Testing high SPF sunscreens: a demonstration of the accuracy and reproducibility of the results of testing high SPF formulations by two methods and at different testing sites.

PubMed

Agin, Patricia Poh; Edmonds, Susan H

2002-08-01

The goals of this study were (i) to demonstrate that existing and widely used sun protection factor (SPF) test methodologies can produce accurate and reproducible 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 reproducibly 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 accurate and reproducible 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.

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.

Month-to-Month and Year-to-Year Reproducibility of High Frequency QRS ECG signals

NASA Technical Reports Server (NTRS)

Batdorf, Niles; Feiveson, Alan H.; Schlegel, Todd T.

2006-01-01

High frequency (HF) electrocardiography analyzing the entire QRS complex in the frequency range of 150 to 250 Hz may prove useful in the detection of coronary artery disease, yet the long-term stability of these waveforms has not been fully characterized. We therefore prospectively investigated the reproducibility of the root mean squared (RMS) voltage, kurtosis, and the presence versus absence of reduced amplitude zones (RAzs) in signal averaged 12-lead HF QRS recordings acquired in the supine position one month apart in 16 subjects and one year apart in 27 subjects. Reproducibility of RMS voltage and kurtosis was excellent over these time intervals in the limb leads, and acceptable in the precordial leads using both the V-lead and CR-lead derivations. The relative error of RMS voltage was 12% month-to-month and 16% year-to-year in the serial recordings when averaged over all 12 leads. RAzs were also reproducible at a rate of up to 87% and 8 1 %, respectively, for the month-to-month and year-to-year recordings. We conclude that 12-lead HF QRS electrocardiograms are sufficiently reproducible for clinical use.

Highly reproducible and sensitive silver nanorod array for the rapid detection of Allura Red in candy

NASA Astrophysics Data System (ADS)

Yao, Yue; Wang, Wen; Tian, Kangzhen; Ingram, Whitney Marvella; Cheng, Jie; Qu, Lulu; Li, Haitao; Han, Caiqin

2018-04-01

Allura Red (AR) is a highly stable synthetic red azo dye, which is widely used in the food industry to dye food and increase its attraction to consumers. However, the excessive consumption of AR can result in adverse health effects to humans. Therefore, a highly reproducible silver nanorod (AgNR) array was developed for surface enhanced Raman scattering (SERS) detection of AR in candy. The relative standard deviation (RSD) of AgNR substrate obtained from the same batch and different batches were 5.7% and 11.0%, respectively, demonstrating the high reproducibility. Using these highly reproducible AgNR arrays as the SERS substrates, AR was detected successfully, and its characteristic peaks were assigned by the density function theory (DFT) calculation. The limit of detection (LOD) of AR was determined to be 0.05 mg/L with a wide linear range of 0.8-100 mg/L. Furthermore, the AgNR SERS arrays can detect AR directly in different candy samples within 3 min without any complicated pretreatment. These results suggest the AgNR array can be used for rapid and qualitative SERS detection of AR, holding a great promise for expanding SERS application in food safety control field.

Preparation of reflective CsI photocathodes with reproducible high quantum efficiency

NASA Astrophysics Data System (ADS)

Maier-Komor, P.; Bauer, B. B.; Friese, J.; Gernhäuser, R.; Kienle, P.; Körner, H. J.; Montermann, G.; Zeitelhack, K.

1995-02-01

CsI as a solid UV-photocathode material has many promising applications in fast gaseous photon detectors. They are proposed in large area Ring Imaging CHerenkov (RICH) devices in forthcoming experiments at various high-energy particle accelerators. A high photon-to-electron conversion efficiency is a basic requirement for the successful operation of these devices. High reproducible quantum efficiencies could be achieved with CsI layers prepared by electron beam evaporation from a water-cooled copper crucible. CsI films were deposited in the thickness range of 30 to 500 μg/cm 2. Absorption coefficients and quantum efficiencies were measured in the wavelength region of 150 nm to 250 nm. The influence of various evaporation parameters on the quantum efficiency were investigated.

Reproducibility in Natural Language Processing: A Case Study of Two R Libraries for Mining PubMed/MEDLINE.

PubMed

Cohen, K Bretonnel; Xia, Jingbo; Roeder, Christophe; Hunter, Lawrence E

2016-05-01

There is currently a crisis in science related to highly publicized failures to reproduce large numbers of published studies. The current work proposes, by way of case studies, a methodology for moving the study of reproducibility in computational work to a full stage beyond that of earlier work. Specifically, it presents a case study in attempting to reproduce the reports of two R libraries for doing text mining of the PubMed/MEDLINE repository of scientific publications. The main findings are that a rational paradigm for reproduction of natural language processing papers can be established; the advertised functionality was difficult, but not impossible, to reproduce; and reproducibility studies can produce additional insights into the functioning of the published system. Additionally, the work on reproducibility lead to the production of novel user-centered documentation that has been accessed 260 times since its publication-an average of once a day per library.

Hexamethylenetetramine-mediated growth of grain-boundary-passivation CH3NH3PbI3 for highly reproducible and stable perovskite solar cells

NASA Astrophysics Data System (ADS)

Zheng, Yan-Zhen; Li, Xi-Tao; Zhao, Er-Fei; Lv, Xin-Ding; Meng, Fan-Li; Peng, Chao; Lai, Xue-Sen; Huang, Meilan; Cao, Guozhong; Tao, Xia; Chen, Jian-Feng

2018-02-01

Simultaneously achieving the long-term device stability and reproducibility has proven challenging in perovskite solar cells because solution-processing produced perovskite film with grain boundary is sensitive to moisture. Herein, we develop a hexamethylenetetramine (HMTA)-mediated one-step solution-processing deposition strategy that leads to the formation of high-purity and grain-boundary-passivation CH3NH3PbI3 film and thereby advances cell optoelectronic performance. Through morphological and structural characterizations and theoretical calculations, we demonstrate that HMTA fully occupies the moisture-exposed surface to build a bridge across grain boundary and coordinates with Pb ions to inhibit the formation of detrimental PbI2. Such HMTA-mediated grown CH3NH3PbI3 films achieves a decent augmentation of power conversion efficiency (PCE) from 12.70% to 17.87%. A full coverage of PbI2-free CH3NH3PbI3 surface on ZnO also boosts the device's stability and reproducibility.

International Interlaboratory Digital PCR Study Demonstrating High Reproducibility for the Measurement of a Rare Sequence Variant.

PubMed

Whale, Alexandra S; Devonshire, Alison S; Karlin-Neumann, George; Regan, Jack; Javier, Leanne; Cowen, Simon; Fernandez-Gonzalez, Ana; Jones, Gerwyn M; Redshaw, Nicholas; Beck, Julia; Berger, Andreas W; Combaret, Valérie; Dahl Kjersgaard, Nina; Davis, Lisa; Fina, Frederic; Forshew, Tim; Fredslund Andersen, Rikke; Galbiati, Silvia; González Hernández, Álvaro; Haynes, Charles A; Janku, Filip; Lacave, Roger; Lee, Justin; Mistry, Vilas; Pender, Alexandra; Pradines, Anne; Proudhon, Charlotte; Saal, Lao H; Stieglitz, Elliot; Ulrich, Bryan; Foy, Carole A; Parkes, Helen; Tzonev, Svilen; Huggett, Jim F

2017-02-07

This study tested the claim that digital PCR (dPCR) can offer highly reproducible quantitative measurements in disparate laboratories. Twenty-one laboratories measured four blinded samples containing different quantities of a KRAS fragment encoding G12D, an important genetic marker for guiding therapy of certain cancers. This marker is challenging to quantify reproducibly using quantitative PCR (qPCR) or next generation sequencing (NGS) due to the presence of competing wild type sequences and the need for calibration. Using dPCR, 18 laboratories were able to quantify the G12D marker within 12% of each other in all samples. Three laboratories appeared to measure consistently outlying results; however, proper application of a follow-up analysis recommendation rectified their data. Our findings show that dPCR has demonstrable reproducibility across a large number of laboratories without calibration. This could enable the reproducible application of molecular stratification to guide therapy and, potentially, for molecular diagnostics.

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

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

Investigation of temporal-resolved emission spectra of highly charged Al ions from laser-produced plasmas

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

Su, M. G., E-mail: sumg@nwnu.edu.cn; Sun, D. X.; Dong, C. Z.

2016-03-15

Temporal evolution of extreme ultraviolet emission from laser-produced aluminum (Al) plasma has been experimentally and theoretically investigated. Al plasmas have been measured by using the temporal-spatially resolved laser-produced plasma technique. The emission lines can be identified from 2p-3s, 3d, 4s, 4d, 5d transition lines from Al{sup 3+} to Al{sup 6+} ions. In order to quickly diagnose the plasma, the assumptions of a normalized Boltzmann distribution among the excited states and a steady-state collisional-radiative model are used to estimate the values of electron temperature and electron density in plasma. We succeeded in reproducing the simulated spectra related to the different timemore » delays, which are in good agreement with experiments. Temporal evolution behavior of highly charged Al ions in plasma has been analyzed, and the exponential decay about electron temperature and electron density has been obtained. The results indicate that the temporal-spatially resolved measurement is essential for accurate understanding of evolution behavior of highly charged ions in laser-produced plasmas.« less

A rapid enzymatic assay for high-throughput screening of adenosine-producing strains

PubMed Central

Dong, Huina; Zu, Xin; Zheng, Ping; Zhang, Dawei

2015-01-01

Adenosine is a major local regulator of tissue function and industrially useful as precursor for the production of medicinal nucleoside substances. High-throughput screening of adenosine overproducers is important for industrial microorganism breeding. An enzymatic assay of adenosine was developed by combined adenosine deaminase (ADA) with indophenol method. The ADA catalyzes the cleavage of adenosine to inosine and NH3, the latter can be accurately determined by indophenol method. The assay system was optimized to deliver a good performance and could tolerate the addition of inorganic salts and many nutrition components to the assay mixtures. Adenosine could be accurately determined by this assay using 96-well microplates. Spike and recovery tests showed that this assay can accurately and reproducibly determine increases in adenosine in fermentation broth without any pretreatment to remove proteins and potentially interfering low-molecular-weight molecules. This assay was also applied to high-throughput screening for high adenosine-producing strains. The high selectivity and accuracy of the ADA assay provides rapid and high-throughput analysis of adenosine in large numbers of samples. PMID:25580842

Reproducibility in Natural Language Processing: A Case Study of Two R Libraries for Mining PubMed/MEDLINE

PubMed Central

Cohen, K. Bretonnel; Xia, Jingbo; Roeder, Christophe; Hunter, Lawrence E.

2018-01-01

There is currently a crisis in science related to highly publicized failures to reproduce large numbers of published studies. The current work proposes, by way of case studies, a methodology for moving the study of reproducibility in computational work to a full stage beyond that of earlier work. Specifically, it presents a case study in attempting to reproduce the reports of two R libraries for doing text mining of the PubMed/MEDLINE repository of scientific publications. The main findings are that a rational paradigm for reproduction of natural language processing papers can be established; the advertised functionality was difficult, but not impossible, to reproduce; and reproducibility studies can produce additional insights into the functioning of the published system. Additionally, the work on reproducibility lead to the production of novel user-centered documentation that has been accessed 260 times since its publication—an average of once a day per library. PMID:29568821

A reproducible approach to high-throughput biological data acquisition and integration

PubMed Central

Rahnavard, Gholamali; Waldron, Levi; McIver, Lauren; Shafquat, Afrah; Franzosa, Eric A.; Miropolsky, Larissa; Sweeney, Christopher

2015-01-01

Modern biological research requires rapid, complex, and reproducible integration of multiple experimental results generated both internally and externally (e.g., from public repositories). Although large systematic meta-analyses are among the most effective approaches both for clinical biomarker discovery and for computational inference of biomolecular mechanisms, identifying, acquiring, and integrating relevant experimental results from multiple sources for a given study can be time-consuming and error-prone. To enable efficient and reproducible integration of diverse experimental results, we developed a novel approach for standardized acquisition and analysis of high-throughput and heterogeneous biological data. This allowed, first, novel biomolecular network reconstruction in human prostate cancer, which correctly recovered and extended the NFκB signaling pathway. Next, we investigated host-microbiome interactions. In less than an hour of analysis time, the system retrieved data and integrated six germ-free murine intestinal gene expression datasets to identify the genes most influenced by the gut microbiota, which comprised a set of immune-response and carbohydrate metabolism processes. Finally, we constructed integrated functional interaction networks to compare connectivity of peptide secretion pathways in the model organisms Escherichia coli, Bacillus subtilis, and Pseudomonas aeruginosa. PMID:26157642

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

Reproducibility of Ultrasound-Guided High Intensity Focused Ultrasound (HIFU) Thermal Lesions in Minimally-Invasive Brain Surgery

NASA Astrophysics Data System (ADS)

Zahedi, Sulmaz

This study aims to prove the feasibility of using Ultrasound-Guided High Intensity Focused Ultrasound (USg-HIFU) to create thermal lesions in neurosurgical applications, allowing for precise ablation of brain tissue, while simultaneously providing real time imaging. To test the feasibility of the system, an optically transparent HIFU compatible tissue-mimicking phantom model was produced. USg-HIFU was then used for ablation of the phantom, with and without targets. Finally, ex vivo lamb brain tissue was imaged and ablated using the USg-HIFU system. Real-time ultrasound images and videos obtained throughout the ablation process showing clear lesion formation at the focal point of the HIFU transducer. Post-ablation gross and histopathology examinations were conducted to verify thermal and mechanical damage in the ex vivo lamb brain tissue. Finally, thermocouple readings were obtained, and HIFU field computer simulations were conducted to verify findings. Results of the study concluded reproducibility of USg-HIFU thermal lesions for neurosurgical applications.

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.

Reproducibility patterns of multiple rapid swallows during high resolution esophageal manometry provide insights into esophageal pathophysiology.

PubMed

Price, L H; Li, Y; Patel, A; Gyawali, C Prakash

2014-05-01

Multiple rapid swallows (MRS) during esophageal high resolution manometry (HRM) assess esophageal neuromuscular integrity by evaluating postdeglutitive inhibition and rebound contraction, but most reports performed only a single MRS sequence. We assessed patterns of MRS reproducibility during clinical HRM in comparison to a normal cohort. Consecutive clinical HRM studies were included if two separate MRS sequences (four to six rapid swallows ≤4 s apart) were successfully performed. Chicago Classification diagnoses were identified; contraction wave abnormalities were additionally recorded. MRS-induced inhibition (contraction ≤3 cm during inhibition phase) and rebound contraction was assessed, and findings compared to 18 controls (28.0 ± 0.7 year, 50.0% female). Reproducibility consisted of similar inhibition and contraction responses with both sequences; discordance was segregated into inhibition and contraction phases. Multiple rapid swallows were successfully performed in 89.3% patients and all controls; 225 subjects (56.2 ± 0.9 year, 62.7% female) met study inclusion criteria. Multiple rapid swallows were reproducible in 76.9% patients and 94.4% controls (inhibition phase: 88.0% vs 94.4%, contraction phase 86.7% vs 100%, respectively, p = ns). A gradient of reproducibility was noted, highest in well-developed motor disorders (achalasia spectrum, hypermotility disorders, and aperistalsis, 91.7-100%, p = ns compared to controls); and lower in lesser motor disorders (contraction wave abnormalities, esophageal body hypomotility) or normal studies (62.2-70.8%, p < 0.0001 compared to well-developed motor disorders). Inhibition phase was most discordant in contraction wave abnormalities, while contraction phase was most discordant when studies were designated normal. Multiple rapid swallows are highly reproducible, especially in well-developed motor disorders, and complement the standard wet swallow manometry protocol. © 2014 John Wiley & Sons Ltd.

Reproducibility of WC-C High-Temperature Fixed Point

NASA Astrophysics Data System (ADS)

Grigoryeva, I. A.; Khlevnoy, B. B.; Solodilov, M. V.

2017-05-01

Reproducibility of the tungsten carbide-carbon peritectic (WC-C) fixed point (3021 K) was investigated by comparing six WC-C blackbody-type cells with each other. All the cells were built at VNIIOFI and had the same design with a cell outer diameter of 24 mm and a cavity opening diameter of 3 mm. Four cells were built using tungsten powder supplied by Alfa Aesar, while the other two cells used powder from Zhuzhou KETE (China). The nominal purity of both suppliers was 99.999 %. All the cells were compared in the same furnace. A reference cell in the second furnace was used for monitoring the stability of a radiation thermometer. Melting temperatures (given by the point of inflection) of all six cells agreed within ±45 mK. The reproducibility, as a standard deviation of the measured temperatures, can be estimated as 35 mK. The Zhuzhou KETE cells showed a slightly lower temperature than the Alfa Aesar cells: by 32 mK on average, which is comparable with repeatability of the measurements.

Highly Reproducible Label Free Quantitative Proteomic Analysis of RNA Polymerase Complexes*

PubMed Central

Mosley, Amber L.; Sardiu, Mihaela E.; Pattenden, Samantha G.; Workman, Jerry L.; Florens, Laurence; Washburn, Michael P.

2011-01-01

The use of quantitative proteomics methods to study protein complexes has the potential to provide in-depth information on the abundance of different protein components as well as their modification state in various cellular conditions. To interrogate protein complex quantitation using shotgun proteomic methods, we have focused on the analysis of protein complexes using label-free multidimensional protein identification technology and studied the reproducibility of biological replicates. For these studies, we focused on three highly related and essential multi-protein enzymes, RNA polymerase I, II, and III from Saccharomyces cerevisiae. We found that label-free quantitation using spectral counting is highly reproducible at the protein and peptide level when analyzing RNA polymerase I, II, and III. In addition, we show that peptide sampling does not follow a random sampling model, and we show the need for advanced computational models to predict peptide detection probabilities. In order to address these issues, we used the APEX protocol to model the expected peptide detectability based on whole cell lysate acquired using the same multidimensional protein identification technology analysis used for the protein complexes. Neither method was able to predict the peptide sampling levels that we observed using replicate multidimensional protein identification technology analyses. In addition to the analysis of the RNA polymerase complexes, our analysis provides quantitative information about several RNAP associated proteins including the RNAPII elongation factor complexes DSIF and TFIIF. Our data shows that DSIF and TFIIF are the most highly enriched RNAP accessory factors in Rpb3-TAP purifications and demonstrate our ability to measure low level associated protein abundance across biological replicates. In addition, our quantitative data supports a model in which DSIF and TFIIF interact with RNAPII in a dynamic fashion in agreement with previously published reports. PMID

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.

Ultimate waveform reproducibility of extreme-ultraviolet pulses by high-harmonic generation in quartz

NASA Astrophysics Data System (ADS)

Garg, M.; Kim, H. Y.; Goulielmakis, E.

2018-05-01

Optical waveforms of light reproducible with subcycle precision underlie applications of lasers in ultrafast spectroscopies, quantum control of matter and light-based signal processing. Nonlinear upconversion of optical pulses via high-harmonic generation in gas media extends these capabilities to the extreme ultraviolet (EUV). However, the waveform reproducibility of the generated EUV pulses in gases is inherently sensitive to intensity and phase fluctuations of the driving field. We used photoelectron interferometry to study the effects of intensity and carrier-envelope phase of an intense single-cycle optical pulse on the field waveform of EUV pulses generated in quartz nanofilms, and contrasted the results with those obtained in gas argon. The EUV waveforms generated in quartz were found to be virtually immune to the intensity and phase of the driving field, implying a non-recollisional character of the underlying emission mechanism. Waveform-sensitive photonic applications and precision measurements of fundamental processes in optics will benefit from these findings.

Stable, fertile, high polyhydroxyalkanoate producing plants and methods of producing them

DOEpatents

Bohmert-Tatarev, Karen; McAvoy, Susan; Peoples, Oliver P.; Snell, Kristi D.

2015-08-04

Transgenic plants that produce high levels of polyhydroxybutyrate and methods of producing them are provided. In a preferred embodiment the transgenic plants are produced using plastid transformation technologies and utilize genes which are codon optimized. Stably transformed plants able to produce greater than 10% dwt PHS in tissues are also provided.

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.

Accessing the reproducibility and specificity of pepsin and other aspartic proteases.

PubMed

Ahn, Joomi; Cao, Min-Jie; Yu, Ying Qing; Engen, John R

2013-06-01

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 reproducibility, both qualitatively and quantitatively, of online and offline pepsin digestion to understand the compliment of reproducible pepsin fragments that can be expected during a typical pepsin digestion. The collection of reproducible peptides was identified from >30 replicate digestions of the same protein and it was found that the number of reproducible 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.

A network-based method to evaluate quality of reproducibility of differential expression in cancer genomics studies

PubMed Central

Geng, Haijiang; Li, Zhihui; Li, Jiabing; Lu, Tao; Yan, Fangrong

2015-01-01

BACKGROUND Personalized cancer treatments depend on the determination of a patient's genetic status according to known genetic profiles for which targeted treatments exist. Such genetic profiles must be scientifically validated before they is applied to general patient population. Reproducibility of findings that support such genetic profiles is a fundamental challenge in validation studies. The percentage of overlapping genes (POG) criterion and derivative methods produce unstable and misleading results. Furthermore, in a complex disease, comparisons between different tumor subtypes can produce high POG scores that do not capture the consistencies in the functions. RESULTS We focused on the quality rather than the quantity of the overlapping genes. We defined the rank value of each gene according to importance or quality by PageRank on basis of a particular topological structure. Then, we used the p-value of the rank-sum of the overlapping genes (PRSOG) to evaluate the quality of reproducibility. Though the POG scores were low in different studies of the same disease, the PRSOG was statistically significant, which suggests that sets of differentially expressed genes might be highly reproducible. CONCLUSIONS Evaluations of eight datasets from breast cancer, lung cancer and four other disorders indicate that quality-based PRSOG method performs better than a quantity-based method. Our analysis of the components of the sets of overlapping genes supports the utility of the PRSOG method. PMID:26556852

Highly uniform and reproducible surface-enhanced Raman scattering from DNA-tailorable nanoparticles with 1-nm interior gap

NASA Astrophysics Data System (ADS)

Lim, Dong-Kwon; Jeon, Ki-Seok; Hwang, Jae-Ho; Kim, Hyoki; Kwon, Sunghoon; Suh, Yung Doug; Nam, Jwa-Min

2011-07-01

An ideal surface-enhanced Raman scattering (SERS) nanostructure for sensing and imaging applications should induce a high signal enhancement, generate a reproducible and uniform response, and should be easy to synthesize. Many SERS-active nanostructures have been investigated, but they suffer from poor reproducibility of the SERS-active sites, and the wide distribution of their enhancement factor values results in an unquantifiable SERS signal. Here, we show that DNA on gold nanoparticles facilitates the formation of well-defined gold nanobridged nanogap particles (Au-NNP) that generate a highly stable and reproducible SERS signal. The uniform and hollow gap (~1 nm) between the gold core and gold shell can be precisely loaded with a quantifiable amount of Raman dyes. SERS signals generated by Au-NNPs showed a linear dependence on probe concentration (R2 > 0.98) and were sensitive down to 10 fM concentrations. Single-particle nano-Raman mapping analysis revealed that >90% of Au-NNPs had enhancement factors greater than 1.0 × 108, which is sufficient for single-molecule detection, and the values were narrowly distributed between 1.0 × 108 and 5.0 × 109.

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.

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

Reproducible, high-throughput synthesis of colloidal nanocrystals for optimization in multidimensional parameter space.

PubMed

Chan, Emory M; Xu, Chenxu; Mao, Alvin W; Han, Gang; Owen, Jonathan S; Cohen, Bruce E; Milliron, Delia J

2010-05-12

While colloidal nanocrystals hold tremendous potential for both enhancing fundamental understanding of materials scaling and enabling advanced technologies, progress in both realms can be inhibited by the limited reproducibility of traditional synthetic methods and by the difficulty of optimizing syntheses over a large number of synthetic parameters. Here, we describe an automated platform for the reproducible synthesis of colloidal nanocrystals and for the high-throughput optimization of physical properties relevant to emerging applications of nanomaterials. This robotic platform enables precise control over reaction conditions while performing workflows analogous to those of traditional flask syntheses. We demonstrate control over the size, size distribution, kinetics, and concentration of reactions by synthesizing CdSe nanocrystals with 0.2% coefficient of variation in the mean diameters across an array of batch reactors and over multiple runs. Leveraging this precise control along with high-throughput optical and diffraction characterization, we effectively map multidimensional parameter space to tune the size and polydispersity of CdSe nanocrystals, to maximize the photoluminescence efficiency of CdTe nanocrystals, and to control the crystal phase and maximize the upconverted luminescence of lanthanide-doped NaYF(4) nanocrystals. On the basis of these demonstrative examples, we conclude that this automated synthesis approach will be of great utility for the development of diverse colloidal nanomaterials for electronic assemblies, luminescent biological labels, electroluminescent devices, and other emerging applications.

High-throughput miniaturized bioreactors for cell culture process development: reproducibility, scalability, and control.

PubMed

Rameez, Shahid; Mostafa, Sigma S; Miller, Christopher; Shukla, Abhinav A

2014-01-01

Decreasing the timeframe for cell culture process development has been a key goal toward accelerating biopharmaceutical development. Advanced Microscale Bioreactors (ambr™) is an automated micro-bioreactor system with miniature single-use bioreactors with a 10-15 mL working volume controlled by an automated workstation. This system was compared to conventional bioreactor systems in terms of its performance for the production of a monoclonal antibody in a recombinant Chinese Hamster Ovary cell line. The miniaturized bioreactor system was found to produce cell culture profiles that matched across scales to 3 L, 15 L, and 200 L stirred tank bioreactors. The processes used in this article involve complex feed formulations, perturbations, and strict process control within the design space, which are in-line with processes used for commercial scale manufacturing of biopharmaceuticals. Changes to important process parameters in ambr™ resulted in predictable cell growth, viability and titer changes, which were in good agreement to data from the conventional larger scale bioreactors. ambr™ was found to successfully reproduce variations in temperature, dissolved oxygen (DO), and pH conditions similar to the larger bioreactor systems. Additionally, the miniature bioreactors were found to react well to perturbations in pH and DO through adjustments to the Proportional and Integral control loop. The data presented here demonstrates the utility of the ambr™ system as a high throughput system for cell culture process development. © 2014 American Institute of Chemical Engineers.

Rapid and highly reproducible analysis of rare earth elements by multiple collector inductively coupled plasma mass spectrometry

NASA Astrophysics Data System (ADS)

Baker, Joel; Waight, Tod; Ulfbeck, David

2002-10-01

A method has been developed for the rapid chemical separation and highly reproducible analysis of the rare earth elements (REE) by isotope dilution analysis by means of a multiple collector inductively coupled plasma mass spectrometer (MC-ICP-MS). This technique is superior in terms of the analytical reproducibility or rapidity of analysis compared with quadrupole ICP-MS or with thermal ionization mass spectrometric isotope dilution techniques. Samples are digested by standard hydrofluoric-nitric acid-based techniques and spiked with two mixed spikes. The bulk REE are separated from the sample on a cation exchange column, collecting the middle-heavy and light REE as two groups, which provides a middle-heavy REE cut with sufficient separation of the light from the heavier REE to render oxide interferences trivial, and a Ba-free light REE cut. The heavy (Er-Lu), middle (Eu-Gd), and light REE (La-Eu) concentrations are determined by three short (1 to 2 min) analyses with a CETAC Aridus desolvating nebulizer introduction system. Replicate digestions of international rock standards demonstrate that concentrations can be reproduced to <1%, which reflects weighing errors during digestion and aliquotting as inter-REE ratios reproduce to ≤0.2% (2 SD). Eu and Ce anomalies reproduce to <0.15%. In addition to determining the concentrations of polyisotopic REE by isotope dilution analysis, the concentration of monoisotopic Pr can be measured during the light REE isotope dilution run, by reference to Pr/Ce and Pr/Nd ratios measured in a REE standard solution. Pr concentrations determined in this way reproduce to <1%, and Pr/REE ratios reproduce to <0.4%. Ce anomalies calculated with La and Pr also reproduce to <0.15% (2 SD). The precise Ce (and Eu) anomaly measurements should allow greater use of these features in studying the recycling of materials with these anomalies into the mantle, or redox-induced effects on the REE during recycling and dehydration of oceanic lithosphere

The Lhc Cryomagnet Supports in Glass-Fiber Reinforced Epoxy: a Large Scale Industrial Production with High Reproducibility in Performance

NASA Astrophysics Data System (ADS)

Poncet, A.; Struik, M.; Trigo, J.; Parma, V.

2008-03-01

The about 1700 LHC main ring super-conducting magnets are supported within their cryostats on 4700 low heat in leak column-type supports. The supports were designed to ensure a precise and stable positioning of the heavy dipole and quadrupole magnets while keeping thermal conduction heat loads within budget. A trade-off between mechanical and thermal properties, as well as cost considerations, led to the choice of glass fibre reinforced epoxy (GFRE). Resin Transfer Moulding (RTM), featuring a high level of automation and control, was the manufacturing process retained to ensure the reproducibility of the performance of the supports throughout the large production. The Spanish aerospace company EADS-CASA Espacio developed the specific RTM process, and produced the total quantity of supports between 2001 and 2004. This paper describes the development and the production of the supports, and presents the production experience and the achieved performance.

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.

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.

"The Pen is the Spear of Today": (Re)producing Gender in the Maasai Schooling Setting

ERIC Educational Resources Information Center

Archambault, Caroline S.

2017-01-01

An essentialist, "traditional", Maasai gender ideology that poorly reflects the day-to-day gender realities of residents is being reproduced and dominating in the modern schooling setting of a Maasai community in Southern Kenya. Through an ethnographic analysis based on long-term fieldwork and mixed-method approaches, this paper explores…

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?

Low-Cost, Disposable, Flexible and Highly Reproducible Screen Printed SERS Substrates for the Detection of Various Chemicals

PubMed Central

Wu, Wei; Liu, Li; Dai, Zhigao; Liu, Juhua; Yang, Shuanglei; Zhou, Li; Xiao, Xiangheng; Jiang, Changzhong; Roy, Vellaisamy A.L.

2015-01-01

Ideal SERS substrates for sensing applications should exhibit strong signal enhancement, generate a reproducible and uniform response, and should be able to fabricate in large-scale and low-cost. Herein, we demonstrate low-cost, highly sensitive, disposable and reproducible SERS substrates by means of screen printing Ag nanoparticles (NPs) on a plastic PET (Polyethylene terephthalate) substrates. While there are many complex methods for the fabrication of SERS substrates, screen printing is suitable for large-area fabrication and overcomes the uneven radial distribution. Using as-printed Ag substrates as the SERS platform, detection of various commonly known chemicals have been done. The SERS detection limit of Rhodamine 6G (R6G) is higher than the concentration of 1 × 10−10 M. The relative standard deviation (RSD) value for 784 points on the detection of R6G and Malachite green (MG) is less than 20% revealing a homogeneous SERS distribution and high reproducibility. Moreover, melamine (MA) is detected in fresh liquid-milk without additional pretreatment, which may accelerate the application of rapid on-line detection of MA in liquid milk. Our screen printing method highlights the use of large-scale printing strategies for the fabrication of well-defined functional nanostructures with applications well beyond the field of SERS sensing. PMID:25974125

Fast gradient separation by very high pressure liquid chromatography: reproducibility of analytical data and influence of delay between successive runs.

PubMed

Stankovicha, Joseph J; Gritti, Fabrice; Beaver, Lois Ann; Stevensona, Paul G; Guiochon, Georges

2013-11-29

Five methods were used to implement fast gradient separations: constant flow rate, constant column-wall temperature, constant inlet pressure at moderate and high pressures (controlled by a pressure controller),and programmed flow constant pressure. For programmed flow constant pressure, the flow rates and gradient compositions are controlled using input into the method instead of the pressure controller. Minor fluctuations in the inlet pressure do not affect the mobile phase flow rate in programmed flow. There producibilities of the retention times, the response factors, and the eluted band width of six successive separations of the same sample (9 components) were measured with different equilibration times between 0 and 15 min. The influence of the length of the equilibration time on these reproducibilities is discussed. The results show that the average column temperature may increase from one separation to the next and that this contributes to fluctuation of the results.

High- and low-temperature-stable thermite composition for producing high-pressure, high-velocity gases

DOEpatents

Halcomb, Danny L.; Mohler, Jonathan H.

1990-10-16

A high- and low-temperature-stable thermite composition for producing high-pressure and high-velocity gases comprises an oxidizable metal, an oxidizing reagent, and a high-temperature-stable gas-producing additive selected from the group consisting of metal carbides and metal nitrides.

PRODUCING HIGH CORN YIELDS.

ERIC Educational Resources Information Center

Illinois Univ., Urbana. Coll. of Agriculture.

RESOURCE MATERIAL ON CORN PRODUCTION FOR HIGH SCHOOL VOCATIONAL AGRICULTURE AND ADULT FARMER CLASSES WAS DESIGNED BY A STATE LEVEL GROUP OF SUBJECT MATTER SPECIALISTS, TEACHER EDUCATORS, SUPERVISORS, AND TEACHERS TO HELP SOLVE PROBLEMS THAT CONFRONT CORN PRODUCERS AT PLANTING TIME. THE SUBJECT MATTER CONCERNS PLANTING TIME, DEPTH, ROW WIDTH,…

Reproducibility of Search Strategies Is Poor in Systematic Reviews Published in High-Impact Pediatrics, Cardiology and Surgery Journals: A Cross-Sectional Study

PubMed Central

2016-01-01

Background A high-quality search strategy is considered an essential component of systematic reviews but many do not contain reproducible search strategies. It is unclear if low reproducibility spans medical disciplines, is affected by librarian/search specialist involvement or has improved with increased awareness of reporting guidelines. Objectives To examine the reporting of search strategies in systematic reviews published in Pediatrics, Surgery or Cardiology journals in 2012 and determine rates and predictors of including a reproducible search strategy. Methods We identified all systematic reviews published in 2012 in the ten highest impact factor journals in Pediatrics, Surgery and Cardiology. Each search strategy was coded to indicate what elements were reported and whether the overall search was reproducible. Reporting and reproducibility rates were compared across disciplines and we measured the influence of librarian/search specialist involvement, discipline or endorsement of a reporting guideline on search reproducibility. Results 272 articles from 25 journals were included. Reporting of search elements ranged widely from 91% of articles naming search terms to 33% providing a full search strategy and 22% indicating the date the search was executed. Only 22% of articles provided at least one reproducible search strategy and 13% provided a reproducible strategy for all databases searched in the article. Librarians or search specialists were reported as involved in 17% of articles. There were strong disciplinary differences on the reporting of search elements. In the multivariable analysis, only discipline (Pediatrics) was a significant predictor of the inclusion of a reproducible search strategy. Conclusions Despite recommendations to report full, reproducible search strategies, many articles still do not. In addition, authors often report a single strategy as covering all databases searched, further decreasing reproducibility. Further research is needed

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

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.

Statecraft and Study Abroad: Imagining, Narrating and Reproducing the State

ERIC Educational Resources Information Center

Lansing, Jade; Farnum, Rebecca L.

2017-01-01

Study abroad in higher education is on the rise, marketed as an effective way to produce global citizens and undermine international boundaries. In practice, however, programmes frequently reify rather than challenge states: participants "study Morocco" rather than "exploring Marrakech." This framing reproduces real and…

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.

Planar heterojunction perovskite solar cells with superior reproducibility

PubMed Central

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

2014-01-01

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 reproducibility of PeSCs ascribed to their inhomogeneously covered film morphology has hindered their practical application. Here, we demonstrate high-performance PeSCs with superior reproducibility 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 reproducible 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

Repeatability and Reproducibility of Virtual Subjective Refraction.

PubMed

Perches, Sara; Collados, M Victoria; Ares, Jorge

2016-10-01

To establish the repeatability and reproducibility 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 reproducibility 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 reproducibility, 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 reproducibility 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.

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.

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.

Imaging of striatal dopamine transporters in rat brain with single pinhole SPECT and co-aligned MRI is highly reproducible.

PubMed

Booij, Jan; de Bruin, Kora; de Win, Maartje M L; Lavini, Cristina; den Heeten, Gerard J; Habraken, Jan B A

2003-08-01

A recently developed pinhole high-resolution SPECT system was used to measure striatal to non-specific binding ratios in rats (n = 9), after injection of the dopamine transporter ligand (123)I-FP-CIT, and to assess its test/retest reproducibility. For co-alignment purposes, the rat brain was imaged on a 1.5 Tesla clinical MRI scanner using a specially developed surface coil. The SPECT images showed clear striatal uptake. On the MR images, cerebral and extra-cerebral structures could be easily delineated. The mean striatal to non-specific [(123)I]FP-CIT binding ratios of the test/retest studies were 1.7 +/- 0.2 and 1.6 +/- 0.2, respectively. The test/retest variability was approximately 9%. We conclude that the assessment of striatal [(123)I]FP-CIT binding ratios in rats is highly reproducible.

Long-term reproducibility of relative sensitivity factors obtained with CAMECA Wf

NASA Astrophysics Data System (ADS)

Gui, D.; Xing, Z. X.; Huang, Y. H.; Mo, Z. Q.; Hua, Y. N.; Zhao, S. P.; Cha, L. Z.

2008-12-01

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 reproducibility 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 reproducibility 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 reproducibility 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 reproducibility results have a practical implication that deviation can be estimated without testing the standards.

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.

Method of producing a high pressure gas

DOEpatents

Bingham, Dennis N.; Klingler, Kerry M.; Zollinger, William T.

