pkg/CFR-2013-title46-vol2/pdf/CFR-2013-title46-vol2-sec54-10-5.pdf','CFR2013'); return false;" href="https://www.gpo.gov/fdsys/pkg/CFR-2013-title46-vol2/pdf/CFR-2013-title46-vol2-sec54-10-5.pdf"><span>46 CFR 54.10-5 - Maximum allowable working pressure (<span class="hlt">reproduces</span> UG-98).</span></a></p> <p><a target="_blank" href="http://www.gpo.gov/fdsys/browse/collectionCfr.action?selectedYearFrom=2013&page.go=Go">Code of Federal Regulations, 2013 CFR</a></p> <p></p> <p>2013-10-01</p> <p>... 46 Shipping 2 2013-10-01 2013-10-01 false Maximum allowable working pressure (<span class="hlt">reproduces</span> UG-98). 54.10-5 Section 54.10-5 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) MARINE ENGINEERING PRESSURE VESSELS Inspection, Reports, and Stamping § 54.10-5 Maximum allowable working pressure (<span class="hlt">reproduces</span> UG-98). (a) The maximum allowable...</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.gpo.gov/fdsys/pkg/CFR-2011-title46-vol2/pdf/CFR-2011-title46-vol2-sec54-10-5.pdf','CFR2011'); return false;" href="https://www.gpo.gov/fdsys/pkg/CFR-2011-title46-vol2/pdf/CFR-2011-title46-vol2-sec54-10-5.pdf"><span>46 CFR 54.10-5 - Maximum allowable working pressure (<span class="hlt">reproduces</span> UG-98).</span></a></p> <p><a target="_blank" href="http://www.gpo.gov/fdsys/browse/collectionCfr.action?selectedYearFrom=2011&page.go=Go">Code of Federal Regulations, 2011 CFR</a></p> <p></p> <p>2011-10-01</p> <p>... 46 Shipping 2 2011-10-01 2011-10-01 false Maximum allowable working pressure (<span class="hlt">reproduces</span> UG-98). 54.10-5 Section 54.10-5 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) MARINE ENGINEERING PRESSURE VESSELS Inspection, Reports, and Stamping § 54.10-5 Maximum allowable working pressure (<span class="hlt">reproduces</span> UG-98). (a) The maximum allowable...</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.gpo.gov/fdsys/pkg/CFR-2014-title46-vol2/pdf/CFR-2014-title46-vol2-sec54-10-5.pdf','CFR2014'); return false;" href="https://www.gpo.gov/fdsys/pkg/CFR-2014-title46-vol2/pdf/CFR-2014-title46-vol2-sec54-10-5.pdf"><span>46 CFR 54.10-5 - Maximum allowable working pressure (<span class="hlt">reproduces</span> UG-98).</span></a></p> <p><a target="_blank" href="http://www.gpo.gov/fdsys/browse/collectionCfr.action?selectedYearFrom=2014&page.go=Go">Code of Federal Regulations, 2014 CFR</a></p> <p></p> <p>2014-10-01</p> <p>... 46 Shipping 2 2014-10-01 2014-10-01 false Maximum allowable working pressure (<span class="hlt">reproduces</span> UG-98). 54.10-5 Section 54.10-5 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) MARINE ENGINEERING PRESSURE VESSELS Inspection, Reports, and Stamping § 54.10-5 Maximum allowable working pressure (<span class="hlt">reproduces</span> UG-98). (a) The maximum allowable...</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.gpo.gov/fdsys/pkg/CFR-2012-title46-vol2/pdf/CFR-2012-title46-vol2-sec54-10-5.pdf','CFR2012'); return false;" href="https://www.gpo.gov/fdsys/pkg/CFR-2012-title46-vol2/pdf/CFR-2012-title46-vol2-sec54-10-5.pdf"><span>46 CFR 54.10-5 - Maximum allowable working pressure (<span class="hlt">reproduces</span> UG-98).</span></a></p> <p><a target="_blank" href="http://www.gpo.gov/fdsys/browse/collectionCfr.action?selectedYearFrom=2012&page.go=Go">Code of Federal Regulations, 2012 CFR</a></p> <p></p> <p>2012-10-01</p> <p>... 46 Shipping 2 2012-10-01 2012-10-01 false Maximum allowable working pressure (<span class="hlt">reproduces</span> UG-98). 54.10-5 Section 54.10-5 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) MARINE ENGINEERING PRESSURE VESSELS Inspection, Reports, and Stamping § 54.10-5 Maximum allowable working pressure (<span class="hlt">reproduces</span> UG-98). (a) The maximum allowable...</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/23968236','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/23968236"><span>Rapid calculation of <span class="hlt">accurate</span> atomic charges for proteins via the electronegativity equalization method.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Ionescu, Crina-Maria; Geidl, Stanislav; Svobodová Vařeková, Radka; Koča, Jaroslav</p> <p>2013-10-28</p> <p>We focused on the parametrization and evaluation of empirical models for fast and <span class="hlt">accurate</span> calculation of conformationally dependent atomic charges in proteins. The models were based on the electronegativity equalization method (EEM), and the parametrization procedure was tailored to proteins. We used large protein fragments as reference structures and fitted the EEM model parameters using atomic charges computed by three population analyses (Mulliken, Natural, iterative Hirshfeld), at the Hartree-Fock level with two basis sets (6-31G*, 6-31G**) and in two environments (gas phase, implicit solvation). We parametrized and successfully validated 24 EEM models. When tested on insulin and ubiquitin, all models <span class="hlt">reproduced</span> quantum mechanics level charges well and were consistent with respect to population analysis and basis set. Specifically, the models showed on average a correlation of 0.961, RMSD 0.097 e, and average absolute error per atom 0.072 e. The EEM models can be used with the freely available EEM implementation EEM_SOLVER.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2014AGUFMOS42A..05K','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2014AGUFMOS42A..05K"><span>Potential utility of three-dimensional temperature and salinity fields estimated from satellite altimetry and Argo data for improving mesoscale <span class="hlt">reproducibility</span> in regional ocean modeling</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Kanki, R.; Uchiyama, Y.; Miyazaki, D.; Takano, A.; Miyazawa, Y.; Yamazaki, H.</p> <p>2014-12-01</p> <p>Mesoscale oceanic structure and variability are required to be <span class="hlt">reproduced</span> as <span class="hlt">accurately</span> as possible in realistic regional ocean modeling. Uchiyama et al. (2012) demonstrated with a submesoscale eddy-resolving JCOPE2-ROMS downscaling oceanic modeling system that the mesoscale <span class="hlt">reproducibility</span> of the Kuroshio meandering along Japan is significantly improved by introducing a simple restoration to data which we call "TS nudging" (a.k.a. robust diagnosis) where the prognostic temperature and salinity fields are weakly nudged four-dimensionally towards the assimilative JCOPE2 reanalysis (Miyazawa et al., 2009). However, there is not always a reliable reanalysis for oceanic downscaling in an arbitrary region and at an arbitrary time, and therefore alternative dataset should be prepared. Takano et al. (2009) proposed an empirical method to estimate mesoscale 3-D thermal structure from the near real-time AVISO altimetry data along with the ARGO float data based on the two-layer model of Goni et al. (1996). In the present study, we consider the TS data derived from this method as a candidate. We thus conduct a synoptic forward modeling of the Kuroshio using the JCOPE2-ROMS downscaling system to explore potential utility of this empirical TS dataset (hereinafter TUM-TS) by carrying out two runs with the T-S nudging towards 1) the JCOPE2-TS and 2) TUM-TS fields. An example of the comparison between the two ROMS test runs is shown in the attached figure showing the annually averaged surface EKE. Both of TUM-TS and JCOPE2-TS are found to help <span class="hlt">reproducing</span> the mesoscale variance of the Koroshio and its extension as well as its mean paths, surface KE and EKE reasonably well. Therefore, the AVISO-ARGO derived empirical 3-D TS estimation is potentially exploitable for the dataset to conduct the T-S nudging to <span class="hlt">reproduce</span> mesoscale oceanic structure.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2673644','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2673644"><span>Evaluation of guidewire path <span class="hlt">reproducibility</span></span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Schafer, Sebastian; Hoffmann, Kenneth R.; Noël, Peter B.; Ionita, Ciprian N.; Dmochowski, Jacek</p> <p>2008-01-01</p> <p>The number of minimally invasive vascular interventions is increasing. In these interventions, a variety of devices are directed to and placed at the site of intervention. The device used in almost all of these interventions is the guidewire, acting as a monorail for all devices which are delivered to the intervention site. However, even with the guidewire in place, clinicians still experience difficulties during the interventions. As a first step toward understanding these difficulties and facilitating guidewire and device guidance, we have investigated the <span class="hlt">reproducibility</span> of the final paths of the guidewire in vessel phantom models on different factors: user, materials and geometry. Three vessel phantoms (vessel diameters ∼4 mm) were constructed having tortuousity similar to the internal carotid artery from silicon tubing and encased in Sylgard elastomer. Several trained users repeatedly passed two guidewires of different flexibility through the phantoms under pulsatile flow conditions. After the guidewire had been placed, rotational c-arm image sequences were acquired (9 in. II mode, 0.185 mm pixel size), and the phantom and guidewire were reconstructed (5123, 0.288 mm voxel size). The reconstructed volumes were aligned. The centerlines of the guidewire and the phantom vessel were then determined using region-growing techniques. Guidewire paths appear similar across users but not across materials. The average root mean square difference of the repeated placement was 0.17±0.02 mm (plastic-coated guidewire), 0.73±0.55 mm (steel guidewire) and 1.15±0.65 mm (steel versus plastic-coated). For a given guidewire, these results indicate that the guidewire path is relatively <span class="hlt">reproducible</span> in shape and position. PMID:18561663</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_21");'>21</a></li> <li><a href="#" onclick='return showDiv("page_22");'>22</a></li> <li class="active"><span>23</span></li> <li><a href="#" onclick='return showDiv("page_24");'>24</a></li> <li><a href="#" onclick='return showDiv("page_25");'>25</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_23 --> <div id="page_24" class="hiddenDiv"> <div class="row"> <div class="col-sm-12"> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_21");'>21</a></li> <li><a href="#" onclick='return showDiv("page_22");'>22</a></li> <li><a href="#" onclick='return showDiv("page_23");'>23</a></li> <li class="active"><span>24</span></li> <li><a href="#" onclick='return showDiv("page_25");'>25</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div> </div> <div class="row"> <div class="col-sm-12"> <ol class="result-class" start="461"> <li> <p><a target="_blank" onclick="trackOutboundLink('http://hdl.handle.net/2060/19970027520','NASA-TRS'); return false;" href="http://hdl.handle.net/2060/19970027520"><span><span class="hlt">Accurate</span> Measurements of the Local Deuterium Abundance from HST Spectra</span></a></p> <p><a target="_blank" href="http://ntrs.nasa.gov/search.jsp">NASA Technical Reports Server (NTRS)</a></p> <p>Linsky, Jeffrey L.</p> <p>1996-01-01</p> <p>An <span class="hlt">accurate</span> measurement of the primordial value of D/H would provide a critical test of nucleosynthesis models for the early universe and the baryon density. I briefly summarize the ongoing HST <span class="hlt">observations</span> of the interstellar H and D Lyman-alpha absorption for lines of sight to nearby stars and comment on recent reports of extragalactic D/H measurements.