2006-07-18

A method of producing a high pressure gas is disclosed and which includes providing a container; supplying the container with a liquid such as water; increasing the pressure of the liquid within the container; supplying a reactant composition such as a chemical hydride to the liquid under pressure in the container and which chemically reacts with the liquid to produce a resulting high pressure gas such as hydrogen at a pressure of greater than about 100 pounds per square inch of pressure; and drawing the resulting high pressure gas from the container.

Reproducing or Challenging Power in the Questions We Ask and the Methods We Use: A Framework for Activist Research in Urban Education

ERIC Educational Resources Information Center

Nygreen, Kysa

2006-01-01

Many have argued that educational research does little to change (and may actually reproduce) the social-structural inequalities shaping the quality of high-poverty urban schools. Building from this premise, this paper asks: How can university-based scholars of urban education do research that encourages, produces, or informs change in urban…

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.

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

Reproducibility of dynamically represented acoustic lung images from healthy individuals

PubMed Central

Maher, T M; Gat, M; Allen, D; Devaraj, A; Wells, A U; Geddes, D M

2008-01-01

Background and aim: Acoustic lung imaging offers a unique method for visualising the lung. This study was designed to demonstrate reproducibility 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. Reproducibility 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 reproducible with an intraclass correlation score of 0.86 (very good agreement). Intraclass correlations for inter-rater agreement and reproducibility 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 reproducible 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

Extended Eden model reproduces growth of an acellular slime mold.

PubMed

Wagner, G; Halvorsrud, R; Meakin, P

1999-11-01

A stochastic growth model was used to simulate the growth of the acellular slime mold Physarum polycephalum on substrates where the nutrients were confined in separate drops. Growth of Physarum on such substrates was previously studied experimentally and found to produce a range of different growth patterns [Phys. Rev. E 57, 941 (1998)]. The model represented the aging of cluster sites and differed from the original Eden model in that the occupation probability of perimeter sites depended on the time of occupation of adjacent cluster sites. This feature led to a bias in the selection of growth directions. A moderate degree of persistence was found to be crucial to reproduce the biological growth patterns under various conditions. Persistence in growth combined quick propagation in heterogeneous environments with a high probability of locating sources of nutrients.

Extended Eden model reproduces growth of an acellular slime mold

NASA Astrophysics Data System (ADS)

Wagner, Geri; Halvorsrud, Ragnhild; Meakin, Paul

1999-11-01

A stochastic growth model was used to simulate the growth of the acellular slime mold Physarum polycephalum on substrates where the nutrients were confined in separate drops. Growth of Physarum on such substrates was previously studied experimentally and found to produce a range of different growth patterns [Phys. Rev. E 57, 941 (1998)]. The model represented the aging of cluster sites and differed from the original Eden model in that the occupation probability of perimeter sites depended on the time of occupation of adjacent cluster sites. This feature led to a bias in the selection of growth directions. A moderate degree of persistence was found to be crucial to reproduce the biological growth patterns under various conditions. Persistence in growth combined quick propagation in heterogeneous environments with a high probability of locating sources of nutrients.

Physics and Psychophysics of High-Fidelity Sound. Part III: The Components of a Sound-Reproducing System: Amplifiers and Loudspeakers.

ERIC Educational Resources Information Center

Rossing, Thomas D.

1980-01-01

Described are the components for a high-fidelity sound-reproducing system which focuses on various program sources, the amplifier, and loudspeakers. Discussed in detail are amplifier power and distortion, air suspension, loudspeaker baffles and enclosures, bass-reflex enclosure, drone cones, rear horn and acoustic labyrinth enclosures, horn…

Massive and Reproducible Production of Liver Buds Entirely from Human Pluripotent Stem Cells.

PubMed

Takebe, Takanori; Sekine, Keisuke; Kimura, Masaki; Yoshizawa, Emi; Ayano, Satoru; Koido, Masaru; Funayama, Shizuka; Nakanishi, Noriko; Hisai, Tomoko; Kobayashi, Tatsuya; Kasai, Toshiharu; Kitada, Rina; Mori, Akira; Ayabe, Hiroaki; Ejiri, Yoko; Amimoto, Naoki; Yamazaki, Yosuke; Ogawa, Shimpei; Ishikawa, Momotaro; Kiyota, Yasujiro; Sato, Yasuhiko; Nozawa, Kohei; Okamoto, Satoshi; Ueno, Yasuharu; Taniguchi, Hideki

2017-12-05

Organoid technology provides a revolutionary paradigm toward therapy but has yet to be applied in humans, mainly because of reproducibility and scalability challenges. Here, we overcome these limitations by evolving a scalable organ bud production platform entirely from human induced pluripotent stem cells (iPSC). By conducting massive "reverse" screen experiments, we identified three progenitor populations that can effectively generate liver buds in a highly reproducible manner: hepatic endoderm, endothelium, and septum mesenchyme. Furthermore, we achieved human scalability by developing an omni-well-array culture platform for mass producing homogeneous and miniaturized liver buds on a clinically relevant large scale (>10 8 ). Vascularized and functional liver tissues generated entirely from iPSCs significantly improved subsequent hepatic functionalization potentiated by stage-matched developmental progenitor interactions, enabling functional rescue against acute liver failure via transplantation. Overall, our study provides a stringent manufacturing platform for multicellular organoid supply, thus facilitating clinical and pharmaceutical applications especially for the treatment of liver diseases through multi-industrial collaborations. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

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

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

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.

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.

Fabrication of bimetallic Cu/Au nanotubes and their sensitive, selective, reproducible and reusable electrochemical sensing of glucose

NASA Astrophysics Data System (ADS)

Tee, Si Yin; Ye, Enyi; Pan, Pei Hua; Lee, Coryl Jing Jun; Hui, Hui Kim; Zhang, Shuang-Yuan; Koh, Leng Duei; Dong, Zhili; Han, Ming-Yong

2015-06-01

Herein, we report a facile two-step approach to produce gold-incorporated copper (Cu/Au) nanostructures through controlled disproportionation of the Cu+-oleylamine complex at 220 °C to form copper nanowires and the subsequent reaction with Au3+ at different temperatures of 140, 220 and 300 °C. In comparison with copper nanowires, these bimetallic Cu/Au nanostructures exhibit their synergistic effect to greatly enhance glucose oxidation. Among them, the shape-controlled Cu/Au nanotubes prepared at 140 °C show the highest electrocatalytic activity for non-enzymatic glucose sensing in alkaline solution. In addition to high sensitivity and fast response, the Cu/Au nanotubes possess high selectivity against interferences from other potential interfering species and excellent reproducibility with long-term stability. By introducing gold into copper nanostructures at a low level of 3, 1 and 0.1 mol% relative to the initial copper precursor, a significant electrocatalytic enhancement of the resulting bimetallic Cu/Au nanostructures starts to occur at 1 mol%. Overall, the present fabrication of stable Cu/Au nanostructures offers a promising low-cost platform for sensitive, selective, reproducible and reusable electrochemical sensing of glucose.Herein, we report a facile two-step approach to produce gold-incorporated copper (Cu/Au) nanostructures through controlled disproportionation of the Cu+-oleylamine complex at 220 °C to form copper nanowires and the subsequent reaction with Au3+ at different temperatures of 140, 220 and 300 °C. In comparison with copper nanowires, these bimetallic Cu/Au nanostructures exhibit their synergistic effect to greatly enhance glucose oxidation. Among them, the shape-controlled Cu/Au nanotubes prepared at 140 °C show the highest electrocatalytic activity for non-enzymatic glucose sensing in alkaline solution. In addition to high sensitivity and fast response, the Cu/Au nanotubes possess high selectivity against interferences from other

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.

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

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.

Handgrip force steadiness in young and older adults: a reproducibility study.

PubMed

Blomkvist, Andreas W; Eika, Fredrik; de Bruin, Eling D; Andersen, Stig; Jorgensen, Martin

2018-04-02

Force steadiness is a quantitative measure of the ability to control muscle tonus. It is an independent predictor of functional performance and has shown to correlate well with different degrees of motor impairment following stroke. Despite being clinically relevant, few studies have assessed the validity of measuring force steadiness. The aim of this study was to explore the reproducibility of handgrip force steadiness, and to assess age difference in steadiness. Intrarater reproducibility (the degree to which a rating gives consistent result on separate occasions) was investigated in a test-retest design with seven days between sessions. Ten young and thirty older adults were recruited and handgrip steadiness was tested at 5%, 10% and 25% of maximum voluntary contraction (MVC) using Nintendo Wii Balance Board (WBB). Coefficients of variation were calculated from the mean force produced (CVM) and the target force (CVT). Area between the force curve and the target force line (Area) was also calculated. For the older adults we explored reliability using intraclass correlation coefficient (ICC) and agreement using standard error of measurement (SEM), limits of agreement (LOA) and smallest real difference (SRD). A systematic improvement in handgrip steadiness was found between sessions for all measures (CVM, CVT, Area). CVM and CVT at 5% of MVC showed good to high reliability, while Area had poor reliability for all percentages of MVC. Averaged ICC for CVM, CVT and Area was 0.815, 0.806 and 0.464, respectively. Averaged ICC on 5%, 10%, and 25% of MVC was 0.751, 0.667 and 0.668, respectively. Measures of agreement showed similar trends with better results for CVM and CVT than for Area. Young adults had better handgrip steadiness than older adults across all measures. The CVM and CVT measures demonstrated good reproducibility at lower percentages of MVC using the WBB, and could become relevant measures in the clinical setting. The Area measure had poor reproducibility

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.

[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.

Paper-based microfluidic approach for surface-enhanced raman spectroscopy and highly reproducible detection of proteins beyond picomolar concentration.

PubMed

Saha, Arindam; Jana, Nikhil R

2015-01-14

Although microfluidic approach is widely used in various point of care diagnostics, its implementation in surface enhanced Raman spectroscopy (SERS)-based detection is challenging. This is because SERS signal depends on plasmonic nanoparticle aggregation induced generation of stable electromagnetic hot spots and in currently available microfluidic platform this condition is difficult to adapt. Here we show that SERS can be adapted using simple paper based microfluidic system where both the plasmonic nanomaterials and analyte are used in mobile phase. This approach allows analyte induced controlled particle aggregation and electromagnetic hot spot generation inside the microfluidic channel with the resultant SERS signal, which is highly reproducible and sensitive. This approach has been used for reproducible detection of protein in the pico to femtomolar concentration. Presented approach is simple, rapid, and cost-effective, and requires low sample volume. Method can be extended for SERS-based detection of other biomolecules.

SiGe epitaxial memory for neuromorphic computing with reproducible high performance based on engineered dislocations

NASA Astrophysics Data System (ADS)

Choi, Shinhyun; Tan, Scott H.; Li, Zefan; Kim, Yunjo; Choi, Chanyeol; Chen, Pai-Yu; Yeon, Hanwool; Yu, Shimeng; Kim, Jeehwan

2018-01-01

Although several types of architecture combining memory cells and transistors have been used to demonstrate artificial synaptic arrays, they usually present limited scalability and high power consumption. Transistor-free analog switching devices may overcome these limitations, yet the typical switching process they rely on—formation of filaments in an amorphous medium—is not easily controlled and hence hampers the spatial and temporal reproducibility of the performance. Here, we demonstrate analog resistive switching devices that possess desired characteristics for neuromorphic computing networks with minimal performance variations using a single-crystalline SiGe layer epitaxially grown on Si as a switching medium. Such epitaxial random access memories utilize threading dislocations in SiGe to confine metal filaments in a defined, one-dimensional channel. This confinement results in drastically enhanced switching uniformity and long retention/high endurance with a high analog on/off ratio. Simulations using the MNIST handwritten recognition data set prove that epitaxial random access memories can operate with an online learning accuracy of 95.1%.

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

Reproducing an extreme flood with uncertain post-event information

NASA Astrophysics Data System (ADS)

Fuentes-Andino, Diana; Beven, Keith; Halldin, Sven; Xu, Chong-Yu; Reynolds, José Eduardo; Di Baldassarre, Giuliano

2017-07-01

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 observed high-water marks within the uncertainty bounds of the evaluation data. This allowed an inundation likelihood map to be produced. Observed high-water marks could not be reproduced 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 reproduce 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

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

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.

Exhaled breath temperature in children: reproducibility and influencing factors.

PubMed

Vermeulen, S; Barreto, M; La Penna, F; Prete, A; Martella, S; Biagiarelli, F; Villa, M P

2014-09-01

This study will investigate the reproducibility 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 reproducible; the second measurement was higher than the first measurement, consistent with a test-retest situation. In 13 subjects, between-session within-day reproducibility 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 reproducible, 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.

A highly reproducible quantitative viral outgrowth assay for the measurement of the replication-competent latent HIV-1 reservoir.

PubMed

Fun, Axel; Mok, Hoi Ping; Wills, Mark R; Lever, Andrew M

2017-02-24

Cure of Human Immunodeficiency Virus (HIV) infection remains elusive due to the persistence of HIV in a latent reservoir. Strategies to eradicate latent infection can only be evaluated with robust, sensitive and specific assays to quantitate reactivatable latent virus. We have taken the standard peripheral blood mononuclear cell (PBMC) based viral outgrowth methodology and from it created a logistically simpler and more highly reproducible assay to quantify replication-competent latent HIV in resting CD4 + T cells, both increasing accuracy and decreasing cost and labour. Purification of resting CD4 + T cells from whole PBMC is expedited and achieved in 3 hours, less than half the time of conventional protocols. Our indicator cell line, SupT1-CCR5 cells (a clonal cell line expressing CD4, CXCR4 and CCR5) provides a readily available standardised readout. Reproducibility compares favourably to other published assays but with reduced cost, labour and assay heterogeneity without compromising sensitivity.

A novel highly reproducible and lethal nonhuman primate model for orthopox virus infection.

PubMed

Kramski, Marit; Mätz-Rensing, Kerstin; Stahl-Hennig, Christiane; Kaup, Franz-Josef; Nitsche, Andreas; Pauli, Georg; Ellerbrok, Heinz

2010-04-29

The intentional re-introduction of Variola virus (VARV), the agent of smallpox, into the human population is of great concern due its bio-terroristic potential. Moreover, zoonotic infections with Cowpox (CPXV) and Monkeypox virus (MPXV) cause severe diseases in humans. Smallpox vaccines presently available can have severe adverse effects that are no longer acceptable. The efficacy and safety of new vaccines and antiviral drugs for use in humans can only be demonstrated in animal models. The existing nonhuman primate models, using VARV and MPXV, need very high viral doses that have to be applied intravenously or intratracheally to induce a lethal infection in macaques. To overcome these drawbacks, the infectivity and pathogenicity of a particular CPXV was evaluated in the common marmoset (Callithrix jacchus).A CPXV named calpox virus was isolated from a lethal orthopox virus (OPV) outbreak in New World monkeys. We demonstrated that marmosets infected with calpox virus, not only via the intravenous but also the intranasal route, reproducibly develop symptoms resembling smallpox in humans. Infected animals died within 1-3 days after onset of symptoms, even when very low infectious viral doses of 5x10(2) pfu were applied intranasally. Infectious virus was demonstrated in blood, saliva and all organs analyzed.We present the first characterization of a new OPV infection model inducing a disease in common marmosets comparable to smallpox in humans. Intranasal virus inoculation mimicking the natural route of smallpox infection led to reproducible infection. In vivo titration resulted in an MID(50) (minimal monkey infectious dose 50%) of 8.3x10(2) pfu of calpox virus which is approximately 10,000-fold lower than MPXV and VARV doses applied in the macaque models. Therefore, the calpox virus/marmoset model is a suitable nonhuman primate model for the validation of vaccines and antiviral drugs. Furthermore, this model can help study mechanisms of OPV pathogenesis.

Uniform neural tissue models produced on synthetic hydrogels using standard culture techniques.

PubMed

Barry, Christopher; Schmitz, Matthew T; Propson, Nicholas E; Hou, Zhonggang; Zhang, Jue; Nguyen, Bao K; Bolin, Jennifer M; Jiang, Peng; McIntosh, Brian E; Probasco, Mitchell D; Swanson, Scott; Stewart, Ron; Thomson, James A; Schwartz, Michael P; Murphy, William L

2017-11-01

The aim of the present study was to test sample reproducibility for model neural tissues formed on synthetic hydrogels. Human embryonic stem (ES) cell-derived precursor cells were cultured on synthetic poly(ethylene glycol) (PEG) hydrogels to promote differentiation and self-organization into model neural tissue constructs. Neural progenitor, vascular, and microglial precursor cells were combined on PEG hydrogels to mimic developmental timing, which produced multicomponent neural constructs with 3D neuronal and glial organization, organized vascular networks, and microglia with ramified morphologies. Spearman's rank correlation analysis of global gene expression profiles and a comparison of coefficient of variation for expressed genes demonstrated that replicate neural constructs were highly uniform to at least day 21 for samples from independent experiments. We also demonstrate that model neural tissues formed on PEG hydrogels using a simplified neural differentiation protocol correlated more strongly to in vivo brain development than samples cultured on tissue culture polystyrene surfaces alone. These results provide a proof-of-concept demonstration that 3D cellular models that mimic aspects of human brain development can be produced from human pluripotent stem cells with high sample uniformity between experiments by using standard culture techniques, cryopreserved cell stocks, and a synthetic extracellular matrix. Impact statement Pluripotent stem (PS) cells have been characterized by an inherent ability to self-organize into 3D "organoids" resembling stomach, intestine, liver, kidney, and brain tissues, offering a potentially powerful tool for modeling human development and disease. However, organoid formation must be quantitatively reproducible for applications such as drug and toxicity screening. Here, we report a strategy to produce uniform neural tissue constructs with reproducible global gene expression profiles for replicate samples from multiple

Enriched reproducing kernel particle method for fractional advection-diffusion equation

NASA Astrophysics Data System (ADS)

Ying, Yuping; Lian, Yanping; Tang, Shaoqiang; Liu, Wing Kam

2018-06-01

The reproducing 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 reproduced, which guarantees a good approximation to the boundary layer. Numerical tests are performed to verify the proposed approach.

The Road to Reproducibility in Animal Research.

PubMed

Jilka, Robert L

2016-07-01

Reproducibility of research findings is the hallmark of scientific advance. However, the recently noted lack of reproducibility 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.

Reproducible fabrication of stable small nano Pt with high activity for sensor applications.

PubMed

Ye, Pingping; Guo, Xiaoyu; Liu, Guiting; Chen, Huifen; Pan, Yuxia; Wen, Ying; Yang, Haifeng

2013-07-26

Pt nanoparticles with an average size of 2-3 nm in diameter were reproducibly synthesized by reduction of H₂PtCl₆ solution containing inositol hexaphosphate (IP₆) as the stabilizing agent. Single crystals with Pt(111) faces of the resulting cubic nanoparticles were revealed by the electron diffraction pattern. The PtNPs-IP₆ nanoparticles were used to modify an electrode as a nonenzymatic sensor for H₂O₂ detection, exhibiting a fast response and high sensitivity. A low detection limit of 2.0 × 10⁻⁷ M (S/N = 3) with two linear ranges between 2.4 × 10⁻⁷ and 1.3 × 10⁻³ M (R² = 0.9987) and between 1.3 × 10⁻³ and 1.3 × 10⁻² M (R² = 0.9980) was achieved. The attractive electrochemical performance of PtNPs-IP₆ enables it to be employed as a promising material for the development of Pt-based analytical systems and other applications.

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.

3-D printing provides a novel approach for standardization and reproducibility of freezing devices

PubMed Central

Hu, E; Childress, William; Tiersch, Terrence R.

2017-01-01

Cryopreservation has become an important and accepted tool for long-term germplasm conservation of animals and plants. To protect genetic resources, repositories have been developed with national and international cooperation. For a repository to be effective, the genetic material submitted must be of good quality and comparable to other submissions. However, due to a variety of reasons, including constraints in knowledge and available resources, cryopreservation methods for aquatic species vary widely across user groups which reduces reproducibility and weakens quality control. Herein we describe a standardizable freezing device produced using 3-dimensional (3-D) printing and introduce the concept of network sharing to achieve aggregate high-throughput cryopreservation for aquatic species. The objectives were to: 1) adapt widely available polystyrene foam products that would be inexpensive, portable, and provide adequate work space; 2) develop a design suitable for 3-D printing that could provide multiple configurations, be inexpensive, and easy to use, and 3) evaluate various configurations to attain freezing rates suitable for various common cryopreservation containers. Through this approach, identical components can be accessed globally, and we demonstrated that 3-D printers can be used to fabricate parts for standardizable freezing devices yielding relevant and reproducible cooling rates across users. With standardized devices for freezing, methods and samples can harmonize into an aggregated high-throughput pathway not currently available for aquatic species repository development. PMID:28465185

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

Highly reproducible and reliable metal/graphene contact by ultraviolet-ozone treatment

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

Li, Wei; Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899; Hacker, Christina A.

2014-03-21

Resist residue from the device fabrication process is a significant source of contamination at the metal/graphene contact interface. Ultraviolet Ozone (UVO) treatment is proven here, by X-ray photoelectron spectroscopy and Raman measurement, to be an effective way of cleaning the metal/graphene interface. Electrical measurements of devices that were fabricated by using UVO treatment of the metal/graphene contact region show that stable and reproducible low resistance metal/graphene contacts are obtained and the electrical properties of the graphene channel remain unaffected.

TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics.

PubMed

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

2016-09-01

Next-generation mass spectrometric (MS) techniques such as SWATH-MS have substantially increased the throughput and reproducibility 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 accurate 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.

Reproducibility of HTS-SQUID magnetocardiography in an unshielded clinical environment.

PubMed

Leder, U; Schrey, F; Haueisen, J; Dörrer, L; Schreiber, J; Liehr, M; Schwarz, G; Solbrig, O; Figulla, H R; Seidel, P

2001-07-01

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 reproducibility 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 reproducibility 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 reproducibility 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 reproducibility 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 reproducibility 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

Using prediction markets to estimate the reproducibility of scientific research.

PubMed

Dreber, Anna; Pfeiffer, Thomas; Almenberg, Johan; Isaksson, Siri; Wilson, Brad; Chen, Yiling; Nosek, Brian A; Johannesson, Magnus

2015-12-15

Concerns about a lack of reproducibility 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 reproducibility of 44 studies published in prominent psychology journals and replicated in the Reproducibility 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 reproducibility 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 reproducibility at low cost and could potentially even be used to determine which studies to replicate to optimally allocate limited resources into replications.

Using prediction markets to estimate the reproducibility of scientific research

PubMed Central

Dreber, Anna; Pfeiffer, Thomas; Almenberg, Johan; Isaksson, Siri; Wilson, Brad; Chen, Yiling; Nosek, Brian A.; Johannesson, Magnus

2015-01-01

Concerns about a lack of reproducibility 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 reproducibility of 44 studies published in prominent psychology journals and replicated in the Reproducibility 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 reproducibility 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 reproducibility at low cost and could potentially even be used to determine which studies to replicate to optimally allocate limited resources into replications. PMID:26553988

Reproducibility of clinical research in critical care: a scoping review.

PubMed

Niven, Daniel J; McCormick, T Jared; Straus, Sharon E; Hemmelgarn, Brenda R; Jeffs, Lianne; Barnes, Tavish R M; Stelfox, Henry T

2018-02-21

The ability to reproduce experiments is a defining principle of science. Reproducibility 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 reproducibility 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 reproducibility 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

Periodontal repair in dogs: examiner reproducibility in the supraalveolar periodontal defect model.

PubMed

Koo, Ki-Tae; Polimeni, Giuseppe; Albandar, Jasim M; Wikesjö, Ulf M E

2004-06-01

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 reproducibility 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 reproducibility 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 reproducibility was somewhat lower compared to the intra-examiner reproducibility. Nevertheless, the ICCs were generally high (ICC range: 0.6-0.9). Histometric evaluations in the supraalveolar periodontal defect model yield highly reproducible results, in particular when a single examiner performs the histometric measurements, even when the examiner was exposed to limited training.

Massive Data, the Digitization of Science, and Reproducibility of Results

ScienceCinema

Stodden, Victoria

2018-04-27

As the scientific enterprise becomes increasingly computational and data-driven, the nature of the information communicated must change. Without inclusion of the code and data with published computational results, we are engendering a credibility crisis in science. Controversies such as ClimateGate, the microarray-based drug sensitivity clinical trials under investigation at Duke University, and retractions from prominent journals due to unverified code suggest the need for greater transparency in our computational science. In this talk I argue that the scientific method be restored to (1) a focus on error control as central to scientific communication and (2) complete communication of the underlying methodology producing the results, ie. reproducibility. I outline barriers to these goals based on recent survey work (Stodden 2010), and suggest solutions such as the “Reproducible Research Standard” (Stodden 2009), giving open licensing options designed to create an intellectual property framework for scientists consonant with longstanding scientific norms.

Apparently low reproducibility of true differential expression discoveries in microarray studies.

PubMed

Zhang, Min; Yao, Chen; Guo, Zheng; Zou, Jinfeng; Zhang, Lin; Xiao, Hui; Wang, Dong; Yang, Da; Gong, Xue; Zhu, Jing; Li, Yanhui; Li, Xia

2008-09-15

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 reproducibility. 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 reproducibility 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 reproducibility 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 reproducibility of discoveries characterized with correlated molecular changes. Supplementaty information: Supplementary data are available at Bioinformatics online.

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.

Equivalence and test-retest reproducibility of conventional and extended-high-frequency audiometric thresholds obtained using pure-tone and narrow-band-noise stimuli.

PubMed

John, Andrew B; Kreisman, Brian M

2017-09-01

Extended high-frequency (EHF) audiometry is useful for evaluating ototoxic exposures and may relate to speech recognition, localisation and hearing aid benefit. There is a need to determine whether common clinical practice for EHF audiometry using tone and noise stimuli is reliable. We evaluated equivalence and compared test-retest (TRT) reproducibility for audiometric thresholds obtained using pure tones and narrowband noise (NBN) from 0.25 to 16 kHz. Thresholds and test-retest reproducibility for stimuli in the conventional (0.25-6 kHz) and EHF (8-16 kHz) frequency ranges were compared in a repeated-measures design. A total of 70 ears of adults with normal hearing. Thresholds obtained using NBN were significantly lower than thresholds obtained using pure tones from 0.5 to 16 kHz, but not 0.25 kHz. Good TRT reproducibility (within 2 dB) was observed for both stimuli at all frequencies. Responses at the lower limit of the presentation range for NBN centred at 14 and 16 kHz suggest unreliability for NBN as a threshold stimulus at these frequencies. Thresholds in the conventional and EHF ranges showed good test-retest reproducibility, but differed between stimulus types. Care should be taken when comparing pure-tone thresholds with NBN thresholds especially at these frequencies.

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

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

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

[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).

Producing high-quality slash pine seeds

Treesearch

James Barnett; Sue Varela

2003-01-01

Slash pine is a desirable species. It serves many purposes and is well adapted to poorly drained flatwoods and seasonally flooded areas along the lower Coastal Plain of the Southeastern US. The use of high-quality seeds has been shown to produce uniform seedlings for outplanting, which is key to silvicultural success along the Coastal Plain and elsewhere. We present...

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.

A Novel Highly Reproducible and Lethal Nonhuman Primate Model for Orthopox Virus Infection

PubMed Central

Kramski, Marit; Mätz-Rensing, Kerstin; Stahl-Hennig, Christiane; Kaup, Franz-Josef; Nitsche, Andreas; Pauli, Georg; Ellerbrok, Heinz

2010-01-01

The intentional re-introduction of Variola virus (VARV), the agent of smallpox, into the human population is of great concern due its bio-terroristic potential. Moreover, zoonotic infections with Cowpox (CPXV) and Monkeypox virus (MPXV) cause severe diseases in humans. Smallpox vaccines presently available can have severe adverse effects that are no longer acceptable. The efficacy and safety of new vaccines and antiviral drugs for use in humans can only be demonstrated in animal models. The existing nonhuman primate models, using VARV and MPXV, need very high viral doses that have to be applied intravenously or intratracheally to induce a lethal infection in macaques. To overcome these drawbacks, the infectivity and pathogenicity of a particular CPXV was evaluated in the common marmoset (Callithrix jacchus). A CPXV named calpox virus was isolated from a lethal orthopox virus (OPV) outbreak in New World monkeys. We demonstrated that marmosets infected with calpox virus, not only via the intravenous but also the intranasal route, reproducibly develop symptoms resembling smallpox in humans. Infected animals died within 1–3 days after onset of symptoms, even when very low infectious viral doses of 5×102 pfu were applied intranasally. Infectious virus was demonstrated in blood, saliva and all organs analyzed. We present the first characterization of a new OPV infection model inducing a disease in common marmosets comparable to smallpox in humans. Intranasal virus inoculation mimicking the natural route of smallpox infection led to reproducible infection. In vivo titration resulted in an MID50 (minimal monkey infectious dose 50%) of 8.3×102 pfu of calpox virus which is approximately 10,000-fold lower than MPXV and VARV doses applied in the macaque models. Therefore, the calpox virus/marmoset model is a suitable nonhuman primate model for the validation of vaccines and antiviral drugs. Furthermore, this model can help study mechanisms of OPV pathogenesis. PMID

HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient

PubMed Central

Yang, Tao; Zhang, Feipeng; Yardımcı, Galip Gürkan; Song, Fan; Hardison, Ross C.; Noble, William Stafford; Yue, Feng; Li, Qunhua

2017-01-01

Hi-C is a powerful technology for studying genome-wide chromatin interactions. However, current methods for assessing Hi-C data reproducibility can produce misleading results because they ignore spatial features in Hi-C data, such as domain structure and distance dependence. We present HiCRep, a framework for assessing the reproducibility of Hi-C data that systematically accounts for these features. In particular, we introduce a novel similarity measure, the stratum adjusted correlation coefficient (SCC), for quantifying the similarity between Hi-C interaction matrices. Not only does it provide a statistically sound and reliable evaluation of reproducibility, SCC can also be used to quantify differences between Hi-C contact matrices and to determine the optimal sequencing depth for a desired resolution. The measure consistently shows higher accuracy than existing approaches in distinguishing subtle differences in reproducibility and depicting interrelationships of cell lineages. The proposed measure is straightforward to interpret and easy to compute, making it well-suited for providing standardized, interpretable, automatable, and scalable quality control. The freely available R package HiCRep implements our approach. PMID:28855260

[Tobacco--a highly efficient producer of vaccines].

PubMed

Budzianowski, Jaromir

2010-01-01

Along with the depreciation of tobacco as a source of nicotine-containing commercial products, the increase of its appreciation as a potential producer of recombinant therapeutical proteins can be observed. Two species of tobacco--Nicotiana tabacum L. and N. benthamiana are easily grown by well established methods of field or green-house cultivation or cell culture, yield high biomass and soluble protein content, can be easily transformed by several methods and are not food for humans or feed for animals. Expression of foreign proteins, including vaccines, can be achieved in those plants either through stable transformation of nuclear or plastid (chloroplast) genomes or by transient transformation using infection with plant virus or bacteria--Agrobacterium tumefaciens (agroinfiltration). The most advanced mode of agrofiltration termed magnifection, which combines benefits of virus and Agrobacterium and depends on using Agrobacterium with viral pro-vectors, enables high-yield and rapid expression of therapeutical proteins, even in a few days, and can be employed on an industrial scale. Expression of many antigenic proteins, which may serve as antiviral, antibacterial, antiprotozoan and anticancer vaccines, and additionally a few autoantigens designed for the treatment of autoimunogenic diseases, like diabetes, have been achieved in tobacco. To date, a vaccine against Newcastle virus disease in poultry produced by tobacco cell culture has been approved for commercial application and several other vaccines are in advanced stage of development. The possibility of a high-level production of vaccines in tobacco against pandemic influenza or anthrax and plague due to a bioterroristic attack, as well as of individualised anticancer vaccines against non-Hodgkin's lymphoma (NHL) in a much shorter period of time than by traditional methods became realistic and hence caused increased interest in tobacco as a high-efficient producer of vaccines not only of specialistic

Cervical vertebrae maturation method morphologic criteria: poor reproducibility.

PubMed

Nestman, Trenton S; Marshall, Steven D; Qian, Fang; Holton, Nathan; Franciscus, Robert G; Southard, Thomas E

2011-08-01

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 reproducibility of the CVM method, and we recently established that the reproducibility of the CVM method was poor when these potential errors were eliminated. The purpose of this study was to further investigate the reproducibility 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 reproducibility 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

Reproducibility of abdominal fat assessment by ultrasound and computed tomography.

PubMed

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

2017-01-01

To test the accuracy and reproducibility 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 reproducibility of ultrasound and CT for the assessment of abdominal fat and found that CT measurements of abdominal fat showed greater reproducibility, 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 reproducibility.

Sandwich ELISA Microarrays: Generating Reliable and Reproducible Assays for High-Throughput Screens

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

Gonzalez, Rachel M.; Varnum, Susan M.; Zangar, Richard C.

The sandwich ELISA microarray is a powerful screening tool in biomarker discovery and validation due to its ability to simultaneously probe for multiple proteins in a miniaturized assay. The technical challenges of generating and processing the arrays are numerous. However, careful attention to possible pitfalls in the development of your antibody microarray assay can overcome these challenges. In this chapter, we describe in detail the steps that are involved in generating a reliable and reproducible sandwich ELISA microarray assay.

An attempt to reproduce high burn-up structure by ion irradiation of SIMFUEL

NASA Astrophysics Data System (ADS)

Baranov, V. G.; Lunev, A. V.; Reutov, V. F.; Tenishev, A. V.; Isaenkova, M. G.; Khlunov, A. V.

2014-09-01

Experiments in IC-100 and U-400 cyclotrons were conducted with SIMFUEL pellets (11.47 wt.% of fission products simulators) to reproduce some aspects of the long-term irradiation conditions in epithermal reactors. Pellets were irradiated with Xe16+, Xe24+ and He+ at energies ranging from 20 keV (He+) to 320 keV (Xe16+) and 1-90 MeV (Xe24+). Some samples were subsequently annealed to obtain larger grain sizes and to study defects recovery. The major microstructural changes consisted in grain sub-division observed on SEM and AFM images and change in composition registered by EPMA (pellets irradiated with 1-90 MeV Xe24+ ions at fluence of 5 × 1015 cm-2). Lattice distortion and increase in dislocation density is also noted according to X-ray data. At low energies and high fluences formation of bubbles (20 keV He+ at 5.5 × 1017 cm-2) was observed. Grain sub-division exhibits full coverage of the grain body and preservation of former grain boundaries. The size of sub-grains depends on local dislocation density and changes from 200 nm to 400 nm along the irradiated surface. Beneath it the size ranges from 150 to 600 nm. Sub-grains are not observed in samples irradiated by low-energy ions even at high dislocation densities.

Fabrication of reproducible, integration-compatible hybrid molecular/si electronics.

PubMed

Yu, Xi; Lovrinčić, Robert; Kraynis, Olga; Man, Gabriel; Ely, Tal; Zohar, Arava; Toledano, Tal; Cahen, David; Vilan, Ayelet

2014-12-29

Reproducible 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 reproducible with a standard deviation in log(J) of 0.2 over a junction diameter change from 3 to 100 μm. Reproducibility 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.

High-resolution 3D coronary vessel wall imaging with near 100% respiratory efficiency using epicardial fat tracking: reproducibility and comparison with standard methods.

PubMed

Scott, Andrew D; Keegan, Jennifer; Firmin, David N

2011-01-01

To quantitatively assess the performance and reproducibility of 3D spiral coronary artery wall imaging with beat-to-beat respiratory-motion-correction (B2B-RMC) compared to navigator gated 2D spiral and turbo-spin-echo (TSE) acquisitions. High-resolution (0.7 × 0.7 mm) cross-sectional right coronary wall acquisitions were performed in 10 subjects using four techniques (B2B-RMC 3D spiral with alternate (2RR) and single (1RR) R-wave gating, navigator-gated 2D spiral (2RR) and navigator-gated 2D TSE (2RR)) on two occasions. Wall thickness measurements were compared with repeated measures analysis of variance (ANOVA). Reproducibility was assessed with the intraclass correlation coefficient (ICC). In all, 91% (73/80) of acquisitions were successful (failures: four TSE, two 3D spiral (1RR) and one 3D spiral (2RR)). Respiratory efficiency of the B2B-RMC was less variable and substantially higher than for navigator gating (99.6 ± 1.2% vs. 39.0 ± 7.5%, P < 0.0001). Coronary wall thicknesses (± standard deviation [SD]) were not significantly different: 1.10 ± 0.14 mm (3D spiral (2RR)), 1.20 ± 0.16 mm (3D spiral (1RR)), 1.14 ± 0.15 mm (2D spiral), and 1.21 ± 0.17 mm (TSE). Wall thickness reproducibility ranged from good (ICC = 0.65, 3D spiral (1RR)) to excellent (ICC = 0.87, 3D spiral (2RR)). High-resolution 3D spiral imaging with B2B-RMC permits coronary vessel wall assessment over multiple thin contiguous slices in a clinically feasible duration. Excellent reproducibility of the technique potentially enables studies of disease progression/regression. Copyright © 2010 Wiley-Liss, Inc.

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

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...

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...

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...

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...

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...

Reproducibility of the spectral components of the electroencephalogram during driver fatigue.

PubMed

Lal, Saroj K L; Craig, Ashley

2005-02-01

To date, no study has tested the reproducibility 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 reproducible. 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 reproducibility 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 reproducibility 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.

Maximizing the quantitative accuracy and reproducibility of Förster resonance energy transfer measurement for screening by high throughput widefield microscopy

PubMed Central

Schaufele, Fred

2013-01-01

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 accurate and reproducible 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 reproducibility 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. Accurate calculation of FRET is realized even from images in which a non-flat background is 10-fold higher than the signal. PMID:23927839

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

PubMed Central

Afgan, Enis; Baker, Dannon; van den Beek, Marius; Blankenberg, Daniel; Bouvier, Dave; Čech, Martin; Chilton, John; Clements, Dave; Coraor, Nate; Eberhard, Carl; Grüning, Björn; Guerler, Aysam; Hillman-Jackson, Jennifer; Von Kuster, Greg; Rasche, Eric; Soranzo, Nicola; Turaga, Nitesh; Taylor, James; Nekrutenko, Anton; Goecks, Jeremy

2016-01-01

High-throughput data production technologies, particularly ‘next-generation’ DNA sequencing, have ushered in widespread and disruptive changes to biomedical research. Making sense of the large datasets produced by these technologies requires sophisticated statistical and computational methods, as well as substantial computational power. This has led to an acute crisis in life sciences, as researchers without informatics training attempt to perform computation-dependent analyses. Since 2005, the Galaxy project has worked to address this problem by providing a framework that makes advanced computational tools usable by non experts. Galaxy seeks to make data-intensive research more accessible, transparent and reproducible by providing a Web-based environment in which users can perform computational analyses and have all of the details automatically tracked for later inspection, publication, or reuse. In this report we highlight recently added features enabling biomedical analyses on a large scale. PMID:27137889

Reproducibility of airway luminal size in asthma measured by HRCT.

PubMed

Brown, Robert H; Henderson, Robert J; Sugar, Elizabeth A; Holbrook, Janet T; Wise, Robert A

2017-10-01

Brown RH, Henderson RJ, Sugar EA, Holbrook JT, Wise RA, on behalf of the American Lung Association Airways Clinical Research Centers. Reproducibility 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 reproducibility. 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 reproducibility 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 reproducibly 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

HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient.

PubMed

Yang, Tao; Zhang, Feipeng; Yardımcı, Galip Gürkan; Song, Fan; Hardison, Ross C; Noble, William Stafford; Yue, Feng; Li, Qunhua

2017-11-01

Hi-C is a powerful technology for studying genome-wide chromatin interactions. However, current methods for assessing Hi-C data reproducibility can produce misleading results because they ignore spatial features in Hi-C data, such as domain structure and distance dependence. We present HiCRep, a framework for assessing the reproducibility of Hi-C data that systematically accounts for these features. In particular, we introduce a novel similarity measure, the stratum adjusted correlation coefficient (SCC), for quantifying the similarity between Hi-C interaction matrices. Not only does it provide a statistically sound and reliable evaluation of reproducibility, SCC can also be used to quantify differences between Hi-C contact matrices and to determine the optimal sequencing depth for a desired resolution. The measure consistently shows higher accuracy than existing approaches in distinguishing subtle differences in reproducibility and depicting interrelationships of cell lineages. The proposed measure is straightforward to interpret and easy to compute, making it well-suited for providing standardized, interpretable, automatable, and scalable quality control. The freely available R package HiCRep implements our approach. © 2017 Yang et al.; Published by Cold Spring Harbor Laboratory Press.

Highly reproducible laser beam scanning device for an internal source laser desorption microprobe Fourier transform mass spectrometer

NASA Astrophysics Data System (ADS)

Scott, Jill R.; Tremblay, Paul L.

2002-03-01

Traditionally, mass spectrometry has relied on manipulating the sample target to provide scanning capabilities for laser desorption microprobes. This has been problematic for an internal source laser desorption Fourier transform mass spectrometer (LD-FTMS) because of the high magnetic field (7 Tesla) and geometric constraints of the superconducting magnet bore. To overcome these limitations, we have implemented a unique external laser scanning mechanism for an internal source LD-FTMS. This mechanism provides adjustable resolution enhancement so that the spatial resolution at the target is not limited to that of the stepper motors at the light source (˜5 μm/step). The spatial resolution is now limited by the practical optical diffraction limit of the final focusing lens. The scanning mechanism employs a virtual source that is wavelength independent up to the final focusing lens, which can be controlled remotely to account for focal length dependence on wavelength. A binary index provides an automatic alignment feature. The virtual source is located ˜9 ft from the sample; therefore, it is completely outside of the vacuum system and beyond the 50 G line of the fringing magnetic field. To eliminate reproducibility problems associated with vacuum pump vibrations, we have taken advantage of the magnetic field inherent to the FTMS to utilize Lenz's law for vibrational dampening. The LD-FTMS microprobe has exceptional reproducibility, which enables successive mapping sequences for depth-profiling studies.

Reproducing a Prospective Clinical Study as a Computational Retrospective Study in MIMIC-II.

PubMed

Kury, Fabrício S P; Huser, Vojtech; Cimino, James J

2015-01-01

In this paper we sought to reproduce, as a computational retrospective study in an EHR database (MIMIC-II), a recent large prospective clinical study: the 2013 publication, by the Japanese Association for Acute Medicine (JAAM), about disseminated intravascular coagulation, in the journal Critical Care (PMID: 23787004). We designed in SQL and Java a set of electronic phenotypes that reproduced the study's data sampling, and used R to perform the same statistical inference procedures. All produced source code is available online at https://github.com/fabkury/paamia2015. Our program identified 2,257 eligible patients in MIMIC-II, and the results remarkably agreed with the prospective study. A minority of the needed data elements was not found in MIMIC-II, and statistically significant inferences were possible in the majority of the cases.

Validity and reproducibility of electrical impedance tomography for measurement of calf blood flow in healthy subjects.

PubMed

Vonk Noordegraaf, A; Kunst, P W; Janse, A; Smulders, R A; Heethaar, R M; Postmus, P E; Faes, T J; de Vries, P M

1997-03-01

The Sheffield electrical impedance tomography; (EIT) system produces images of changes in the distribution of resistivity within tissue. The paper reports on the application of electrical impedance tomography in monitoring volume changes in the limb during venous occlusion. The aim of the study is to assess the feasibility, reproducibility and validity of calf blood flow measurements by EIT. In 14 healthy volunteers calf blood flow is compared, as determined in a calf segment by strain-gauge plethysmography (SGP), with the impedance changes measured by EIT during rest and post-ischaemic hyperaemia. The measurements are repeated to assess reproducibility. The reproducibility for the EIT, assessed from the repeated measurements and expressed as a reproducibility coefficient, is 0.88 during rest and 0.89 during hyperaemia. The reproducibility coefficient for SGP data is 0.83 at rest and 0.67 during hyperaemia. Flow measurements, assessed by means of two methods, correlate well at rest (r = 0.89), but only moderately during hyperaemia (r = 0.51). The correlation coefficient for the pooled flow measurements is 0.98. It is concluded that EIT is a valid and reliable method for assessing blood flow in the limb. Possible applications of EIT in localising fluid changes are discussed.

Reproducibility of peripapillary retinal nerve fiber layer thickness with spectral domain cirrus high-definition optical coherence tomography in normal eyes.

PubMed

Hong, Samin; Kim, Chan Yun; Lee, Won Seok; Seong, Gong Je

2010-01-01

To assess the reproducibility of the new spectral domain Cirrus high-definition optical coherence tomography (HD-OCT; Carl Zeiss Meditec, Dublin, CA, USA) for analysis of peripapillary retinal nerve fiber layer (RNFL) thickness in healthy eyes. Thirty healthy Korean volunteers were enrolled. Three optic disc cube 200 x 200 Cirrus HD-OCT scans were taken on the same day in discontinuous sessions by the same operator without using the repeat scan function. The reproducibility of the calculated RNFL thickness and probability code were determined by the intraclass correlation coefficient (ICC), coefficient of variation (CV), test-retest variability, and Fleiss' generalized kappa (kappa). Thirty-six eyes were analyzed. For average RNFL thickness, the ICC was 0.970, CV was 2.38%, and test-retest variability was 4.5 microm. For all quadrants except the nasal, ICCs were 0.972 or higher and CVs were 4.26% or less. Overall test-retest variability ranged from 5.8 to 8.1 microm. The kappa value of probability codes for average RNFL thickness was 0.690. The kappa values of quadrants and clock-hour sectors were lower in the nasal areas than in other areas. The reproducibility of Cirrus HD-OCT to analyze peripapillary RNFL thickness in healthy eyes was excellent compared with the previous reports for time domain Stratus OCT. For the calculated RNFL thickness and probability code, variability was relatively higher in the nasal area, and more careful analyses are needed.

Reproducibility of abdominal fat assessment by ultrasound and computed tomography

PubMed Central

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

2017-01-01

Objective: To test the accuracy and reproducibility 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 reproducibility of ultrasound and CT for the assessment of abdominal fat and found that CT measurements of abdominal fat showed greater reproducibility, 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 reproducibility. PMID:28670024

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.

Community-based Approaches to Improving Accuracy, Precision, and Reproducibility in U-Pb and U-Th Geochronology

NASA Astrophysics Data System (ADS)

McLean, N. M.; Condon, D. J.; Bowring, S. A.; Schoene, B.; Dutton, A.; Rubin, K. H.

2015-12-01

The last two decades have seen a grassroots effort by the international geochronology community to "calibrate Earth history through teamwork and cooperation," both as part of the EARTHTIME initiative and though several daughter projects with similar goals. Its mission originally challenged laboratories "to produce temporal constraints with uncertainties approaching 0.1% of the radioisotopic ages," but EARTHTIME has since exceeded its charge in many ways. Both the U-Pb and Ar-Ar chronometers first considered for high-precision timescale calibration now regularly produce dates at the sub-per mil level thanks to instrumentation, laboratory, and software advances. At the same time new isotope systems, including U-Th dating of carbonates, have developed comparable precision. But the larger, inter-related scientific challenges envisioned at EARTHTIME's inception remain - for instance, precisely calibrating the global geologic timescale, estimating rates of change around major climatic perturbations, and understanding evolutionary rates through time - and increasingly require that data from multiple geochronometers be combined. To solve these problems, the next two decades of uranium-daughter geochronology will require further advances in accuracy, precision, and reproducibility. The U-Th system has much in common with U-Pb, in that both parent and daughter isotopes are solids that can easily be weighed and dissolved in acid, and have well-characterized reference materials certified for isotopic composition and/or purity. For U-Pb, improving lab-to-lab reproducibility has entailed dissolving precisely weighed U and Pb metals of known purity and isotopic composition together to make gravimetric solutions, then using these to calibrate widely distributed tracers composed of artificial U and Pb isotopes. To mimic laboratory measurements, naturally occurring U and Pb isotopes were also mixed in proportions to mimic samples of three different ages, to be run as internal

Microbial community development in a dynamic gut model is reproducible, colon region specific, and selective for Bacteroidetes and Clostridium cluster IX.

PubMed

Van den Abbeele, Pieter; Grootaert, Charlotte; Marzorati, Massimo; Possemiers, Sam; Verstraete, Willy; Gérard, Philippe; Rabot, Sylvie; Bruneau, Aurélia; El Aidy, Sahar; Derrien, Muriel; Zoetendal, Erwin; Kleerebezem, Michiel; Smidt, Hauke; Van de Wiele, Tom

2010-08-01

Dynamic, multicompartment in vitro gastrointestinal simulators are often used to monitor gut microbial dynamics and activity. These reactors need to harbor a microbial community that is stable upon inoculation, colon region specific, and relevant to in vivo conditions. Together with the reproducibility of the colonization process, these criteria are often overlooked when the modulatory properties from different treatments are compared. We therefore investigated the microbial colonization process in two identical simulators of the human intestinal microbial ecosystem (SHIME), simultaneously inoculated with the same human fecal microbiota with a high-resolution phylogenetic microarray: the human intestinal tract chip (HITChip). Following inoculation of the in vitro colon compartments, microbial community composition reached steady state after 2 weeks, whereas 3 weeks were required to reach functional stability. This dynamic colonization process was reproducible in both SHIME units and resulted in highly diverse microbial communities which were colon region specific, with the proximal regions harboring saccharolytic microbes (e.g., Bacteroides spp. and Eubacterium spp.) and the distal regions harboring mucin-degrading microbes (e.g., Akkermansia spp.). Importantly, the shift from an in vivo to an in vitro environment resulted in an increased Bacteroidetes/Firmicutes ratio, whereas Clostridium cluster IX (propionate producers) was enriched compared to clusters IV and XIVa (butyrate producers). This was supported by proportionally higher in vitro propionate concentrations. In conclusion, high-resolution analysis of in vitro-cultured gut microbiota offers new insight on the microbial colonization process and indicates the importance of digestive parameters that may be crucial in the development of new in vitro models.

Junior High Students Produce Daily TV Today Program

ERIC Educational Resources Information Center

Worzala, Louise Hicks

1976-01-01

Describes the seven-minute, closed-circuit television program for 500 students and teachers which is entirely planned and produced by an eighth grade broadcast journalism class at a McHenry (Illinois) junior high school. (JM)

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.

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

Method for producing high quality thin layer films on substrates

DOEpatents

Strongin, M.; Ruckman, M.; Strongin, D.

1994-04-26

A method for producing high quality, thin layer films of inorganic compounds upon the surface of a substrate is disclosed. The method involves condensing a mixture of preselected molecular precursors on the surface of a substrate and subsequently inducing the formation of reactive species using high energy photon or charged particle irradiation. The reactive species react with one another to produce a film of the desired compound upon the surface of the substrate. 4 figures.

Method for producing high quality thin layer films on substrates

DOEpatents

Strongin, Myron; Ruckman, Mark; Strongin, Daniel

1994-01-01

A method for producing high quality, thin layer films of inorganic compounds upon the surface of a substrate is disclosed. The method involves condensing a mixture of preselected molecular precursors on the surface of a substrate and subsequently inducing the formation of reactive species using high energy photon or charged particle irradiation. The reactive species react with one another to produce a film of the desired compound upon the surface of the substrate.

Molecular crowding of collagen: a pathway to produce highly-organized collagenous structures.

PubMed

Saeidi, Nima; Karmelek, Kathryn P; Paten, Jeffrey A; Zareian, Ramin; DiMasi, Elaine; Ruberti, Jeffrey W

2012-10-01

Collagen in vertebrate animals is often arranged in alternating lamellae or in bundles of aligned fibrils which are designed to withstand in vivo mechanical loads. The formation of these organized structures is thought to result from a complex, large-area integration of individual cell motion and locally-controlled synthesis of fibrillar arrays via cell-surface fibripositors (direct matrix printing). The difficulty of reproducing such a process in vitro has prevented tissue engineers from constructing clinically useful load-bearing connective tissue directly from collagen. However, we and others have taken the view that long-range organizational information is potentially encoded into the structure of the collagen molecule itself, allowing the control of fibril organization to extend far from cell (or bounding) surfaces. We here demonstrate a simple, fast, cell-free method capable of producing highly-organized, anistropic collagen fibrillar lamellae de novo which persist over relatively long-distances (tens to hundreds of microns). Our approach to nanoscale organizational control takes advantage of the intrinsic physiochemical properties of collagen molecules by inducing collagen association through molecular crowding and geometric confinement. To mimic biological tissues which comprise planar, aligned collagen lamellae (e.g. cornea, lamellar bone or annulus fibrosus), type I collagen was confined to a thin, planar geometry, concentrated through molecular crowding and polymerized. The resulting fibrillar lamellae show a striking resemblance to native load-bearing lamellae in that the fibrils are small, generally aligned in the plane of the confining space and change direction en masse throughout the thickness of the construct. The process of organizational control is consistent with embryonic development where the bounded planar cell sheets produced by fibroblasts suggest a similar confinement/concentration strategy. Such a simple approach to nanoscale

The flux qubit revisited to enhance coherence and reproducibility

PubMed Central

Yan, Fei; Gustavsson, Simon; Kamal, Archana; Birenbaum, Jeffrey; Sears, Adam P; Hover, David; Gudmundsen, Ted J.; Rosenberg, Danna; Samach, Gabriel; Weber, S; Yoder, Jonilyn L.; Orlando, Terry P.; Clarke, John; Kerman, Andrew J.; Oliver, William D.

2016-01-01

The scalable application of quantum information science will stand on reproducible and controllable high-coherence quantum bits (qubits). Here, we revisit the design and fabrication of the superconducting flux qubit, achieving a planar device with broad-frequency tunability, strong anharmonicity, high reproducibility and relaxation times in excess of 40 μs at its flux-insensitive point. Qubit relaxation times T1 across 22 qubits are consistently matched with a single model involving resonator loss, ohmic charge noise and 1/f-flux noise, a noise source previously considered primarily in the context of dephasing. We furthermore demonstrate that qubit dephasing at the flux-insensitive point is dominated by residual thermal-photons in the readout resonator. The resulting photon shot noise is mitigated using a dynamical decoupling protocol, resulting in T2≈85 μs, approximately the 2T1 limit. In addition to realizing an improved flux qubit, our results uniquely identify photon shot noise as limiting T2 in contemporary qubits based on transverse qubit–resonator interaction. PMID:27808092

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.

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.

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.

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.

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.

"People in Stockholm Are Smarter than Countryside Folks"--Reproducing Urban and Rural Imaginaries in Film and Life

ERIC Educational Resources Information Center

Eriksson, Madeleine

2010-01-01

This article explores the celebrated film "The Hunters" (Swedish title: "Jagarna") within the context of the discourse of "Internal Orientalism." By juxtaposing a contemporary Swedish film with historical accounts and contemporary news media, I demonstrate how the film reworks and (re)produces representations of the…

Empirical evaluation of cross-site reproducibility in radiomic features for characterizing prostate MRI

NASA Astrophysics Data System (ADS)

Chirra, Prathyush; Leo, Patrick; Yim, Michael; Bloch, B. Nicolas; Rastinehad, Ardeshir R.; Purysko, Andrei; Rosen, Mark; Madabhushi, Anant; Viswanath, Satish

2018-02-01

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 reproducible 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 reproducibility 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 reproducible they were within a relatively homogeneous non-tumor tissue region; using 2 different measures of reproducibility: Multivariate Coefficient of Variation and Instability Score. Our results demonstrated that Haralick features were most reproducible between all 4 sites. By comparison, Laws features were among the least reproducible between sites, as well as performing highly variably across their entire parameter space. Similarly, the Gabor feature family demonstrated good cross-site reproducibility, 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 reproducible enough for use within radiomics-based machine learning classifier schemes.

Optogenetic stimulation of infralimbic PFC reproduces ketamine's rapid and sustained antidepressant actions.

PubMed

Fuchikami, Manabu; Thomas, Alexandra; Liu, Rongjian; Wohleb, Eric S; Land, Benjamin B; DiLeone, Ralph J; Aghajanian, George K; Duman, Ronald S

2015-06-30

Ketamine produces rapid and sustained antidepressant actions in depressed patients, but the precise cellular mechanisms underlying these effects have not been identified. Here we determined if modulation of neuronal activity in the infralimbic prefrontal cortex (IL-PFC) underlies the antidepressant and anxiolytic actions of ketamine. We found that neuronal inactivation of the IL-PFC completely blocked the antidepressant and anxiolytic effects of systemic ketamine in rodent models and that ketamine microinfusion into IL-PFC reproduced these behavioral actions of systemic ketamine. We also found that optogenetic stimulation of the IL-PFC produced rapid and long-lasting antidepressant and anxiolytic effects and that these effects are associated with increased number and function of spine synapses of layer V pyramidal neurons. The results demonstrate that ketamine infusions or optogenetic stimulation of IL-PFC are sufficient to produce long-lasting antidepressant behavioral and synaptic responses similar to the effects of systemic ketamine administration.

Reproducibility and validity of the Nintendo Wii Balance Board for measuring shoulder sensorimotor control in prone lying.

PubMed

Eshoj, H; Juul-Kristensen, Birgit; Jørgensen, Rene Gam Bender; Søgaard, Karen

2017-02-01

For the lower limbs, the Nintendo Wii Balance Board (NWBB) has been widely used to measure postural control. However, this has not been performed for upper limb measurements. Further, the NWBB has shown to produce more background noise with decreasing loads, which may be of concern when used for upper limb testing. The aim was to investigate reproducibility and validity of the NWBB. A test-retest design was performed with 68 subjects completing three different prone lying, upper limb weight-bearing balance tasks on a NWBB: two-arms, eyes closed (1) one-arm, non-dominant/non-injured (2) and one-arm, dominant/injured (3). Each task was repeated three times over the course of two test sessions with a 30-min break in between. Further, the level of background noise from a NWBB was compared with a force platform through systematic loading of both boards with increasing deadweights ranging from 5 to 90kg. Test-retest reproducibility was high with ICCs ranging from 0.95 to 0.97 (95% CI 0.92 to 0.98). However, systematic bias and tendencies for funnel effects in the Bland Altman plots for both one-armed tests were present. The concurrent validity of the NWBB was low (CCC 0.17 (95% CI 0.12-0.22)) due to large differences between the NWBB and force platform in noise sensitivity at low deadweights (especially below 50kg). The NWBB prone lying, shoulder sensorimotor control test was highly reproducible. Though, concurrent validity of the NWBB was poor compared to a force platform. Further investigation of the impact of the background noise, especially at low loads, is needed. Copyright © 2016 Elsevier B.V. All rights reserved.

MetaboAnalystR: an R package for flexible and reproducible analysis of metabolomics data.

PubMed

Chong, Jasmine; Xia, Jianguo

2018-06-28

The MetaboAnalyst web application has been widely used for metabolomics data analysis and interpretation. Despite its user-friendliness, the web interface has presented its inherent limitations (especially for advanced users) with regard to flexibility in creating customized workflow, support for reproducible analysis, and capacity in dealing with large data. To address these limitations, we have developed a companion R package (MetaboAnalystR) based on the R code base of the web server. The package has been thoroughly tested to ensure that the same R commands will produce identical results from both interfaces. MetaboAnalystR complements the MetaboAnalyst web server to facilitate transparent, flexible and reproducible analysis of metabolomics data. MetaboAnalystR is freely available from https://github.com/xia-lab/MetaboAnalystR. Supplementary data are available at Bioinformatics online.

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

PubMed

Jurj, Adriana L; Wen, Wanqing; Xiang, Yong-Bing; Matthews, Charles E; Liu, Dake; Zheng, Wei; Shu, Xiao-Ou

2007-05-15

Reproducibility and validity of the physical activity questionnaire (PAQ) used in the Shanghai Men's Health Study (2003-2006, People's Republic of China) was evaluated in a random sample of 196 participants aged 40-74 years. Participants completed a PAQ at baseline and again 1 year later, 12 monthly 7-day physical activity recalls, and four quarterly 1-week physical activity logs. Reproducibility was evaluated by using the two PAQs and validity by comparing the PAQs with 1-year averages of the two criterion measures: 7-day physical activity recall and physical activity log. The PAQ had moderate to high reproducibility for measuring adult exercise participation (kappa = 0.60) and energy expenditure (r(s) = 0.68), nonexercise activities (correlation coefficients = 0.42-0.68), and total daily energy expenditure (r(s) = 0.68, kappa(quartiles) = 0.47). Correlations between the PAQ and criterion measures of adult exercise were 0.45 (7-day physical activity recall) and 0.51 (physical activity log) for the first PAQ and 0.62 (7-day physical activity recall) and 0.71 (physical activity log) for the second PAQ. Correlations between PAQ nonexercise activities and the physical activity log and 7-day physical activity recall were 0.31-0.86. Correlations for total energy expenditure were high (0.62-0.77). Results indicate that the Shanghai Men's Health Study PAQ has reasonable reproducibility and validity for classifying men by their level of exercise and nonexercise activities in this cohort.

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.

Reproducibility and Knowledge Capture Architecture for the NASA Earth Exchange (NEX)

NASA Astrophysics Data System (ADS)

Votava, P.; Michaelis, A.; Nemani, R. R.

2015-12-01

NASA Earth Exchange (NEX) is a data, supercomputing and knowledge collaboratory that houses NASA satellite, climate and ancillary data where a focused community can come together to address large-scale challenges in Earth sciences. As NEX has been growing into a platform for analysis, experiments and production of data on the order of petabytes in volume, it has been increasingly important to enable users to easily retrace their steps, identify what datasets were produced by which process or chain of processes, and give them ability to readily reproduce their results. This can be a tedious and difficult task even for a small project, but is almost impossible on large processing pipelines. For example, the NEX Landsat pipeline is deployed to process hundreds of thousands of Landsat scenes in a non-linear production workflow with many-to-many mappings of files between 40 separate processing stages where over 100 million processes get executed. At this scale it is almost impossible to easily examine the entire provenance of each file, let alone easily reproduce it. We have developed an initial solution for the NEX system - a transparent knowledge capture and reproducibility architecture that does not require any special code instrumentation and other actions on user's part. Users can automatically capture their work through a transparent provenance tracking system and the information can subsequently be queried and/or converted into workflows. The provenance information is streamed to a MongoDB document store and a subset is converted to an RDF format and inserted into our triple-store. The triple-store already contains semantic information about other aspects of the NEX system and adding provenance enhances the ability to relate workflows and data to users, locations, projects and other NEX concepts that can be queried in a standard way. The provenance system has the ability to track data throughout NEX and across number of executions and can recreate and re

Peripapillary nerve fiber layer thickness measurement reproducibility using optical coherence tomography.

PubMed

Villain, Max A; Greenfield, David S

2003-01-01

To assess reproducibility of quadrantic and clock hour sectors of retinal nerve fiber layer thickness in normal eyes using optical coherence tomography. Normal eyes of healthy volunteers meeting eligibility criteria were imaged by two inexperienced operators. Six 360 degrees circular scans with a diameter of 3.4 mm centered on the optic disc were obtained during each scanning session, and a baseline image was formed using 3 high-quality images defined by the software. Images were obtained on three different days within a 4-week period. Variance and coefficient of variation (CV) were calculated for quadrantic and retinal nerve fiber layer clock hour sectors obtained from the baseline image. Five normal eyes were scanned. Intraoperator reproducibility was high. The mean (+/- SD) CV for total retinal nerve fiber layer thickness was 5.3 +/- 3.82% and 4.33 +/- 3.7% for operators 1 and 2, respectively. Interoperator reproducibility was good with statistically similar variance for all quadrantic and clock hour retinal nerve fiber layer parameters (P = .42 to .99). The nasal retinal nerve fiber layer was the most variable sector for both operators (mean CV: 10.42% and 7.83% for operators 1 and 2, respectively). Differences in mean total, nasal, temporal, and superior retinal nerve fiber layer thickness were not statistically significant between operators for all eyes; however, for inferior retinal nerve fiber layer thickness, there was a significant (P = .0007) difference between operators in one eye. Peripapillary retinal nerve fiber layer thickness assessments using optical coherence tomography have good intraoperator and interoperator reproducibility. Inexperienced operators can generate useful measurement data with acceptable levels of variance.

Modernized Approach for Generating Reproducible Heterogeneity Using Transmitted-Light for Flow Visualization Experiments

NASA Astrophysics Data System (ADS)

Jones, A. A.; Holt, R. M.

2017-12-01

Image capturing in flow experiments has been used for fluid mechanics research since the early 1970s. Interactions of fluid flow between the vadose zone and permanent water table are of great interest because this zone is responsible for all recharge waters, pollutant transport and irrigation efficiency for agriculture. Griffith, et al. (2011) developed an approach where constructed reproducible "geologically realistic" sand configurations are deposited in sandfilled experimental chambers for light-transmitted flow visualization experiments. This method creates reproducible, reverse graded, layered (stratified) thin-slab sand chambers for point source experiments visualizing multiphase flow through porous media. Reverse-graded stratification of sand chambers mimic many naturally occurring sedimentary deposits. Sandfilled chambers use light as nonintrusive tools for measuring water saturation in two-dimensions (2-D). Homogeneous and heterogeneous sand configurations can be produced to visualize the complex physics of the unsaturated zone. The experimental procedure developed by Griffith, et al. (2011) was designed using now outdated and obsolete equipment. We have modernized this approach with new Parker Deadel linear actuator and programed projects/code for multiple configurations. We have also updated the Roper CCD software and image processing software with the latest in industry standards. Modernization of transmitted-light source, robotic equipment, redesigned experimental chambers, and newly developed analytical procedures have greatly reduced time and cost per experiment. We have verified the ability of the new equipment to generate reproducible heterogeneous sand-filled chambers and demonstrated the functionality of the new equipment and procedures by reproducing several gravity-driven fingering experiments conducted by Griffith (2008).

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...

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...

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

High beta plasma operation in a toroidal plasma producing device

DOEpatents

Clarke, John F.

1978-01-01

A high beta plasma is produced in a plasma producing device of toroidal configuration by ohmic heating and auxiliary heating. The plasma pressure is continuously monitored and used in a control system to program the current in the poloidal field windings. Throughout the heating process, magnetic flux is conserved inside the plasma and the distortion of the flux surfaces drives a current in the plasma. As a consequence, the total current increases and the poloidal field windings are driven with an equal and opposing increasing current. The spatial distribution of the current in the poloidal field windings is determined by the plasma pressure. Plasma equilibrium is maintained thereby, and high temperature, high beta operation results.

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

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.

Cypress surrogate mother produces haploid progeny from alien pollen.

PubMed

Pichot, Christian; Liens, Benjamin; Nava, Juana L Rivera; Bachelier, Julien B; El Maâtaoui, Mohamed

2008-01-01

Although most living organisms reproduce sexually, some have developed a uniparental reproduction where the embryo usually derives from the female parent. A unique case of paternal apomixis in plants has been recently reported in Cupressus dupreziana, an endangered Mediterranean conifer. This species produces unreduced pollen that develop into all-paternal embryos within the seed tissues. We analyzed seedlings produced by open-pollinated C. dupreziana seed trees using morphological descriptors, ploidy levels assessed through flow cytometry, and AFLP genetic diversity. In situ C. dupreziana seed trees (from Algeria) produced only diploid C. dupreziana progeny. In contrast, only one-third of the progeny produced by ex situ C. dupreziana seed trees planted in French collections were similar to C. dupreziana seedlings; the other progeny were haploid or diploid C. sempervirens seedlings. These results demonstrate that C. dupreziana ovules allow for the development of all-paternal embryos from pollen produced by another species, C. sempervirens. Thus, the in planta androgenesis is achieved through the combination of the embryogenic behavior of pollen grains and the ability of seed tree ovules to act as a surrogate mother. This phenomenon offers a unique opportunity to produce, by natural means, highly valuable material for genetic studies and selection of sterile cultivars.

Isolation and Characterization of a Novel, Highly Selective Astaxanthin-Producing Marine Bacterium.

PubMed

Asker, Dalal

2017-10-18

A high-throughput screening approach for astaxanthin-producing bacteria led to the discovery of a novel, highly selective astaxanthin-producing marine bacterium (strain N-5). Phylogenetic analysis based on partial 16S rRNA gene and phenotypic metabolic testing indicated it belongs to the genus Brevundimonas. Therefore, it was designated as Brevundimonas sp. strain N-5. To identify and quantify carotenoids produced by strain N-5, HPLC-DAD and HPLC-MS methods were used. The culture conditions including media, shaking, and time had significant effects on cell growth and carotenoids production including astaxanthin. The total carotenoids were ∼601.2 μg g -1 dry cells including a remarkable amount (364.6 μg g -1 dry cells) of optically pure astaxanthin (3S, 3'S) isomer, with high selectivity (∼60.6%) under medium aeration conditions. Notably, increasing the culture aeration enhanced astaxanthin production up to 85% of total carotenoids. This is the first report that describes a natural, highly selective astaxanthin-producing marine bacterium.

On the origin of reproducible sequential activity in neural circuits

NASA Astrophysics Data System (ADS)

Afraimovich, V. S.; Zhigulin, V. P.; Rabinovich, M. I.

2004-12-01

Robustness and reproducibility 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 reproducible 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 reproducible 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.

On the origin of reproducible sequential activity in neural circuits.

PubMed

Afraimovich, V S; Zhigulin, V P; Rabinovich, M I

2004-12-01

Robustness and reproducibility 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 reproducible 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 reproducible 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.

The Harm Done to Reproducibility by the Culture of Null Hypothesis Significance Testing.

PubMed

Lash, Timothy L

2017-09-15

In the last few years, stakeholders in the scientific community have raised alarms about a perceived lack of reproducibility of scientific results. In reaction, guidelines for journals have been promulgated and grant applicants have been asked to address the rigor and reproducibility 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 reproducible 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 reproducibility 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 reproducibility 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.

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

Method for producing highly reflective metal surfaces

DOEpatents

Arnold, J.B.; Steger, P.J.; Wright, R.R.

1982-03-04

The invention is a novel method for producing mirror surfaces which are extremely smooth and which have high optical reflectivity. The method includes depositing, by electrolysis, an amorphous layer of nickel on an article and then diamond-machining the resulting nickel surface to increase its smoothness and reflectivity. The machined nickel surface then is passivated with respect to the formation of bonds with electrodeposited nickel. Nickel then is electrodeposited on the passivated surface to form a layer of electroplated nickel whose inside surface is a replica of the passivated surface. The mandrel then may be-re-passivated and provided with a layer of electrodeposited nickel, which is then recovered from the mandrel providing a second replica. The mandrel can be so re-used to provide many such replicas. As compared with producing each mirror-finished article by plating and diamond-machining, the new method is faster and less expensive.

Reproducibility of African giant pouched rats detecting Mycobacterium tuberculosis.

PubMed

Ellis, Haylee; Mulder, Christiaan; Valverde, Emilio; Poling, Alan; Edwards, Timothy

2017-04-24

African pouched rats sniffing sputum samples provided by local clinics have significantly increased tuberculosis case findings in Tanzania and Mozambique. The objective of this study was to determine the reproducibility of rat results. Over an 18-month period 11,869 samples were examined by the rats. Intra-rater reliability was assessed through Yule's Q. Inter-rater reliability was assessed with Krippendorff's alpha. Intra-rater reliability was high, with a mean Yule's Q of 0.9. Inter-rater agreement was fair, with Krippendorf's alpha ranging from 0.15 to 0.45. Both Intra- and Inter-rater reliability was independent of the sex of the animals, but they were positively correlated with age. Both intra- and inter-rater agreement was lowest for samples designated as smear-negative by the clinics. Overall, the reproducibility of tuberculosis detection rat results was fair and diagnostic results were therefore independent of the rats used.

OpenMS - A platform for reproducible analysis of mass spectrometry data.

PubMed

Pfeuffer, Julianus; Sachsenberg, Timo; Alka, Oliver; Walzer, Mathias; Fillbrunn, Alexander; Nilse, Lars; Schilling, Oliver; Reinert, Knut; Kohlbacher, Oliver

2017-11-10

In recent years, several mass spectrometry-based omics technologies emerged to investigate qualitative and quantitative changes within thousands of biologically active components such as proteins, lipids and metabolites. The research enabled through these methods potentially contributes to the diagnosis and pathophysiology of human diseases as well as to the clarification of structures and interactions between biomolecules. Simultaneously, technological advances in the field of mass spectrometry leading to an ever increasing amount of data, demand high standards in efficiency, accuracy and reproducibility of potential analysis software. This article presents the current state and ongoing developments in OpenMS, a versatile open-source framework aimed at enabling reproducible analyses of high-throughput mass spectrometry data. It provides implementations of frequently occurring processing operations on MS data through a clean application programming interface in C++ and Python. A collection of 185 tools and ready-made workflows for typical MS-based experiments enable convenient analyses for non-developers and facilitate reproducible research without losing flexibility. OpenMS will continue to increase its ease of use for developers as well as users with improved continuous integration/deployment strategies, regular trainings with updated training materials and multiple sources of support. The active developer community ensures the incorporation of new features to support state of the art research. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

A Reproducible Oral Microcosm Biofilm Model for Testing Dental Materials

PubMed Central

Rudney, J.D.; Chen, R.; Lenton, P.; Li, J.; Li, Y.; Jones, R.S.; Reilly, C.; Fok, A.S.; Aparicio, C.

2012-01-01

Aims Most studies of biofilm effects on dental materials use single-species biofilms, or consortia. Microcosm biofilms grown directly from saliva or plaque are much more diverse, but difficult to characterize. We used the Human Oral Microbial Identification Microarray (HOMIM) to validate a reproducible oral microcosm model. Methods and Results Saliva and dental plaque were collected from adults and children. Hydroxyapatite and dental composite disks were inoculated with either saliva or plaque, and microcosm biofilms were grown in a CDC biofilm reactor. In later experiments, the reactor was pulsed with sucrose. DNA from inoculums and microcosms were analyzed by HOMIM for 272 species. Microcosms included about 60% of species from the original inoculum. Biofilms grown on hydroxyapatite and composites were extremely similar. Sucrose-pulsing decreased diversity and pH, but increased the abundance of Streptococcus and Veilonella. Biofilms from the same donor, grown at different times, clustered together. Conclusions This model produced reproducible microcosm biofilms that were representative of the oral microbiota. Sucrose induced changes associated with dental caries. Significance and Impact of the Study This is the first use of HOMIM to validate an oral microcosm model that can be used to study the effects of complex biofilms on dental materials. PMID:22925110

Reproducibility of ZrO2-based freeze casting for biomaterials.

PubMed

Naleway, Steven E; Fickas, Kate C; Maker, Yajur N; Meyers, Marc A; McKittrick, Joanna

2016-04-01

The processing technique of freeze casting has been intensely researched for its potential to create porous scaffold and infiltrated composite materials for biomedical implants and structural materials. However, in order for this technique to be employed medically or commercially, it must be able to reliably produce materials in great quantities with similar microstructures and properties. Here we investigate the reproducibility of the freeze casting process by independently fabricating three sets of eight ZrO2-epoxy composite scaffolds with the same processing conditions but varying solid loading (10, 15 and 20 vol.%). Statistical analyses (One-way ANOVA and Tukey's HSD tests) run upon measurements of the microstructural dimensions of these composite scaffold sets show that, while the majority of microstructures are similar, in all cases the composite scaffolds display statistically significant variability. In addition, composite scaffolds where mechanically compressed and statistically analyzed. Similar to the microstructures, almost all of their resultant properties displayed significant variability though most composite scaffolds were similar. These results suggest that additional research to improve control of the freeze casting technique is required before scaffolds and composite scaffolds can reliably be reproduced for commercial or medical applications. Copyright © 2015 Elsevier B.V. All rights reserved.