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=5638246','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=5638246"><span><span class="hlt">Reproducibility</span> of shear wave elastography (SWE) in patients with chronic liver disease</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Salomone Megna, Angelo; Ragucci, Monica; De Luca, Massimo; Marino Marsilia, Giuseppina; Nardone, Gerardo; Coccoli, Pietro; Prinster, Anna; Mannelli, Lorenzo; Vergara, Emilia; Monti, Serena; Liuzzi, Raffaele; Incoronato, Mariarosaria</p> <p>2017-01-01</p> <p>The presence of significant fibrosis is an indicator for liver disease staging and prognosis. The aim of the study was to determine <span class="hlt">reproducibility</span> of real-time shear wave elastography using a hepatic biopsy as the reference standard to identify patients with chronic liver disease. Forty patients with chronic liver disease and 12 normal subjects received shear wave elastography performed by skilled operators. Interoperator <span class="hlt">reproducibility</span> was studied in 29 patients. Fibrosis was evaluated using the Metavir score. The median and range shear wave elastography values in chronic liver disease subjects were 6.15 kPa and 3.14–16.7 kPa and were 4.49 kPa and 2.92–7.32 kPa in normal subjects, respectively. With respect to fibrosis detected by liver biopsy, shear wave elastography did not change significantly between F0 and F1 (p = 0.334), F1 and F2 (p = 0.611), or F3 and F4 (0.327); a significant difference was <span class="hlt">observed</span> between the F0-F2 and F3-F4 groups (p = 0.002). SWE also correlated with inflammatory activity (Rs = 0.443, p = 0.0023) and ALT levels (Rs = 0.287, p = 0.0804). Age, sex and body mass index did not affect shear wave elastography measurements. Using receiver operator characteristic curves, two threshold values for shear wave elastography were identified: 5.62 kPa for patients with fibrosis (≥F2; sensitivity 80%, specificity 69.4%, and accuracy 77%) and 7.04 kPa for patients with severe fibrosis (≥F3; sensitivity 88.9%, specificity 81%, and accuracy 89%). Overall interobserver agreement was excellent and was analysed using an interclass correlation coefficient (0.94; CI 0.87–0.97).This study shows that shear wave elastography executed by skilled operators can be performed on almost all chronic liver disease patients with high <span class="hlt">reproducibility</span>. It is not influenced by age, sex or body mass index, identifies severely fibrotic patients and is also related to inflammatory activity. PMID:29023554</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4627782','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=4627782"><span><span class="hlt">Reproducibility</span> and Temporal Structure in Weekly Resting-State fMRI over a Period of 3.5 Years</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Choe, Ann S.; Jones, Craig K.; Joel, Suresh E.; Muschelli, John; Belegu, Visar; Caffo, Brian S.; Lindquist, Martin A.; van Zijl, Peter C. M.; Pekar, James J.</p> <p>2015-01-01</p> <p>Resting-state functional MRI (rs-fMRI) permits study of the brain’s functional networks without requiring participants to perform tasks. Robust changes in such resting state networks (RSNs) have been <span class="hlt">observed</span> in neurologic disorders, and rs-fMRI outcome measures are candidate biomarkers for monitoring clinical trials, including trials of extended therapeutic interventions for rehabilitation of patients with chronic conditions. In this study, we aim to present a unique longitudinal dataset reporting on a healthy adult subject scanned weekly over 3.5 years and identify rs-fMRI outcome measures appropriate for clinical trials. Accordingly, we assessed the <span class="hlt">reproducibility</span>, and characterized the temporal structure of, rs-fMRI outcome measures derived using independent component analysis (ICA). Data was compared to a 21-person dataset acquired on the same scanner in order to confirm that the values of the single-subject RSN measures were within the expected range as assessed from the multi-participant dataset. Fourteen RSNs were identified, and the inter-session <span class="hlt">reproducibility</span> of outcome measures—network spatial map, temporal signal fluctuation magnitude, and between-network connectivity (BNC)–was high, with executive RSNs showing the highest <span class="hlt">reproducibility</span>. Analysis of the weekly outcome measures also showed that many rs-fMRI outcome measures had a significant linear trend, annual periodicity, and persistence. Such temporal structure was most prominent in spatial map similarity, and least prominent in BNC. High <span class="hlt">reproducibility</span> supports the candidacy of rs-fMRI outcome measures as biomarkers, but the presence of significant temporal structure needs to be taken into account when such outcome measures are considered as biomarkers for rehabilitation-style therapeutic interventions in chronic conditions. PMID:26517540</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/21567210','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/21567210"><span><span class="hlt">Reproducibility</span> of straylight measurement by C-Quant for assessment of retinal straylight using the compensation comparison method.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Guber, Ivo; Bachmann, Lucas M; Guber, Josef; Bochmann, Frank; Lange, Alex P; Thiel, Michael A</p> <p>2011-09-01</p> <p>Straylight gives the appearance of a veil of light thrown over a person's retinal image when there is a strong light source present. We examined the <span class="hlt">reproducibility</span> of the measurements by C-Quant, and assessed its correlation to characteristics of the eye and subjects' age. Five repeated straylight measurements were taken using the dominant eye of 45 healthy subjects (age 21-59) with a BCVA of 20/20: 14 emmetropic, 16 myopic, eight hyperopic and seven with astigmatism. We assessed the extent of <span class="hlt">reproducibility</span> of straylight measures using the intraclass correlation coefficient. The mean straylight value of all measurements was 1.01 (SD 0.23, median 0.97, interquartile range 0.85-1.1). Per 10 years of age, straylight increased in average by 0.10 (95%CI 0.04 to 0.16, p < 0.01]. We found no independent association of refraction (range -5.25 dpt to +2 dpt) on straylight values (0.001; 95%CI -0.022 to 0.024, p = 0.92). Compared to emmetropic subjects, myopia reduced straylight (-.011; -0.024 to 0.02, p = 0.11), whereas higher straylight values (0.09; -0.01 to 0.20, p = 0.09) were <span class="hlt">observed</span> in subjects with blue irises as compared to dark-colored irises when correcting for age. The intraclass correlation coefficient (ICC) of repeated measurements was 0.83 (95%CI 0.76 to 0.90). Our study showed that straylight measurements with the C-Quant had a high <span class="hlt">reproducibility</span>, i.e. a lack of large intra-<span class="hlt">observer</span> variability, making it appropriate to be applied in long-term follow-up studies assessing the long-term effect of surgical procedures on the quality of vision.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.osti.gov/pages/biblio/1184294-using-molecular-dynamics-quantify-electrical-double-layer-examine-potential-its-direct-observation-situ-tem','SCIGOV-DOEP'); return false;" href="https://www.osti.gov/pages/biblio/1184294-using-molecular-dynamics-quantify-electrical-double-layer-examine-potential-its-direct-observation-situ-tem"><span>Using Molecular Dynamics to quantify the electrical double layer and examine the potential for its direct <span class="hlt">observation</span> in the in-situ TEM</span></a></p> <p><a target="_blank" href="http://www.osti.gov/pages">DOE PAGES</a></p> <p>Welch, David A.; Mehdi, Beata L.; Hatchell, Hanna J.; ...</p> <p>2015-03-25</p> <p>Understanding the fundamental processes taking place at the electrode-electrolyte interface in batteries will play a key role in the development of next generation energy storage technologies. One of the most fundamental aspects of the electrode-electrolyte interface is the electrical double layer (EDL). Given the recent development of high spatial resolution in-situ electrochemical cells for scanning transmission electron microscopy (STEM), there now exists the possibility that we can directly <span class="hlt">observe</span> the formation and dynamics of the EDL. In this paper we predict electrolyte structure within the EDL using classical models and atomistic Molecular Dynamics (MD) simulations. The MD simulations show thatmore » the classical models fail to <span class="hlt">accurately</span> <span class="hlt">reproduce</span> concentration profiles that exist within the electrolyte. It is thus suggested that MD must be used in order to <span class="hlt">accurately</span> predict STEM images of the electrode-electrolyte interface. Using MD and image simulations together for a high contrast electrolyte (the high atomic number CsCl electrolyte), it is determined that, for a smooth interface, concentration profiles within the EDL should be visible experimentally. When normal experimental parameters such as rough interfaces and low-Z electrolytes (like those used in Li-ion batteries) are considered, <span class="hlt">observation</span> of the EDL appears to be more difficult.« less</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2018GeoRL..45.3136G','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2018GeoRL..45.3136G"><span>Reconstructed Solar-Induced Fluorescence: A Machine Learning Vegetation Product Based on MODIS Surface Reflectance to <span class="hlt">Reproduce</span> GOME-2 Solar-Induced Fluorescence</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Gentine, P.; Alemohammad, S. H.</p> <p>2018-04-01</p> <p>Solar-induced fluorescence (SIF) <span class="hlt">observations</span> from space have resulted in major advancements in estimating gross primary productivity (GPP). However, current SIF <span class="hlt">observations</span> remain spatially coarse, infrequent, and noisy. Here we develop a machine learning approach using surface reflectances from Moderate Resolution Imaging Spectroradiometer (MODIS) channels to <span class="hlt">reproduce</span> SIF normalized by clear sky surface irradiance from the Global Ozone Monitoring Experiment-2 (GOME-2). The resulting product is a proxy for ecosystem photosynthetically active radiation absorbed by chlorophyll (fAPARCh). Multiplying this new product with a MODIS estimate of photosynthetically active radiation provides a new MODIS-only reconstruction of SIF called Reconstructed SIF (RSIF). RSIF exhibits much higher seasonal and interannual correlation than the original SIF when compared with eddy covariance estimates of GPP and two reference global GPP products, especially in dry and cold regions. RSIF also <span class="hlt">reproduces</span> intense productivity regions such as the U.S. Corn Belt contrary to typical vegetation indices and similarly to SIF.