Revisiting the scientific method to improve rigor and reproducibility of immunohistochemistry in reproductive science.

PubMed

Manuel, Sharrón L; Johnson, Brian W; Frevert, Charles W; Duncan, Francesca E

2018-04-21

Immunohistochemistry (IHC) is a robust scientific tool whereby cellular components are visualized within a tissue, and this method has been and continues to be a mainstay for many reproductive biologists. IHC is highly informative if performed and interpreted correctly, but studies have shown that the general use and reporting of appropriate controls in IHC experiments is low. This omission of the scientific method can result in data that lacks rigor and reproducibility. In this editorial, we highlight key concepts in IHC controls and describe an opportunity for our field to partner with the Histochemical Society to adopt their IHC guidelines broadly as researchers, authors, ad hoc reviewers, editorial board members, and editors-in-chief. Such cross-professional society interactions will ensure that we produce the highest quality data as new technologies emerge that still rely upon the foundations of classic histological and immunohistochemical principles.

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.

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

Evaluation of the reproducibility of lung motion probability distribution function (PDF) using dynamic MRI.

PubMed

Cai, Jing; Read, Paul W; Altes, Talissa A; Molloy, Janelle A; Brookeman, James R; Sheng, Ke

2007-01-21

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 reproducibility of the PDF. In this paper, we investigated the dependences of the PDF reproducibility 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 reproducibility were evaluated as a function of scan time and frame rate. As results, the PDF reproducibility 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 reproducibility 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 reproducibility of the PDF affects the dosimetric accuracy substantially. This study provides a reference for acquiring MR-based PDF of structures in the lung.

Method for producing highly reflective metal surfaces

DOEpatents

Arnold, Jones B.; Steger, Philip J.; Wright, Ralph R.

1983-01-01

The invention is a novel method for producing mirror surfaces which are extremely smooth and which have high optical reflectivity. The method includes electrolessly depositing an amorphous layer of nickel on an article and then diamond-machining the resulting nickel surface to increase its smoothness and reflectivity. The machined nickel surface then is passivated with respect to the formation of bonds with electrodeposited nickel. Nickel then is electrodeposited on the passivated surface to form a layer of electroplated nickel whose inside surface is a replica of the passivated surface. The electroplated nickel layer then is separated from the passivated surface. The mandrel then may be re-passivated and provided with a layer of electrodeposited nickel, which is then recovered from the mandrel providing a second replica. The mandrel can be so re-used to provide many such replicas. As compared with producing each mirror-finished article by plating and diamond-machining, the new method is faster and less expensive.

State-of-the-art exposure chamber for highly controlled and reproducible THz biological effects studies

NASA Astrophysics Data System (ADS)

Cerna, Cesario Z.; Elam, David P.; Echchgadda, Ibtissam; Sloan, Mark A.; Wilmink, Gerald J.

2014-03-01

Terahertz (THz) imaging and sensing technologies are increasingly being used at international airports for security screening purposes and at major medical centers for cancer and burn diagnosis. The emergence of new THz applications has directly resulted in an increased interest regarding the biological effects associated with this frequency range. Knowledge of THz biological effects is also desired for the safe use of THz systems, identification of health hazards, and development of empirically-based safety standards. In this study, we developed a state-of-the-art exposure chamber that allowed for highly controlled and reproducible studies of THz biological effects. This innovative system incorporated an industry grade cell incubator system that permitted a highly controlled exposure environment, where temperatures could be maintained at 37 °C +/- 0.1 °C, carbon dioxide (CO2) levels at 5% +/- 0.1%, and relative humidity (RH) levels at 95% +/- 1%. To maximize the THz power transmitted to the cell culture region inside the humid incubator, a secondary custom micro-chamber was fabricated and incorporated into the system. This micro-chamber shields the THz beam from the incubator environment and could be nitrogen-purged to eliminate water absorption effects. Additionally, a microscope that allowed for real-time visualization of the live cells before, during, and after THz exposure was integrated into the exposure system.

The substorm cycle as reproduced by global MHD models

NASA Astrophysics Data System (ADS)

Gordeev, E.; Sergeev, V.; Tsyganenko, N.; Kuznetsova, M.; Rastäetter, L.; Raeder, J.; Tóth, G.; Lyon, J.; Merkin, V.; Wiltberger, M.

2017-01-01

Recently, Gordeev et al. (2015) suggested a method to test global MHD models against statistical empirical data. They showed that four community-available global MHD models supported by the Community Coordinated Modeling Center (CCMC) produce a reasonable agreement with reality for those key parameters (the magnetospheric size, magnetic field, and pressure) that are directly related to the large-scale equilibria in the outer magnetosphere. Based on the same set of simulation runs, here we investigate how the models reproduce the global loading-unloading cycle. We found that in terms of global magnetic flux transport, three examined CCMC models display systematically different response to idealized 2 h north then 2 h south interplanetary magnetic field (IMF) Bz variation. The LFM model shows a depressed return convection and high loading rate during the growth phase as well as enhanced return convection and high unloading rate during the expansion phase, with the amount of loaded/unloaded magnetotail flux and the growth phase duration being the closest to their observed empirical values during isolated substorms. Two other models exhibit drastically different behavior. In the BATS-R-US model the plasma sheet convection shows a smooth transition to the steady convection regime after the IMF southward turning. In the Open GGCM a weak plasma sheet convection has comparable intensities during both the growth phase and the following slow unloading phase. We also demonstrate potential technical problem in the publicly available simulations which is related to postprocessing interpolation and could affect the accuracy of magnetic field tracing and of other related procedures.

The Substorm Cycle as Reproduced by Global MHD Models

NASA Technical Reports Server (NTRS)

Gordeev, E.; Sergee, V.; Tsyganenko, N.; Kuznetsova, M.; Rastaetter, Lutz; Raeder, J.; Toth, G.; Lyon, J.; Merkin, V.; Wiltberger, M.

2017-01-01

Recently, Gordeev et al. (2015) suggested a method to test global MHD models against statistical empirical data. They showed that four community-available global MHD models supported by the Community Coordinated Modeling Center (CCMC) produce a reasonable agreement with reality for those key parameters (the magnetospheric size, magnetic field, and pressure) that are directly related to the large-scale equilibria in the outer magnetosphere. Based on the same set of simulation runs, here we investigate how the models reproduce the global loading-unloading cycle. We found that in terms of global magnetic flux transport, three examined CCMC models display systematically different response to idealized2 h north then 2 h south interplanetary magnetic field (IMF) Bz variation. The LFM model shows a depressed return convection and high loading rate during the growth phase as well as enhanced return convection and high unloading rate during the expansion phase, with the amount of loaded unloaded magnetotail flux and the growth phase duration being the closest to their observed empirical values during isolated substorms. Two other models exhibit drastically different behavior. In the BATS-R-US model the plasma sheet convection shows a smooth transition to the steady convection regime after the IMF southward turning. In the Open GGCM a weak plasma sheet convection has comparable intensities during both the growth phase and the following slow unloading phase. We also demonstrate potential technical problem in the publicly available simulations which is related to post processing interpolation and could affect the accuracy of magnetic field tracing and of other related procedures.

Parametric studies on droplet generation reproducibility for applications with biological relevant fluids

PubMed Central

Eichler, Marko; Römer, Robert; Grodrian, Andreas; Lemke, Karen; Nagel, Krees; Klages, Claus‐Peter; Gastrock, Gunter

2017-01-01

Abstract Although the great potential of droplet based microfluidic technologies for routine applications in industry and academia has been successfully demonstrated over the past years, its inherent potential is not fully exploited till now. Especially regarding to the droplet generation reproducibility and stability, two pivotally important parameters for successful applications, there is still a need for improvement. This is even more considerable when droplets are created to investigate tissue fragments or cell cultures (e.g. suspended cells or 3D cell cultures) over days or even weeks. In this study we present microfluidic chips composed of a plasma coated polymer, which allow surfactants‐free, highly reproducible and stable droplet generation from fluids like cell culture media. We demonstrate how different microfluidic designs and different flow rates (and flow rate ratios) affect the reproducibility of the droplet generation process and display the applicability for a wide variety of bio(techno)logically relevant media. PMID:29399017

SeqBox: RNAseq/ChIPseq reproducible analysis on a consumer game computer.

PubMed

Beccuti, Marco; Cordero, Francesca; Arigoni, Maddalena; Panero, Riccardo; Amparore, Elvio G; Donatelli, Susanna; Calogero, Raffaele A

2018-03-01

Short reads sequencing technology has been used for more than a decade now. However, the analysis of RNAseq and ChIPseq data is still computational demanding and the simple access to raw data does not guarantee results reproducibility between laboratories. To address these two aspects, we developed SeqBox, a cheap, efficient and reproducible RNAseq/ChIPseq hardware/software solution based on NUC6I7KYK mini-PC (an Intel consumer game computer with a fast processor and a high performance SSD disk), and Docker container platform. In SeqBox the analysis of RNAseq and ChIPseq data is supported by a friendly GUI. This allows access to fast and reproducible analysis also to scientists with/without scripting experience. Docker container images, docker4seq package and the GUI are available at http://www.bioinformatica.unito.it/reproducibile.bioinformatics.html. beccuti@di.unito.it. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

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.

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

Introduction to the special issue on recentering science: Replication, robustness, and reproducibility in psychophysiology.

PubMed

Kappenman, Emily S; Keil, Andreas

2017-01-01

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 reproducibility 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 observations. 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, reproducible results in the field of psychophysiology. © 2016 Society for Psychophysiological Research.

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.

In vivo reproducibility of robotic probe placement for a novel ultrasound-guided radiation therapy system

PubMed Central

Lediju Bell, Muyinatu A.; Sen, H. Tutkun; Iordachita, Iulian; Kazanzides, Peter; Wong, John

2014-01-01

Abstract. Ultrasound can provide real-time image guidance of radiation therapy, but the probe-induced tissue deformations cause local deviations from the treatment plan. If placed during treatment planning, the probe causes streak artifacts in required computed tomography (CT) images. To overcome these challenges, we propose robot-assisted placement of an ultrasound probe, followed by replacement with a geometrically identical, CT-compatible model probe. In vivo reproducibility was investigated by implanting a canine prostate, liver, and pancreas with three 2.38-mm spherical markers in each organ. The real probe was placed to visualize the markers and subsequently replaced with the model probe. Each probe was automatically removed and returned to the same position or force. Under position control, the median three-dimensional reproducibility of marker positions was 0.6 to 0.7 mm, 0.3 to 0.6 mm, and 1.1 to 1.6 mm in the prostate, liver, and pancreas, respectively. Reproducibility was worse under force control. Probe substitution errors were smallest for the prostate (0.2 to 0.6 mm) and larger for the liver and pancreas (4.1 to 6.3 mm), where force control generally produced larger errors than position control. Results indicate that position control is better than force control for this application, and the robotic approach has potential, particularly for relatively constrained organs and reproducibility errors that are smaller than established treatment margins. PMID:26158038

Union Texas hopes to reproduce its Pakistan Badin experience

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

Petzet, G.A.

1997-11-03

Union Texas Petroleum Holdings Inc. has resolved to transplant elsewhere in the world the success of tis 20 year old grass-roots exploration effort on the Badin block in Pakistan. Union Texas Pakistan Inc. (UTP) is actively seeking exploration concessions in Pakistan, and the parent company is on an international bent aimed at finding other areas where it might reproduce its performance in Pakistan. The 104 exploratory wells drilled through April 1, 1997, resulted in 47 discoveries and 57 dry holes for a 45% success rate. Some oil and gas are produced from the Middle Sand units, and some gas ismore » produced from the Basal Sand units. The 1997 Badin exploration plan called for 11 exploratory wells, including one, Tarai Deep-3, that would test a new play concept in Jurassic Chiltan. It also called for Badin`s first 3D seismic surveys, at South Buzdar and Tangri fields on the northern part of the block, and 146 km of 2D seismic acquisition. The paper discusses Badin development, drilling status, operating challenges, oil price and sales, gas markets, local effects, and future developments.« less

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

Reproducibility of the retinal vascular response to flicker light in Asians.

PubMed

Nguyen, Thanh T; Kreis, Andreas J; Kawasaki, Ryo; Wang, Jie Jin; Seifert, Bernd-U; Vilser, Walthard; Nagel, Edgar; Wong, Tien Y

2009-12-01

Dilation of retinal vessels in response to diffuse luminance flicker may reflect endothelial function. Although this has previously been shown to be reproducible in whites, there have been no similar data in Asians. We assess the reproducibility of repeated measurements of this response in Asians. Healthy Asians (n = 33) with normal vision and no history of glaucoma, age-related macular degeneration, cataract, or retinal arterial/venous occlusion participated in this study. Repeated measures from the same subjects were taken 30-60 min apart using the Dynamic Vessel Analyser (DVA, IMEDOS, Jena, Germany). Modification was made to the shape of the light source for Asian participants. Correlations of the first and second measures were assessed using Pearson correlation (R(2)), and agreement between the two measures was shown using Bland-Altman plots. After modification to the shape of the light source, almost perfect correlation was found between the 1st and 2nd measurements of baseline arteriolar (R(2) = 0.95) and venular diameters (R(2) = 0.98) of arteriolar maximum dilation (R(2) = 0.85). Substantially high correlation between the 1st and 2nd measurements of venular maximum dilation was found (R(2) = 0.80). Measurements of the dilation response of retinal vessels to diffuse luminance flicker an Asian sample using the DVA show high reproducibility for repeated measures over a short period of time. Such measurements may allow non-invasive quantification of endothelial function to study its association with systemic and ocular diseases.

Reproducibility of myelin content-based human habenula segmentation at 3 Tesla.

PubMed

Kim, Joo-Won; Naidich, Thomas P; Joseph, Joshmi; Nair, Divya; Glasser, Matthew F; O'halloran, Rafael; Doucet, Gaelle E; Lee, Won Hee; Krinsky, Hannah; Paulino, Alejandro; Glahn, David C; Anticevic, Alan; Frangou, Sophia; Xu, Junqian

2018-03-26

In vivo morphological study of the human habenula, a pair of small epithalamic nuclei adjacent to the dorsomedial thalamus, has recently gained significant interest for its role in reward and aversion processing. However, segmenting the habenula from in vivo magnetic resonance imaging (MRI) is challenging due to the habenula's small size and low anatomical contrast. Although manual and semi-automated habenula segmentation methods have been reported, the test-retest reproducibility of the segmented habenula volume and the consistency of the boundaries of habenula segmentation have not been investigated. In this study, we evaluated the intra- and inter-site reproducibility of in vivo human habenula segmentation from 3T MRI (0.7-0.8 mm isotropic resolution) using our previously proposed semi-automated myelin contrast-based method and its fully-automated version, as well as a previously published manual geometry-based method. The habenula segmentation using our semi-automated method showed consistent boundary definition (high Dice coefficient, low mean distance, and moderate Hausdorff distance) and reproducible volume measurement (low coefficient of variation). Furthermore, the habenula boundary in our semi-automated segmentation from 3T MRI agreed well with that in the manual segmentation from 7T MRI (0.5 mm isotropic resolution) of the same subjects. Overall, our proposed semi-automated habenula segmentation showed reliable and reproducible habenula localization, while its fully-automated version offers an efficient way for large sample analysis. © 2018 Wiley Periodicals, Inc.

High-efficiency holograms fixed in lithium niobate after recording using a digital fringe stabilization system.

PubMed

Arizmendi, Luis; Ambite, Emilio J

2012-02-20

We used a digital feedback control loop system to produce reproducible fixed volume transmission holograms of high diffraction efficiency. Different strategies were investigated to obtain holograms of good quality and the highest refractive index modulation depth. Using this control system, we were able to record holograms with stationary fringes. Additionally to using the stationary fringe recording, a double recording-fixing schedule resulted in being the most appropriate one to produce reproducible holograms of better characteristics. This strategy is discussed and compared with other already established ones. © 2012 Optical Society of America

Reproducing oil paint gloss in print for the purpose of creating reproductions of Old Masters

NASA Astrophysics Data System (ADS)

Elkhuizen, Willemijn S.; Lenseigne, Boris A. J.; Baar, Teun; Verhofstad, Wim; Tempelman, Erik; Geraedts, Jo M. P.; Dik, Joris

2015-03-01

In the field of Fine Art reproduction, 3D scanning plus 3D printing, combined with dedicated software, now allows to capture and reproduce the color and texture of oil paintings. However, for life-like reproduction of the material appearance of such paintings, the typical gloss and translucency must also be included, which is currently not the case. The aim of this paper is to elaborate on the challenges and results of capturing and reproducing oil paint gloss (next to texture and color) using a scanning and printing system. A sample was hand-made using oil paint and acrylic varnish, and its gloss was then reproduced. A gloss map of the painted sample was acquired using a high end DLSR camera and a simple acquisition protocol. Next, Océ High Resolution 3D printing technology was used to create samples with spatially varying gloss. For this, two different strategies were combined: (1) multilevel half-toning of the colors was used to reproduce matte color layers, and (2) varnish was half-toned on top in increasing coverage to recreate increasing gloss levels. This paper presents an overview of the state-of-the-art literature in gloss reproduction and perception, our process of reproduction as well as the visual evaluation of the quality of the created reproduction.

A Pilot Study on the Ability of Young Children and Adults to Identify and Reproduce Novel Speech Sounds.

ERIC Educational Resources Information Center

Yeni-Komshian, Grace; And Others

This study was designed to compare children and adults on their initial ability to identify and reproduce novel speech sounds and to evaluate their performance after receiving several training sessions in producing these sounds. The novel speech sounds used were two voiceless fricatives which are consonant phonemes in Arabic but which are…

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.

Facile one-step synthesis of Ag@Fe3O4 core-shell nanospheres for reproducible SERS substrates

NASA Astrophysics Data System (ADS)

Sun, Lijuan; He, Jiang; An, Songsong; Zhang, Junwei; Ren, Dong

2013-08-01

A facile approach has been developed to synthesize Ag@Fe3O4 core-shell nanospheres, in which the Ag nanoparticle core was well wrapped by a permeable Fe3O4 shell. An in situ reduction of AgNO3 and Fe(NO3)3 was the basis of this one-step method with ethylene glycol as the reducing agent. The as-obtained Ag@Fe3O4 nanospheres were a highly efficient surface-enhanced Raman scattering (SERS) substrate; high reproducibility, stability, and reusability were obtained by employing 4-aminothiophenol (4-ATP) and rhodamine 6G (R6G) as the Raman probe molecules. It was revealed that the SERS signals of 4-ATP and R6G on the Ag@Fe3O4 nanospheres were much stronger than those on the pure Ag nanoparticles, demonstrating that the magnetic enrichment procedures can improve SERS detection sensitivity efficiently. A highly efficient and recyclable SERS substrate was produced by the new model system that has potential applications in chemical and biomolecular assays.

Potential miRNA regulators of differential HPG axis gene expression between low egg producing and high egg producing turkey hens

USDA-ARS?s Scientific Manuscript database

Expression differences exist in key genes of the hypothalamo-pituitary-gonadal (HPG) axis in low egg producing hens (LEPH) and high egg producing hens (HEPH); however, regulation of these differences is unknown. MicroRNAs (miRNAs) are small non-coding RNAs that play a role in post-transcriptional re...

Reproducibility for Heart Rate Variability Analysis during 6-Min Walk Test in Patients with Heart Failure and Agreement between Devices.

PubMed

Braga, Lays Magalhães; Prado, Gustavo Faibischew; Umeda, Iracema Ioco Kikuchi; Kawauchi, Tatiana Satie; Taboada, Adriana Marques Fróes; Azevedo, Raymundo Soares; Pereira Filho, Horacio Gomes; Grupi, César José; Souza, Hayala Cristina Cavenague; Moreira, Dalmo Antônio Ribeiro; Nakagawa, Naomi Kondo

2016-01-01

Heart rate variability (HRV) analysis is a useful method to assess abnormal functioning in the autonomic nervous system and to predict cardiac events in patients with heart failure (HF). HRV measurements with heart rate monitors have been validated with an electrocardiograph in healthy subjects but not in patients with HF. We explored the reproducibility of HRV in two consecutive six-minute walk tests (6MW), 60-minute apart, using a heart rate monitor (PolarS810i) and a portable electrocardiograph (called Holter) in 50 HF patients (mean age 59 years, NYHA II, left ventricular ejection fraction ~35%). The reproducibility for each device was analysed using a paired t-test or the Wilcoxon signed-rank test. Additionally, we assessed the agreement between the two devices based on the HRV indices at rest, during the 6MW and during recovery using concordance correlation coefficients (CCC), 95% confidence intervals and Bland-Altman plots. The test-retest for the HRV analyses was reproducible using Holter and PolarS810i at rest but not during recovery. In the second 6MW, patients showed significant increases in rMSSD and walking distance. The PolarS810i measurements had remarkably high concordance correlation [0.86reproducibility of HRV at rest in two consecutive 6MW using Holter and PolarS810i. Additionally, PolarS810i produced good agreements in short-term HRV indices based on Holter simultaneous recordings at rest, during the 6MW and recovery in HF patients.

Diversity, Stability, and Reproducibility in Stochastically Assembled Microbial Ecosystems

NASA Astrophysics Data System (ADS)

Goyal, Akshit; Maslov, Sergei

2018-04-01

Microbial ecosystems are remarkably diverse, stable, and usually consist of a mixture of core and peripheral species. Here we propose a conceptual model exhibiting all these emergent properties in quantitative agreement with real ecosystem data, specifically species abundance and prevalence distributions. Resource competition and metabolic commensalism drive the stochastic ecosystem assembly in our model. We demonstrate that even when supplied with just one resource, ecosystems can exhibit high diversity, increasing stability, and partial reproducibility between samples.

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

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

Reproducibility of image quality for moving objects using respiratory-gated computed tomography: a study using a phantom model

PubMed Central

Fukumitsu, Nobuyoshi; Ishida, Masaya; Terunuma, Toshiyuki; Mizumoto, Masashi; Hashimoto, Takayuki; Moritake, Takashi; Okumura, Toshiyuki; Sakae, Takeji; Tsuboi, Koji; Sakurai, Hideyuki

2012-01-01

To investigate the reproducibility of computed tomography (CT) imaging quality in respiratory-gated radiation treatment planning is essential in radiotherapy of movable tumors. Seven series of regular and six series of irregular respiratory motions were performed using a thorax dynamic phantom. For the regular respiratory motions, the respiratory cycle was changed from 2.5 to 4 s and the amplitude was changed from 4 to 10 mm. For the irregular respiratory motions, a cycle of 2.5 to 4 or an amplitude of 4 to 10 mm was added to the base data (i.e. 3.5-s cycle, 6-mm amplitude) every three cycles. Images of the object were acquired six times using respiratory-gated data acquisition. The volume of the object was calculated and the reproducibility of the volume was decided based on the variety. The registered image of the object was added and the reproducibility of the shape was decided based on the degree of overlap of objects. The variety in the volumes and shapes differed significantly as the respiratory cycle changed according to regular respiratory motions. In irregular respiratory motion, shape reproducibility was further inferior, and the percentage of overlap among the six images was 35.26% in the 2.5- and 3.5-s cycle mixed group. Amplitude changes did not produce significant differences in the variety of the volumes and shapes. Respiratory cycle changes reduced the reproducibility of the image quality in respiratory-gated CT. PMID:22966173

Development of high-sensitive, reproducible colloidal surface-enhanced Raman spectroscopy active substrate using silver nanocubes for potential biosensing applications

NASA Astrophysics Data System (ADS)

Hasna, Kudilatt; Lakshmi, Kiran; Ezhuthachan Jayaraj, Madambi Kunjukuttan; Kumar, Kumaran Rajeev; Matham, Murukeshan Vadakke

2016-04-01

Surface-enhanced Raman spectroscopy (SERS) has emerged as one of the thrust research areas that could find potential applications in bio and chemical sensing. We developed colloidal SERS active substrate with excellent sensitivity and high reproducibility using silver nanocube (AgNC) synthesized via the solvothermal method. Finite-difference time-domain simulation was carried out in detail to visualize dipole generation in the nanocube during localized surface plasmon resonance and to locate the respective hot spots in AgNC responsible for the huge Raman enhancement. The prediction is verified by the SERS analysis of the synthesized nanocubes using Rhodamine 6G molecule. An excellent sensitivity with a detection limit of 10-17 M and a very high enhancement factor of 1.2×108 confirms the "hot spots" in the nanocube. SERS activity is also carried out for crystal violet and for food adulterant Sudan I molecule. Finally, label-free DNA detection is performed to demonstrate the versatility of SERS as a potential biosensor.

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

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...

TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics

PubMed Central

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

2016-01-01

Large scale, quantitative proteomic studies have become essential for the analysis of clinical cohorts, large perturbation experiments and systems biology studies. While next-generation mass spectrometric techniques such as SWATH-MS have substantially increased throughput and reproducibility, ensuring consistent quantification of thousands of peptide analytes across multiple LC-MS/MS runs remains a challenging and laborious manual process. To produce highly consistent and quantitatively accurate proteomics data matrices in an automated fashion, we have developed the TRIC software which utilizes fragment ion data to perform cross-run alignment, consistent peak-picking and quantification for high throughput targeted proteomics. TRIC uses a graph-based alignment strategy based on non-linear retention time correction to integrate peak elution information from all LC-MS/MS runs acquired in a study. When compared to state-of-the-art SWATH-MS data analysis, the algorithm was able to reduce the identification error by more than 3-fold at constant recall, while correcting for highly non-linear chromatographic effects. On a pulsed-SILAC experiment performed on human induced pluripotent stem (iPS) cells, TRIC was able to automatically align and quantify thousands of light and heavy isotopic peak groups and substantially increased the quantitative completeness and biological information in the data, providing insights into protein dynamics of iPS cells. Overall, this study demonstrates the importance of consistent quantification in highly challenging experimental setups, and proposes an algorithm to automate this task, constituting the last missing piece in a pipeline for automated analysis of massively parallel targeted proteomics datasets. PMID:27479329

Hydrological Modeling Reproducibility Through Data Management and Adaptors for Model Interoperability

NASA Astrophysics Data System (ADS)

Turner, M. A.

2015-12-01

Because of a lack of centralized planning and no widely-adopted standards among hydrological modeling research groups, research communities, and the data management teams meant to support research, there is chaos when it comes to data formats, spatio-temporal resolutions, ontologies, and data availability. All this makes true scientific reproducibility and collaborative integrated modeling impossible without some glue to piece it all together. Our Virtual Watershed Integrated Modeling System provides the tools and modeling framework hydrologists need to accelerate and fortify new scientific investigations by tracking provenance and providing adaptors for integrated, collaborative hydrologic modeling and data management. Under global warming trends where water resources are under increasing stress, reproducible hydrological modeling will be increasingly important to improve transparency and understanding of the scientific facts revealed through modeling. The Virtual Watershed Data Engine is capable of ingesting a wide variety of heterogeneous model inputs, outputs, model configurations, and metadata. We will demonstrate one example, starting from real-time raw weather station data packaged with station metadata. Our integrated modeling system will then create gridded input data via geostatistical methods along with error and uncertainty estimates. These gridded data are then used as input to hydrological models, all of which are available as web services wherever feasible. Models may be integrated in a data-centric way where the outputs too are tracked and used as inputs to "downstream" models. This work is part of an ongoing collaborative Tri-state (New Mexico, Nevada, Idaho) NSF EPSCoR Project, WC-WAVE, comprised of researchers from multiple universities in each of the three states. The tools produced and presented here have been developed collaboratively alongside watershed scientists to address specific modeling problems with an eye on the bigger picture of

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

Reproducibility of studies on text mining for citation screening in systematic reviews: Evaluation and checklist.

PubMed

Olorisade, Babatunde Kazeem; Brereton, Pearl; Andras, Peter

2017-09-01

Independent validation of published scientific results through study replication is a pre-condition for accepting the validity of such results. In computation research, full replication is often unrealistic for independent results validation, therefore, study reproduction has been justified as the minimum acceptable standard to evaluate the validity of scientific claims. The application of text mining techniques to citation screening in the context of systematic literature reviews is a relatively young and growing computational field with high relevance for software engineering, medical research and other fields. However, there is little work so far on reproduction studies in the field. In this paper, we investigate the reproducibility of studies in this area based on information contained in published articles and we propose reporting guidelines that could improve reproducibility. The study was approached in two ways. Initially we attempted to reproduce results from six studies, which were based on the same raw dataset. Then, based on this experience, we identified steps considered essential to successful reproduction of text mining experiments and characterized them to measure how reproducible is a study given the information provided on these steps. 33 articles were systematically assessed for reproducibility using this approach. Our work revealed that it is currently difficult if not impossible to independently reproduce the results published in any of the studies investigated. The lack of information about the datasets used limits reproducibility of about 80% of the studies assessed. Also, information about the machine learning algorithms is inadequate in about 27% of the papers. On the plus side, the third party software tools used are mostly free and available. The reproducibility potential of most of the studies can be significantly improved if more attention is paid to information provided on the datasets used, how they were partitioned and utilized, and

Repeatability and Reproducibility of Decisions by Latent Fingerprint Examiners

PubMed Central

Ulery, Bradford T.; Hicklin, R. Austin; Buscaglia, JoAnn; Roberts, Maria Antonia

2012-01-01

The interpretation of forensic fingerprint evidence relies on the expertise of latent print examiners. We tested latent print examiners on the extent to which they reached consistent decisions. This study assessed intra-examiner repeatability by retesting 72 examiners on comparisons of latent and exemplar fingerprints, after an interval of approximately seven months; each examiner was reassigned 25 image pairs for comparison, out of total pool of 744 image pairs. We compare these repeatability results with reproducibility (inter-examiner) results derived from our previous study. Examiners repeated 89.1% of their individualization decisions, and 90.1% of their exclusion decisions; most of the changed decisions resulted in inconclusive decisions. Repeatability of comparison decisions (individualization, exclusion, inconclusive) was 90.0% for mated pairs, and 85.9% for nonmated pairs. Repeatability and reproducibility were notably lower for comparisons assessed by the examiners as “difficult” than for “easy” or “moderate” comparisons, indicating that examiners' assessments of difficulty may be useful for quality assurance. No false positive errors were repeated (n = 4); 30% of false negative errors were repeated. One percent of latent value decisions were completely reversed (no value even for exclusion vs. of value for individualization). Most of the inter- and intra-examiner variability concerned whether the examiners considered the information available to be sufficient to reach a conclusion; this variability was concentrated on specific image pairs such that repeatability and reproducibility were very high on some comparisons and very low on others. Much of the variability appears to be due to making categorical decisions in borderline cases. PMID:22427888

Gold@silver bimetal nanoparticles/pyramidal silicon 3D substrate with high reproducibility for high-performance SERS

NASA Astrophysics Data System (ADS)

Zhang, Chao; Jiang, Shou Zhen; Yang, Cheng; Li, Chong Hui; Huo, Yan Yan; Liu, Xiao Yun; Liu, Ai Hua; Wei, Qin; Gao, Sai Sai; Gao, Xing Guo; Man, Bao Yuan

2016-05-01

A novel and efficient surface enhanced Raman scattering (SERS) substrate has been presented based on Gold@silver/pyramidal silicon 3D substrate (Au@Ag/3D-Si). By combining the SERS activity of Ag, the chemical stability of Au and the large field enhancement of 3D-Si, the Au@Ag/3D-Si substrate possesses perfect sensitivity, homogeneity, reproducibility and chemical stability. Using R6G as probe molecule, the SERS results imply that the Au@Ag/3D-Si substrate is superior to the 3D-Si, Ag/3D-Si and Au/3D-Si substrate. We also confirmed these excellent behaviors in theory via a commercial COMSOL software. The corresponding experimental and theoretical results indicate that our proposed Au@Ag/3D-Si substrate is expected to develop new opportunities for label-free SERS detections in biological sensors, biomedical diagnostics and food safety.

Development of High Cordycepin-Producing Cordyceps militaris Strains.

PubMed

Kang, Naru; Lee, Hyun-Hee; Park, Inmyoung; Seo, Young-Su

2017-03-01

Cordyceps militaris , known as Dong-Chong-Xia-Cao, produces the most cordycepin among Cordyceps species and can be cultured artificially. For these reasons, C. militaris is widely used as herb or functional food in the East Asia. In this study, we developed a new strain of C. militaris that produces higher cordycepin content than parent strains through mating-based sexual reproduction. Twenty parent strains were collected and identified as C. militaris based on internal trasncrived spacer and rDNA sequences. Seven single spores of MAT 1-1 idiomorph and five single spores of MAT 1-2 idiomorph were isolated from 12 parent strains. When 35 combinations were mated on the brown rice medium with the isolated single spores, eight combinations formed a stroma with a normal perithecia and confirmed mated strains. High pressure liquid chromatography analysis showed that mated strain KSP8 produced the most cordycepin in all the media among all the tested strains. This result showed due to genetic recombination occurring during the sexual reproduction of C. militaris . The development of C. militaris strain with increased cordycepin content by this approach can help not only to generate new C. militaris strains, but also to contribute to the health food or medicine industry.

Development of High Cordycepin-Producing Cordyceps militaris Strains

PubMed Central

Kang, Naru; Lee, Hyun-Hee; Park, Inmyoung

2017-01-01

Cordyceps militaris, known as Dong-Chong-Xia-Cao, produces the most cordycepin among Cordyceps species and can be cultured artificially. For these reasons, C. militaris is widely used as herb or functional food in the East Asia. In this study, we developed a new strain of C. militaris that produces higher cordycepin content than parent strains through mating-based sexual reproduction. Twenty parent strains were collected and identified as C. militaris based on internal trasncrived spacer and rDNA sequences. Seven single spores of MAT 1-1 idiomorph and five single spores of MAT 1-2 idiomorph were isolated from 12 parent strains. When 35 combinations were mated on the brown rice medium with the isolated single spores, eight combinations formed a stroma with a normal perithecia and confirmed mated strains. High pressure liquid chromatography analysis showed that mated strain KSP8 produced the most cordycepin in all the media among all the tested strains. This result showed due to genetic recombination occurring during the sexual reproduction of C. militaris. The development of C. militaris strain with increased cordycepin content by this approach can help not only to generate new C. militaris strains, but also to contribute to the health food or medicine industry. PMID:28435352

Miniature whirlwinds produced in the laboratory by high-voltage electrical discharges.

PubMed

Ryan, R T; Vonnegut, B

1970-06-12

Laboratory experiments showed that under certain conditions of vorticity the electrical heatinig produced by a high-voltage discharge at atmospheric pressure can cause the formation of a miniature tornado-like vortex. Once it forms, this vortex stabilizes the electrical discharge along its axis and changes its character from that of a spark to high-pressure variety of a glow discharge. Electrical and dynamic parameters were measured. By relating observations and measurements made in these experiments to previous work and to analogous situations in nature, it is concluded that the heating produced by electrical discharges in a large storm may play a significant role in forming and maintaining natural tornadoes.

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.

Reproducibility of an aerobic endurance test for nonexpert swimmers.

PubMed

Veronese da Costa, Adalberto; Costa, Manoel da Cunha; Carlos, Daniel Medeiros; Guerra, Luis Marcos de Medeiros; Silva, Antônio José; Barbosa, Tiago Manoel Cabral Dos Santos

2012-01-01

nonexpert swimmers produces comparable results for noncompetitive swimmers with a favorable degree of reproducibility, thus presenting possible applications for researching the physiological performance of nonexpert swimmers.

Validity and reproducibility of self-reported working hours among Japanese male employees.

PubMed

Imai, Teppei; Kuwahara, Keisuke; Miyamoto, Toshiaki; Okazaki, Hiroko; Nishihara, Akiko; Kabe, Isamu; Mizoue, Tetsuya; Dohi, Seitaro

2016-07-22

Working long hours is a potential health hazard. Although self-reporting of working hours in various time frames has been used in epidemiologic studies, its validity is unclear. The objective of this study was to examine the validity and reproducibility of self-reported working hours among Japanese male employees. The participants were 164 male employees of four large-scale companies in Japan. For validity, the Spearman correlation between self-reported working hours in the second survey and the working hours recorded by the company was calculated for the following four time frames: daily working hours, monthly overtime working hours in the last month, average overtime working hours in the last 3 months, and the frequency of long working months (≥45 h/month) within the last 12 months. For reproducibility, the intraclass correlation between the first (September 2013) and second surveys (December 2013) was calculated for each of the four time frames. The Spearman correlations between self-reported working hours and those based on company records were 0.74, 0.81, 0.85, and 0.89 for daily, monthly, 3-monthly, and yearly time periods, respectively. The intraclass correlations for self-reported working hours between the two questionnaire surveys were 0.63, 0.66, 0.73, and 0.87 for the respective time frames. The results of the present study among Japanese male employees suggest that the validity of self-reported working hours is high for all four time frames, whereas the reproducibility is moderate to high.

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.

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.

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.

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

Reproducibility of the measurement of sweet taste preferences.

PubMed

Asao, Keiko; Luo, Wendy; Herman, William H

2012-12-01

Developing interventions to prevent and treat obesity are medical and public health imperatives. Taste is a major determinant of food intake and reliable methods to measure taste preferences need to be established. This study aimed to establish the short-term reproducibility of sweet taste preference measurements using 5-level sucrose concentrations in healthy adult volunteers. We defined sweet taste preference as the geometric mean of the preferred sucrose concentration determined from two series of two-alternative, forced-choice staircase procedures administered 10min apart on a single day. We repeated the same procedures at a second visit 3-7days later. Twenty-six adults (13 men and 13 women, age 33.2±12.2years) completed the measurements. The median number of pairs presented for each series was three (25th and 75th percentiles: 3, 4). The intraclass correlation coefficients between the measurements was 0.82 (95% confidence interval [CI]: 0.63-0.92) within a few days. This study showed high short-term reproducibility of a simple, 5-level procedure for measuring sweet taste preferences. This method may be useful for assessing sweet taste preferences and the risks resulting from those preferences. Copyright © 2012 Elsevier Ltd. All rights reserved.

Development of Reproducible EST-derived SSR Markers and Assessment of Genetic Diversity in Panax ginseng Cultivars and Related Species

PubMed Central

Choi, Hong-Il; Kim, Nam Hoon; Kim, Jun Ha; Choi, Beom Soon; Ahn, In-Ok; Lee, Joon-Soo; Yang, Tae-Jin

2011-01-01

Little is known about the genetics or genomics of Panax ginseng. In this study, we developed 70 expressed sequence tag-derived polymorphic simple sequence repeat markers by trials of 140 primer pairs. All of the 70 markers showed reproducible polymorphism among four Panax speciesand 19 of them were polymorphic in six P. ginseng cultivars. These markers segregated 1:2:1 manner of Mendelian inheritance in an F2 population of a cross between two P. ginseng cultivars, ‘Yunpoong’ and ‘Chunpoong’, indicating that these are reproducible and inheritable mappable markers. A phylogenetic analysis using the genotype data showed three distinctive groups: a P. ginseng-P. japonicus clade, P. notoginseng and P. quinquefolius, with similarity coefficients of 0.70. P. japonicus was intermingled with P. ginseng cultivars, indicating that both species have similar genetic backgrounds. P. ginseng cultivars were subdivided into three minor groups: an independent cultivar ‘Chunpoong’, a subgroup with three accessions including two cultivars, ‘Gumpoong’ and ‘Yunpoong’ and one landrace ‘Hwangsook’ and another subgroup with two accessions including one cultivar, ‘Gopoong’ and one landrace ‘Jakyung’. Each primer pair produced 1 to 4 bands, indicating that the ginseng genome has a highly replicated paleopolyploid genome structure. PMID:23717085

Semiautomated, Reproducible Batch Processing of Soy

NASA Technical Reports Server (NTRS)

Thoerne, Mary; Byford, Ivan W.; Chastain, Jack W.; Swango, Beverly E.

2005-01-01

A computer-controlled apparatus processes batches of soybeans into one or more of a variety of food products, under conditions that can be chosen by the user and reproduced from batch to batch. Examples of products include soy milk, tofu, okara (an insoluble protein and fiber byproduct of soy milk), and whey. Most processing steps take place without intervention by the user. This apparatus was developed for use in research on processing of soy. It is also a prototype of other soy-processing apparatuses for research, industrial, and home use. Prior soy-processing equipment includes household devices that automatically produce soy milk but do not automatically produce tofu. The designs of prior soy-processing equipment require users to manually transfer intermediate solid soy products and to press them manually and, hence, under conditions that are not consistent from batch to batch. Prior designs do not afford choices of processing conditions: Users cannot use previously developed soy-processing equipment to investigate the effects of variations of techniques used to produce soy milk (e.g., cold grinding, hot grinding, and pre-cook blanching) and of such process parameters as cooking times and temperatures, grinding times, soaking times and temperatures, rinsing conditions, and sizes of particles generated by grinding. In contrast, the present apparatus is amenable to such investigations. The apparatus (see figure) includes a processing tank and a jacketed holding or coagulation tank. The processing tank can be capped by either of two different heads and can contain either of two different insertable mesh baskets. The first head includes a grinding blade and heating elements. The second head includes an automated press piston. One mesh basket, designated the okara basket, has oblong holes with a size equivalent to about 40 mesh [40 openings per inch (.16 openings per centimeter)]. The second mesh basket, designated the tofu basket, has holes of 70 mesh [70 openings

Sensitivity Gains, Linearity, and Spectral Reproducibility in Nonuniformly Sampled Multidimensional MAS NMR Spectra of High Dynamic Range.

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

Suiter, Christopher L.; Paramasivam, Sivakumar; Hou, Guangjin

Recently, we have demonstrated that considerable inherent sensitivity gains are attained in MAS NMR spectra acquired by nonuniform sampling (NUS) and introduced maximum entropy interpolation (MINT) processing that assures the linearity of transformation between the time and frequency domains. In this report, we examine the utility of the NUS/MINT approach in multidimensional datasets possessing high dynamic range, such as homonuclear 13C–13C correlation spectra. We demonstrate on model compounds and on 1–73-(U-13C,15N)/74–108-(U-15N) E. coli thioredoxin reassembly, that with appropriately constructed 50 % NUS schedules inherent sensitivity gains of 1.7–2.1-fold are readily reached in such datasets. We show that both linearity andmore » line width are retained under these experimental conditions throughout the entire dynamic range of the signals. Furthermore, we demonstrate that the reproducibility of the peak intensities is excellent in the NUS/MINT approach when experiments are repeated multiple times and identical experimental and processing conditions are employed. Finally, we discuss the principles for design and implementation of random exponentially biased NUS sampling schedules for homonuclear 13C–13C MAS correlation experiments that yield high quality artifact-free datasets.« less

Sensitivity gains, linearity, and spectral reproducibility in nonuniformly sampled multidimensional MAS NMR spectra of high dynamic range

PubMed Central

Suiter, Christopher L.; Paramasivam, Sivakumar; Hou, Guangjin; Sun, Shangjin; Rice, David; Hoch, Jeffrey C.; Rovnyak, David

2014-01-01

Recently, we have demonstrated that considerable inherent sensitivity gains are attained in MAS NMR spectra acquired by nonuniform sampling (NUS) and introduced maximum entropy interpolation (MINT) processing that assures the linearity of transformation between the time and frequency domains. In this report, we examine the utility of the NUS/MINT approach in multidimensional datasets possessing high dynamic range, such as homonuclear 13C–13C correlation spectra. We demonstrate on model compounds and on 1–73-(U-13C, 15N)/74–108-(U-15N) E. coli thioredoxin reassembly, that with appropriately constructed 50 % NUS schedules inherent sensitivity gains of 1.7–2.1-fold are readily reached in such datasets. We show that both linearity and line width are retained under these experimental conditions throughout the entire dynamic range of the signals. Furthermore, we demonstrate that the reproducibility of the peak intensities is excellent in the NUS/MINT approach when experiments are repeated multiple times and identical experimental and processing conditions are employed. Finally, we discuss the principles for design and implementation of random exponentially biased NUS sampling schedules for homonuclear 13C–13C MAS correlation experiments that yield high-quality artifact-free datasets. PMID:24752819

Parameter optimization for reproducible cardiac 1 H-MR spectroscopy at 3 Tesla.

PubMed

de Heer, Paul; Bizino, Maurice B; Lamb, Hildo J; Webb, Andrew G

2016-11-01

frequency selective excitation water suppression (7.0%). Using the optimized parameters an intrasession limits of agreement of the myocardial triglyceride content of -0.11% to +0.04%, and an intersession of -0.15% to +0.9%, were achieved. The coefficient of variation was 5% for the intrasession reproducibility and 6.5% for the intersession reproducibility. Using approaches designed to optimize SNR and minimize the variation in inter-average signal intensities and frequencies/phases, a protocol was developed to perform cardiac MR spectroscopy on a clinical 3T system with high reproducibility. J. Magn. Reson. Imaging 2016;44:1151-1158. © 2016 International Society for Magnetic Resonance in Medicine.

The construction of a two-dimensional reproducing kernel function and its application in a biomedical model.

PubMed

Guo, Qi; Shen, Shu-Ting

2016-04-29

There are two major classes of cardiac tissue models: the ionic model and the FitzHugh-Nagumo model. During computer simulation, each model entails solving a system of complex ordinary differential equations and a partial differential equation with non-flux boundary conditions. The reproducing kernel method possesses significant applications in solving partial differential equations. The derivative of the reproducing kernel function is a wavelet function, which has local properties and sensitivities to singularity. Therefore, study on the application of reproducing kernel would be advantageous. Applying new mathematical theory to the numerical solution of the ventricular muscle model so as to improve its precision in comparison with other methods at present. A two-dimensional reproducing kernel function inspace is constructed and applied in computing the solution of two-dimensional cardiac tissue model by means of the difference method through time and the reproducing kernel method through space. Compared with other methods, this method holds several advantages such as high accuracy in computing solutions, insensitivity to different time steps and a slow propagation speed of error. It is suitable for disorderly scattered node systems without meshing, and can arbitrarily change the location and density of the solution on different time layers. The reproducing kernel method has higher solution accuracy and stability in the solutions of the two-dimensional cardiac tissue model.

Fluctuation and reproducibility of exposure and effect of insulin glargine in healthy subjects.

PubMed

Becker, R H A; Frick, A D; Teichert, L; Nosek, L; Heinemann, L; Heise, T; Rave, K

2008-11-01

Low diurnal fluctuation and high day-to-day reproducibility in exposure and effect characterize beneficial basal insulin products. Two insulin glargine (LANTUS) formulations [without (R) or with polysorbate-20 (T)], added to minimize unfolding of proteins and subsequent formation of fibril structures, were assessed for equivalence in exposure and effect, and aspects of fluctuation and reproducibility in time-concentration and time-action profiles. A dose of 0.4 U/kg was subcutaneously administered to 24 healthy subjects in a two-sequence (R-T-R-T or T-R-T-R), randomized, four-way crossover trial utilizing 30-h Biostator-based euglycaemic glucose clamps. Identical serum insulin glargine concentration and time-action profiles established average, individual and population equivalence in insulin exposure and effect. Point estimates for 24-h area under the curve for insulin (INS-AUC(0-24) (h)) and glucose infusion rates (GIR-AUC(0-24) (h)) were 97% [90% confidence interval (CI): 91-103%] and 100% (88-114%), respectively. Within-subject variability (coefficient of variation) for INS-AUC(0-24) (h) and GIR-AUC(0-24) (h) were 19% (95% CI: 14-25%) and 34% (24-43%), respectively. The diurnal relative fluctuation of the serum insulin glargine concentration was 20% (95% CI: 19-21%). Insulin glargine in either formulation presents with a high day-to-day reproducibility of a uniform release after injection enabling an effective basal insulin supplementation.

Chimeric Mice with Competent Hematopoietic Immunity Reproduce Key Features of Severe Lassa Fever.

PubMed

Oestereich, Lisa; Lüdtke, Anja; Ruibal, Paula; Pallasch, Elisa; Kerber, Romy; Rieger, Toni; Wurr, Stephanie; Bockholt, Sabrina; Pérez-Girón, José V; Krasemann, Susanne; Günther, Stephan; Muñoz-Fontela, César

2016-05-01

Lassa fever (LASF) is a highly severe viral syndrome endemic to West African countries. Despite the annual high morbidity and mortality caused by LASF, very little is known about the pathophysiology of the disease. Basic research on LASF has been precluded due to the lack of relevant small animal models that reproduce the human disease. Immunocompetent laboratory mice are resistant to infection with Lassa virus (LASV) and, to date, only immunodeficient mice, or mice expressing human HLA, have shown some degree of susceptibility to experimental infection. Here, transplantation of wild-type bone marrow cells into irradiated type I interferon receptor knockout mice (IFNAR-/-) was used to generate chimeric mice that reproduced important features of severe LASF in humans. This included high lethality, liver damage, vascular leakage and systemic virus dissemination. In addition, this model indicated that T cell-mediated immunopathology was an important component of LASF pathogenesis that was directly correlated with vascular leakage. Our strategy allows easy generation of a suitable small animal model to test new vaccines and antivirals and to dissect the basic components of LASF pathophysiology.

Reflectance confocal microscopy and features of melanocytic lesions: an internet-based study of the reproducibility of terminology.

PubMed

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

2009-10-01

To test the interobserver and intraobserver reproducibility 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 reproducibility 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 reproducibility. However, less-than-ideal reproducibility 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 reproducibly recognized by independent observers.

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

APPARATUS FOR PRODUCING HIGH VELOCITY SHOCK WAVES IN GASES

DOEpatents

Scott, F.R.; Josephson, V.

1960-02-01

>A device for producing a high-energy ionized gas region comprises an evacuated tapered insulating vessel and a substantially hemispherical insulating cap hermetically affixed to the large end of the vessel, an annular electrode having a diameter equal to and supported in the interior wall of the vessel at the large end and having a conductive portion inside the vessel, a second electrode supported at the small end of the vessel, means connected to the vessel for introducing a selected gas therein, a source of high potential having two poles. means for connecting one pole of the high potential source to the annular electrode, and means for connecting the other pole of the potential source to the second electrode.

Method for producing through extrusion an anisotropic magnet with high energy product

DOEpatents

Chandhok, Vijay K.

2004-09-07

A method for producing an anisotropic magnet with high energy product through extrusion and, more specifically, by placing a particle charge of a composition from the which magnet is to be produced in a noncircular container, heating the container and particle charge and extruding the container and particle charge through a noncircular extrusion die in such a manner that one of the cross-sectional axes or dimension of the container and particle charge is held substantially constant during the extrusion to compact the particle charge to substantially full density by mechanical deformation produced during the extrusion to achieve a magnet with anisotropic magnetic properties along the axes or dimension thereof and, more specifically, a high energy product along the transverse of the smallest cross-sectional dimension of the extruded magnet.

Course Enrollment in the High School: The Perspective of Working-Class Females.

ERIC Educational Resources Information Center

Gaskell, Jane

1985-01-01

Interviews with high school senior girls in Vancouver, Canada, who selected business courses are used to illustrate how students' knowledge of the school and of the society produces course choices that in turn tend to reproduce class and gender categories. (RM)

Spiking Neural Network With Distributed Plasticity Reproduces Cerebellar Learning in Eye Blink Conditioning Paradigms.

PubMed

Antonietti, Alberto; Casellato, Claudia; Garrido, Jesús A; Luque, Niceto R; Naveros, Francisco; Ros, Eduardo; D' Angelo, Egidio; Pedrocchi, Alessandra

2016-01-01

In this study, we defined a realistic cerebellar model through the use of artificial spiking neural networks, testing it in computational simulations that reproduce associative motor tasks in multiple sessions of acquisition and extinction. By evolutionary algorithms, we tuned the cerebellar microcircuit to find out the near-optimal plasticity mechanism parameters that better reproduced human-like behavior in eye blink classical conditioning, one of the most extensively studied paradigms related to the cerebellum. We used two models: one with only the cortical plasticity and another including two additional plasticity sites at nuclear level. First, both spiking cerebellar models were able to well reproduce the real human behaviors, in terms of both "timing" and "amplitude", expressing rapid acquisition, stable late acquisition, rapid extinction, and faster reacquisition of an associative motor task. Even though the model with only the cortical plasticity site showed good learning capabilities, the model with distributed plasticity produced faster and more stable acquisition of conditioned responses in the reacquisition phase. This behavior is explained by the effect of the nuclear plasticities, which have slow dynamics and can express memory consolidation and saving. We showed how the spiking dynamics of multiple interactive neural mechanisms implicitly drive multiple essential components of complex learning processes.  This study presents a very advanced computational model, developed together by biomedical engineers, computer scientists, and neuroscientists. Since its realistic features, the proposed model can provide confirmations and suggestions about neurophysiological and pathological hypotheses and can be used in challenging clinical applications.

Reproducibility of flap thickness with IntraLase FS and Moria LSK-1 and M2 microkeratomes.

PubMed

Talamo, Jonathan H; Meltzer, Jeremy; Gardner, John

2006-06-01

To compare flap thickness reproducibility of the femtosecond laser and two mechanical microkeratomes. Flap thickness for all eyes was measured as the difference between the preoperative (day of surgery) full corneal thickness and post-flap creation central stromal bed thickness using ultrasonic pachymetry. Flap thickness values produced by three different microkeratome systems were compared for accuracy and reproducibility. For 99 flaps created using the IntraLase FS laser with an intended thickness of 110 microm, the mean achieved thickness was 119 +/- 12 microm (range: 82 to 149 microm). In 100 eyes treated with the Moria LSK-1 microkeratome with an intended flap thickness of 160 microm, the mean achieved thickness was 130 +/- 19 microm (range: 71 to 186 microm). In 135 eyes treated with the Moria M2 microkeratome with an intended flap thickness of 130 microm, mean thickness was 142 +/- 24 microm (range: 84 to 203 microm). The standard deviation and range of corneal flap thickness created with the IntraLase FS laser was significantly smaller than either mechanical microkeratome (P < .0001). When compared to two commonly used mechanical microkeratomes, mean achieved flap thickness was more reproducible with the IntraLase FS laser, reducing the comparative risk of overly thick flaps.

Female fecundity variation affects reproducibility of experiments on host plant preference and acceptance in a phytophagous insect

PubMed Central

Schäpers, Alexander; Petrén, Hampus; Wheat, Christopher W.; Wiklund, Christer

2017-01-01

Reproducibility is a scientific cornerstone. Many recent studies, however, describe a reproducibility crisis and call for assessments of reproducibility across scientific domains. Here, we explore the reproducibility of a classic ecological experiment—that of assessing female host plant preference and acceptance in phytophagous insects, a group in which host specialization is a key driver of diversification. We exposed multiple cohorts of Pieris napi butterflies from the same population to traditional host acceptance and preference tests on three Brassicaceae host species. Whereas the host plant rank order was highly reproducible, the propensity to oviposit on low-ranked hosts varied significantly even among cohorts exposed to similar conditions. Much variation could be attributed to among-cohort variation in female fecundity, a trait strongly correlated both to female size and to the size of the nuptial gift a female receives during mating. Small males provide small spermatophores, and in our experiment small females that mated with small males had a disproportionally low propensity to oviposit on low-ranked hosts. Hence, our results provide empirical support to the theoretical prediction that female host utilization is strongly affected by non-genetic, environmental variation, and that such variation can affect the reproducibility of ecological experiments even under seemingly identical conditions. PMID:28202813

HIGH ENERGY, HIGH BRIGHTNESS X-RAYS PRODUCED BY COMPTON BACKSCATTERING AT THE LIVERMORE PLEIADES FACILITY

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

Tremaine, A M; Anderson, S G; Betts, S

2005-05-19

PLEIADES (Picosecond Laser Electron Interaction for the Dynamic Evaluation of Structures) produces tunable 30-140 keV x-rays with 0.3-5 ps pulse lengths and up to 10{sup 7} photons/pulse by colliding a high brightness electron beam with a high power laser. The electron beam is created by an rf photo-injector system, accelerated by a 120 MeV linac, and focused to 20 {micro}m with novel permanent magnet quadrupoles. To produce Compton back scattered x-rays, the electron bunch is overlapped with a Ti:Sapphire laser that delivers 500 mJ, 100 fs, pulses to the interaction point. K-edge radiography at 115 keV on Uranium has verifiedmore » the angle correlated energy spectrum inherent in Compton scattering and high-energy tunability of the Livermore source. Current upgrades to the facility will allow laser pumping of targets synchronized to the x-ray source enabling dynamic diffraction and time-resolved studies of high Z materials. Near future plans include extending the radiation energies to >400 keV, allowing for nuclear fluorescence studies of materials.« less

Faster, More Reproducible DESI-MS for Biological Tissue Imaging

NASA Astrophysics Data System (ADS)

Tillner, Jocelyn; Wu, Vincen; Jones, Emrys A.; Pringle, Steven D.; Karancsi, Tamas; Dannhorn, Andreas; Veselkov, Kirill; McKenzie, James S.; Takats, Zoltan

2017-10-01

A new, more robust sprayer for desorption electrospray ionization (DESI) mass spectrometry imaging is presented. The main source of variability in DESI is thought to be the uncontrolled variability of various geometric parameters of the sprayer, primarily the position of the solvent capillary, or more specifically, its positioning within the gas capillary or nozzle. If the solvent capillary is off-center, the sprayer becomes asymmetrical, making the geometry difficult to control and compromising reproducibility. If the stiffness, tip quality, and positioning of the capillary are improved, sprayer reproducibility can be improved by an order of magnitude. The quality of the improved sprayer and its potential for high spatial resolution imaging are demonstrated on human colorectal tissue samples by acquisition of images at pixel sizes of 100, 50, and 20 μm, which corresponds to a lateral resolution of 40-60 μm, similar to the best values published in the literature. The high sensitivity of the sprayer also allows combination with a fast scanning quadrupole time-of-flight mass spectrometer. This provides up to 30 times faster DESI acquisition, reducing the overall acquisition time for a 10 mm × 10 mm rat brain sample to approximately 1 h. Although some spectral information is lost with increasing analysis speed, the resulting data can still be used to classify tissue types on the basis of a previously constructed model. This is particularly interesting for clinical applications, where fast, reliable diagnosis is required. [Figure not available: see fulltext.

Consistency and reproducibility of the VMAT plan delivery using three independent validation methods

PubMed Central

Chandraraj, Varatharaj; Manickam, Ravikumar; Esquivel, Carlos; Supe, Sanjay S; Papanikolaou, Nikos

2010-01-01

The complexity of VMAT delivery requires new methods and potentially new tools for the commissioning of these systems. It appears that great consideration is needed for quality assurance (QA) of these treatments since there are limited devices that are dedicated to the QA of rotational delivery. In this present study, we have evaluated the consistency and reproducibility of one prostate and one lung VMAT plans for 31 consecutive days using three different approaches: 1) MLC DynaLog files, 2) in vivo measurements using the multiwire ionization chamber DAVID, and 3) using PTWseven29 2D ARRAY with the OCTAVIUS phantom at our Varian Clinac linear accelerator. Overall, the three methods of testing the reproducibility and consistency of the VMAT delivery were in agreement with each other. All methods showed minimal daily deviations that contributed to clinically insignificant dose variations from day to day. Based on our results, we conclude that the VMAT delivery using a Varian 2100CD linear accelerator equipped with 120 MLC is highly reproducible. PACS numbers: 87.55.Qr and 87.56.Fc

Assessment of high and low enterotoxin A producing Staphylococcus aureus strains on pork sausage.

PubMed

Zeaki, Nikoleta; Cao, Rong; Skandamis, Panagiotis N; Rådström, Peter; Schelin, Jenny

2014-07-16

Three Staphylococcus aureus strains representing different alleles of the Siphoviridae prophage-encoded enterotoxin A (SEA) gene, including two high-SEA-producing strains and one low-SEA-producing strain were studied to investigate sea expression and SEA formation on a frankfurter type of sausage. The effect of lactic acid, an antimicrobial compound used as a preservative in food, was also investigated on the same product. All three strains were grown on pork sausages at 15°C for 14days in the presence or absence of lactic acid (1 or 2% v/v). Growth, sea mRNA expression and SEA formation were regularly monitored and compared between non-treated and treated sausages. For all experiments performed, the extracellular SEA formation significantly differed between the high- and low-SEA-producing strains, although growth and viability were overall the same. For the low producer (Sa51), the accumulated amount of extracellular SEA formed after 14days was close to the detection limit (less than 1ng/g) in all conditions; while Sa21 and Sa17, the two high-producing strains, formed 250±25.37ng/g and 750±82.65ng/g in non-treated sausage and 150±75.75ng/g and 300±83.89ng/g when treated with 1% lactic acid, respectively, after 14days. Sausages treated with 2% lactic acid followed the same pattern as above, but with an extended lag phase to 4days and reduced levels of enterotoxin formed for all strains. The difference in the level of SEA between the two high-producing strains is most likely due to the different clonal lineages of the sea-encoded Siphoviridae phages where induction of the prophage potentially could be the reason for higher production of SEA in one of the lines. Furthermore, a prolonged expression of sea gene in the two high-producing strains was observed during the entire incubation period, while the sea expression was under the detection limit in the low-producing strain. This study indicates that the high-SEA-producing strains, especially the strains with the

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...

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...

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

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

Highlights: Black-Right-Pointing-Pointer We design an innovative small-scale composting device including six 4-l reactors. Black-Right-Pointing-Pointer We investigate the performance and reproducibility of composting on a small scale. Black-Right-Pointing-Pointer Thermophilic conditions are established by self-heating in all replicates. Black-Right-Pointing-Pointer Biochemical transformations, organic matter losses and stabilisation are realistic. Black-Right-Pointing-Pointer The organic matter evolution exhibits good reproducibility for all six replicates. - Abstract: 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 creatingmore » 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{sub 2} consumption and CO{sub 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

Highly Sensitive, Uniform, and Reproducible Surface-Enhanced Raman Spectroscopy Substrate with Nanometer-Scale Quasi-periodic Nanostructures.

PubMed

Jin, Yuanhao; Wang, Yingcheng; Chen, Mo; Xiao, Xiaoyang; Zhang, Tianfu; Wang, Jiaping; Jiang, Kaili; Fan, Shoushan; Li, Qunqing

2017-09-20

We introduce a simple and cost-effective approach for fabrication of effective surface-enhanced Raman spectroscopy (SERS) substrates. It is shown that the as-fabricated substrates show excellent SERS effects in various probe molecules with high sensitivity, that is, picomolar level detection, and also good reliability. With a SERS enhancement factor beyond 10 8 and excellent reproducibility (deviation less than 5%) of signal intensity, the fabrication of the SERS substrate is realized on a four-inch wafer and proven to be effective in pesticide residue detection. The SERS substrate is realized first through the fabrication of quasi-periodic nanostructured silicon with dimension features in tens of nanometers using superaligned carbon nanotubes networks as an etching mask, after which a large amount of hot spots with nanometer gaps are formed through deposition of a gold film. With rigorous nanostructure design, the enhanced performance of electromagnetic field distribution for nanostructures is optimized. With the advantage of cost-effective large-area preparation, it is believed that the as-fabricated SERS substrate could be used in a wide variety of actual applications where detection of trace amounts is necessary.

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.

The substorm loading-unloading cycle as reproduced by community-available global MHD magnetospheric models

NASA Astrophysics Data System (ADS)

Gordeev, Evgeny; Sergeev, Victor; Tsyganenko, Nikolay; Kuznetsova, Maria; Rastaetter, Lutz; Raeder, Joachim; Toth, Gabor; Lyon, John; Merkin, Vyacheslav; Wiltberger, Michael

2017-04-01

In this study we investigate how well the three community-available global MHD models, supported by the Community Coordinated Modeling Center (CCMC NASA), reproduce the global magnetospheric dynamics, including the loading-unloading substorm cycle. We found that in terms of global magnetic flux transport CCMC models display systematically different response to idealized 2-hour north then 2-hour south IMF Bz variation. The LFM model shows a depressed return convection in the tail plasma sheet and high rate of magnetic flux loading into the lobes during the growth phase, as well as enhanced return convection and high unloading rate during the expansion phase, with the amount of loaded/unloaded magnetotail flux and the growth phase duration being the closest to their observed empirical values during isolated substorms. BATSRUS and Open GGCM models exhibit drastically different behavior. In the BATS-R-US model the plasma sheet convection shows a smooth transition to the steady convection regime after the IMF southward turning. In the Open GGCM a weak plasma sheet convection has comparable intensities during both the growth phase and the following slow unloading phase. Our study shows that different CCMC models under the same solar wind conditions (north to south IMF variation) produce essentially different solutions in terms of global magnetospheric convection.

Repeatability and reproducibility of optic nerve head perfusion measurements using optical coherence tomography angiography

NASA Astrophysics Data System (ADS)

Chen, Chieh-Li; Bojikian, Karine D.; Xin, Chen; Wen, Joanne C.; Gupta, Divakar; Zhang, Qinqin; Mudumbai, Raghu C.; Johnstone, Murray A.; Chen, Philip P.; Wang, Ruikang K.

2016-06-01

Optical coherence tomography angiography (OCTA) has increasingly become a clinically useful technique in ophthalmic imaging. We evaluate the repeatability and reproducibility of blood perfusion in the optic nerve head (ONH) measured using optical microangiography (OMAG)-based OCTA. Ten eyes from 10 healthy volunteers are recruited and scanned three times with a 68-kHz Cirrus HD-OCT 5000-based OMAG prototype system (Carl Zeiss Meditec Inc., Dublin, California) centered at the ONH involving two separate visits within six weeks. Vascular images are generated with OMAG processing by detecting the differences in OCT signals between consecutive B-scans acquired at the same retina location. ONH perfusion is quantified as flux, vessel area density, and normalized flux within the ONH for the prelaminar, lamina cribrosa, and the full ONH. Coefficient of variation (CV) and intraclass correlation coefficient (ICC) are used to evaluate intravisit and intervisit repeatability, and interobserver reproducibility. ONH perfusion measurements show high repeatability [CV≤3.7% (intravisit) and ≤5.2% (intervisit)] and interobserver reproducibility (ICC≤0.966) in all three layers by three metrics. OCTA provides a noninvasive method to visualize and quantify ONH perfusion in human eyes with excellent repeatability and reproducibility, which may add additional insight into ONH perfusion in clinical practice.

Validity and reproducibility of self-reported working hours among Japanese male employees

PubMed Central

Imai, Teppei; Kuwahara, Keisuke; Miyamoto, Toshiaki; Okazaki, Hiroko; Nishihara, Akiko; Kabe, Isamu; Mizoue, Tetsuya; Dohi, Seitaro

2016-01-01

Objective: Working long hours is a potential health hazard. Although self-reporting of working hours in various time frames has been used in epidemiologic studies, its validity is unclear. The objective of this study was to examine the validity and reproducibility of self-reported working hours among Japanese male employees. Methods: The participants were 164 male employees of four large-scale companies in Japan. For validity, the Spearman correlation between self-reported working hours in the second survey and the working hours recorded by the company was calculated for the following four time frames: daily working hours, monthly overtime working hours in the last month, average overtime working hours in the last 3 months, and the frequency of long working months (≥45 h/month) within the last 12 months. For reproducibility, the intraclass correlation between the first (September 2013) and second surveys (December 2013) was calculated for each of the four time frames. Results: The Spearman correlations between self-reported working hours and those based on company records were 0.74, 0.81, 0.85, and 0.89 for daily, monthly, 3-monthly, and yearly time periods, respectively. The intraclass correlations for self-reported working hours between the two questionnaire surveys were 0.63, 0.66, 0.73, and 0.87 for the respective time frames. Conclusions: The results of the present study among Japanese male employees suggest that the validity of self-reported working hours is high for all four time frames, whereas the reproducibility is moderate to high. PMID:27265530

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.

Reproducible and controllable induction voltage adder for scaled beam experiments

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

Sakai, Yasuo; Nakajima, Mitsuo; Horioka, Kazuhiko

2016-08-15

A reproducible 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 reproducible modulation voltages with jitter less than 0.3 ns. Preliminary beam compression experiments indicated that the induction adder can improve the reproducibility of modulation voltages and advance the beam physics experiments.

Method for producing high carrier concentration p-Type transparent conducting oxides

DOEpatents

Li, Xiaonan; Yan, Yanfa; Coutts, Timothy J.; Gessert, Timothy A.; Dehart, Clay M.

2009-04-14

A method for producing transparent p-type conducting oxide films without co-doping plasma enhancement or high temperature comprising: a) introducing a dialkyl metal at ambient temperature and a saturated pressure in a carrier gas into a low pressure deposition chamber, and b) introducing NO alone or with an oxidizer into the chamber under an environment sufficient to produce a metal-rich condition to enable NO decomposition and atomic nitrogen incorporation into the formed transparent metal conducting oxide.

Data Identifiers and Citations Enable Reproducible Science

NASA Astrophysics Data System (ADS)

Tilmes, C.

2011-12-01

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 reproduce 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 reproducibility. 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 reproduce the analyses and experiments to confirm the results. Describing the experiment to a sufficient extent to reproduce the research enforces a formal approach that lends credibility to the results, and ultimately, to the policies of decision makers depending on that research.

Intrathoracic Fat Measurements Using Multidetector Computed Tomography (MDCT): Feasibility and Reproducibility

PubMed Central

Stojanovska, Jadranka; Ibrahim, El-Sayed H.; Chughtai, Aamer R.; Jackson, Elizabeth A.; Gross, Barry H.; Jacobson, Jon A.; Tsodikov, Alexander; Daneshvar, Brian; Long, Benjamin D.; Chenevert, Thomas L.; Kazerooni, Ella A.

2017-01-01

Intrathoracic fat volume, more specifically, epicardial fat volume, is an emerging imaging biomarker of adverse cardiovascular events. The purpose of this work is to show the feasibility and reproducibility of intrathoracic fat volume measurement applied to contrast-enhanced multidetector computed tomography images. A retrospective cohort study of 62 subjects free of cardiovascular disease (55% females, age = 49 ± 11 years) conducted from 2008 to 2011 formed the study group. Intrathoracic fat volume was defined as all fat voxels measuring −50 to −250 Hounsfield Unit within the intrathoracic cavity from the level of the pulmonary artery bifurcation to the heart apex. The intrathoracic fat was separated into epicardial and extrapericardial fat by tracing the pericardium. The measurements were obtained by 2 readers and compared for interrater reproducibility. The fat volume measurements for the study group were 141 ± 72 cm3 for intrathoracic fat, 58 ± 27 cm3 for epicardial fat, and 84 ± 50 cm3 for extrapericardial fat. There was no statistically significant difference in intrathoracic fat volume measurements between the 2 readers, with correlation coefficients of 0.88 (P = .55) for intrathoracic fat volume and −0.12 (P = .33) for epicardial fat volume. Voxel-based measurement of intrathoracic fat, including the separation into epicardial and extrapericardial fat, is feasible and highly reproducible from multidetector computed tomography scans. PMID:28626797

Pulsed discharges produced by high-power surface waves

NASA Astrophysics Data System (ADS)

Böhle, A.; Ivanov, O.; Kolisko, A.; Kortshagen, U.; Schlüter, H.; Vikharev, A.

1996-02-01

The mechanisms of the ionization front advance in surface-wave-produced discharges are investigated using two experimental set-ups. The high-power surface waves are excited in a 3 cm wavelength band by a surfaguide and a novel type of launcher (an E-plane junction). The ionization front velocity of the surface wave is measured for a wide range of gas pressures, incident microwave power and initial pre-ionization. The experimental results are compared with theoretical ones based on three different models. The comparison between theory and experiment allows one to suggest a new interpretation of the ionization front's advance. The ionization front velocity is determined by a breakdown wave or an ionization wave in the electric field of a high-power surface wave in the zone near the ionization front.

A Novel Extraction Method Combining Plasma with a Whole-Blood Fraction Shows Excellent Sensitivity and Reproducibility for Patients at High Risk for Invasive Aspergillosis

PubMed Central

Springer, Jan; Schloßnagel, Hannes; Heinz, Werner; Doedt, Thomas; Soeller, Rainer; Einsele, Hermann

2012-01-01

Diagnosis of invasive aspergillosis (IA) is still a major problem in routine clinical practice. Early diagnosis is essential for a good patient prognosis. PCR is a highly sensitive method for the detection of nucleic acids and could play an important role in improving the diagnosis of fungal infections. Therefore, a novel DNA extraction method, ultraclean production (UCP), was developed allowing purification of both cellular and cell-free circulating fungal DNA. In this prospective study we evaluated the commercially available UCP extraction system and compared it to an in-house system. Sixty-three patients at high risk for IA were screened twice weekly, and DNA extracted by both methods was cross-analyzed, in triplicate, by two different real-time PCR assays. The negative predictive values were high for all methods (94.3 to 100%), qualifying them as screening methods, but the sensitivity and diagnostic odds ratios were higher using the UCP extraction method. Sensitivity ranged from 33.3 to 66.7% using the in-house extracts to 100% using the UCP extraction method. Most of the unclassified patients showed no positive PCR results; however, single-positive PCR replicates were observed in some cases. These can bear clinical relevance but should be interpreted with additional clinical and laboratory data. The PCR assays from the UCP extracts showed greater reproducibility than the in-house method for probable IA patients. The standardized UCP extraction method yielded superior results, with regard to sensitivity and reproducibility, than the in-house method. This was independent of the PCR assay used to detect fungal DNA in the sample extracts. PMID:22593600

Method and apparatus for producing high purity silicon

DOEpatents

Olson, Jerry M.

1984-01-01

A method for producing high purity silicon includes forming a copper silie alloy and positioning the alloy within an enclosure. A filament member is also placed within the enclosure opposite the alloy. The enclosure is then filled with a chemical vapor transport gas adapted for transporting silicon. Finally, both the filament member and the alloy are heated to temperatures sufficient to cause the gas to react with silicon at the alloy surface and deposit the reacted silicon on the filament member. In addition, an apparatus for carrying out this method is also disclosed.

Method and apparatus for producing high purity silicon

DOEpatents

Olson, J.M.

1983-05-27

A method for producing high purity silicon includes forming a copper silicide alloy and positioning the alloy within an enclosure. A filament member is also placed within the enclosure opposite the alloy. The enclosure is then filled with a chemical vapor transport gas adapted for transporting silicon. Finally, both the filament member and the alloy are heated to temperatures sufficient to cause the gas to react with silicon at the alloy surface and deposit the reacted silicon on the filament member. In addition, an apparatus for carrying out this method is also disclosed.

Reproducible research in vadose zone sciences

USDA-ARS?s Scientific Manuscript database

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 reproducing and building o...