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2016JPS...310..137P','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2016JPS...310..137P"><span>Highly <span class="hlt">accurate</span> apparatus for electrochemical characterization of the felt electrodes used in redox flow batteries</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Park, Jong Ho; Park, Jung Jin; Park, O. Ok; Jin, Chang-Soo; Yang, Jung Hoon</p> <p>2016-04-01</p> <p>Because of the rise in renewable energy use, the redox flow battery (RFB) has attracted extensive attention as an energy storage system. Thus, many studies have focused on improving the performance of the felt electrodes used in RFBs. However, existing analysis cells are unsuitable for characterizing felt electrodes because of their complex 3-dimensional structure. Analysis is also greatly affected by the measurement conditions, viz. compression ratio, contact area, and contact strength between the felt and current collector. To address the growing need for practical analytical apparatus, we report a new analysis cell for <span class="hlt">accurate</span> electrochemical characterization of felt electrodes under various conditions, and compare it with previous ones. In this cell, the measurement conditions can be exhaustively controlled with a compression supporter. The cell showed excellent <span class="hlt">reproducibility</span> in cyclic voltammetry analysis and the results agreed well with actual RFB charge-discharge performance.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/1989RScI...60..795A','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/1989RScI...60..795A"><span><span class="hlt">Accurate</span> electron gun-positioning mechanism for electron beam-mapping of large cross-section magnetic surfaces</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Anderson, F. S. B.; Middleton, F.; Colchin, R. J.; Million, D.</p> <p>1989-04-01</p> <p>A method of <span class="hlt">accurately</span> supporting and positioning an electron source inside a large cross-sectional area magnetic field which provides very low electron beam occlusion is reported. The application of electrical discharge machining to the fabrication of a 1-m truss support structure has provided an extremely long, rigid and mechanically strong electron gun support. <span class="hlt">Reproducible</span> electron gun positioning to within 1 mm has been achieved at any location within a 1×0.6-m2 area. The extremely thin sections of the support truss (≤1.5 mm) have kept the electron beam occlusion to less than 3 mm. The support and drive mechanism have been designed and fabricated at the University of Wisconsin for application to the mapping of the magnetic surface structure of the Advanced Toroidal Facility torsatron1 at the Oak Ridge National Laboratory.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/24289323','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/24289323"><span>Economical and <span class="hlt">accurate</span> protocol for calculating hydrogen-bond-acceptor strengths.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>El Kerdawy, Ahmed; Tautermann, Christofer S; Clark, Timothy; Fox, Thomas</p> <p>2013-12-23</p> <p>A series of density functional/basis set combinations and second-order Møller-Plesset calculations have been used to test their ability to <span class="hlt">reproduce</span> the trends <span class="hlt">observed</span> experimentally for the strengths of hydrogen-bond acceptors in order to identify computationally efficient techniques for routine use in the computational drug-design process. The effects of functionals, basis sets, counterpoise corrections, and constraints on the optimized geometries were tested and analyzed, and recommendations (M06-2X/cc-pVDZ and X3LYP/cc-pVDZ with single-point counterpoise corrections or X3LYP/aug-cc-pVDZ without counterpoise) were made for suitable moderately high-throughput techniques.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/26617403','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/26617403"><span><span class="hlt">Reproducibility</span> of 3D kinematics and surface electromyography measurements of mastication.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Remijn, Lianne; Groen, Brenda E; Speyer, Renée; van Limbeek, Jacques; Nijhuis-van der Sanden, Maria W G</p> <p>2016-03-01</p> <p>The aim of this study was to determine the measurement <span class="hlt">reproducibility</span> for a procedure evaluating the mastication process and to estimate the smallest detectable differences of 3D kinematic and surface electromyography (sEMG) variables. Kinematics of mandible movements and sEMG activity of the masticatory muscles were obtained over two sessions with four conditions: two food textures (biscuit and bread) of two sizes (small and large). Twelve healthy adults (mean age 29.1 years) completed the study. The second to the fifth chewing cycle of 5 bites were used for analyses. The <span class="hlt">reproducibility</span> per outcome variable was calculated with an intraclass correlation coefficient (ICC) and a Bland-Altman analysis was applied to determine the standard error of measurement relative error of measurement and smallest detectable differences of all variables. ICCs ranged from 0.71 to 0.98 for all outcome variables. The outcome variables consisted of four bite and fourteen chewing cycle variables. The relative standard error of measurement of the bite variables was up to 17.3% for 'time-to-swallow', 'time-to-transport' and 'number of chewing cycles', but ranged from 31.5% to 57.0% for 'change of chewing side'. The relative standard error of measurement ranged from 4.1% to 24.7% for chewing cycle variables and was smaller for kinematic variables than sEMG variables. In general, measurements obtained with 3D kinematics and sEMG are <span class="hlt">reproducible</span> techniques to assess the mastication process. The duration of the chewing cycle and frequency of chewing were the best <span class="hlt">reproducible</span> measurements. Change of chewing side could not be <span class="hlt">reproduced</span>. The published measurement error and smallest detectable differences will aid the interpretation of the results of future clinical studies using the same study variables. Copyright © 2015 Elsevier Inc. All rights reserved.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/29648497','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/29648497"><span>Low <span class="hlt">reproducibility</span> between oral radiologists and general dentists with regards to radiographic diagnosis of caries.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Pakbaznejad Esmaeili, Elmira; Pakkala, Tuomas; Haukka, Jari; Siukosaari, Päivi</p> <p>2018-04-12</p> <p>Early clinical and radiological diagnosis of dental caries is one of the fundamental objectives of clinical dentistry because of the high frequency of the disease and severe complications if caries remains untreated, especially among the elderly and patients with immunodeficiency. Dental panoramic tomography (DPT) is a common radiographic method for evaluating dentition when indicated, especially in an adult population. The aim of this study was to assess the <span class="hlt">reproducibility</span> of diagnosis between specialists in oral radiology and general dentists with regards to caries lesions based on DPTs of adults. One-hundred DPTs taken from adult patients (average age 35) and then analyzed and reported on by 42 general dentists were then analyzed independently by two specialists in oral radiology with respect to caries lesions in the premolar and molar areas using radiographic criteria established for caries diagnosis. The general dentists versus oral radiologists were not calibrated before. Level of agreement between specialists and general dentists was measured using Cohen's kappa. Comparison between <span class="hlt">observations</span> of general dentists and specialists in oral radiology showed that 61% of the caries lesions on proximal surfaces of premolars and molars <span class="hlt">observed</span> by specialists went unobserved by general dentists. Cohen's kappa value for specialists was 0.85 (p < .001) and for each specialist and general dentists 0.48 (p < .001) and 0.44 (p < .001). The <span class="hlt">reproducibility</span> between specialists in oral radiology and general dentists for detecting caries in DPTs was low.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2011AGUFM.B43F0359L','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2011AGUFM.B43F0359L"><span>The synergistic use of models and <span class="hlt">observations</span>: understanding the mechanisms behind <span class="hlt">observed</span> biomass dynamics at 14 Amazonian field sites and the implications for future biomass change</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Levine, N. M.; Galbraith, D.; Christoffersen, B. J.; Imbuzeiro, H. A.; Restrepo-Coupe, N.; Malhi, Y.; Saleska, S. R.; Costa, M. H.; Phillips, O.; Andrade, A.; Moorcroft, P. R.</p> <p>2011-12-01</p> <p>The Amazonian rainforests play a vital role in global water, energy and carbon cycling. The sensitivity of this system to natural and anthropogenic disturbances therefore has important implications for the global climate. Some global models have predicted large-scale forest dieback and the savannization of Amazonia over the next century [Meehl et al., 2007]. While several studies have demonstrated the sensitivity of dynamic global vegetation models to changes in temperature, precipitation, and dry season length [e.g. Galbraith et al., 2010; Good et al., 2011], the ability of these models to <span class="hlt">accurately</span> <span class="hlt">reproduce</span> ecosystem dynamics of present-day transitional or low biomass tropical forests has not been demonstrated. A model-data intercomparison was conducted with four state-of-the-art terrestrial ecosystem models to evaluate the ability of these models to <span class="hlt">accurately</span> represent structure, function, and long-term biomass dynamics over a range of Amazonian ecosystems. Each modeling group conducted a series of simulations for 14 sites including mature forest, transitional forest, savannah, and agricultural/pasture sites. All models were run using standard physical parameters and the same initialization procedure. Model results were compared against forest inventory and dendrometer data in addition to flux tower measurements. While the models compared well against field <span class="hlt">observations</span> for the mature forest sites, significant differences were <span class="hlt">observed</span> between predicted and measured ecosystem structure and dynamics for the transitional forest and savannah sites. The length of the dry season and soil sand content were good predictors of model performance. In addition, for the big leaf models, model performance was highest for sites dominated by late successional trees and lowest for sites with predominantly early and mid-successional trees. This study provides insight into tropical forest function and sensitivity to environmental conditions that will aid in predictions of the</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.osti.gov/servlets/purl/1221578','SCIGOV-STC'); return false;" href="https://www.osti.gov/servlets/purl/1221578"><span>Towards <span class="hlt">Accurate</span> Application Characterization for Exascale (APEX)</span></a></p> <p><a target="_blank" href="http://www.osti.gov/search">DOE Office of Scientific and Technical Information (OSTI.GOV)</a></p> <p>Hammond, Simon David</p> <p></p> <p>Sandia National Laboratories has been engaged in hardware and software codesign activities for a number of years, indeed, it might be argued that prototyping of clusters as far back as the CPLANT machines and many large capability resources including ASCI Red and RedStorm were examples of codesigned solutions. As the research supporting our codesign activities has moved closer to investigating on-node runtime behavior a nature hunger has grown for detailed analysis of both hardware and algorithm performance from the perspective of low-level operations. The Application Characterization for Exascale (APEX) LDRD was a project concieved of addressing some of these concerns.more » Primarily the research was to intended to focus on generating <span class="hlt">accurate</span> and <span class="hlt">reproducible</span> low-level performance metrics using tools that could scale to production-class code bases. Along side this research was an advocacy and analysis role associated with evaluating tools for production use, working with leading industry vendors to develop and refine solutions required by our code teams and to directly engage with production code developers to form a context for the application analysis and a bridge to the research community within Sandia. On each of these accounts significant progress has been made, particularly, as this report will cover, in the low-level analysis of operations for important classes of algorithms. This report summarizes the development of a collection of tools under the APEX research program and leaves to other SAND and L2 milestone reports the description of codesign progress with Sandia’s production users/developers.