Comparative Proteome Analysis between High Lipid-Producing Strain Mucor circinelloides WJ11 and Low Lipid-Producing Strain CBS 277.49.

PubMed

Tang, Xin; Chen, Haiqin; Gu, Zhennan; Zhang, Hao; Chen, Yong Q; Song, Yuanda; Chen, Wei

2017-06-21

Mucor circinelloides is one of few oleaginous fungi that produces a useful oil rich in γ-linolenic acid, but it usually only produces <25% total lipid. Nevertheless, we isolated a new strain WJ11 that can produce up to 36% lipid of cell dry weight. In this study, we have systematically analyzed the global changes in protein levels between the high lipid-producing strain WJ11 and the low lipid-producing strain CBS 277.49 (15%, lipid/cell dry weight) at lipid accumulation phase through comparative proteome analysis. Proteome analysis demonstrated that the branched-chain amino acid and lysine metabolism, glycolytic pathway, and pentose phosphate pathway in WJ11 were up-regulated, while the activities of tricarboxylic acid cycle and branch point enzyme for synthesis of isoprenoids were retarded compared with CBS 277.49. The coordinated regulation at proteome level indicate that more acetyl-CoA and NADPH are provided for fatty acid biosynthesis in WJ11 compared with CBS 277.49.

Heavily loaded ferrite-polymer composites to produce high refractive index materials at centimetre wavelengths

NASA Astrophysics Data System (ADS)

Parke, L.; Hooper, I. R.; Hicken, R. J.; Dancer, C. E. J.; Grant, P. S.; Youngs, I. J.; Sambles, J. R.; Hibbins, A. P.

2013-10-01

A cold-pressing technique has been developed for fabricating composites composed of a polytetrafluoroethylene-polymer matrix and a wide range of volume-fractions of MnZn-ferrite filler (0%-80%). The electromagnetic properties at centimetre wavelengths of all prepared composites exhibited good reproducibility, with the most heavily loaded composites possessing simultaneously high permittivity (180 ± 10) and permeability (23 ± 2). The natural logarithm of both the relative complex permittivity and permeability shows an approximately linear dependence with the volume fraction of ferrite. Thus, this simple method allows for the manufacture of bespoke materials required in the design and construction of devices based on the principles of transformation optics.

An Open Science and Reproducible Research Primer for Landscape Ecologists

EPA Science Inventory

In recent years many funding agencies, some publishers, and even the United States government have enacted policies that encourage open science and strive for reproducibility; however, the knowledge and skills to implement open science and enable reproducible research are not yet...

High-strength, creep-resistant molybdenum alloy and process for producing the same

DOEpatents

Bianco, Robert; Buckman, Jr., R. William; Geller, Clint B.

1999-01-01

A wet-doping process for producing an oxide-dispersion strengthened (ODS), creep-resistant molybdenum alloy is disclosed. The alloy is made by adding nitrate or acetate salts of lanthanum, cerium, thorium, or yttrium to molybdenum oxide to produce a slurry, heating the slurry in a hydrogen atmosphere to produce a powder, mixing and cold isostatically pressing the powder, sintering in a hydrogen atmosphere, and thermomechanically processing (swaging, extruding, cold drawing) the product. The ODS molybdenum alloy produced by the process contains 2-4% by volume (.about.1-4% by weight) of an oxide of lanthanum, cerium, thorium, or yttrium. The alloy has high strength and improved creep-resistance at temperatures greater than 0.55T.sub.m of molybdenum.

Reproducible culture and differentiation of mouse embryonic stem cells using an automated microwell platform☆

PubMed Central

Hussain, Waqar; Moens, Nathalie; Veraitch, Farlan S.; Hernandez, Diana; Mason, Chris; Lye, Gary J.

2013-01-01

The use of embryonic stem cells (ESCs) and their progeny in high throughput drug discovery and regenerative medicine will require production at scale of well characterized cells at an appropriate level of purity. The adoption of automated bioprocessing techniques offers the possibility to overcome the lack of consistency and high failure rates seen with current manual protocols. To build the case for increased use of automation this work addresses the key question: “can an automated system match the quality of a highly skilled and experienced person working manually?” To answer this we first describe an integrated automation platform designed for the ‘hands-free’ culture and differentiation of ESCs in microwell formats. Next we outline a framework for the systematic investigation and optimization of key bioprocess variables for the rapid establishment of validatable Standard Operating Procedures (SOPs). Finally the experimental comparison between manual and automated bioprocessing is exemplified by expansion of the murine Oct-4-GiP ESC line over eight sequential passages with their subsequent directed differentiation into neural precursors. Our results show that ESCs can be effectively maintained and differentiated in a highly reproducible manner by the automated system described. Statistical analysis of the results for cell growth over single and multiple passages shows up to a 3-fold improvement in the consistency of cell growth kinetics with automated passaging. The quality of the cells produced was evaluated using a panel of biological markers including cell growth rate and viability, nutrient and metabolite profiles, changes in gene expression and immunocytochemistry. Automated processing of the ESCs had no measurable negative effect on either their pluripotency or their ability to differentiate into the three embryonic germ layers. Equally important is that over a 6-month period of culture without antibiotics in the medium, we have not had any cases

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

Diffusion Properties and 3D Architecture of Human Lower Leg Muscles Assessed with Ultra-High-Field-Strength Diffusion-Tensor MR Imaging and Tractography: Reproducibility and Sensitivity to Sex Difference and Intramuscular Variability.

PubMed

Fouré, Alexandre; Ogier, Augustin C; Le Troter, Arnaud; Vilmen, Christophe; Feiweier, Thorsten; Guye, Maxime; Gondin, Julien; Besson, Pierre; Bendahan, David

2018-05-01

Purpose To demonstrate the reproducibility of the diffusion properties and three-dimensional structural organization measurements of the lower leg muscles by using diffusion-tensor imaging (DTI) assessed with ultra-high-field-strength (7.0-T) magnetic resonance (MR) imaging and tractography of skeletal muscle fibers. On the basis of robust statistical mapping analyses, this study also aimed at determining the sensitivity of the measurements to sex difference and intramuscular variability. Materials and Methods All examinations were performed with ethical review board approval; written informed consent was obtained from all volunteers. Reproducibility of diffusion tensor indexes assessment including eigenvalues, mean diffusivity, and fractional anisotropy (FA) as well as muscle volume and architecture (ie, fiber length and pennation angle) were characterized in lower leg muscles (n = 8). Intramuscular variability and sex differences were characterized in young healthy men and women (n = 10 in each group). Student t test, statistical parametric mapping, correlation coefficients (Spearman rho and Pearson product-moment) and coefficient of variation (CV) were used for statistical data analysis. Results High reproducibility of measurements (mean CV ± standard deviation, 4.6% ± 3.8) was determined in diffusion properties and architectural parameters. Significant sex differences were detected in FA (4.2% in women for the entire lower leg; P = .001) and muscle volume (21.7% in men for the entire lower leg; P = .008), whereas architecture parameters were almost identical across sex. Additional differences were found independently of sex in diffusion properties and architecture along several muscles of the lower leg. Conclusion The high-spatial-resolution DTI assessed with 7.0-T MR imaging allows a reproducible assessment of structural organization of superficial and deep muscles, giving indirect information on muscle function. © RSNA, 2018 Online supplemental material is

Understanding high wintertime ozone pollution events in an oil- and natural gas-producing region of the western US

NASA Astrophysics Data System (ADS)

Ahmadov, R.; McKeen, S.; Trainer, M.; Banta, R.; Brewer, A.; Brown, S.; Edwards, P. M.; de Gouw, J. A.; Frost, G. J.; Gilman, J.; Helmig, D.; Johnson, B.; Karion, A.; Koss, A.; Langford, A.; Lerner, B.; Olson, J.; Oltmans, S.; Peischl, J.; Pétron, G.; Pichugina, Y.; Roberts, J. M.; Ryerson, T.; Schnell, R.; Senff, C.; Sweeney, C.; Thompson, C.; Veres, P. R.; Warneke, C.; Wild, R.; Williams, E. J.; Yuan, B.; Zamora, R.

2015-01-01

Recent increases in oil and natural gas (NG) production throughout the western US have come with scientific and public interest in emission rates, air quality and climate impacts related to this industry. This study uses a regional-scale air quality model (WRF-Chem) to simulate high ozone (O3) episodes during the winter of 2013 over the Uinta Basin (UB) in northeastern Utah, which is densely populated by thousands of oil and NG wells. The high-resolution meteorological simulations are able qualitatively to reproduce the wintertime cold pool conditions that occurred in 2013, allowing the model to reproduce the observed multi-day buildup of atmospheric pollutants and the accompanying rapid photochemical ozone formation in the UB. Two different emission scenarios for the oil and NG sector were employed in this study. The first emission scenario (bottom-up) was based on the US Environmental Protection Agency (EPA) National Emission Inventory (NEI) (2011, version 1) for the oil and NG sector for the UB. The second emission scenario (top-down) was based on estimates of methane (CH4) emissions derived from in situ aircraft measurements and a regression analysis for multiple species relative to CH4 concentration measurements in the UB. Evaluation of the model results shows greater underestimates of CH4 and other volatile organic compounds (VOCs) in the simulation with the NEI-2011 inventory than in the case when the top-down emission scenario was used. Unlike VOCs, the NEI-2011 inventory significantly overestimates the emissions of nitrogen oxides (NOx), while the top-down emission scenario results in a moderate negative bias. The model simulation using the top-down emission case captures the buildup and afternoon peaks observed during high O3 episodes. In contrast, the simulation using the bottom-up inventory is not able to reproduce any of the observed high O3 concentrations in the UB. Simple emission reduction scenarios show that O3 production is VOC sensitive and NOx

Deposition method for producing silicon carbide high-temperature semiconductors

DOEpatents

Hsu, George C.; Rohatgi, Naresh K.

1987-01-01

An improved deposition method for producing silicon carbide high-temperature semiconductor material comprising placing a semiconductor substrate composed of silicon carbide in a fluidized bed silicon carbide deposition reactor, fluidizing the bed particles by hydrogen gas in a mildly bubbling mode through a gas distributor and heating the substrate at temperatures around 1200.degree.-1500.degree. C. thereby depositing a layer of silicon carbide on the semiconductor substrate.

A new paradigm for reproducing and analyzing N-body simulations of planetary systems

NASA Astrophysics Data System (ADS)

Rein, Hanno; Tamayo, Daniel

2017-05-01

The reproducibility of experiments is one of the main principles of the scientific method. However, numerical N-body experiments, especially those of planetary systems, are currently not reproducible. In the most optimistic scenario, they can only be replicated in an approximate or statistical sense. Even if authors share their full source code and initial conditions, differences in compilers, libraries, operating systems or hardware often lead to qualitatively different results. We provide a new set of easy-to-use, open-source tools that address the above issues, allowing for exact (bit-by-bit) reproducibility of N-body experiments. In addition to generating completely reproducible integrations, we show that our framework also offers novel and innovative ways to analyse these simulations. As an example, we present a high-accuracy integration of the Solar system spanning 10 Gyr, requiring several weeks to run on a modern CPU. In our framework, we can not only easily access simulation data at predefined intervals for which we save snapshots, but at any time during the integration. We achieve this by integrating an on-demand reconstructed simulation forward in time from the nearest snapshot. This allows us to extract arbitrary quantities at any point in the saved simulation exactly (bit-by-bit), and within seconds rather than weeks. We believe that the tools we present in this paper offer a new paradigm for how N-body simulations are run, analysed and shared across the community.

SUSHI: an exquisite recipe for fully documented, reproducible and reusable NGS data analysis.

PubMed

Hatakeyama, Masaomi; Opitz, Lennart; Russo, Giancarlo; Qi, Weihong; Schlapbach, Ralph; Rehrauer, Hubert

2016-06-02

Next generation sequencing (NGS) produces massive datasets consisting of billions of reads and up to thousands of samples. Subsequent bioinformatic analysis is typically done with the help of open source tools, where each application performs a single step towards the final result. This situation leaves the bioinformaticians with the tasks to combine the tools, manage the data files and meta-information, document the analysis, and ensure reproducibility. We present SUSHI, an agile data analysis framework that relieves bioinformaticians from the administrative challenges of their data analysis. SUSHI lets users build reproducible data analysis workflows from individual applications and manages the input data, the parameters, meta-information with user-driven semantics, and the job scripts. As distinguishing features, SUSHI provides an expert command line interface as well as a convenient web interface to run bioinformatics tools. SUSHI datasets are self-contained and self-documented on the file system. This makes them fully reproducible and ready to be shared. With the associated meta-information being formatted as plain text tables, the datasets can be readily further analyzed and interpreted outside SUSHI. SUSHI provides an exquisite recipe for analysing NGS data. By following the SUSHI recipe, SUSHI makes data analysis straightforward and takes care of documentation and administration tasks. Thus, the user can fully dedicate his time to the analysis itself. SUSHI is suitable for use by bioinformaticians as well as life science researchers. It is targeted for, but by no means constrained to, NGS data analysis. Our SUSHI instance is in productive use and has served as data analysis interface for more than 1000 data analysis projects. SUSHI source code as well as a demo server are freely available.

How reproducible is cutaneous electrogastrography? An in-depth evidence-based study.

PubMed

Jonderko, K; Kasicka-Jonderko, A; Krusiec-Swidergoł, B; Dzielicki, M; Strój, L; Doliński, M; Doliński, K; Błońska-Fajfrowska, B

2005-12-01

To check on reproducibility 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 reproducibility, whereas fair reproducibility 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 reproducibility any worse than the short term one. Categorical data analysis revealed that the relative time share of normogastria postprandially exhibited a better reproducibility than in the fasted period. The Cohen's kappa-value of 0.459 for the DeltaDP for the medium term reproducibility 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 reproducibility. The feasibility of some electrogastrographic parameters to convey clinically useful information may be hampered by their fair reproducibility. Recoding of parameters of the cutaneous electrogastrogram from primary continuous to secondary categorical may help achieve a better agreement between repeat examinations.

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.

Polarized Th2 like cells, in the absence of Th0 cells, are responsible for lymphocyte produced IL-4 in high IgE-producer schistosomiasis patients.

PubMed

Dutra, Walderez O; Correa-Oliveira, Rodrigo; Dunne, David; Cecchini, Luiza Fosenca; Fraga, Lúcia; Roberts, Morven; Soares-Silveira, Alda Maria; Webster, Michelle; Yssel, Hans; Gollob, Kenneth J

2002-07-06

Human resistance to re-infection with S. mansoni is correlated with high levels of anti-soluble adult worm antigens (SWAP) IgE. Although it has been shown that IL-4 and IL-5 are crucial in establishing IgE responses in vitro, the active in vivo production of these cytokines by T cells, and the degree of polarization of Th2 vs. Th0 in human schistosomiasis is not known. To address this question, we determined the frequency of IL-4 and IFN-gamma or IL-5 and IL-2 producing lymphocytes from schistosomiasis patients with high or low levels of IgE anti-SWAP. Our analysis showed that high and low IgE-producers responded equally to schistosomiasis antigens as determined by proliferation. Moreover, patients from both groups displayed similar percentages of circulating lymphocytes. However, high IgE-producers had an increased percentage of activated CD4+ T cells as compared to the low IgE-producers. Moreover, intracellular cytokine analysis, after short-term stimulation with anti-CD3/CD28 mAbs, showed that IgE high-producers display an increase in the percentage of T lymphocytes expressing IL-4 and IL-5 as compared to IgE low-responders. A coordinate control of the frequency of IL-4 and IL-5 producing lymphocytes in IgE high, but not IgE low-responders, was observed. High IgE phenotype human schistosomiasis patients exhibit a coordinate regulation of IL-4 and IL-5 producing cells and the lymphocyte derived IL-4 comes from true polarized Th2 like cells, in the absence of measurable Th0 cells as measured by co-production of IL-4 and IFN-gamma.

Polarized Th2 like cells, in the absence of Th0 cells, are responsible for lymphocyte produced IL-4 in high IgE-producer schistosomiasis patients

PubMed Central

Dutra, Walderez O; Correa-Oliveira, Rodrigo; Dunne, David; Cecchini, Luiza Fosenca; Fraga, Lúcia; Roberts, Morven; Soares-Silveira, Alda Maria; Webster, Michelle; Yssel, Hans; Gollob, Kenneth J

2002-01-01

Background Human resistance to re-infection with S. mansoni is correlated with high levels of anti-soluble adult worm antigens (SWAP) IgE. Although it has been shown that IL-4 and IL-5 are crucial in establishing IgE responses in vitro, the active in vivo production of these cytokines by T cells, and the degree of polarization of Th2 vs. Th0 in human schistosomiasis is not known. To address this question, we determined the frequency of IL-4 and IFN-γ or IL-5 and IL-2 producing lymphocytes from schistosomiasis patients with high or low levels of IgE anti-SWAP. Results Our analysis showed that high and low IgE-producers responded equally to schistosomiasis antigens as determined by proliferation. Moreover, patients from both groups displayed similar percentages of circulating lymphocytes. However, high IgE-producers had an increased percentage of activated CD4+ T cells as compared to the low IgE-producers. Moreover, intracellular cytokine analysis, after short-term stimulation with anti-CD3/CD28 mAbs, showed that IgE high-producers display an increase in the percentage of T lymphocytes expressing IL-4 and IL-5 as compared to IgE low-responders. A coordinate control of the frequency of IL-4 and IL-5 producing lymphocytes in IgE high, but not IgE low-responders, was observed. Conclusions High IgE phenotype human schistosomiasis patients exhibit a coordinate regulation of IL-4 and IL-5 producing cells and the lymphocyte derived IL-4 comes from true polarized Th2 like cells, in the absence of measurable Th0 cells as measured by co-production of IL-4 and IFN-γ. PMID:12100735

Measures of low back function: a review of reproducibility studies.

PubMed

Essendrop, Morten; Maul, Irina; Läubli, Thomas; Riihimäki, Hilkka; Schibye, Bente

2002-05-01

The objective of the present study was to make a systematic literature review with preset quality criteria concerning reproducibility 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 reproducibility 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 reproducibility 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 reproducibility 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 reproducibility will be helpful both as a survey of tests, and to provide information on the usefulness in relation to the level of reproducibility.

Benchmarking contactless acquisition sensor reproducibility for latent fingerprint trace evidence

NASA Astrophysics Data System (ADS)

Hildebrandt, Mario; Dittmann, Jana

2015-03-01

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 reproducibility 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 reproducibility 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 reproducibility 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 (reproducible) and large differences (non-reproducible). Furthermore, we suggest comparing the classification results with biometric verification scores (calculated with NBIS, with threshold of 40) as biometric reproducibility 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.

The MIMIC Code Repository: enabling reproducibility in critical care research.

PubMed

Johnson, Alistair Ew; Stone, David J; Celi, Leo A; Pollard, Tom J

2018-01-01

Lack of reproducibility 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 reproducible 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 reproduce 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 reproduce 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 reproducible. By providing open source code alongside the freely accessible MIMIC-III database, we enable end-to-end reproducible analysis of electronic health records. © The Author 2017. Published by Oxford University Press on behalf of the American Medical Informatics Association.

Reproducibility of an aerobic endurance test for nonexpert swimmers

PubMed Central

Veronese da Costa, Adalberto; Costa, Manoel da Cunha; Carlos, Daniel Medeiros; Guerra, Luis Marcos de Medeiros; Silva, Antônio José; Barbosa, Tiago Manoel Cabral dos Santos

2012-01-01

of swimmers. Conclusion: The Progressive Swim Test for nonexpert swimmers produces comparable results for noncompetitive swimmers with a favorable degree of reproducibility, thus presenting possible applications for researching the physiological performance of nonexpert swimmers. PMID:23055740

Estimating high mosquito-producing rice fields using spectral and spatial data

NASA Technical Reports Server (NTRS)

Wood, B. L.; Beck, L. R.; Washino, R. K.; Hibbard, K. A.; Salute, J. S.

1992-01-01

The cultivation of irrigated rice provides ideal larval habitat for a number of anopheline vectors of malaria throughout the world. Anopheles freeborni, a potential vector of human malaria, is associated with the nearly 240,000 hectares of irrigated rice grown annually in Northern and Central California; therefore, this species can serve as a model for the study of rice field anopheline population dynamics. Analysis of field data revealed that rice fields with early season canopy development, that are located near bloodmeal sources (i.e., pastures with livestock) were more likely to produce anopheline larvae than fields with less developed canopies located further from pastures. Remote sensing reflectance measurements of early-season canopy development and geographic information system (GIS) measurements of distanes between rice fields and pastures with livestock were combined to distinguish between high and low mosquito-producing rice fields. Using spectral and distance measures in either a discriminant or Bayesian analysis, the identification of high mosquito-producing fields was made with 85 percent accuracy nearly two months before anopheline larval populations peaked. Since omission errors were also minimized by these approaches, they could provide a new basis for directing abatement techniques for the control of malaria vectors.

Sensitivity, specificity, and reproducibility of four measures of laboratory turnaround time.

PubMed

Valenstein, P N; Emancipator, K

1989-04-01

The authors studied the performance of four measures of laboratory turnaround time: the mean, median, 90th percentile, and proportion of tests reported within a predetermined cut-off interval (proportion of acceptable tests [PAT]). Measures were examined with the use of turnaround time data from 11,070 stat partial thromboplastin times, 16,761 urine cultures, and 28,055 stat electrolyte panels performed by a single laboratory. For laboratories with long turnaround times, the most important quality of a turnaround time measure is high reproducibility, so that improvement in reporting speed can be distinguished from random variation resulting from sampling. The mean was found to be the most reproducible of the four measures, followed by the median. The mean achieved acceptable precision with sample sizes of 100-500 tests. For laboratories with normally rapid turnaround times, the most important quality of a measure is high sensitivity and specificity for detecting whether turnaround time has dropped below standards. The PAT was found to be the best measure of turnaround time in this setting but required sample sizes of at least 500 tests to achieve acceptable accuracy. Laboratory turnaround time may be measured for different reasons. The method of measurement should be chosen with an eye toward its intended application.

Reproducibility of food consumption frequencies derived from the Children's Eating Habits Questionnaire used in the IDEFICS study.

PubMed

Lanfer, A; Hebestreit, A; Ahrens, W; Krogh, V; Sieri, S; Lissner, L; Eiben, G; Siani, A; Huybrechts, I; Loit, H-M; Papoutsou, S; Kovács, E; Pala, V

2011-04-01

To investigate the reproducibility of food consumption frequencies derived from the food frequency section of the Children's Eating Habits Questionnaire (CEHQ-FFQ) that was developed and used in the IDEFICS (Identification and prevention of dietary- and lifestyle-induced health effects in children and infants) project to assess food habits in 2- to 9-year-old European children. From a subsample of 258 children who participated in the IDEFICS baseline examination, parental questionnaires of the CEHQ were collected twice to assess reproducibility of questionnaire results from 0 to 354 days after the first examination. Weighted Cohen's kappa coefficients (κ) and Spearman's correlation coefficients (r) were calculated to assess agreement between the first and second questionnaires for each food item of the CEHQ-FFQ. Stratification was performed for sex, age group, geographical region and length of period between the first and second administrations. Fisher's Z transformation was applied to test correlation coefficients for significant differences between strata. For all food items analysed, weighted Cohen's kappa coefficients (κ) and Spearman's correlation coefficients (r) were significant and positive (P<0.001). Reproducibility was lowest for diet soft drinks (κ=0.23, r=0.32) and highest for sweetened milk (κ=0.68, r=0.76). Correlation coefficients were comparable to those of previous studies on FFQ reproducibility in children and adults. Stratification did not reveal systematic differences in reproducibility by sex and age group. Spearman's correlation coefficients differed significantly between northern and southern European countries for 10 food items. In nine of them, the lower respective coefficient was still high enough to conclude acceptable reproducibility. As expected, longer time (>128 days) between the first and second administrations resulted in a generally lower, yet still acceptable, reproducibility. Results indicate that the CEHQ-FFQ gives

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.

High-strength, creep-resistant molybdenum alloy and process for producing the same

DOEpatents

Bianco, R.; Buckman, R.W. Jr.; Geller, C.B.

1999-02-09

A wet-doping process for producing an oxide-dispersion strengthened (ODS), creep-resistant molybdenum alloy is disclosed. The alloy is made by adding nitrate or acetate salts of lanthanum, cerium, thorium, or yttrium to molybdenum oxide to produce a slurry, heating the slurry in a hydrogen atmosphere to produce a powder, mixing and cold isostatically pressing the powder, sintering in a hydrogen atmosphere, and thermomechanically processing (swaging, extruding, cold drawing) the product. The ODS molybdenum alloy produced by the process contains 2--4% by volume (ca. 1--4% by weight) of an oxide of lanthanum, cerium, thorium, or yttrium. The alloy has high strength and improved creep-resistance at temperatures greater than 0.55T{sub m} of molybdenum. 10 figs.

Process for producing high purity isoolefins and dimers thereof by dissociation of ethers

DOEpatents

Smith, L.A. Jr.; Jones, E.M. Jr.; Hearn, D.

1984-05-08

Alkyl tertiary butyl ether or alkyl tertiary amyl ether is dissociated by vapor phase contact with a cation acidic exchange resin at temperatures in the range of 150 to 250 F at LHSV of 0.1 to 20 to produce a stream consisting of unreacted ether, isobutene or isoamylene and an alcohol corresponding to the alkyl radical. After the alcohol is removed, the ether/isoolefin stream may be fractionated to obtain a high purity isoolefin (99+%) or the ether/isoolefin stream can be contacted in liquid phase with a cation acidic exchange resin to selectively dimerize the isoolefin in a highly exothermic reaction, followed by fractionation of the dimerization product to produce high purity diisoolefin (97+%). In the case where the alkyl is C[sub 3] to C[sub 6] and the corresponding alcohol is produced on dissociation of the ether, combined dissociation-distillation may be carried out such that isoolefin is the overhead product and alcohol the bottom. 2 figs.

Process for producing high purity isoolefins and dimers thereof by dissociation of ethers

DOEpatents

Smith, Jr., Lawrence A.; Jones, Jr., Edward M.; Hearn, Dennis

1984-01-01

Alkyl tertiary butyl ether or alkyl tertiary amyl ether is dissociated by vapor phase contact with a cation acidic exchange resin at temperatures in the range of 150.degree. to 250.degree. F. at LHSV of 0.1 to 20 to produce a stream consisting of unreacted ether, isobutene or isoamylene and an alcohol corresponding to the alkyl radical. After the alcohol is removed, the ether/isoolefin stream may be fractionated to obtain a high purity isoolefin (99+%) or the ether/isoolefin stream can be contacted in liquid phase with a cation acidic exchange resin to selectively dimerize the isoolefin in a highly exothermic reaction, followed by fractionation of the dimerization product to produce high purity diisoolefin (97+%). In the case where the alkyl is C.sub.3 to C.sub.6 and the corresponding alcohol is produced on dissociation of the ether, combined dissociation-distillation may be carried out such that isoolefin is the overhead product and alcohol the bottom.

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.

Desalination and reuse of high-salinity shale gas produced water: drivers, technologies, and future directions.

PubMed

Shaffer, Devin L; Arias Chavez, Laura H; Ben-Sasson, Moshe; Romero-Vargas Castrillón, Santiago; Yip, Ngai Yin; Elimelech, Menachem

2013-09-03

In the rapidly developing shale gas industry, managing produced water is a major challenge for maintaining the profitability of shale gas extraction while protecting public health and the environment. We review the current state of practice for produced water management across the United States and discuss the interrelated regulatory, infrastructure, and economic drivers for produced water reuse. Within this framework, we examine the Marcellus shale play, a region in the eastern United States where produced water is currently reused without desalination. In the Marcellus region, and in other shale plays worldwide with similar constraints, contraction of current reuse opportunities within the shale gas industry and growing restrictions on produced water disposal will provide strong incentives for produced water desalination for reuse outside the industry. The most challenging scenarios for the selection of desalination for reuse over other management strategies will be those involving high-salinity produced water, which must be desalinated with thermal separation processes. We explore desalination technologies for treatment of high-salinity shale gas produced water, and we critically review mechanical vapor compression (MVC), membrane distillation (MD), and forward osmosis (FO) as the technologies best suited for desalination of high-salinity produced water for reuse outside the shale gas industry. The advantages and challenges of applying MVC, MD, and FO technologies to produced water desalination are discussed, and directions for future research and development are identified. We find that desalination for reuse of produced water is technically feasible and can be economically relevant. However, because produced water management is primarily an economic decision, expanding desalination for reuse is dependent on process and material improvements to reduce capital and operating costs.

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

Chronic systemic pesticide exposure reproduces features of Parkinson's disease.

PubMed

Betarbet, R; Sherer, T B; MacKenzie, G; Garcia-Osuna, M; Panov, A V; Greenamyre, J T

2000-12-01

The cause of Parkinson's disease (PD) is unknown, but epidemiological studies suggest an association with pesticides and other environmental toxins, and biochemical studies implicate a systemic defect in mitochondrial complex I. We report that chronic, systemic inhibition of complex I by the lipophilic pesticide, rotenone, causes highly selective nigrostriatal dopaminergic degeneration that is associated behaviorally with hypokinesia and rigidity. Nigral neurons in rotenone-treated rats accumulate fibrillar cytoplasmic inclusions that contain ubiquitin and alpha-synuclein. These results indicate that chronic exposure to a common pesticide can reproduce the anatomical, neurochemical, behavioral and neuropathological features of PD.

One-Step Printable Perovskite Films Fabricated under Ambient Conditions for Efficient and Reproducible Solar Cells.

PubMed

Jung, Yen-Sook; Hwang, Kyeongil; Heo, Youn-Jung; Kim, Jueng-Eun; Lee, Donmin; Lee, Cheol-Ho; Joh, Han-Ik; Yeo, Jun-Seok; Kim, Dong-Yu

2017-08-23

Despite the potential of roll-to-roll processing for the fabrication of perovskite films, the realization of highly efficient and reproducible perovskite solar cells (PeSCs) through continuous coating techniques and low-temperature processing is still challenging. Here, we demonstrate that efficient and reliable CH 3 NH 3 PbI 3 (MAPbI 3 ) films fabricated by a printing process can be achieved through synergetic effects of binary processing additives, N-cyclohexyl-2-pyrrolidone (CHP) and dimethyl sulfoxide (DMSO). Notably, these perovskite films are deposited from premixed perovskite solutions for facile one-step processing under a room-temperature and ambient atmosphere. The CHP molecules result in the uniform and homogeneous perovskite films even in the one-step slot-die system, which originate from the high boiling point and low vapor pressure of CHP. Meanwhile, the DMSO molecules facilitate the growth of perovskite grains by forming intermediate states with the perovskite precursor molecules. Consequently, fully printed PeSC based on the binary additive system exhibits a high PCE of 12.56% with a high reproducibility.

Quantification of atrial dynamics using cardiovascular magnetic resonance: inter-study reproducibility.

PubMed

Kowallick, Johannes T; Morton, Geraint; Lamata, Pablo; Jogiya, Roy; Kutty, Shelby; Hasenfuß, Gerd; Lotz, Joachim; Nagel, Eike; Chiribiri, Amedeo; Schuster, Andreas

2015-05-17

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 reproducibility 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 reproducibility. Morning and afternoon scans were compared to address possible diurnal variation of atrial function. Inter-study reproducibility was within acceptable limits for all LA and RA volumetric, strain and SR parameters. Inter-study reproducibility 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 reproducibility (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, reproducibility 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 reproducibility for CMR-based derivation of LA and RA functions is acceptable using either volumetric, strain or SR parameters with LA function showing higher reproducibility than RA function assessment. Amongst the different functional components

Advancements in RNASeqGUI towards a Reproducible Analysis of RNA-Seq Experiments

PubMed Central

Russo, Francesco; Righelli, Dario

2016-01-01

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 reproducible research and shows how it has been incorporated in RNASeqGUI to provide reproducible (computational) results. The novel version of RNASeqGUI combines graphical interfaces with tools for reproducible 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 reproducible way. Moreover, this paper represents a proof of concept, showing a simple way to develop computational tools for Life Science in the spirit of reproducible research. PMID:26977414

Reproducible Preparation of Au/TS-1 with High Reaction Rate for Gas Phase Epoxidation of Propylene

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

Lee W. S.; Stach E.; Akatay, M.C.

2012-03-01

A refined and reliable synthesis procedure for Au/TS-1(Si/Ti molar ratio {approx}100) with high reaction rate for the direct gas phase epoxidation of propylene has been developed by studying the effects of pH of the gold slurry solution, mixing time, and preparation temperature for deposition precipitation (DP) of Au on TS-1 supports. Au/TS-1 catalysts prepared at optimal DP conditions (pH {approx} 7.3, mixing for 9.5 h, room temperature) showed an average PO rate {approx} 160 g{sub PO} h{sup -1} kg{sub Cat}{sup -1} at 200 C at 1 atm. A reproducibility better than {+-}10% was demonstrated by nine independent samples prepared atmore » the same conditions. These are the highest rates yet reported at 200 C. No visible gold particles were observed by the HRTEM analysis in the fresh Au/TS-1 with gold loading up to {approx}0.1 wt%, indicating that the gold species were smaller than 1 nm. Additionally, the rate per gram of Au and the catalyst stability increased as the Au loading decreased, giving a maximum value of 500 g{sub PO} h{sup -1} g{sub Au}{sup -1}, and Si/Ti molar ratios of {approx}100 gave the highest rates.« less

Evaluating reproducibility of differential expression discoveries in microarray studies by considering correlated molecular changes.

PubMed

Zhang, Min; Zhang, Lin; Zou, Jinfeng; Yao, Chen; Xiao, Hui; Liu, Qing; Wang, Jing; Wang, Dong; Wang, Chenguang; Guo, Zheng

2009-07-01

According to current consistency metrics such as percentage of overlapping genes (POG), lists of differentially expressed genes (DEGs) detected from different microarray studies for a complex disease are often highly inconsistent. This irreproducibility problem also exists in other high-throughput post-genomic areas such as proteomics and metabolism. A complex disease is often characterized with many coordinated molecular changes, which should be considered when evaluating the reproducibility of discovery lists from different studies. We proposed metrics percentage of overlapping genes-related (POGR) and normalized POGR (nPOGR) to evaluate the consistency between two DEG lists for a complex disease, considering correlated molecular changes rather than only counting gene overlaps between the lists. Based on microarray datasets of three diseases, we showed that though the POG scores for DEG lists from different studies for each disease are extremely low, the POGR and nPOGR scores can be rather high, suggesting that the apparently inconsistent DEG lists may be highly reproducible in the sense that they are actually significantly correlated. Observing different discovery results for a disease by the POGR and nPOGR scores will obviously reduce the uncertainty of the microarray studies. The proposed metrics could also be applicable in many other high-throughput post-genomic areas.

Cocaine Self-Administration Produces a Persistent Increase in Dopamine D2High Receptors

PubMed Central

Briand, Lisa A.; Flagel, Shelly B.; Seeman, Philip; Robinson, Terry E.

2008-01-01

Cocaine addicts are reported to have decreased numbers of striatal dopamine D2 receptors. However, in rodents, repeated cocaine administration consistently produces hypersensitivity to the psychomotor activating effects of both indirect dopamine agonists, such as cocaine itself, and importantly, to direct-acting D2 receptor agonists. The current study reports a possible resolution to this long-standing paradox. The dopamine D2 receptor exists in both a low and a high affinity state, and dopamine exerts its effects via the more functionally relevant high-affinity D2 receptor (D2High). We report here that cocaine self-administration experience produces a large (approximately 150%) increase in the proportion of D2High receptors in the striatum with no change in the total number of D2 receptors, and this effect is evident both 3 and 30 days after the discontinuation of cocaine self-administration. Changes in D2High receptors would not be evident with the probes used in human (and non-human primate) imaging studies. We suggest, therefore, that cocaine addicts and animals previously treated with cocaine may be hyper-responsive to dopaminergic drugs in part because an increase in D2High receptors results in dopamine supersensitivity. This may also help explain why stimuli that increase dopamine neurotransmission, including drugs themselves, are so effective in producing relapse in individuals with a history of exposure to cocaine. PMID:18284941

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

Producing high-quality negatives from ERTS black-and-white transparancies

Treesearch

Richard J. Myhre

1973-01-01

A method has been devised for producing high-quality black-and-white negatives quickly and efficiently from dense transparencies orgininating from Earth Resources Technology Satellite imagery. Transparencies are evaluated on a standard light source to determine exposure and processing information needed for making negatives. A “System ASA Rating” was developed by...

Methods to increase reproducibility in differential gene expression via meta-analysis

PubMed Central

Sweeney, Timothy E.; Haynes, Winston A.; Vallania, Francesco; Ioannidis, John P.; Khatri, Purvesh

2017-01-01

Findings from clinical and biological studies are often not reproducible 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 reproducible. Compared to single-study analysis, gene expression meta-analysis can improve reproducibility 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 reproducibility. 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 reproducibility with more-stringent effect size thresholds with relaxed significance thresholds; relatively lower reproducibility 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

36 CFR 903.12 - Fees for furnishing and reproducing records.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 36 Parks, Forests, and Public Property 3 2010-07-01 2010-07-01 false Fees for furnishing and reproducing records. 903.12 Section 903.12 Parks, Forests, and Public Property PENNSYLVANIA AVENUE DEVELOPMENT CORPORATION PRIVACY ACT § 903.12 Fees for furnishing and reproducing records. (a) Individuals will not be...

Depth dependency of neutron density produced by cosmic rays in the lunar subsurface

NASA Astrophysics Data System (ADS)

Ota, S.; Sihver, L.; Kobayashi, S.; Hasebe, N.