« less</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=5506257','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=5506257"><span><span class="hlt">Reproducibility</span> of Centric Relation Techniques by means of Condyle Position Analysis</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Galeković, Nikolina Holen; Fugošić, Vesna; Braut, Vedrana</p> <p>2017-01-01</p> <p>Purpose The aim of this study was to determine the <span class="hlt">reproducibility</span> of clinical centric relation (CR) registration techniques (bimanual manipulation, chin point guidance and Roth's method) by means of condyle position analysis. Material and methods Thirty two fully dentate asymptomatic subjects (16 female and 16 male) with normal occlusal relations (Angle class I) participated in the study (mean age, 22.6 ± 4.7 years). The mandibular position indicator (MPI) was used to analyze the three-dimensional (anteroposterior (ΔX), superoinferior (ΔZ), mediolateral (ΔY)) condylar shift generated by the difference between the centric relation position (CR) and the maximal intercuspation position (MI) <span class="hlt">observed</span> in dental arches. Results The mean value and standard deviation of three-dimensional condylar shift of the tested clinical CR techniques was 0.19 ± 0.34 mm. Significant differences within the tested clinical CR registration techniques were found for anteroposterior condylar shift on the right side posterior (Δ Xrp; P ≤ 0.012); and superoinferior condylar shift on the left side inferior (Δ Zli; P ≤ 0.011), whereas between the tested CR registration techniques were found for anteroposterior shift on the right side posterior (ΔXrp, P ≤ 0.037) and superoinferior shift on the right side inferior (ΔZri, P ≤ 0.004), on the left side inferior (ΔZli, P ≤ 0.005) and on the left side superior (ΔZls, P ≤ 0.007). Conclusion Bimanual manipulation, chin point guidance and Roth's method are clinical CR registration techniques of equal accuracy and <span class="hlt">reproducibility</span> in asymptomatic subjects with normal occlusal relationship. PMID:28740266</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/28740266','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/28740266"><span><span class="hlt">Reproducibility</span> of Centric Relation Techniques by means of Condyle Position Analysis.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Galeković, Nikolina Holen; Fugošić, Vesna; Braut, Vedrana; Ćelić, Robert</p> <p>2017-03-01</p> <p>The aim of this study was to determine the <span class="hlt">reproducibility</span> of clinical centric relation (CR) registration techniques (bimanual manipulation, chin point guidance and Roth's method) by means of condyle position analysis. Thirty two fully dentate asymptomatic subjects (16 female and 16 male) with normal occlusal relations (Angle class I) participated in the study (mean age, 22.6 ± 4.7 years). The mandibular position indicator (MPI) was used to analyze the three-dimensional (anteroposterior (ΔX), superoinferior (ΔZ), mediolateral (ΔY)) condylar shift generated by the difference between the centric relation position (CR) and the maximal intercuspation position (MI) <span class="hlt">observed</span> in dental arches. The mean value and standard deviation of three-dimensional condylar shift of the tested clinical CR techniques was 0.19 ± 0.34 mm. Significant differences within the tested clinical CR registration techniques were found for anteroposterior condylar shift on the right side posterior (Δ Xrp; P ≤ 0.012); and superoinferior condylar shift on the left side inferior (Δ Zli; P ≤ 0.011), whereas between the tested CR registration techniques were found for anteroposterior shift on the right side posterior (ΔXrp, P ≤ 0.037) and superoinferior shift on the right side inferior (ΔZri, P ≤ 0.004), on the left side inferior (ΔZli, P ≤ 0.005) and on the left side superior (ΔZls, P ≤ 0.007). Bimanual manipulation, chin point guidance and Roth's method are clinical CR registration techniques of equal accuracy and <span class="hlt">reproducibility</span> in asymptomatic subjects with normal occlusal relationship.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/28938715','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/28938715"><span>The Harm Done to <span class="hlt">Reproducibility</span> by the Culture of Null Hypothesis Significance Testing.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Lash, Timothy L</p> <p>2017-09-15</p> <p>In the last few years, stakeholders in the scientific community have raised alarms about a perceived lack of <span class="hlt">reproducibility</span> of scientific results. In reaction, guidelines for journals have been promulgated and grant applicants have been asked to address the rigor and <span class="hlt">reproducibility</span> of their proposed projects. Neither solution addresses a primary culprit, which is the culture of null hypothesis significance testing that dominates statistical analysis and inference. In an innovative research enterprise, selection of results for further evaluation based on null hypothesis significance testing is doomed to yield a low proportion of <span class="hlt">reproducible</span> results and a high proportion of effects that are initially overestimated. In addition, the culture of null hypothesis significance testing discourages quantitative adjustments to account for systematic errors and quantitative incorporation of prior information. These strategies would otherwise improve <span class="hlt">reproducibility</span> and have not been previously proposed in the widely cited literature on this topic. Without discarding the culture of null hypothesis significance testing and implementing these alternative methods for statistical analysis and inference, all other strategies for improving <span class="hlt">reproducibility</span> will yield marginal gains at best. © The Author(s) 2017. Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/25098545','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/25098545"><span>Fabrication of <span class="hlt">reproducible</span>, integration-compatible hybrid molecular/si electronics.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Yu, Xi; Lovrinčić, Robert; Kraynis, Olga; Man, Gabriel; Ely, Tal; Zohar, Arava; Toledano, Tal; Cahen, David; Vilan, Ayelet</p> <p>2014-12-29</p> <p><span class="hlt">Reproducible</span> molecular junctions can be integrated within standard CMOS technology. Metal-molecule-semiconductor junctions are fabricated by direct Si-C binding of hexadecane or methyl-styrene onto oxide-free H-Si(111) surfaces, with the lateral size of the junctions defined by an etched SiO2 well and with evaporated Pb as the top contact. The current density, J, is highly <span class="hlt">reproducible</span> with a standard deviation in log(J) of 0.2 over a junction diameter change from 3 to 100 μm. <span class="hlt">Reproducibility</span> over such a large range indicates that transport is truly across the molecules and does not result from artifacts like edge effects or defects in the molecular monolayer. Device fabrication is tested for two n-Si doping levels. With highly doped Si, transport is dominated by tunneling and reveals sharp conductance onsets at room temperature. Using the temperature dependence of current across medium-doped n-Si, the molecular tunneling barrier can be separated from the Si-Schottky one, which is a 0.47 eV, in agreement with the molecular-modified surface dipole and quite different from the bare Si-H junction. This indicates that Pb evaporation does not cause significant chemical changes to the molecules. The ability to manufacture reliable devices constitutes important progress toward possible future hybrid Si-based molecular electronics. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1308157','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1308157"><span><span class="hlt">Observation</span> procedure, <span class="hlt">observer</span> gender, and behavior valence as determinants of sampling error in a behavior assessment analogue</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Farkas, Gary M.; Tharp, Roland G.</p> <p>1980-01-01</p> <p>Several factors thought to influence the representativeness of behavioral assessment data were examined in an analogue study using a multifactorial design. Systematic and unsystematic methods of <span class="hlt">observing</span> group behavior were investigated using 18 male and 18 female <span class="hlt">observers</span>. Additionally, valence properties of the <span class="hlt">observed</span> behaviors were inspected. <span class="hlt">Observers</span>' assessments of a videotape were compared to a criterion code that defined the population of behaviors. Results indicated that systematic <span class="hlt">observation</span> procedures were more <span class="hlt">accurate</span> than unsystematic procedures, though this factor interacted with gender of <span class="hlt">observer</span> and valence of behavior. Additionally, males tended to sample more representatively than females. A third finding indicated that the negatively valenced behavior was overestimated, whereas the neutral and positively valenced behaviors were <span class="hlt">accurately</span> assessed. PMID:16795631</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/24475860','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/24475860"><span>Liver diffusion-weighted MR imaging: <span class="hlt">reproducibility</span> comparison of ADC measurements obtained with multiple breath-hold, free-breathing, respiratory-triggered, and navigator-triggered techniques.