2014-11-01

Depth dependency of neutrons produced by cosmic rays (CRs) in the lunar subsurface was estimated using the three-dimensional Monte Carlo particle and heavy ion transport simulation code, PHITS, incorporating the latest high energy nuclear data, JENDL/HE-2007. The PHITS simulations of equilibrium neutron density profiles in the lunar subsurface were compared with the measurement by Apollo 17 Lunar Neutron Probe Experiment (LNPE). Our calculations reproduced the LNPE data except for the 350-400 mg/cm2 region under the improved condition using the CR spectra model based on the latest observations, well-tested nuclear interaction models with systematic cross section data, and JENDL/HE-2007.

Winter Photochemistry Underlying High Ozone in an Oil and Gas Producing Region

NASA Astrophysics Data System (ADS)

Brown, S. S.; Edwards, P. M.; Roberts, J. M.; Ahmadov, R.; Banta, R. M.; De Gouw, J. A.; Dube, W. P.; Field, R. A.; Gilman, J.; Graus, M.; Helmig, D.; Koss, A.; Langford, A. O.; Lefer, B. L.; Lerner, B. M.; McKeen, S. A.; Li, S. M.; Murphy, S. M.; Parrish, D. D.; Senff, C. J.; Stutz, J.; Thompson, C. R.; Trainer, M.; Veres, P. R.; Warneke, C.; Wild, R. J.; Young, C.; Yuan, B.; Zamora, R. J.; Washenfelder, R. A.

2014-12-01

Ozone formation during wintertime in oil and gas producing basins of the Rocky Mountain West now accounts for some of the highest ozone pollutant concentrations observed in the U.S. These events are scientifically challenging, occurring only during cold, snow covered periods when meteorological inversions concentrate pollutants near the surface, but when incident solar actinic flux that initiates photochemical reactions is at or near its minimum. A near-explicit chemical model that incorporates detailed measurements obtained during three successive winter field studies in the Uintah Basin, Utah, accurately reproduces the observed buildup of ozone and other photochemically generated species. It also identifies the sources of free radicals that drive this unusual photochemistry, and quantifies their relative contributions. Although sharing the same basic atmospheric chemistry, winter ozone formation differs from its summertime, urban counterpart in its dependence upon the relative concentrations of volatile organic compounds (VOCs) and nitrogen oxide (NOx) precursors. Observed NO­­x mixing ratios in the Uintah basin are lower than is typical of urban areas, while VOC levels are significantly larger. These extreme VOC concentrations allow for nearly optimal efficiency of ozone production from the available NO­x. This analysis will inform the design of mitigation strategies and provide insight into the response of winter ozone to primary air pollutants in other regions, particularly those where oil and gas development is contemplated.

Emotional Climate and High Quality Learning Experiences in Science Teacher Education

ERIC Educational Resources Information Center

Bellocchi, Alberto; Ritchie, Stephen M.; Tobin, Kenneth; King, Donna; Sandhu, Maryam; Henderson, Senka

2014-01-01

The role of emotion during learning encounters in science teacher education is under-researched and under-theorized. In this case study, we explore the emotional climates (ECs), that is, the collective states of emotional arousal, of a preservice secondary science education class to illuminate practice for producing and reproducing high quality…

Microbiologic tests in epidemiologic studies: are they reproducible?

PubMed

Aass, A M; Preus, H R; Zambon, J J; Gjermo, P

1994-12-01

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 reproducibility 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 reproducibility of the four methods was low. The IIF and the cultivation methods showed somewhat higher reproducibility 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 reproducibility of the second test was improved, indicating that the detection level of the system may influence the reliability.

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.

Fluctuation-Driven Neural Dynamics Reproduce Drosophila Locomotor Patterns

PubMed Central

Cruchet, Steeve; Gustafson, Kyle; Benton, Richard; Floreano, Dario

2015-01-01

The neural mechanisms determining the timing of even simple actions, such as when to walk or rest, are largely mysterious. One intriguing, but untested, hypothesis posits a role for ongoing activity fluctuations in neurons of central action selection circuits that drive animal behavior from moment to moment. To examine how fluctuating activity can contribute to action timing, we paired high-resolution measurements of freely walking Drosophila melanogaster with data-driven neural network modeling and dynamical systems analysis. We generated fluctuation-driven network models whose outputs—locomotor bouts—matched those measured from sensory-deprived Drosophila. From these models, we identified those that could also reproduce a second, unrelated dataset: the complex time-course of odor-evoked walking for genetically diverse Drosophila strains. Dynamical models that best reproduced both Drosophila basal and odor-evoked locomotor patterns exhibited specific characteristics. First, ongoing fluctuations were required. In a stochastic resonance-like manner, these fluctuations allowed neural activity to escape stable equilibria and to exceed a threshold for locomotion. Second, odor-induced shifts of equilibria in these models caused a depression in locomotor frequency following olfactory stimulation. Our models predict that activity fluctuations in action selection circuits cause behavioral output to more closely match sensory drive and may therefore enhance navigation in complex sensory environments. Together these data reveal how simple neural dynamics, when coupled with activity fluctuations, can give rise to complex patterns of animal behavior. PMID:26600381

Highly controlled, reproducible measurements of aerosol emissions from combustion of a common African biofuel source

NASA Astrophysics Data System (ADS)

Haslett, Sophie L.; Thomas, J. Chris; Morgan, William T.; Hadden, Rory; Liu, Dantong; Allan, James D.; Williams, Paul I.; Keita, Sekou; Liousse, Cathy; Coe, Hugh

2018-01-01

Particulate emissions from biomass burning can both alter the atmosphere's radiative balance and cause significant harm to human health. However, due to the large effect on emissions caused by even small alterations to the way in which a fuel burns, it is difficult to study particulate production of biomass combustion mechanistically and in a repeatable manner. In order to address this gap, in this study, small wood samples sourced from Côte D'Ivoire in West Africa were burned in a highly controlled laboratory environment. The shape and mass of samples, available airflow and surrounding thermal environment were carefully regulated. Organic aerosol and refractory black carbon emissions were measured in real time using an Aerosol Mass Spectrometer and a Single Particle Soot Photometer, respectively. This methodology produced remarkably repeatable results, allowing aerosol emissions to be mapped directly onto different phases of combustion. Emissions from pyrolysis were visible as a distinct phase before flaming was established. After flaming combustion was initiated, a black-carbon-dominant flame was observed during which very little organic aerosol was produced, followed by a period that was dominated by organic-carbon-producing smouldering combustion, despite the presence of residual flaming. During pyrolysis and smouldering, the two phases producing organic aerosol, distinct mass spectral signatures that correspond to previously reported variations in biofuel emissions measured in the atmosphere are found. Organic aerosol emission factors averaged over an entire combustion event were found to be representative of the time spent in the pyrolysis and smouldering phases, rather than reflecting a coupling between emissions and the mass loss of the sample. Further exploration of aerosol yields from similarly carefully controlled fires and a careful comparison with data from macroscopic fires and real-world emissions will help to deliver greater constraints on the

Using Docker Containers to Extend Reproducibility Architecture for the NASA Earth Exchange (NEX)

NASA Technical Reports Server (NTRS)

Votava, Petr; Michaelis, Andrew; Spaulding, Ryan; Becker, Jeffrey C.

2016-01-01

NASA Earth Exchange (NEX) is a data, supercomputing and knowledge collaboratory that houses NASA satellite, climate and ancillary data where a focused community can come together to address large-scale challenges in Earth sciences. As NEX has been growing into a petabyte-size platform for analysis, experiments and data production, it has been increasingly important to enable users to easily retrace their steps, identify what datasets were produced by which process chains, and give them ability to readily reproduce their results. This can be a tedious and difficult task even for a small project, but is almost impossible on large processing pipelines. We have developed an initial reproducibility and knowledge capture solution for the NEX, however, if users want to move the code to another system, whether it is their home institution cluster, laptop or the cloud, they have to find, build and install all the required dependencies that would run their code. This can be a very tedious and tricky process and is a big impediment to moving code to data and reproducibility outside the original system. The NEX team has tried to assist users who wanted to move their code into OpenNEX on Amazon cloud by creating custom virtual machines with all the software and dependencies installed, but this, while solving some of the issues, creates a new bottleneck that requires the NEX team to be involved with any new request, updates to virtual machines and general maintenance support. In this presentation, we will describe a solution that integrates NEX and Docker to bridge the gap in code-to-data migration. The core of the solution is saemi-automatic conversion of science codes, tools and services that are already tracked and described in the NEX provenance system, to Docker - an open-source Linux container software. Docker is available on most computer platforms, easy to install and capable of seamlessly creating and/or executing any application packaged in the appropriate format. We

Using Docker Containers to Extend Reproducibility Architecture for the NASA Earth Exchange (NEX)

NASA Astrophysics Data System (ADS)

Votava, P.; Michaelis, A.; Spaulding, R.; Becker, J. C.

2016-12-01

NASA Earth Exchange (NEX) is a data, supercomputing and knowledge collaboratory that houses NASA satellite, climate and ancillary data where a focused community can come together to address large-scale challenges in Earth sciences. As NEX has been growing into a petabyte-size platform for analysis, experiments and data production, it has been increasingly important to enable users to easily retrace their steps, identify what datasets were produced by which process chains, and give them ability to readily reproduce their results. This can be a tedious and difficult task even for a small project, but is almost impossible on large processing pipelines. We have developed an initial reproducibility and knowledge capture solution for the NEX, however, if users want to move the code to another system, whether it is their home institution cluster, laptop or the cloud, they have to find, build and install all the required dependencies that would run their code. This can be a very tedious and tricky process and is a big impediment to moving code to data and reproducibility outside the original system. The NEX team has tried to assist users who wanted to move their code into OpenNEX on Amazon cloud by creating custom virtual machines with all the software and dependencies installed, but this, while solving some of the issues, creates a new bottleneck that requires the NEX team to be involved with any new request, updates to virtual machines and general maintenance support. In this presentation, we will describe a solution that integrates NEX and Docker to bridge the gap in code-to-data migration. The core of the solution is saemi-automatic conversion of science codes, tools and services that are already tracked and described in the NEX provenance system, to Docker - an open-source Linux container software. Docker is available on most computer platforms, easy to install and capable of seamlessly creating and/or executing any application packaged in the appropriate format. We

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

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

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.

Highly sensitive, reproducible and stable SERS substrate based on reduced graphene oxide/silver nanoparticles coated weighing paper

NASA Astrophysics Data System (ADS)

Xiao, Guina; Li, Yunxiang; Shi, Wangzhou; Shen, Leo; Chen, Qi; Huang, Lei

2017-05-01

Paper-based surface-enhanced Raman scattering (SERS) substrates receive a great deal of attention due to low cost and high flexibility. Herein, we developed an efficient SERS substrate by gravure printing of sulfonated reduced graphene-oxide (S-RGO) thin film and inkjet printing of silver nanoparticles (AgNPs) on weighing paper successively. Malachite green (MG) and rhodamine 6G (R6G) were chosen as probe molecules to evaluate the enhanced performance of the fabricated SERS-active substrates. It was found that the S-RGO/AgNPs composite structure possessed higher enhancement ability than the pure AgNPs. The Raman enhancement factor of S-RGO/AgNPs was calculated to be as large as 109. The minimum detection limit for MG and R6G was down to 10-7 M with good linear responses (R2 = 0.9996, 0.9983) range from 10-4 M to 10-7 M. In addition, the S-RGO/AgNPs exhibited good uniformity with a relative standard deviation (RSD) of 7.90% measured by 572 points, excellent reproducibility with RSD smaller than 3.36%, and long-term stability with RSD less than 7.19%.

SERS Detection of Biomolecules by Highly Sensitive and Reproducible Raman-Enhancing Nanoparticle Array

NASA Astrophysics Data System (ADS)

Chan, Tzu-Yi; Liu, Ting-Yu; Wang, Kuan-Syun; Tsai, Kun-Tong; Chen, Zhi-Xin; Chang, Yu-Chi; Tseng, Yi-Qun; Wang, Chih-Hao; Wang, Juen-Kai; Wang, Yuh-Lin

2017-05-01

This paper describes the preparation of nanoarrays composed of silver nanoparticles (AgNPs: 20-50 nm) for use as surface-enhanced Raman scattering (SERS) substrates. The AgNPs were grown on porous anodic aluminum oxide (AAO) templates by electrochemical plating, and the inter-channel gap of AAO channels is between 10 and 20 nm. The size and interparticle gap of silver particles were adjusted in order to achieve optimal SERS signals and characterized by scanning electron microscopy, atomic force microscopy, and Raman spectroscopy. The fluctuation of SERS intensity is about 10-20% when measuring adenine solutions, showing a great reproducible SERS sensing. The nanoparticle arrays offer a large potential for practical applications as shown by the SERS-based quantitative detection and differentiation of adenine (A), thymine (T), cytosine (C), guanine (G), β-carotene, and malachite green. The respective detection limits are <1 ppb for adenine and <0.63 ppm for β-carotene and malachite green, respectively.

Determining the optimal number of independent components for reproducible transcriptomic data analysis.

PubMed

Kairov, Ulykbek; Cantini, Laura; Greco, Alessandro; Molkenov, Askhat; Czerwinska, Urszula; Barillot, Emmanuel; Zinovyev, Andrei

2017-09-11

Independent Component Analysis (ICA) is a method that models gene expression data as an action of a set of statistically independent hidden factors. The output of ICA depends on a fundamental parameter: the number of components (factors) to compute. The optimal choice of this parameter, related to determining the effective data dimension, remains an open question in the application of blind source separation techniques to transcriptomic data. Here we address the question of optimizing the number of statistically independent components in the analysis of transcriptomic data for reproducibility of the components in multiple runs of ICA (within the same or within varying effective dimensions) and in multiple independent datasets. To this end, we introduce ranking of independent components based on their stability in multiple ICA computation runs and define a distinguished number of components (Most Stable Transcriptome Dimension, MSTD) corresponding to the point of the qualitative change of the stability profile. Based on a large body of data, we demonstrate that a sufficient number of dimensions is required for biological interpretability of the ICA decomposition and that the most stable components with ranks below MSTD have more chances to be reproduced in independent studies compared to the less stable ones. At the same time, we show that a transcriptomics dataset can be reduced to a relatively high number of dimensions without losing the interpretability of ICA, even though higher dimensions give rise to components driven by small gene sets. We suggest a protocol of ICA application to transcriptomics data with a possibility of prioritizing components with respect to their reproducibility that strengthens the biological interpretation. Computing too few components (much less than MSTD) is not optimal for interpretability of the results. The components ranked within MSTD range have more chances to be reproduced in independent studies.

Indirect monitoring shot-to-shot shock waves strength reproducibility during pump-probe experiments

NASA Astrophysics Data System (ADS)

Pikuz, T. A.; Faenov, A. Ya.; Ozaki, N.; Hartley, N. J.; Albertazzi, B.; Matsuoka, T.; Takahashi, K.; Habara, H.; Tange, Y.; Matsuyama, S.; Yamauchi, K.; Ochante, R.; Sueda, K.; Sakata, O.; Sekine, T.; Sato, T.; Umeda, Y.; Inubushi, Y.; Yabuuchi, T.; Togashi, T.; Katayama, T.; Yabashi, M.; Harmand, M.; Morard, G.; Koenig, M.; Zhakhovsky, V.; Inogamov, N.; Safronova, A. S.; Stafford, A.; Skobelev, I. Yu.; Pikuz, S. A.; Okuchi, T.; Seto, Y.; Tanaka, K. A.; Ishikawa, T.; Kodama, R.

2016-07-01

We present an indirect method of estimating the strength of a shock wave, allowing on line monitoring of its reproducibility in each laser shot. This method is based on a shot-to-shot measurement of the X-ray emission from the ablated plasma by a high resolution, spatially resolved focusing spectrometer. An optical pump laser with energy of 1.0 J and pulse duration of ˜660 ps was used to irradiate solid targets or foils with various thicknesses containing Oxygen, Aluminum, Iron, and Tantalum. The high sensitivity and resolving power of the X-ray spectrometer allowed spectra to be obtained on each laser shot and to control fluctuations of the spectral intensity emitted by different plasmas with an accuracy of ˜2%, implying an accuracy in the derived electron plasma temperature of 5%-10% in pump-probe high energy density science experiments. At nano- and sub-nanosecond duration of laser pulse with relatively low laser intensities and ratio Z/A ˜ 0.5, the electron temperature follows Te ˜ Ilas2/3. Thus, measurements of the electron plasma temperature allow indirect estimation of the laser flux on the target and control its shot-to-shot fluctuation. Knowing the laser flux intensity and its fluctuation gives us the possibility of monitoring shot-to-shot reproducibility of shock wave strength generation with high accuracy.

Reproducibility in cyclostratigraphy: initiating an intercomparison project

NASA Astrophysics Data System (ADS)

Sinnesael, Matthias; De Vleeschouwer, David; Zeeden, Christian; Claeys, Philippe

2017-04-01

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 reproducibility, uncertainties and standardization of results. The radioisotopic dating community, in particular, has done far-reaching efforts to improve reproducibility 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 reproducibility 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 reproducibility 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

Ultra-high-pressure homogenization (UHPH) system for producing high-quality vegetable-based beverages: physicochemical, microbiological, nutritional and toxicological characteristics.

PubMed

Ferragut, Victoria; Hernández-Herrero, Manuela; Veciana-Nogués, María Teresa; Borras-Suarez, Miquel; González-Linares, Javier; Vidal-Carou, María Carmen; Guamis, Buenaventura

2015-03-30

A relatively new technology based on a continuous system of ultra-high-pressure homogenization (UHPH) was used for producing high-quality soy and almond beverages as an alternative to conventional heat treatments (pasteurization and UHT). The aim of this study was to compare those treatments by analyzing the most relevant quality parameters with a broad vision from the production to the potential toxicological changes, passing through the main nutritional characteristics. UHPH treatment at 200 MPa, 55 °C T(in) produced a higher reduction of microorganisms than pasteurization. UHPH treatment at 300 MPa, 75 °C T(in) led to complete inactivation of microorganisms, similar to UHT treatment. A much better colloidal stability was observed in both UHPH-treated almond and soy beverages compared with those processed by conventional heat treatments. UHPH treatments led to the same increase in digestibility as heat treatments and did not produce a reduction in the availability of lysine. In addition, UHPH samples of soy beverage seem to be less allergenic based on their lower gut immune response in comparison with heat-treated samples. UHPH treatments could be used to produce high-quality commercial vegetable beverages with different quality standards (fresh or long-life storage) according to consumer preference. © 2014 Society of Chemical Industry.

Progress toward openness, transparency, and reproducibility in cognitive neuroscience.

PubMed

Gilmore, Rick O; Diaz, Michele T; Wyble, Brad A; Yarkoni, Tal

2017-05-01

Accumulating evidence suggests that many findings in psychological science and cognitive neuroscience may prove difficult to reproduce; 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 reproducibility, 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 reproducibility, statistical power, and transparency in ways that will ultimately accelerate discovery. © 2017 New York Academy of Sciences.

The quest for improved reproducibility in MALDI mass spectrometry.

PubMed

O'Rourke, Matthew B; Djordjevic, Steven P; Padula, Matthew P

2018-03-01

Reproducibility 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 reproducibility 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 reproducibility. 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.

Apparent diffusion coefficient is highly reproducible on preclinical imaging systems: Evidence from a seven-center multivendor study.

PubMed

Doblas, Sabrina; Almeida, Gilberto S; Blé, François-Xavier; Garteiser, Philippe; Hoff, Benjamin A; McIntyre, Dominick J O; Wachsmuth, Lydia; Chenevert, Thomas L; Faber, Cornelius; Griffiths, John R; Jacobs, Andreas H; Morris, David M; O'Connor, James P B; Robinson, Simon P; Van Beers, Bernard E; Waterton, John C

2015-12-01

To evaluate between-site agreement of apparent diffusion coefficient (ADC) measurements in preclinical magnetic resonance imaging (MRI) systems. A miniaturized thermally stable ice-water phantom was devised. ADC (mean and interquartile range) was measured over several days, on 4.7T, 7T, and 9.4T Bruker, Agilent, and Magnex small-animal MRI systems using a common protocol across seven sites. Day-to-day repeatability was expressed as percent variation of mean ADC between acquisitions. Cross-site reproducibility was expressed as 1.96 × standard deviation of percent deviation of ADC values. ADC measurements were equivalent across all seven sites with a cross-site ADC reproducibility of 6.3%. Mean day-to-day repeatability of ADC measurements was 2.3%, and no site was identified as presenting different measurements than others (analysis of variance [ANOVA] P = 0.02, post-hoc test n.s.). Between-slice ADC variability was negligible and similar between sites (P = 0.15). Mean within-region-of-interest ADC variability was 5.5%, with one site presenting a significantly greater variation than the others (P = 0.0013). Absolute ADC values in preclinical studies are comparable between sites and equipment, provided standardized protocols are employed. © 2015 Wiley Periodicals, Inc.

An Open, Large-Scale, Collaborative Effort to Estimate the Reproducibility of Psychological Science.

PubMed

2012-11-01

Reproducibility 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 Reproducibility Project is an open, large-scale, collaborative effort to systematically examine the rate and predictors of reproducibility 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 reproducibility. Whatever the result, a better understanding of reproducibility will ultimately improve confidence in scientific methodology and findings. © The Author(s) 2012.

Reproducibility of structural strength and stiffness for graphite-epoxy aircraft spoilers

NASA Technical Reports Server (NTRS)

Howell, W. E.; Reese, C. D.

1978-01-01

Structural strength reproducibility 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 reproducibility of full scale component structural properties was within the reproducibility range of data from material property tests.

Robust estimation of fractal measures for characterizing the structural complexity of the human brain: optimization and reproducibility

PubMed Central

Goñi, Joaquín; Sporns, Olaf; Cheng, Hu; Aznárez-Sanado, Maite; Wang, Yang; Josa, Santiago; Arrondo, Gonzalo; Mathews, Vincent P; Hummer, Tom A; Kronenberger, William G; Avena-Koenigsberger, Andrea; Saykin, Andrew J.; Pastor, María A.

2013-01-01

High-resolution isotropic three-dimensional reconstructions of human brain gray and white matter structures can be characterized to quantify aspects of their shape, volume and topological complexity. In particular, methods based on fractal analysis have been applied in neuroimaging studies to quantify the structural complexity of the brain in both healthy and impaired conditions. The usefulness of such measures for characterizing individual differences in brain structure critically depends on their within-subject reproducibility in order to allow the robust detection of between-subject differences. This study analyzes key analytic parameters of three fractal-based methods that rely on the box-counting algorithm with the aim to maximize within-subject reproducibility of the fractal characterizations of different brain objects, including the pial surface, the cortical ribbon volume, the white matter volume and the grey matter/white matter boundary. Two separate datasets originating from different imaging centers were analyzed, comprising, 50 subjects with three and 24 subjects with four successive scanning sessions per subject, respectively. The reproducibility of fractal measures was statistically assessed by computing their intra-class correlations. Results reveal differences between different fractal estimators and allow the identification of several parameters that are critical for high reproducibility. Highest reproducibility with intra-class correlations in the range of 0.9–0.95 is achieved with the correlation dimension. Further analyses of the fractal dimensions of parcellated cortical and subcortical gray matter regions suggest robustly estimated and region-specific patterns of individual variability. These results are valuable for defining appropriate parameter configurations when studying changes in fractal descriptors of human brain structure, for instance in studies of neurological diseases that do not allow repeated measurements or for disease

Reproducibility Between Brain Uptake Ratio Using Anatomic Standardization and Patlak-Plot Methods.

PubMed

Shibutani, Takayuki; Onoguchi, Masahisa; Noguchi, Atsushi; Yamada, Tomoki; Tsuchihashi, Hiroko; Nakajima, Tadashi; Kinuya, Seigo

2015-12-01

The Patlak-plot and conventional methods of determining brain uptake ratio (BUR) have some problems with reproducibility. We formulated a method of determining BUR using anatomic standardization (BUR-AS) in a statistical parametric mapping algorithm to improve reproducibility. The objective of this study was to demonstrate the inter- and intraoperator reproducibility 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. Reproducibility was evaluated using coefficient of variation and Bland-Altman plotting. For both inter- and intraoperator reproducibility, 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 reproducibility. Compared with the Patlak-plot and BUR-C methods, the BUR-AS method provides greater inter- and intraoperator reproducibility of cerebral blood flow measurement. © 2015 by the Society of Nuclear Medicine and Molecular Imaging, Inc.

Reproducing Domestic Laborers through Office Education.

ERIC Educational Resources Information Center

Valli, Linda R.

Scholars have long acknowledged the role schools have in reproducing 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…

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.

Inter-study reproducibility of left ventricular torsion and torsion rate quantification using MR myocardial feature tracking.

PubMed

Kowallick, Johannes T; Morton, Geraint; Lamata, Pablo; Jogiya, Roy; Kutty, Shelby; Lotz, Joachim; Hasenfuß, Gerd; Nagel, Eike; Chiribiri, Amedeo; Schuster, Andreas

2016-01-01

To determine the inter-study reproducibility of MR feature tracking (MR-FT) derived left ventricular (LV) torsion and torsion rates for a combined assessment of systolic and diastolic myocardial function. Steady-state free precession (SSFP) cine LV short-axis stacks were acquired at 9:00 (Exam A), 9:30 (Exam B), and 14:00 (Exam C) in 16 healthy volunteers at 3 Tesla. SSFP images were analyzed offline using MR-FT to assess rotational displacement in apical and basal slices. Global peak torsion, peak systolic and peak diastolic torsion rates were calculated using different definitions ("twist", "normalized twist" and "circumferential-longitudinal (CL) shear angle"). Exam A and B were compared to assess the inter-study reproducibility. Morning and afternoon scans were compared to address possible diurnal variation. The different methods showed good inter-study reproducibility for global peak torsion (intraclass correlation coefficient [ICC]: 0.90-0.92; coefficient of variation [CoV]: 19.0-20.3%) and global peak systolic torsion rate (ICC: 0.82-0.84; CoV: 25.9-29.0%). Conversely, global peak diastolic torsion rate showed little inter-study reproducibility (ICC: 0.34-0.47; CoV: 40.8-45.5%). Global peak torsion as determined by the CL shear angle showed the best inter-study reproducibility (ICC: 0.90;CoV: 19.0%). MR-FT results were not measurably affected by diurnal variation between morning and afternoon scans (CL shear angle: 4.8 ± 1.4°, 4.8 ± 1.5°, and 4.1 ± 1.6° for Exam A, B, and C, respectively; P = 0.21). MR-FT based derivation of myocardial peak torsion and peak systolic torsion rate has high inter-study reproducibility as opposed to peak diastolic torsion rate. The CL shear angle was the most reproducible parameter independently of cardiac anatomy and may develop into a robust tool to quantify cardiac rotational mechanics in longitudinal MR-FT patient studies. © 2015 Wiley Periodicals, Inc.

Reproducibility of the cutoff probe for the measurement of electron density

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

Kim, D. W.; Oh, W. Y.; You, S. J., E-mail: sjyou@cnu.ac.kr

2016-06-15

Since a plasma processing control based on plasma diagnostics attracted considerable attention in industry, the reproducibility 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 reproducibility of the cutoff probe measurement becomes quit important in the cutoff probe application research. To test the reproducibility 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 reproducibility 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

Efficient and reproducible mammalian cell bioprocesses without probes and controllers?

PubMed

Tissot, Stéphanie; Oberbek, Agata; Reclari, Martino; Dreyer, Matthieu; Hacker, David L; Baldi, Lucia; Farhat, Mohamed; Wurm, Florian M

2011-07-01

Bioprocesses for recombinant protein production with mammalian cells are typically controlled for several physicochemical parameters including the pH and dissolved oxygen concentration (DO) of the culture medium. Here we studied whether these controls are necessary for efficient and reproducible bioprocesses in an orbitally shaken bioreactor (OSR). Mixing, gas transfer, and volumetric power consumption (P(V)) were determined in both a 5-L OSR and a 3-L stirred-tank bioreactor (STR). The two cultivation systems had a similar mixing intensity, but the STR had a lower volumetric mass transfer coefficient of oxygen (k(L)a) and a higher P(V) than the OSR. Recombinant CHO cell lines expressing either tumor necrosis factor receptor as an Fc fusion protein (TNFR:Fc) or an anti-RhesusD monoclonal antibody were cultivated in the two systems. The 5-L OSR was operated in an incubator shaker with 5% CO(2) in the gas environment but without pH and DO control whereas the STR was operated with or without pH and DO control. Higher cell densities and recombinant protein titers were obtained in the OSR as compared to both the controlled and the non-controlled STRs. To test the reproducibility of a bioprocess in a non-controlled OSR, the two CHO cell lines were each cultivated in parallel in six 5-L OSRs. Similar cell densities, cell viabilities, and recombinant protein titers along with similar pH and DO profiles were achieved in each group of replicates. Our study demonstrated that bioprocesses can be performed in OSRs without pH or DO control in a highly reproducible manner, at least at the scale of operation studied here. Copyright © 2011 Elsevier B.V. All rights reserved.

Reproducibility of the Internal Load and Performance-Based Responses to Simulated Amateur Boxing.

PubMed

Thomson, Edward D; Lamb, Kevin L

2017-12-01

Thomson, ED and Lamb, KL. Reproducibility of the internal load and performance-based responses to simulated amateur boxing. J Strength Cond Res 31(12): 3396-3402, 2017-The aim of this study was to examine the reproducibility of the internal load and performance-based responses to repeated bouts of a three-round amateur boxing simulation protocol (boxing conditioning and fitness test [BOXFIT]). Twenty-eight amateur boxers completed 2 familiarization trials before performing 2 complete trials of the BOXFIT, separated by 4-7 days. To characterize the internal load, mean (HRmean) and peak (HRpeak) heart rate, breath-by-breath oxygen uptake (V[Combining Dot Above]O2), aerobic energy expenditure, excess carbon dioxide production (CO2excess), and ratings of perceived exertion were recorded throughout each round, and blood lactate determined post-BOXFIT. Additionally, an indication of the performance-based demands of the BOXFIT was provided by a measure of acceleration of the punches thrown in each round. Analyses revealed there were no significant differences (p > 0.05) between repeated trials in any round for all dependent measures. The typical error (coefficient variation %) for all but 1 marker of internal load (CO2excess) was 1.2-16.5% and reflected a consistency that was sufficient for the detection of moderate changes in variables owing to an intervention. The reproducibility of the punch accelerations was high (coefficient of variance % range = 2.1-2.7%). In general, these findings suggest that the internal load and performance-based efforts recorded during the BOXFIT are reproducible and, thereby, offer practitioners a method by which meaningful changes impacting on performance could be identified.

Modest validity and fair reproducibility of dietary patterns derived by cluster analysis.

PubMed

Funtikova, Anna N; Benítez-Arciniega, Alejandra A; Fitó, Montserrat; Schröder, Helmut

2015-03-01

Cluster analysis is widely used to analyze dietary patterns. We aimed to analyze the validity and reproducibility 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 reproducibility 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 (reproducibility), and for 67.0% in FFQ2 and 24-HDR (validity). Spearman correlation analysis showed reasonable reproducibility, especially in the "fruits & vegetables" pattern, and lower validity also especially in the "fruits & vegetables" pattern. κ statistic revealed a fair validity and reproducibility of clusters. Our findings indicate a reasonable reproducibility and fair to modest validity of dietary patterns derived by cluster analysis. Copyright © 2015 Elsevier Inc. All rights reserved.

Reproducible and sustained regulation of Gαs signalling using a metazoan opsin as an optogenetic tool.

PubMed

Bailes, Helena J; Zhuang, Ling-Yu; Lucas, Robert J

2012-01-01

Originally developed to regulate neuronal excitability, optogenetics is increasingly also used to control other cellular processes with unprecedented spatiotemporal resolution. Optogenetic modulation of all major G-protein signalling pathways (Gq, Gi and Gs) has been achieved using variants of mammalian rod opsin. We show here that the light response driven by such rod opsin-based tools dissipates under repeated exposure, consistent with the known bleaching characteristics of this photopigment. We continue to show that replacing rod opsin with a bleach resistant opsin from Carybdea rastonii, the box jellyfish, (JellyOp) overcomes this limitation. Visible light induced high amplitude, reversible, and reproducible increases in cAMP in mammalian cells expressing JellyOp. While single flashes produced a brief cAMP spike, repeated stimulation could sustain elevated levels for 10s of minutes. JellyOp was more photosensitive than currently available optogenetic tools, responding to white light at irradiances ≥1 µW/cm(2). We conclude that JellyOp is a promising new tool for mimicking the activity of Gs-coupled G protein coupled receptors with fine spatiotemporal resolution.

High Contrast Internal and External Coronagraph Masks Produced by Various Techniques

NASA Technical Reports Server (NTRS)

Balasubramanian, Kunjithapatha; Wilson, Daniel; White, Victor; Muller, Richard; Dickie, Matthew; Yee, Karl; Ruiz, Ronald; Shaklan, Stuart; Cady, Eric; Kern, Brian;

Understanding high wintertime ozone pollution events in an oil and natural gas producing region of the western US

NASA Astrophysics Data System (ADS)

Ahmadov, R.; McKeen, S.; Trainer, M.; Banta, R.; Brewer, A.; Brown, S.; Edwards, P. M.; de Gouw, J. A.; Frost, G. J.; Gilman, J.; Helmig, D.; Johnson, B.; Karion, A.; Koss, A.; Langford, A.; Lerner, B.; Olson, J.; Oltmans, S.; Peischl, J.; Pétron, G.; Pichugina, Y.; Roberts, J. M.; Ryerson, T.; Schnell, R.; Senff, C.; Sweeney, C.; Thompson, C.; Veres, P.; Warneke, C.; Wild, R.; Williams, E. J.; Yuan, B.; Zamora, R.

2014-08-01

Recent increases in oil and natural gas (NG) production throughout the western US have come with scientific and public interest in emission rates, air quality and climate impacts related to this industry. This study uses a regional scale air quality model WRF-Chem to simulate high ozone (O3) episodes during the winter of 2013 over the Uinta Basin (UB) in northeastern Utah, which is densely populated by thousands of oil and NG wells. The high resolution meteorological simulations are able to qualitatively reproduce the wintertime cold pool conditions that occurred in 2013, allowing the model to reproduce the observed multi-day buildup of atmospheric pollutants and accompanying rapid photochemical ozone formation in the UB. Two different emission scenarios for the oil and NG sector were employed in this study. The first emission scenario (bottom-up) was based on the US EPA National Emission Inventory (NEI) (2011, version 1) for the oil and NG sector for the UB. The second emission scenario (top-down) was based on the previously derived estimates of methane (CH4) emissions and a regression analysis for multiple species relative to CH4 concentration measurements in the UB. WRF-Chem simulations using the two emission data sets resulted in significant differences for concentrations of most gas-phase species. Evaluation of the model results shows greater underestimates of CH4 and other volatile organic compounds (VOCs) in the simulation with the NEI-2011 inventory than the case when the top-down emission scenario was used. Unlike VOCs, the NEI-2011 inventory significantly overestimates the emissions of nitrogen oxides (NOx), while the top-down emission scenario results in a moderate negative bias. Comparison of simulations using the two emission data sets reveals that the top-down case captures the high O3 episodes. In contrast, the simulation case using the bottom-up inventory is not able to reproduce any of the observed high O3 concentrations in the UB. A sensitivity

An empirical analysis of journal policy effectiveness for computational reproducibility.

PubMed

Stodden, Victoria; Seiler, Jennifer; Ma, Zhaokun

2018-03-13

A key component of scientific communication is sufficient information for other researchers in the field to reproduce 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 reproducibility 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 reproduce 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 reproducibility.

An empirical analysis of journal policy effectiveness for computational reproducibility

PubMed Central

Seiler, Jennifer; Ma, Zhaokun

2018-01-01

A key component of scientific communication is sufficient information for other researchers in the field to reproduce 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 reproducibility 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 reproduce 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 reproducibility. PMID:29531050

Natural Disasters: Earth Science Readings. Reproducibles.

ERIC Educational Resources Information Center

Lobb, Nancy

Natural Disasters is a reproducible 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,…

Zwitterionic Antifouling Coatings for the Purification of High-Salinity Shale Gas Produced Water.

PubMed

Yang, Rong; Goktekin, Esma; Gleason, Karen K

2015-11-03

Fouling refers to the undesirable attachment of organic molecules and microorganisms to submerged surfaces. It is an obstacle to the purification of shale gas produced water and is currently without an effective solution due to the highly contaminated nature of produced water. Here, we demonstrate the direct vapor application of a robust zwitterionic coating to a variety of substrates. The coating remains unprecedentedly hydrophilic, smooth, and effectively antifouling in extremely high salinity solutions (with salt concentration of 200,000 ppm). The fouling resistance is assessed rapidly and quantitatively with a molecular force spectroscopy-based method and corroborated using quartz crystal microbalance system with dissipation monitoring. Grazing angle attenuated total reflectance Fourier transform infrared is used in combination with X-ray photoelectron spectroscopy, atomic force microscope, and in situ spectroscopic ellipsometry to lend insight into the underlying mechanism for the exceptional stability and effectiveness of the zwitterionic coating under high-salinity conditions. A unique coating architecture, where the surface is concentrated with mobile zwitterionic moieties while the bulk is cross-linked to enhance coating durability, was discovered to be the origin of its stable fouling resistance under high salinity. Combined with previously reported exceptional stability in highly oxidative environments and strong fouling resistance to oil and grease, the zwitterionic surface here has the potential to enable low-cost, membrane-based techniques for the purification of produced water and to eventually balance the favorable economics and the concerning environmental impacts of the hydraulic fracturing industry.