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Chen, Xin; Qin, Lei; Pan, Dan; Huang, Yanqi; Yan, Lifen; Wang, Guangyi; Liu, Yubao; Liang, Changhong; Liu, Zaiyi</p> <p>2014-04-01</p> <p>To prospectively compare the <span class="hlt">reproducibility</span> of normal liver apparent diffusion coefficient (ADC) measurements by using different respiratory motion compensation techniques with multiple breath-hold (MBH), free-breathing (FB), respiratory-triggered (RT), and navigator-triggered (NT) diffusion-weighted (DW) imaging and to compare the ADCs at different liver anatomic locations. The study protocol was approved by the institutional review board, and written informed consent was obtained from each participant. Thirty-nine volunteers underwent liver DW imaging twice. Imaging was performed with a 1.5-T MR imager with MBH, FB, RT, and NT techniques (b = 0, 100, and 500 sec/mm(2)). Three representative sections--superior, central, and inferior--were selected on left and right liver lobes, respectively. On each selected section, three regions of interest were drawn, and ADCs were measured. Analysis of variance was used to assess ADCs among the four techniques and various anatomic locations. <span class="hlt">Reproducibility</span> of ADCs was assessed with the Bland-Altman method. ADCs obtained with MBH (range: right lobe, [1.641-1.662] × 10(-3)mm(2)/sec; left lobe, [2.034-2.054] ×10(-3)mm(2)/sec) were higher than those obtained with FB (right, [1.349-1.391] ×10(-3)mm(2)/sec; left, [1.630-1.700] ×10(-3)mm(2)/sec), RT (right, [1.439-1.455] ×10(-3)mm(2)/sec; left, [1.720-1.755] ×10(-3)mm(2)/sec), or NT (right, [1.387-1.400] ×10(-3)mm(2)/sec; left, [1.661-1.736] ×10(-3)mm(2)/sec) techniques (P < .001); however, no significant difference was <span class="hlt">observed</span> between ADCs obtained with FB, RT, and NT techniques (P = .130 to P >.99). ADCs showed a trend to decrease moving from left to right. <span class="hlt">Reproducibility</span> in the left liver lobe was inferior to that in the right, and the central middle segment in the right lobe had the most <span class="hlt">reproducible</span> ADC. Statistical differences in ADCs were <span class="hlt">observed</span> in the left-right direction in the right lobe (P < .001), but they were not <span class="hlt">observed</span> in the superior-inferior direction</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://rosap.ntl.bts.gov/view/dot/5898','DOTNTL'); return false;" href="https://rosap.ntl.bts.gov/view/dot/5898"><span>Improved estimates of fixed <span class="hlt">reproducible</span> tangible wealth, 1929-95</span></a></p> <p><a target="_blank" href="http://ntlsearch.bts.gov/tris/index.do">DOT National Transportation Integrated Search</a></p> <p></p> <p>1997-05-01</p> <p>This article presents revised estimates of the value of fixed <span class="hlt">reproducible</span> tangible wealth in the United States for 192995; these estimates incorporate the definitional and statistical : improvements introduced in last years comprehensive revis...</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_21");'>21</a></li> <li><a href="#" onclick='return showDiv("page_22");'>22</a></li> <li><a href="#" onclick='return showDiv("page_23");'>23</a></li> <li class="active"><span>24</span></li> <li><a href="#" onclick='return showDiv("page_25");'>25</a></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_24 --> <div id="page_25" class="hiddenDiv"> <div class="row"> <div class="col-sm-12"> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_21");'>21</a></li> <li><a href="#" onclick='return showDiv("page_22");'>22</a></li> <li><a href="#" onclick='return showDiv("page_23");'>23</a></li> <li><a href="#" onclick='return showDiv("page_24");'>24</a></li> <li class="active"><span>25</span></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div> </div> <div class="row"> <div class="col-sm-12"> <ol class="result-class" start="481"> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.osti.gov/biblio/22410267-accurate-coarse-grained-models-mixtures-colloids-linear-polymers-under-good-solvent-conditions','SCIGOV-STC'); return false;" href="https://www.osti.gov/biblio/22410267-accurate-coarse-grained-models-mixtures-colloids-linear-polymers-under-good-solvent-conditions"><span><span class="hlt">Accurate</span> coarse-grained models for mixtures of colloids and linear polymers under good-solvent conditions</span></a></p> <p><a target="_blank" href="http://www.osti.gov/search">DOE Office of Scientific and Technical Information (OSTI.GOV)</a></p> <p>D’Adamo, Giuseppe, E-mail: giuseppe.dadamo@sissa.it; Pelissetto, Andrea, E-mail: andrea.pelissetto@roma1.infn.it; Pierleoni, Carlo, E-mail: carlo.pierleoni@aquila.infn.it</p> <p>2014-12-28</p> <p>A coarse-graining strategy, previously developed for polymer solutions, is extended here to mixtures of linear polymers and hard-sphere colloids. In this approach, groups of monomers are mapped onto a single pseudoatom (a blob) and the effective blob-blob interactions are obtained by requiring the model to <span class="hlt">reproduce</span> some large-scale structural properties in the zero-density limit. We show that an <span class="hlt">accurate</span> parametrization of the polymer-colloid interactions is obtained by simply introducing pair potentials between blobs and colloids. For the coarse-grained (CG) model in which polymers are modelled as four-blob chains (tetramers), the pair potentials are determined by means of the iterative Boltzmannmore » inversion scheme, taking full-monomer (FM) pair correlation functions at zero-density as targets. For a larger number n of blobs, pair potentials are determined by using a simple transferability assumption based on the polymer self-similarity. We validate the model by comparing its predictions with full-monomer results for the interfacial properties of polymer solutions in the presence of a single colloid and for thermodynamic and structural properties in the homogeneous phase at finite polymer and colloid density. The tetramer model is quite <span class="hlt">accurate</span> for q ≲ 1 (q=R{sup ^}{sub g}/R{sub c}, where R{sup ^}{sub g} is the zero-density polymer radius of gyration and R{sub c} is the colloid radius) and reasonably good also for q = 2. For q = 2, an <span class="hlt">accurate</span> coarse-grained description is obtained by using the n = 10 blob model. We also compare our results with those obtained by using single-blob models with state-dependent potentials.« less</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2014A%26A...568A.120P','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2014A%26A...568A.120P"><span>Simulating AIA <span class="hlt">observations</span> of a flux rope ejection</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Pagano, P.; Mackay, D. H.; Poedts, S.</p> <p>2014-08-01</p> <p>Context. Coronal mass ejections (CMEs) are the most violent phenomena <span class="hlt">observed</span> on the Sun. Currently, extreme ultraviolet (EUV) images from the Atmospheric Imaging Assembly (AIA) on board the Solar Dynamic Observatory (SDO) are providing new insights into the early phase of CME evolution. In particular, <span class="hlt">observations</span> now show the ejection of magnetic flux ropes from the solar corona and how they evolve into CMEs. While this is the case, these <span class="hlt">observations</span> are difficult to interpret in terms of basic physical mechanisms and quantities. To fully understand CMEs we need to compare equivalent quantities derived from both <span class="hlt">observations</span> and theoretical models. This will aid in bridging the gap between <span class="hlt">observations</span> and models. Aims: To this end, we aim to produce synthesised AIA <span class="hlt">observations</span> from simulations of a flux rope ejection. To carry this out we include the role of thermal conduction and radiative losses, both of which are important for determining the temperature distribution of the solar corona during a CME. Methods: We perform a simulation where a flux rope is ejected from the solar corona. From the density and temperature of the plasma in the simulation we synthesise AIA <span class="hlt">observations</span>. The emission is then integrated along the line of sight using the instrumental response function of AIA. Results: We sythesise <span class="hlt">observations</span> of AIA in the channels at 304 Å, 171 Å, 335 Å, and 94 Å. The synthesised <span class="hlt">observations</span> show a number of features similar to actual <span class="hlt">observations</span> and in particular <span class="hlt">reproduce</span> the general development of CMEs in the low corona as <span class="hlt">observed</span> by AIA. In particular we <span class="hlt">reproduce</span> an erupting and expanding arcade in the 304 Å and 171 Å channels with a high density core. Conclusions: The ejection of a flux rope <span class="hlt">reproduces</span> many of the features found in the AIA <span class="hlt">observations</span>. This work is therefore a step forward in bridging the gap between <span class="hlt">observations</span> and models, and can lead to more direct interpretations of EUV <span class="hlt">observations</span> in terms of flux rope</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.osti.gov/biblio/21269195-rico-new-approach-fast-accurate-representation-cosmological-recombination-history','SCIGOV-STC'); return false;" href="https://www.osti.gov/biblio/21269195-rico-new-approach-fast-accurate-representation-cosmological-recombination-history"><span>RICO: A NEW APPROACH FOR FAST AND <span class="hlt">ACCURATE</span> REPRESENTATION OF THE COSMOLOGICAL RECOMBINATION HISTORY</span></a></p> <p><a target="_blank" href="http://www.osti.gov/search">DOE Office of Scientific and Technical Information (OSTI.GOV)</a></p> <p>Fendt, W. A.; Wandelt, B. D.; Chluba, J.</p> <p>2009-04-15</p> <p>We present RICO, a code designed to compute the ionization fraction of the universe during the epoch of hydrogen and helium recombination with an unprecedented combination of speed and accuracy. This is accomplished by training the machine learning code PICO on the calculations of a multilevel cosmological recombination code which self-consistently includes several physical processes that were neglected previously. After training, RICO is used to fit the free electron fraction as a function of the cosmological parameters. While, for example, at low redshifts (z {approx}< 900), much of the net change in the ionization fraction can be captured by loweringmore » the hydrogen fudge factor in RECFAST by about 3%, RICO provides a means of effectively using the <span class="hlt">accurate</span> ionization history of the full recombination code in the standard cosmological parameter estimation framework without the need to add new or refined fudge factors or functions to a simple recombination model. Within the new approach presented here, it is easy to update RICO whenever a more <span class="hlt">accurate</span> full recombination code becomes available. Once trained, RICO computes the cosmological ionization history with negligible fitting error in {approx}10 ms, a speedup of at least 10{sup 6} over the full recombination code that was used here. Also RICO is able to <span class="hlt">reproduce</span> the ionization history of the full code to a level well below 0.1%, thereby ensuring that the theoretical power spectra of cosmic microwave background (CMB) fluctuations can be computed to sufficient accuracy and speed for analysis from upcoming CMB experiments like Planck. Furthermore, it will enable cross-checking different recombination codes across cosmological parameter space, a comparison that will be very important in order to assure the <span class="hlt">accurate</span> interpretation of future CMB data.« less</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://www.dtic.mil/docs/citations/ADA597898','DTIC-ST'); return false;" href="http://www.dtic.mil/docs/citations/ADA597898"><span><span class="hlt">Accurate</span> Arabic Script Language/Dialect Classification</span></a></p> <p><a target="_blank" href="http://www.dtic.mil/">DTIC Science & Technology</a></p> <p></p> <p>2014-01-01</p> <p>Army Research Laboratory <span class="hlt">Accurate</span> Arabic Script Language/Dialect Classification by Stephen C. Tratz ARL-TR-6761 January 2014 Approved for public...1197 ARL-TR-6761 January 2014 <span class="hlt">Accurate</span> Arabic Script Language/Dialect Classification Stephen C. Tratz Computational and Information Sciences...Include area code) Standard Form 298 (Rev. 8/98) Prescribed by ANSI Std. Z39.18 January 2014 Final <span class="hlt">Accurate</span> Arabic Script Language/Dialect Classification</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/17202620','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/17202620"><span>Evaluation of the <span class="hlt">reproducibility</span> of lung motion probability distribution function (PDF) using dynamic MRI.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Cai, Jing; Read, Paul W; Altes, Talissa A; Molloy, Janelle A; Brookeman, James R; Sheng, Ke</p> <p>2007-01-21</p> <p>Treatment planning based on probability distribution function (PDF) of patient geometries has been shown a potential off-line strategy to incorporate organ motion, but the application of such approach highly depends upon the <span class="hlt">reproducibility</span> of the PDF. In this paper, we investigated the dependences of the PDF <span class="hlt">reproducibility</span> on the imaging acquisition parameters, specifically the scan time and the frame rate. Three healthy subjects underwent a continuous 5 min magnetic resonance (MR) scan in the sagittal plane with a frame rate of approximately 10 f s-1, and the experiments were repeated with an interval of 2 to 3 weeks. A total of nine pulmonary vessels from different lung regions (upper, middle and lower) were tracked and the dependences of their displacement PDF <span class="hlt">reproducibility</span> were evaluated as a function of scan time and frame rate. As results, the PDF <span class="hlt">reproducibility</span> error decreased with prolonged scans and appeared to approach equilibrium state in subjects 2 and 3 within the 5 min scan. The PDF accuracy increased in the power function with the increase of frame rate; however, the PDF <span class="hlt">reproducibility</span> showed less sensitivity to frame rate presumably due to the randomness of breathing which dominates the effects. As the key component of the PDF-based treatment planning, the <span class="hlt">reproducibility</span> of the PDF affects the dosimetric accuracy substantially. This study provides a reference for acquiring MR-based PDF of structures in the lung.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/11461747','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/11461747"><span><span class="hlt">Reproducibility</span> of HTS-SQUID magnetocardiography in an unshielded clinical environment.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Leder, U; Schrey, F; Haueisen, J; Dörrer, L; Schreiber, J; Liehr, M; Schwarz, G; Solbrig, O; Figulla, H R; Seidel, P</p> <p>2001-07-01</p> <p>A new technology has been developed which measures the magnetic field of the human heart (magnetocardiogram, MCG) by using high temperature superconducting (HTS) sensors. These sensors can be operated at the temperature of liquid nitrogen without electromagnetic shielding. We tested the <span class="hlt">reproducibility</span> of HTS-MCG measurements in healthy volunteers. Unshielded HTS-MCG measurements were performed in 18 healthy volunteers in left precordial position in two separate sessions in a clinical environment. The heart cycles of 10 min were averaged, smoothed, the baselines were adjusted, and the data were standardized to the respective areas under the curves (AUC) of the absolute values of the QRST amplitudes. The QRS complexes and the ST-T intervals were used to assess the <span class="hlt">reproducibility</span> of the two measurements. Ratios (R(QRS), R(STT)) were calculated by dividing the AUC of the first measurement by the ones of the second measurement. The linear correlation coefficients (CORR(QRS), CORR(STT)) of the time intervals of the two measurements were calculated, too. The HTS-MCG signal was completely concealed by the high noise level in the raw data. The averaging and smoothing algorithms unmasked the QRS complex and the ST segment. A high <span class="hlt">reproducibility</span> was found for the QRS complex (R(QRS)=1.2+/-0.3, CORR(QRS)=0.96+/-0.06). Similarly to the shape of the ECG it was characterized by three bends, the Q, R, and S waves. In the ST-T interval, the <span class="hlt">reproducibility</span> was considerably lower (R(STT)=0.9+/-0.2, CORR(STT)=0.66+/-0.28). In contrast to the shape of the ECG, a baseline deflection after the T wave which may belong to U wave activity was found in a number of volunteers. HTS-MCG devices can be operated in a clinical environment without shielding. Whereas the <span class="hlt">reproducibility</span> was found to be high for the depolarization interval, it was considerably lower for the ST segment and for the T wave. Therefore, before clinically applying HTS-MCG systems to the detection of repolarization</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2017AGUFMGC33E1118L','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2017AGUFMGC33E1118L"><span>Evaluation of CMIP5 Ability to <span class="hlt">Reproduce</span> 20th Century Regional Trends in Surface Air Temperature and Precipitation over CONUS</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Lee, J.; Waliser, D. E.; Lee, H.; Loikith, P. C.; Kunkel, K.</p> <p>2017-12-01</p> <p>Monitoring temporal changes in key climate variables, such as surface air temperature and precipitation, is an integral part of the ongoing efforts of the United States National Climate Assessment (NCA). Climate models participating in CMIP5 provide future trends for four different emissions scenarios. In order to have confidence in the future projections of surface air temperature and precipitation, it is crucial to evaluate the ability of CMIP5 models to <span class="hlt">reproduce</span> <span class="hlt">observed</span> trends for three different time periods (1895-1939, 1940-1979, and 1980-2005). Towards this goal, trends in surface air temperature and precipitation obtained from the NOAA nClimGrid 5 km gridded station <span class="hlt">observation</span>-based product are compared during all three time periods to the 206 CMIP5 historical simulations from 48 unique GCMs and their multi-model ensemble (MME) for NCA-defined climate regions during summer (JJA) and winter (DJF). This evaluation quantitatively examines the biases of simulated trends of the spatially averaged temperature and precipitation in the NCA climate regions. The CMIP5 MME <span class="hlt">reproduces</span> historical surface air temperature trends for JJA for all time period and all regions, except the Northern Great Plains from 1895-1939 and Southeast during 1980-2005. Likewise, for DJF, the MME <span class="hlt">reproduces</span> historical surface air temperature trends across all time periods over all regions except the Southeast from 1895-1939 and the Midwest during 1940-1979. The Regional Climate Model Evaluation System (RCMES), an analysis tool which supports the NCA by providing access to data and tools for regional climate model validation, facilitates the comparisons between the models and <span class="hlt">observation</span>. The RCMES Toolkit is designed to assist in the analysis of climate variables and the procedure of the evaluation of climate projection models to support the decision-making processes. This tool is used in conjunction with the above analysis and results will be presented to demonstrate its capability to</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/25552691','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/25552691"><span><span class="hlt">Reproducibility</span> in science: improving the standard for basic and preclinical research.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Begley, C Glenn; Ioannidis, John P A</p> <p>2015-01-02</p> <p>Medical and scientific advances are predicated on new knowledge that is robust and reliable and that serves as a solid foundation on which further advances can be built. In biomedical research, we are in the midst of a revolution with the generation of new data and scientific publications at a previously unprecedented rate. However, unfortunately, there is compelling evidence that the majority of these discoveries will not stand the test of time. To a large extent, this <span class="hlt">reproducibility</span> crisis in basic and preclinical research may be as a result of failure to adhere to good scientific practice and the desperation to publish or perish. This is a multifaceted, multistakeholder problem. No single party is solely responsible, and no single solution will suffice. Here we review the <span class="hlt">reproducibility</span> problems in basic and preclinical biomedical research, highlight some of the complexities, and discuss potential solutions that may help improve research quality and <span class="hlt">reproducibility</span>. © 2015 American Heart Association, Inc.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2017MMAS...40.7240M','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2017MMAS...40.7240M"><span>Aveiro method in <span class="hlt">reproducing</span> kernel Hilbert spaces under complete dictionary</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Mai, Weixiong; Qian, Tao</p> <p>2017-12-01</p> <p>Aveiro Method is a sparse representation method in <span class="hlt">reproducing</span> kernel Hilbert spaces (RKHS) that gives orthogonal projections in linear combinations of <span class="hlt">reproducing</span> kernels over uniqueness sets. It, however, suffers from determination of uniqueness sets in the underlying RKHS. In fact, in general spaces, uniqueness sets are not easy to be identified, let alone the convergence speed aspect with Aveiro Method. To avoid those difficulties we propose an anew Aveiro Method based on a dictionary and the matching pursuit idea. What we do, in fact, are more: The new Aveiro method will be in relation to the recently proposed, the so called Pre-Orthogonal Greedy Algorithm (P-OGA) involving completion of a given dictionary. The new method is called Aveiro Method Under Complete Dictionary (AMUCD). The complete dictionary consists of all directional derivatives of the underlying <span class="hlt">reproducing</span> kernels. We show that, under the boundary vanishing condition, bring available for the classical Hardy and Paley-Wiener spaces, the complete dictionary enables an efficient expansion of any given element in the Hilbert space. The proposed method reveals new and advanced aspects in both the Aveiro Method and the greedy algorithm.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2004Chaos..14.1123A','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2004Chaos..14.1123A"><span>On the origin of <span class="hlt">reproducible</span> sequential activity in neural circuits</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Afraimovich, V. S.; Zhigulin, V. P.; Rabinovich, M. I.</p> <p>2004-12-01</p> <p>Robustness and <span class="hlt">reproducibility</span> of sequential spatio-temporal responses is an essential feature of many neural circuits in sensory and motor systems of animals. The most common mathematical images of dynamical regimes in neural systems are fixed points, limit cycles, chaotic attractors, and continuous attractors (attractive manifolds of neutrally stable fixed points). These are not suitable for the description of <span class="hlt">reproducible</span> transient sequential neural dynamics. In this paper we present the concept of a stable heteroclinic sequence (SHS), which is not an attractor. SHS opens the way for understanding and modeling of transient sequential activity in neural circuits. We show that this new mathematical object can be used to describe robust and <span class="hlt">reproducible</span> sequential neural dynamics. Using the framework of a generalized high-dimensional Lotka-Volterra model, that describes the dynamics of firing rates in an inhibitory network, we present analytical results on the existence of the SHS in the phase space of the network. With the help of numerical simulations we confirm its robustness in presence of noise in spite of the transient nature of the corresponding trajectories. Finally, by referring to several recent neurobiological experiments, we discuss possible applications of this new concept to several problems in neuroscience.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/15568926','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/15568926"><span>On the origin of <span class="hlt">reproducible</span> sequential activity in neural circuits.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Afraimovich, V S; Zhigulin, V P; Rabinovich, M I</p> <p>2004-12-01</p> <p>Robustness and <span class="hlt">reproducibility</span> of sequential spatio-temporal responses is an essential feature of many neural circuits in sensory and motor systems of animals. The most common mathematical images of dynamical regimes in neural systems are fixed points, limit cycles, chaotic attractors, and continuous attractors (attractive manifolds of neutrally stable fixed points). These are not suitable for the description of <span class="hlt">reproducible</span> transient sequential neural dynamics. In this paper we present the concept of a stable heteroclinic sequence (SHS), which is not an attractor. SHS opens the way for understanding and modeling of transient sequential activity in neural circuits. We show that this new mathematical object can be used to describe robust and <span class="hlt">reproducible</span> sequential neural dynamics. Using the framework of a generalized high-dimensional Lotka-Volterra model, that describes the dynamics of firing rates in an inhibitory network, we present analytical results on the existence of the SHS in the phase space of the network. With the help of numerical simulations we confirm its robustness in presence of noise in spite of the transient nature of the corresponding trajectories. Finally, by referring to several recent neurobiological experiments, we discuss possible applications of this new concept to several problems in neuroscience.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/15142212','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/15142212"><span>Periodontal repair in dogs: examiner <span class="hlt">reproducibility</span> in the supraalveolar periodontal defect model.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Koo, Ki-Tae; Polimeni, Giuseppe; Albandar, Jasim M; Wikesjö, Ulf M E</p> <p>2004-06-01</p> <p>Histometric assessments are routinely used to evaluate biologic events ascertained in histologic sections acquired from animal and human studies. The objective of this study was to evaluate the intra- and inter-examiner <span class="hlt">reproducibility</span> of histometric assessments in the supraalveolar periodontal defect model. Histometric analysis using incandescent and polarized light microscopy, an attached digital camera system, and a PC-based image analysis system including a custom program for the supraalveolar periodontal defect model was performed on histologic sections acquired from one jaw quadrant in each of 12 dogs. The animals had received an experimental protocol including implantation of a coral biomaterial and guided tissue regeneration (GTR) barrier devices, and were evaluated following a 4-week healing interval. Histometric parameters were recorded and repeated within a 3-month interval by two examiners following brief training. Intra- and inter-examiner <span class="hlt">reproducibility</span> was assessed using the intra-class correlation coefficient (ICC). Most parameters showed high intra-examiner ICCs. Parameters including defect height, connective tissue repair, bone regeneration (height/area), formation of a junctional epithelium, positioning of the GTR device, ankylosis, root resorption, and defect area yielded an ICC> or 0..9. The ICCs for bone density and biomaterial density were somewhat lower (0.8 and 0.7, respectively). The inter-examiner <span class="hlt">reproducibility</span> was somewhat lower compared to the intra-examiner <span class="hlt">reproducibility</span>. Nevertheless, the ICCs were generally high (ICC range: 0.6-0.9). Histometric evaluations in the supraalveolar periodontal defect model yield highly <span class="hlt">reproducible</span> results, in particular when a single examiner performs the histometric measurements, even when the examiner was exposed to limited training.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2018AcMSn..34..515Y','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2018AcMSn..34..515Y"><span>Enriched <span class="hlt">reproducing</span> kernel particle method for fractional advection-diffusion equation</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Ying, Yuping; Lian, Yanping; Tang, Shaoqiang; Liu, Wing Kam</p> <p>2018-06-01</p> <p>The <span class="hlt">reproducing</span> kernel particle method (RKPM) has been efficiently applied to problems with large deformations, high gradients and high modal density. In this paper, it is extended to solve a nonlocal problem modeled by a fractional advection-diffusion equation (FADE), which exhibits a boundary layer with low regularity. We formulate this method on a moving least-square approach. Via the enrichment of fractional-order power functions to the traditional integer-order basis for RKPM, leading terms of the solution to the FADE can be exactly <span class="hlt">reproduced</span>, which guarantees a good approximation to the boundary layer. Numerical tests are performed to verify the proposed approach.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=5809762','PMC'); return false;" href="https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=5809762"><span>Are Registration of Disease Codes for Adult Anaphylaxis <span class="hlt">Accurate</span> in the Emergency Department?</span></a></p> <p><a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pmc">PubMed Central</a></p> <p>Choi, Byungho; Lee, Hyeji</p> <p>2018-01-01</p> <p>Purpose There has been active research on anaphylaxis, but many study subjects are limited to patients registered with anaphylaxis codes. However, anaphylaxis codes tend to be underused. The aim of this study was to investigate the accuracy of anaphylaxis code registration and the clinical characteristics of <span class="hlt">accurate</span> and inaccurate anaphylaxis registration in anaphylactic patients. Methods This retrospective study evaluated the medical records of adult patients who visited the university hospital emergency department between 2012 and 2016. The study subjects were divided into the groups with <span class="hlt">accurate</span> and inaccurate anaphylaxis codes registered under anaphylaxis and other allergy-related codes and symptom-related codes, respectively. Results Among 211,486 patients, 618 (0.29%) had anaphylaxis. Of these, 161 and 457 were assigned to the <span class="hlt">accurate</span> and inaccurate coding groups, respectively. The average age, transportation to the emergency department, past anaphylaxis history, cancer history, and the cause of anaphylaxis differed between the 2 groups. Cutaneous symptom manifested more frequently in the inaccurate coding group, while cardiovascular and neurologic symptoms were more frequently <span class="hlt">observed</span> in the <span class="hlt">accurate</span> group. Severe symptoms and non-alert consciousness were more common in the <span class="hlt">accurate</span> group. Oxygen supply, intubation, and epinephrine were more commonly used as treatments for anaphylaxis in the <span class="hlt">accurate</span> group. Anaphylactic patients with cardiovascular symptoms, severe symptoms, and epinephrine use were more likely to be <span class="hlt">accurately</span> registered with anaphylaxis disease codes. Conclusions In case of anaphylaxis, more patients were registered inaccurately under other allergy-related codes and symptom-related codes rather than <span class="hlt">accurately</span> under anaphylaxis disease codes. Cardiovascular symptoms, severe symptoms, and epinephrine treatment were factors associated with <span class="hlt">accurate</span> registration with anaphylaxis disease codes in patients with anaphylaxis. PMID:29411554</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/27016265','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/27016265"><span>Parameter optimization for <span class="hlt">reproducible</span> cardiac 1 H-MR spectroscopy at 3 Tesla.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>de Heer, Paul; Bizino, Maurice B; Lamb, Hildo J; Webb, Andrew G</p> <p>2016-11-01</p> <p>To optimize data acquisition parameters in cardiac proton MR spectroscopy, and to evaluate the intra- and intersession variability in myocardial triglyceride content. Data acquisition parameters at 3 Tesla (T) were optimized and <span class="hlt">reproducibility</span> measured using, in total, 49 healthy subjects. The signal-to-noise-ratio (SNR) and the variance in metabolite amplitude between averages were measured for: (i) global versus local power optimization; (ii) static magnetic field (B 0 ) shimming performed during free-breathing or within breathholds; (iii) post R-wave peak measurement times between 50 and 900 ms; (iv) without respiratory compensation, with breathholds and with navigator triggering; and (v) frequency selective excitation, Chemical Shift Selective (CHESS) and Multiply Optimized Insensitive Suppression Train (MOIST) water suppression techniques. Using the optimized parameters intra- and intersession myocardial triglyceride content <span class="hlt">reproducibility</span> was measured. Two cardiac proton spectra were acquired with the same parameters and compared (intrasession <span class="hlt">reproducibility</span>) after which the subject was removed from the scanner and placed back in the scanner and a third spectrum was acquired which was compared with the first measurement (intersession <span class="hlt">reproducibility</span>). Local power optimization increased SNR on average by 22% compared with global power optimization (P = 0.0002). The average linewidth was not significantly different for pencil beam B 0 shimming using free-breathing or breathholds (19.1 Hz versus 17.5 Hz; P = 0.15). The highest signal stability occurred at a cardiac trigger delay around 240 ms. The mean amplitude variation was significantly lower for breathholds versus free-breathing (P = 0.03) and for navigator triggering versus free-breathing (P = 0.03) as well as for navigator triggering versus breathhold (P = 0.02). The mean residual water signal using CHESS (1.1%, P = 0.01) or MOIST (0.7%, P = 0.01) water suppression was significantly lower than using</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/26251184','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/26251184"><span><span class="hlt">Reproducibility</span> of Echocardiograph-Derived Multilevel Left Ventricular Apical Twist Mechanics.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Stewart, Glenn M; Yamada, Akira; Kavanagh, Justin J; Haseler, Luke J; Chan, Jonathan; Sabapathy, Surendran</p> <p>2016-02-01</p> <p>Left ventricular (LV) twist mechanics are routinely assessed via echocardiography in clinical and research trials investigating the function of obliquely oriented myocardial fibers. However, echocardiograph-derived measures of LV twist may be compromised by nonstandardized acquisition of the apical image. This study examined the <span class="hlt">reproducibility</span> of echocardiograph-derived parameters of apical twist mechanics at multiple levels of the apical myocardium. Two sets of 2D LV parasternal short-axis images were obtained in 30 healthy subjects (24 men; 19-57 year) via echocardiography. Images were acquired immediately distal to the papillary muscles (apical image 1), immediately above the point of LV cavity obliteration at end systole (apical image 3), and midway between apical image 1 and apical image 3 (apical image 2). Repeat scans were performed within 1 hour, and twist mechanics (rotation and rotation rate) were calculated via frame-by-frame tracking of natural acoustic echocardiographic markers (speckle tracking). The magnitude of apical rotation increased progressively toward the apex (apical image 1: 4.2 ± 2.1°, apical image 2: 7.2 ± 3.9°, apical image 3: 11.8 ± 4.6°). apical images 1, 2, and 3 each had moderate to good correlations between repeat scans (ICC: 0.531-0.856). When apical images 1, 2, and 3 were averaged, rotation was 7.7 ± 2.7° and between-scan correlation was excellent (ICC: 0.910). Similar results were <span class="hlt">observed</span> for systolic and diastolic rotation rates. Averaging multiple standardized apical images, tending progressively toward the apex, generated the most <span class="hlt">reproducible</span> rotation indices and may be optimal for the assessment of LV twist mechanics across therapeutic, interventional, and research studies; however, care should be taken given the influence of acquisition level on the magnitude of apical rotation. © 2015, Wiley Periodicals, Inc.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/28428032','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/28428032"><span>Does semi-automatic bone-fragment segmentation improve the <span class="hlt">reproducibility</span> of the Letournel acetabular fracture classification?</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Boudissa, M; Orfeuvre, B; Chabanas, M; Tonetti, J</p> <p>2017-09-01</p> <p>The Letournel classification of acetabular fracture shows poor <span class="hlt">reproducibility</span> in inexperienced <span class="hlt">observers</span>, despite the introduction of 3D imaging. We therefore developed a method of semi-automatic segmentation based on CT data. The present prospective study aimed to assess: (1) whether semi-automatic bone-fragment segmentation increased the rate of correct classification; (2) if so, in which fracture types; and (3) feasibility using the open-source itksnap 3.0 software package without incurring extra cost for users. Semi-automatic segmentation of acetabular fractures significantly increases the rate of correct classification by orthopedic surgery residents. Twelve orthopedic surgery residents classified 23 acetabular fractures. Six used conventional 3D reconstructions provided by the center's radiology department (conventional group) and 6 others used reconstructions obtained by semi-automatic segmentation using the open-source itksnap 3.0 software package (segmentation group). Bone fragments were identified by specific colors. Correct classification rates were compared between groups on Chi 2 test. Assessment was repeated 2 weeks later, to determine intra-<span class="hlt">observer</span> <span class="hlt">reproducibility</span>. Correct classification rates were significantly higher in the "segmentation" group: 114/138 (83%) versus 71/138 (52%); P<0.0001. The difference was greater for simple (36/36 (100%) versus 17/36 (47%); P<0.0001) than complex fractures (79/102 (77%) versus 54/102 (53%); P=0.0004). Mean segmentation time per fracture was 27±3min [range, 21-35min]. The segmentation group showed excellent intra-<span class="hlt">observer</span> correlation coefficients, overall (ICC=0.88), and for simple (ICC=0.92) and complex fractures (ICC=0.84). Semi-automatic segmentation, identifying the various bone fragments, was effective in increasing the rate of correct acetabular fracture classification on the Letournel system by orthopedic surgery residents. It may be considered for routine use in education and training. III: prospective</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.ncbi.nlm.nih.gov/pubmed/29458233','PUBMED'); return false;" href="https://www.ncbi.nlm.nih.gov/pubmed/29458233"><span>Pharmacokinetic Modelling to Predict FVIII:C Response to Desmopressin and Its <span class="hlt">Reproducibility</span> in Nonsevere Haemophilia A Patients.</span></a></p> <p><a target="_blank" href="https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed">PubMed</a></p> <p>Schütte, Lisette M; van Hest, Reinier M; Stoof, Sara C M; Leebeek, Frank W G; Cnossen, Marjon H; Kruip, Marieke J H A; Mathôt, Ron A A</p> <p>2018-04-01</p> <p> Nonsevere haemophilia A (HA) patients can be treated with desmopressin. Response of factor VIII activity (FVIII:C) differs between patients and is difficult to predict.  Our aims were to describe FVIII:C response after desmopressin and its <span class="hlt">reproducibility</span> by population pharmacokinetic (PK) modelling.  Retrospective data of 128 nonsevere HA patients (age 7-75 years) receiving an intravenous or intranasal dose of desmopressin were used. PK modelling of FVIII:C was performed by nonlinear mixed effect modelling. <span class="hlt">Reproducibility</span> of FVIII:C response was defined as less than 25% difference in peak FVIII:C between administrations.  A total of 623 FVIII:C measurements from 142 desmopressin administrations were available; 14 patients had received two administrations at different occasions. The FVIII:C time profile was best described by a two-compartment model with first-order absorption and elimination. Interindividual variability of the estimated baseline FVIII:C, central volume of distribution and clearance were 37, 43 and 50%, respectively. The most recently measured FVIII:C (FVIII-recent) was significantly associated with FVIII:C response to desmopressin ( p  < 0.001). Desmopressin administration resulted in an absolute FVIII:C increase of 0.47 IU/mL (median, interquartile range: 0.32-0.65 IU/mL, n  = 142). C response was <span class="hlt">reproducible</span> in 6 out of 14 patients receiving two desmopressin administrations.  FVIII:C response to desmopressin in nonsevere HA patients was adequately described by a population PK model. Large variability in FVIII:C response was <span class="hlt">observed</span>, which could only partially be explained by FVIII-recent. C response was not <span class="hlt">reproducible</span> in a small subset of patients. Therefore, monitoring FVIII:C around surgeries or bleeding might be considered. Research is needed to study this further. Schattauer Stuttgart.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('http://adsabs.harvard.edu/abs/2001APS..MARN27004N','NASAADS'); return false;" href="http://adsabs.harvard.edu/abs/2001APS..MARN27004N"><span><span class="hlt">Reproducible</span> fabrication and applications of superconducting scanning tunneling microscope tips</span></a></p> <p><a target="_blank" href="http://adsabs.harvard.edu/abstract_service.html">NASA Astrophysics Data System (ADS)</a></p> <p>Naaman, Ofer; Teizer, Winfried; Dynes, Robert C.</p> <p>2001-03-01</p> <p>We report on a method developed in our lab, for the fabrication of superconducting scanning tunneling microscope (STM) tips in a <span class="hlt">reproducible</span> fashion. The fabrication process relies on sequential deposition of superconducting Pb and a proximity-coupled Ag capping layer onto a Pt/Ir tip. The tips were characterized by tunneling into both normal-metal and superconducting films, and the results confirm that the tips are superconducting with Tc and Δ close to that of bulk lead. The lead phonon structure in the tunneling density of states was <span class="hlt">observed</span>, indicating a single step tunneling process. In an attempt to form STM Josephson junctions, we used our tips to form S/I/S junctions with R_NN ~50-100 kΩ. Results from spectroscopic measurements of these junctions at 2.0 K are discussed within the framework of the Ivanchenko and Zil'berman theory (Soviet Physics JETP, vol.28, 1272; 1969) of Josephson tunneling in the presence of strong phase fluctuations.</p> </li> <li> <p><a target="_blank" onclick="trackOutboundLink('https://www.osti.gov/biblio/1029211-stable-spectrally-accurate-schemes-navier-stokes-equations','SCIGOV-STC'); return false;" href="https://www.osti.gov/biblio/1029211-stable-spectrally-accurate-schemes-navier-stokes-equations"><span>Stable and Spectrally <span class="hlt">Accurate</span> Schemes for the Navier-Stokes Equations</span></a></p> <p><a target="_blank" href="http://www.osti.gov/search">DOE Office of Scientific and Technical Information (OSTI.GOV)</a></p> <p>Jia, Jun; Liu, Jie</p> <p>2011-01-01</p> <p>In this paper, we present an <span class="hlt">accurate</span>, efficient and stable numerical method for the incompressible Navier-Stokes equations (NSEs). The method is based on (1) an equivalent pressure Poisson equation formulation of the NSE with proper pressure boundary conditions, which facilitates the design of high-order and stable numerical methods, and (2) the Krylov deferred correction (KDC) accelerated method of lines transpose (mbox MoL{sup T}), which is very stable, efficient, and of arbitrary order in time. Numerical tests with known exact solutions in three dimensions show that the new method is spectrally <span class="hlt">accurate</span> in time, and a numerical order of convergence 9more » was <span class="hlt">observed</span>. Two-dimensional computational results of flow past a cylinder and flow in a bifurcated tube are also reported.« less</p> </li> </ol> <div class="pull-right"> <ul class="pagination"> <li><a href="#" onclick='return showDiv("page_1");'>«</a></li> <li><a href="#" onclick='return showDiv("page_21");'>21</a></li> <li><a href="#" onclick='return showDiv("page_22");'>22</a></li> <li><a href="#" onclick='return showDiv("page_23");'>23</a></li> <li><a href="#" onclick='return showDiv("page_24");'>24</a></li> <li class="active"><span>25</span></li> <li><a href="#" onclick='return showDiv("page_25");'>»</a></li> </ul> </div> </div><!-- col-sm-12 --> </div><!-- row --> </div><!-- page_25 --> <div class="footer-extlink text-muted" style="margin-bottom:1rem; text-align:center;">Some links on this page may take you to non-federal websites. 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