Reproducibility and day time bias correction of optoelectronic leg volumetry: a prospective cohort study.

PubMed

Engelberger, Rolf P; Blazek, Claudia; Amsler, Felix; Keo, Hong H; Baumann, Frédéric; Blättler, Werner; Baumgartner, Iris; Willenberg, Torsten

2011-10-05

Leg edema is a common manifestation of various underlying pathologies. Reliable measurement tools are required to quantify edema and monitor therapeutic interventions. Aim of the present work was to investigate the reproducibility of optoelectronic leg volumetry over 3 weeks' time period and to eliminate daytime related within-individual variability. Optoelectronic leg volumetry was performed in 63 hairdressers (mean age 45 ± 16 years, 85.7% female) in standing position twice within a minute for each leg and repeated after 3 weeks. Both lower leg (legBD) and whole limb (limbBF) volumetry were analysed. Reproducibility was expressed as analytical and within-individual coefficients of variance (CVA, CVW), and as intra-class correlation coefficients (ICC). A total of 492 leg volume measurements were analysed. Both legBD and limbBF volumetry were highly reproducible with CVA of 0.5% and 0.7%, respectively. Within-individual reproducibility of legBD and limbBF volumetry over a three weeks' period was high (CVW 1.3% for both; ICC 0.99 for both). At both visits, the second measurement revealed a significantly higher volume compared to the first measurement with a mean increase of 7.3 ml ± 14.1 (0.33% ± 0.58%) for legBD and 30.1 ml ± 48.5 ml (0.52% ± 0.79%) for limbBF volume. A significant linear correlation between absolute and relative leg volume differences and the difference of exact day time of measurement between the two study visits was found (P < .001). A therefore determined time-correction formula permitted further improvement of CVW. Leg volume changes can be reliably assessed by optoelectronic leg volumetry at a single time point and over a 3 weeks' time period. However, volumetry results are biased by orthostatic and daytime-related volume changes. The bias for day-time related volume changes can be minimized by a time-correction formula.

Short term reproducibility of a high contrast 3-D isotropic optic nerve imaging sequence in healthy controls

NASA Astrophysics Data System (ADS)

Harrigan, Robert L.; Smith, Alex K.; Mawn, Louise A.; Smith, Seth A.; Landman, Bennett A.

2016-03-01

The optic nerve (ON) plays a crucial role in human vision transporting all visual information from the retina to the brain for higher order processing. There are many diseases that affect the ON structure such as optic neuritis, anterior ischemic optic neuropathy and multiple sclerosis. Because the ON is the sole pathway for visual information from the retina to areas of higher level processing, measures of ON damage have been shown to correlate well with visual deficits. Increased intracranial pressure has been shown to correlate with the size of the cerebrospinal fluid (CSF) surrounding the ON. These measures are generally taken at an arbitrary point along the nerve and do not account for changes along the length of the ON. We propose a high contrast and high-resolution 3-D acquired isotropic imaging sequence optimized for ON imaging. We have acquired scan-rescan data using the optimized sequence and a current standard of care protocol for 10 subjects. We show that this sequence has superior contrast-to-noise ratio to the current standard of care while achieving a factor of 11 higher resolution. We apply a previously published automatic pipeline to segment the ON and CSF sheath and measure the size of each individually. We show that these measures of ON size have lower short- term reproducibility than the population variance and the variability along the length of the nerve. We find that the proposed imaging protocol is (1) useful in detecting population differences and local changes and (2) a promising tool for investigating biomarkers related to structural changes of the ON.

Short Term Reproducibility of a High Contrast 3-D Isotropic Optic Nerve Imaging Sequence in Healthy Controls.

PubMed

Harrigan, Robert L; Smith, Alex K; Mawn, Louise A; Smith, Seth A; Landman, Bennett A

2016-02-27

The optic nerve (ON) plays a crucial role in human vision transporting all visual information from the retina to the brain for higher order processing. There are many diseases that affect the ON structure such as optic neuritis, anterior ischemic optic neuropathy and multiple sclerosis. Because the ON is the sole pathway for visual information from the retina to areas of higher level processing, measures of ON damage have been shown to correlate well with visual deficits. Increased intracranial pressure has been shown to correlate with the size of the cerebrospinal fluid (CSF) surrounding the ON. These measures are generally taken at an arbitrary point along the nerve and do not account for changes along the length of the ON. We propose a high contrast and high-resolution 3-D acquired isotropic imaging sequence optimized for ON imaging. We have acquired scan-rescan data using the optimized sequence and a current standard of care protocol for 10 subjects. We show that this sequence has superior contrast-to-noise ratio to the current standard of care while achieving a factor of 11 higher resolution. We apply a previously published automatic pipeline to segment the ON and CSF sheath and measure the size of each individually. We show that these measures of ON size have lower short-term reproducibility than the population variance and the variability along the length of the nerve. We find that the proposed imaging protocol is (1) useful in detecting population differences and local changes and (2) a promising tool for investigating biomarkers related to structural changes of the ON.

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.

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.

Producing citizens, reproducing the "French race": immigration, demography, and pronatalism in early twentieth-century France.

PubMed

Camiscioli, E

2001-01-01

This essay examines how, in the context of depopulation and mass immigration, members of the French pronatalist movement advanced a policy favouring immigrants from Italy, Spain, and Poland. Because the 'demographic crisis' created a shortage of citizens as well as workers, pronatalists held that foreign workers must also be assimilable, and able to produce French offspring. While the racial difference of colonial subjects was deemed immutable, pronatalists called for the immigration of white foreigners whose less 'modern' condition promoted fecundity, traditionalism, and gender dimorphism. Evidence is drawn from demographic studies, the press of France's largest pronatalist movement, and a pronatalist advisory committee created by the Ministry of Health in 1920.

Reproducible Bioconductor workflows using browser-based interactive notebooks and containers.

PubMed

Almugbel, Reem; Hung, Ling-Hong; Hu, Jiaming; Almutairy, Abeer; Ortogero, Nicole; Tamta, Yashaswi; Yeung, Ka Yee

2018-01-01

Bioinformatics publications typically include complex software workflows that are difficult to describe in a manuscript. We describe and demonstrate the use of interactive software notebooks to document and distribute bioinformatics research. We provide a user-friendly tool, BiocImageBuilder, that allows users to easily distribute their bioinformatics protocols through interactive notebooks uploaded to either a GitHub repository or a private server. We present four different interactive Jupyter notebooks using R and Bioconductor workflows to infer differential gene expression, analyze cross-platform datasets, process RNA-seq data and KinomeScan data. These interactive notebooks are available on GitHub. The analytical results can be viewed in a browser. Most importantly, the software contents can be executed and modified. This is accomplished using Binder, which runs the notebook inside software containers, thus avoiding the need to install any software and ensuring reproducibility. All the notebooks were produced using custom files generated by BiocImageBuilder. BiocImageBuilder facilitates the publication of workflows with a point-and-click user interface. We demonstrate that interactive notebooks can be used to disseminate a wide range of bioinformatics analyses. The use of software containers to mirror the original software environment ensures reproducibility of results. Parameters and code can be dynamically modified, allowing for robust verification of published results and encouraging rapid adoption of new methods. Given the increasing complexity of bioinformatics workflows, we anticipate that these interactive software notebooks will become as necessary for documenting software methods as traditional laboratory notebooks have been for documenting bench protocols, and as ubiquitous. © The Author 2017. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com

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

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.

Indirect monitoring shot-to-shot shock waves strength reproducibility during pump–probe experiments

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

Pikuz, T. A., E-mail: tatiana.pikuz@eie.eng.osaka-u.ac.jp; Photon Pioneers Center, Osaka University, Suita, Osaka 565-0871 Japan; Joint Institute for High Temperatures, Russian Academy of Sciences, Moscow 125412

We present an indirect method of estimating the strength of a shock wave, allowing on line monitoring of its reproducibility in each laser shot. This method is based on a shot-to-shot measurement of the X-ray emission from the ablated plasma by a high resolution, spatially resolved focusing spectrometer. An optical pump laser with energy of 1.0 J and pulse duration of ∼660 ps was used to irradiate solid targets or foils with various thicknesses containing Oxygen, Aluminum, Iron, and Tantalum. The high sensitivity and resolving power of the X-ray spectrometer allowed spectra to be obtained on each laser shot and tomore » control fluctuations of the spectral intensity emitted by different plasmas with an accuracy of ∼2%, implying an accuracy in the derived electron plasma temperature of 5%–10% in pump–probe high energy density science experiments. At nano- and sub-nanosecond duration of laser pulse with relatively low laser intensities and ratio Z/A ∼ 0.5, the electron temperature follows T{sub e} ∼ I{sub las}{sup 2/3}. Thus, measurements of the electron plasma temperature allow indirect estimation of the laser flux on the target and control its shot-to-shot fluctuation. Knowing the laser flux intensity and its fluctuation gives us the possibility of monitoring shot-to-shot reproducibility of shock wave strength generation with high accuracy.« less

Effect of soil moisture content on the splash phenomenon reproducibility.

PubMed

Ryżak, Magdalena; Bieganowski, Andrzej; Polakowski, Cezary

2015-01-01

One of the methods for testing splash (the first phase of water erosion) may be an analysis of photos taken using so-called high-speed cameras. The aim of this study was to determine the reproducibility of measurements using a single drop splash of simulated precipitation. The height from which the drops fell resulted in a splash of 1.5 m. Tests were carried out using two types of soil: Eutric Cambisol (loamy silt) and Orthic Luvisol (sandy loam); three initial pressure heads were applied equal to 16 kPa, 3.1 kPa, and 0.1 kPa. Images for one, five, and 10 drops were recorded at a rate of 2000 frames per second. It was found that (i) the dispersion of soil caused by the striking of the 1st drop was significantly different from the splash impact caused by subsequent drops; (ii) with every drop, the splash phenomenon proceeded more reproducibly, that is, the number of particles of soil and/or water that splashed were increasingly close to each other; (iii) the number of particles that were detached during the splash were strongly correlated with its surface area; and (iv) the higher the water film was on the surface the smaller the width of the crown was.

Effect of Soil Moisture Content on the Splash Phenomenon Reproducibility

PubMed Central

Ryżak, Magdalena; Bieganowski, Andrzej; Polakowski, Cezary

2015-01-01

One of the methods for testing splash (the first phase of water erosion) may be an analysis of photos taken using so-called high-speed cameras. The aim of this study was to determine the reproducibility of measurements using a single drop splash of simulated precipitation. The height from which the drops fell resulted in a splash of 1.5 m. Tests were carried out using two types of soil: Eutric Cambisol (loamy silt) and Orthic Luvisol (sandy loam); three initial pressure heads were applied equal to 16 kPa, 3.1 kPa, and 0.1 kPa. Images for one, five, and 10 drops were recorded at a rate of 2000 frames per second. It was found that (i) the dispersion of soil caused by the striking of the 1st drop was significantly different from the splash impact caused by subsequent drops; (ii) with every drop, the splash phenomenon proceeded more reproducibly, that is, the number of particles of soil and/or water that splashed were increasingly close to each other; (iii) the number of particles that were detached during the splash were strongly correlated with its surface area; and (iv) the higher the water film was on the surface the smaller the width of the crown was. PMID:25785859

Reproducibility of the dynamics of facial expressions in unilateral facial palsy.

PubMed

Alagha, M A; Ju, X; Morley, S; Ayoub, A

2018-02-01

The aim of this study was to assess the reproducibility 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 reproducibility 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 reproducibility 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 reproducible. Facial expressions of maximum smile and forceful eye closure were not reproducible. The limited coordination of various groups of facial muscles contributed to the lack of reproducibility 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.

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.

Comparison of multi-fiber reproducibility of PAS-MRI and Q-ball with empirical multiple b-value HARDI

NASA Astrophysics Data System (ADS)

Nath, Vishwesh; Schilling, Kurt G.; Blaber, Justin A.; Ding, Zhaohua; Anderson, Adam W.; Landman, Bennett A.

2017-02-01

Crossing fibers are prevalent in human brains and a subject of intense interest for neuroscience. Diffusion tensor imaging (DTI) can resolve tissue orientation but is blind to crossing fibers. Many advanced diffusion-weighted magnetic resolution imaging (MRI) approaches have been presented to extract crossing-fibers from high angular resolution diffusion imaging (HARDI), but the relative sensitivity and specificity of approaches remains unclear. Here, we examine two leading approaches (PAS and q-ball) in the context of a large-scale, single subject reproducibility study. A single healthy individual was scanned 11 times with 96 diffusion weighted directions and 10 reference volumes for each of five b-values (1000, 1500, 2000, 2500, 3000 s/mm2) for a total of 5830 volumes (over the course of three sessions). We examined the reproducibility of the number of fibers per voxel, volume fraction, and crossing-fiber angles. For each method, we determined the minimum resolvable angle for each acquisition. Reproducibility of fiber counts per voxel was generally high ( 80% consensus for PAS and 70% for q-ball), but there was substantial bias between individual repetitions and model estimated with all data ( 10% lower consensus for PAS and 15% lower for q-ball). Both PAS and q-ball predominantly discovered fibers crossing at near 90 degrees, but reproducibility was higher for PAS across most measures. Within voxels with low anisotropy, q-ball finds more intra-voxel structure; meanwhile, PAS resolves multiple fibers at greater than 75 degrees for more voxels. These results can inform researchers when deciding between HARDI approaches or interpreting findings across studies.

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

PubMed Central

2012-01-01

Background Affinity-Purification Mass-Spectrometry (AP-MS) provides a powerful means of identifying protein complexes and interactions. Several important challenges exist in interpreting the results of AP-MS experiments. First, the reproducibility of AP-MS experimental replicates can be low, due both to technical variability and the dynamic nature of protein interactions in the cell. Second, the identification of true protein-protein interactions in AP-MS experiments is subject to inaccuracy due to high false negative and false positive rates. Several experimental approaches can be used to mitigate these drawbacks, including the use of replicated and control experiments and relative quantification to sensitively distinguish true interacting proteins from false ones. Methods To address the issues of reproducibility and accuracy of protein-protein interactions, we introduce a two-step method, called ROCS, which makes use of Indicator Prey Proteins to select reproducible AP-MS experiments, and of Confidence Scores to select specific protein-protein interactions. The Indicator Prey Proteins account for measures of protein identifiability as well as protein reproducibility, effectively allowing removal of outlier experiments that contribute noise and affect downstream inferences. The filtered set of experiments is then used in the Protein-Protein Interaction (PPI) scoring step. Prey protein scoring is done by computing a Confidence Score, which accounts for the probability of occurrence of prey proteins in the bait experiments relative to the control experiment, where the significance cutoff parameter is estimated by simultaneously controlling false positives and false negatives against metrics of false discovery rate and biological coherence respectively. In summary, the ROCS method relies on automatic objective criterions for parameter estimation and error-controlled procedures. Results We illustrate the performance of our method by applying it to five previously

Reproducibility of intraocular pressure peak and fluctuation of the water-drinking test.

PubMed

Hatanaka, Marcelo; Alencar, Luciana M; De Moraes, Carlos G; Susanna, Remo

2013-01-01

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 reproducible results with consistent measurements. This study was performed to verify the reproducibility 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. Reproducibility was assessed using the intraclass correlation coefficient. Peak and fluctuation of intraocular pressure obtained with the water-drinking test were analysed for reproducibility. 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, reproducibility 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 reproducibility, whereas the reproducibility of fluctuation was considered fair. © 2012 The Authors. Clinical and Experimental Ophthalmology © 2012 Royal Australian and New Zealand College of Ophthalmologists.

Reproducibility, Controllability, and Optimization of Lenr Experiments

NASA Astrophysics Data System (ADS)

Nagel, David J.

2006-02-01

Low-energy nuclear reaction (LENR) measurements are significantly and increasingly reproducible. 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.

Intact cell mass spectrometry (ICMS) used to type methicillin-resistant Staphylococcus aureus: media effects and inter-laboratory reproducibility.

PubMed

Walker, J; Fox, A J; Edwards-Jones, V; Gordon, D B

2002-02-01

Intact cell mass spectrometry (ICMS) rapidly analyses the surface composition of microorganisms providing rapid, discriminatory fingerprints for identification and subtyping of important nosocomial pathogens such as methicillin resistant Staphylocccus aureus (MRSA). In this study, ICMS using matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI TOF/MS) was assessed for the identification and subtyping of MRSA. An intra- and inter-laboratory reproducibility study was carried out and the effects of culture media (an important source of variation for ICMS) were also studied. Several media used for the cultural identification of MRSA were examined using a panel of well-characterised staphylococcal isolates (n=26). Six MRSA isolates were analysed over a 1-month period for intra-laboratory reproducibility on the same instrument and three different culture media. Spectra were consistent for each isolate between the four experiments on the same culture medium. Individual isolates produced different spectral profiles on different culture media. Spectra from organisms grown on Columbia blood agar contained more peaks (approximately 120) compared to Columbia agar (approximately 50) and methicillin mannitol salt agar (approximately 25). All 26 staphylococcal isolates were subjected to an inter-laboratory study on two MALDI instruments. For each isolate, the overall spectral profile was the same for each of the two instruments but the baseline threshold values was adjusted due to instrument differences in detector sensitivities. Differences between certain regions of the spectra reproducibly identified isolates belonging to the two major MRSA strains (EMRSA phage group 15 and 16). These results demonstrate ICMS with appropriate media selection is a rapid and reproducible technique for identification and discrimination of MRSA.

Report of high quantum efficiency photocathode at Milano

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

Michelato, P.

R D activity on high quantum efficiency alkali antimonide photocathode is in progress at Milano, in the context of the ARES program. Inside a preliminary preparation chamber, Cs[sub 3]Sb layers with qunatum efficiency up to 9% (at [lambda]=543.5 nm) and lifetime of some days has been recently produced on copper, stainless steel and niobium, using a reproducible deposition procedure adapted to the material of the different substrata.

"Elementary, My Dear Shakespeare." Producing a Shakespearean Festival in the Elementary Schools.

ERIC Educational Resources Information Center

Engen, Barbara; Campbell, Joy

Intended to give teachers usable information and prepared materials that are ready-to-reproduce for students, this book compiles research, tips, and teaching ideas into a sourcebook on teaching and producing William Shakespeare's plays in the elementary classroom. It is designed to bring the student into an awareness of Shakespeare's art and…

Reproducible detection of disease-associated markers from gene expression data.

PubMed

Omae, Katsuhiro; Komori, Osamu; Eguchi, Shinto

2016-08-18

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 reproducible 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 reproducibility 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 reproducible 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 reproducibility.

Reproducibility studies for experimental epitope detection in macrophages (EDIM).

PubMed

Japink, Dennis; Nap, Marius; Sosef, Meindert N; Nelemans, Patty J; Coy, Johannes F; Beets, Geerard; von Meyenfeldt, Maarten F; Leers, Math P G

2014-05-01

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 reproducibility, while inter-assay variation showed reproducibility 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, reproducible and transferable. Biological variation over time needs further assessment in future work. Copyright © 2014 Elsevier B.V. All rights reserved.

PSYCHOLOGY. Estimating the reproducibility of psychological science.

PubMed

2015-08-28

Reproducibility is a defining feature of science, but the extent to which it characterizes current research is unknown. We conducted replications of 100 experimental and correlational studies published in three psychology journals using high-powered designs and original materials when available. Replication effects were half the magnitude of original effects, representing a substantial decline. Ninety-seven percent of original studies had statistically significant results. Thirty-six percent of replications had statistically significant results; 47% of original effect sizes were in the 95% confidence interval of the replication effect size; 39% of effects were subjectively rated to have replicated the original result; and if no bias in original results is assumed, combining original and replication results left 68% with statistically significant effects. Correlational tests suggest that replication success was better predicted by the strength of original evidence than by characteristics of the original and replication teams. Copyright © 2015, American Association for the Advancement of Science.

Examining the Reproducibility of 6 Published Studies in Public Health Services and Systems Research.

PubMed

Harris, Jenine K; B Wondmeneh, Sarah; Zhao, Yiqiang; Leider, Jonathon P

2018-02-23

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. Reproducibility, or reanalysis of data to verify published findings, is one proposed minimum alternative standard. While a lack of research reproducibility 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 reproducibility of public health research. We examined reproducibility 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 reproduced 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 reproducibility, 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 reproducibility of science through several strategies including publishing data and statistical code, using guidelines to write clear and complete methods sections, conducting reproducibility reviews, and incentivizing reproducible science.

Reproducibility of electronic tooth colour measurements.

PubMed

Ratzmann, Anja; Klinke, Thomas; Schwahn, Christian; Treichel, Anja; Gedrange, Tomasz

2008-10-01

Clinical methods of investigation, such as tooth colour determination, should be simple, quick and reproducible. 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 reproducibility. 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.

Reproducible Growth of High-Quality Cubic-SiC Layers

NASA Technical Reports Server (NTRS)

Neudeck, Philip G.; Powell, J. Anthony

2004-01-01

Semiconductor electronic devices and circuits based on silicon carbide (SiC) are being developed for use in high-temperature, high-power, and/or high-radiation conditions under which devices made from conventional semiconductors cannot adequately perform. The ability of SiC-based devices to function under such extreme conditions is expected to enable significant improvements in a variety of applications and systems. These include greatly improved high-voltage switching for saving energy in public electric power distribution and electric motor drives; more powerful microwave electronic circuits for radar and communications; and sensors and controls for cleaner-burning, more fuel-efficient jet aircraft and automobile engines.

Exploratory results from a new rotary shear designed to reproduce the extreme deformation conditions of crustal earthquakes

NASA Astrophysics Data System (ADS)

Di Toro, G.; Nielsen, S. B.; Spagnuolo, E.; Smith, S.; Violay, M. E.; Niemeijer, A. R.; Di Felice, F.; Di Stefano, G.; Romeo, G.; Scarlato, P.

2011-12-01

A challenging goal in experimental rock deformation is to reproduce the extreme deformation conditions typical of coseismic slip in crustal earthquakes: large slip (up to 50 m), slip rates (0.1-10 m/s), accelerations (> 10 m/s2) and normal stress (> 50 MPa). Moreover, fault zones usually contain non-cohesive rocks (gouges) and fluids. The integration of all these deformation conditions is such a technical challenge that there is currently no apparatus in the world that can reproduce seismic slip. Yet, the determination of rock friction at seismic slip rates remains one of the main unknowns in earthquake physics, as it cannot be determined (or very approximately) by seismic wave inversion analysis. In the last thirty years, rotary shear apparatus were designed that combine large normal stresses and slip but low slip rates (high-pressure rotary shears first designed by Tullis) or low normal stresses but large slip rates and slip (rotary shears first designed by Shimamoto). Here we present the results of experiments using a newly-constructed Slow to HIgh Velocity Apparatus (SHIVA), installed at INGV in Rome, which extends the combination of normal stress, slip and slip rate achieved by previous apparatus and reproduces the conditions likely to occur during an earthquake in the shallow crust. SHIVA uses two brushless engines (max power 300 kW, max torque 930 Nm) and an air actuator (thrust 5 tons) in a rotary shear configuration (nominally infinite displacement) to slide hollow rock cylinders (30/50 mm int./ext. diameter) at slip rates ranging from 10 micron/s up to 6.5 m/s, accelerations up to 80 m/s2 and normal stresses up to 50 MPa. SHIVA can also perform experiments in which the torque on the sample (rather than the slip rate) is progressively increased until spontaneous failure occurs: this experimental capability should better reproduce natural conditions. The apparatus is equipped with a sample chamber to carry out experiments in the presence of fluids (up to 15

Reproducibility of graph metrics of human brain structural networks.

PubMed

Duda, Jeffrey T; Cook, Philip A; Gee, James C

2014-01-01

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 reproducibility 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 reproducibility 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 reproducibility 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 reproducibility 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.

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.

On the Reproducibility of Label-Free Quantitative Cross-Linking/Mass Spectrometry

NASA Astrophysics Data System (ADS)

Müller, Fränze; Fischer, Lutz; Chen, Zhuo Angel; Auchynnikava, Tania; Rappsilber, Juri

2018-02-01

Quantitative cross-linking/mass spectrometry (QCLMS) is an emerging approach to study conformational changes of proteins and multi-subunit complexes. Distinguishing protein conformations requires reproducibly 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 reproducible 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 reproducibility of QCLMS is in line with the reproducibility of general quantitative proteomics and we establish a robust workflow for MS1-based quantitation of cross-linked peptides.

Identifying Reproducible Molecular Biomarkers for Gastric Cancer Metastasis with the Aid of Recurrence Information

PubMed Central

Li, Mengyao; Hong, Guini; Cheng, Jun; Li, Jing; Cai, Hao; Li, Xiangyu; Guan, Qingzhou; Tong, Mengsha; Li, Hongdong; Guo, Zheng

2016-01-01

To precisely diagnose metastasis state is important for tailoring treatments for gastric cancer patients. However, the routinely employed radiological and pathologic tests for tumour metastasis have considerable high false negative rates, which may retard the identification of reproducible metastasis-related molecular biomarkers for gastric cancer. In this research, using three datasets, we firstly shwed that differentially expressed genes (DEGs) between metastatic tissue samples and non-metastatic tissue samples could hardly be reproducibly detected with a proper statistical control when the metastatic and non-metastatic samples were defined by TNM stage alone. Then, assuming that undetectable micrometastases are the prime cause for recurrence of early stage patients with curative resection, we reclassified all the “non-metastatic” samples as metastatic samples whenever the patients experienced tumour recurrence during follow-up after tumour resection. In this way, we were able to find distinct and reproducible DEGs between the reclassified metastatic and non-metastatic tissue samples and concordantly significant DNA methylation alterations distinguishing metastatic tissues and non-metastatic tissues of gastric cancer. Our analyses suggested that the follow-up recurrence information for patients should be employed in the research of tumour metastasis in order to decrease the confounding effects of false non-metastatic samples with undetected micrometastases. PMID:27109211

The reliability and reproducibility of cephalometric measurements: a comparison of conventional and digital methods

PubMed Central

AlBarakati, SF; Kula, KS; Ghoneima, AA

2012-01-01

Objective The aim of this study was to assess the reliability and reproducibility 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 reproducibility 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 observed 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 reproducibility of the two methods showed some statistically significant differences, most differences were not clinically significant. PMID:22184624

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

GUIdock: Using Docker Containers with a Common Graphics User Interface to Address the Reproducibility of Research

PubMed Central

Yeung, Ka Yee

2016-01-01

Reproducibility is vital in science. For complex computational methods, it is often necessary, not just to recreate the code, but also the software and hardware environment to reproduce results. Virtual machines, and container software such as Docker, make it possible to reproduce the exact environment regardless of the underlying hardware and operating system. However, workflows that use Graphical User Interfaces (GUIs) remain difficult to replicate on different host systems as there is no high level graphical software layer common to all platforms. GUIdock allows for the facile distribution of a systems biology application along with its graphics environment. Complex graphics based workflows, ubiquitous in systems biology, can now be easily exported and reproduced on many different platforms. GUIdock uses Docker, an open source project that provides a container with only the absolutely necessary software dependencies and configures a common X Windows (X11) graphic interface on Linux, Macintosh and Windows platforms. As proof of concept, we present a Docker package that contains a Bioconductor application written in R and C++ called networkBMA for gene network inference. Our package also includes Cytoscape, a java-based platform with a graphical user interface for visualizing and analyzing gene networks, and the CyNetworkBMA app, a Cytoscape app that allows the use of networkBMA via the user-friendly Cytoscape interface. PMID:27045593

GUIdock: Using Docker Containers with a Common Graphics User Interface to Address the Reproducibility of Research.

PubMed

Hung, Ling-Hong; Kristiyanto, Daniel; Lee, Sung Bong; Yeung, Ka Yee

2016-01-01

Reproducibility is vital in science. For complex computational methods, it is often necessary, not just to recreate the code, but also the software and hardware environment to reproduce results. Virtual machines, and container software such as Docker, make it possible to reproduce the exact environment regardless of the underlying hardware and operating system. However, workflows that use Graphical User Interfaces (GUIs) remain difficult to replicate on different host systems as there is no high level graphical software layer common to all platforms. GUIdock allows for the facile distribution of a systems biology application along with its graphics environment. Complex graphics based workflows, ubiquitous in systems biology, can now be easily exported and reproduced on many different platforms. GUIdock uses Docker, an open source project that provides a container with only the absolutely necessary software dependencies and configures a common X Windows (X11) graphic interface on Linux, Macintosh and Windows platforms. As proof of concept, we present a Docker package that contains a Bioconductor application written in R and C++ called networkBMA for gene network inference. Our package also includes Cytoscape, a java-based platform with a graphical user interface for visualizing and analyzing gene networks, and the CyNetworkBMA app, a Cytoscape app that allows the use of networkBMA via the user-friendly Cytoscape interface.

Jupyter meets Earth: Creating Comprehensible and Reproducible Scientific Workflows with Jupyter Notebooks and Google Earth Engine

NASA Astrophysics Data System (ADS)

Erickson, T.

2016-12-01

Deriving actionable information from Earth observation data obtained from sensors or models can be quite complicated, and sharing those insights with others in a form that they can understand, reproduce, and improve upon is equally difficult. Journal articles, even if digital, commonly present just a summary of an analysis that cannot be understood in depth or reproduced without major effort on the part of the reader. Here we show a method of improving scientific literacy by pairing a recently developed scientific presentation technology (Jupyter Notebooks) with a petabyte-scale platform for accessing and analyzing Earth observation and model data (Google Earth Engine). Jupyter Notebooks are interactive web documents that mix live code with annotations such as rich-text markup, equations, images, videos, hyperlinks and dynamic output. Notebooks were first introduced as part of the IPython project in 2011, and have since gained wide acceptance in the scientific programming community, initially among Python programmers but later by a wide range of scientific programming languages. While Jupyter Notebooks have been widely adopted for general data analysis, data visualization, and machine learning, to date there have been relatively few examples of using Jupyter Notebooks to analyze geospatial datasets. Google Earth Engine is cloud-based platform for analyzing geospatial data, such as satellite remote sensing imagery and/or Earth system model output. Through its Python API, Earth Engine makes petabytes of Earth observation data accessible, and provides hundreds of algorithmic building blocks that can be chained together to produce high-level algorithms and outputs in real-time. We anticipate that this technology pairing will facilitate a better way of creating, documenting, and sharing complex analyses that derive information on our Earth that can be used to promote broader understanding of the complex issues that it faces. http://jupyter.orghttps://earthengine.google.com

Adapting to blur produced by ocular high-order aberrations

PubMed Central

Sawides, Lucie; de Gracia, Pablo; Dorronsoro, Carlos; Webster, Michael; Marcos, Susana

2011-01-01

The perceived focus of an image can be strongly biased by prior adaptation to a blurred or sharpened image. We examined whether these adaptation effects can occur for the natural patterns of retinal image blur produced by high-order aberrations (HOAs) in the optics of the eye. Focus judgments were measured for 4 subjects to estimate in a forced choice procedure (sharp/blurred) their neutral point after adaptation to different levels of blur produced by scaled increases or decreases in their HOAs. The optical blur was simulated by convolution of the PSFs from the 4 different HOA patterns, with Zernike coefficients (excluding tilt, defocus, and astigmatism) multiplied by a factor between 0 (diffraction limited) and 2 (double amount of natural blur). Observers viewed the images through an Adaptive Optics system that corrected their aberrations and made settings under neutral adaptation to a gray field or after adapting to 5 different blur levels. All subjects adapted to changes in the level of blur imposed by HOA regardless of which observer’s HOA was used to generate the stimuli, with the perceived neutral point proportional to the amount of blur in the adapting image. PMID:21712375

Adapting to blur produced by ocular high-order aberrations.

PubMed

Sawides, Lucie; de Gracia, Pablo; Dorronsoro, Carlos; Webster, Michael; Marcos, Susana

2011-06-28

The perceived focus of an image can be strongly biased by prior adaptation to a blurred or sharpened image. We examined whether these adaptation effects can occur for the natural patterns of retinal image blur produced by high-order aberrations (HOAs) in the optics of the eye. Focus judgments were measured for 4 subjects to estimate in a forced choice procedure (sharp/blurred) their neutral point after adaptation to different levels of blur produced by scaled increases or decreases in their HOAs. The optical blur was simulated by convolution of the PSFs from the 4 different HOA patterns, with Zernike coefficients (excluding tilt, defocus, and astigmatism) multiplied by a factor between 0 (diffraction limited) and 2 (double amount of natural blur). Observers viewed the images through an Adaptive Optics system that corrected their aberrations and made settings under neutral adaptation to a gray field or after adapting to 5 different blur levels. All subjects adapted to changes in the level of blur imposed by HOA regardless of which observer's HOA was used to generate the stimuli, with the perceived neutral point proportional to the amount of blur in the adapting image.

Highly oil-producing microalgae selected through directed-evolution on a microfludic chip

NASA Astrophysics Data System (ADS)

Mestler, Troy; Estevez-Torres, Andre; Lambert, Guillaume; Austin, Robert H.

2009-03-01

Some species of photosynthetic microalgae produce signi?cant amounts of oil which can be easily converted to diesel fuel. However, as it stands today, biodiesel is signi?cantly more expensive than fossil fuels. We wish to improve the oil yield and production rate of a single species of microalgae through directed evolution. We propose to utilize our microfabication technology to create microhabitats to control the nutrient environment of the species, monitor oil production through Raman Spectroscopy, and punish colonies of algae which have low oil yield. We believe this process will produce a mutant species with a high oil yield.

Relevant principal factors affecting the reproducibility of insect primary culture.

PubMed

Ogata, Norichika; Iwabuchi, Kikuo

2017-06-01

The primary culture of insect cells often suffers from problems with poor reproducibility 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 reproducibility 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 reproducibility 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.

Magnetic resonance elastography of the pancreas: Measurement reproducibility and relationship with age.

PubMed

Kolipaka, Arunark; Schroeder, Samuel; Mo, Xiaokui; Shah, Zarine; Hart, Phil A; Conwell, Darwin L

2017-10-01

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 reproducibility 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 reproducibility 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 observed 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 reproducible 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.

Discriminatory Power and Reproducibility of Novel DNA Typing Methods for Mycobacterium tuberculosis Complex Strains

PubMed Central

Kremer, Kristin; Arnold, Catherine; Cataldi, Angel; Gutiérrez, M. Cristina; Haas, Walter H.; Panaiotov, Stefan; Skuce, Robin A.; Supply, Philip; van der Zanden, Adri G. M.; van Soolingen, Dick

2005-01-01

In recent years various novel DNA typing methods have been developed which are faster and easier to perform than the current internationally standardized IS6110 restriction fragment length polymorphism typing method. However, there has been no overview of the utility of these novel typing methods, and it is largely unknown how they compare to previously published methods. In this study, the discriminative power and reproducibility of nine recently described PCR-based typing methods for Mycobacterium tuberculosis were investigated using the strain collection of the interlaboratory study of Kremer et al. (J. Clin. Microbiol. 37:2607-2618, 1999). This strain collection contains 90 M. tuberculosis complex and 10 non-M. tuberculosis complex mycobacterial strains, as well as 31 duplicated DNA samples to assess reproducibility. The highest reproducibility was found with variable numbers of tandem repeat typing using mycobacterial interspersed repetitive units (MIRU VNTR) and fast ligation-mediated PCR (FLiP), followed by second-generation spoligotyping, ligation-mediated PCR (LM-PCR), VNTR typing using five repeat loci identified at the Queens University of Belfast (QUB VNTR), and the Amadio speciation PCR. Poor reproducibility was associated with fluorescent amplified fragment length polymorphism typing, which was performed in three different laboratories. The methods were ordered from highest discrimination to lowest by the Hunter-Gaston discriminative index as follows: QUB VNTR typing, MIRU VNTR typing, FLiP, LM-PCR, and spoligotyping. We conclude that both VNTR typing methods and FLiP typing are rapid, highly reliable, and discriminative epidemiological typing methods for M. tuberculosis and that VNTR typing is the epidemiological typing method of choice for the near future. PMID:16272496

Method to Produce Flexible Ceramic Thermal Protection System Resistant to High Aeroacoustic Noise

NASA Technical Reports Server (NTRS)

Sawko, Paul M. (Inventor); Calamito, Dominic P. (Inventor); Jong, Anthony (Inventor)

1997-01-01

A method of producing a three dimensional angle interlock ceramic fiber which is stable to high aeroacoustic noise of about 170 decibels and to high temperatures of about 2500 F is disclosed. The method uses multiple separate strands of a ceramic fiber or ceramic tow suitable for weaving having multiple warp fibers and multiple fill fibers woven with a modified fly-shuttle loom or rapier shuttleless loom which has nip rolls, a modified fabric advancement mechanism and at least eight harnesses in connection with a Dobby pattern chain utilizing sufficient heddles for each warp fiber and a reed which accommodates at least 168 ends per inch. The method produces a multilayered top fabric, rib fabric and single-layered bottom fabric.

Reproducibility and Temporal Structure in Weekly Resting-State fMRI over a Period of 3.5 Years

PubMed Central

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.

2015-01-01

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 observed 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 reproducibility, 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 reproducibility of outcome measures—network spatial map, temporal signal fluctuation magnitude, and between-network connectivity (BNC)–was high, with executive RSNs showing the highest reproducibility. 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 reproducibility 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

Real-time PCR assays for detection and quantification of aflatoxin-producing molds in foods.

PubMed

Rodríguez, Alicia; Rodríguez, Mar; Luque, M Isabel; Martín, Alberto; Córdoba, Juan J

2012-08-01

Aflatoxins are among the most toxic mycotoxins. Early detection and quantification of aflatoxin-producing species is crucial to improve food safety. In the present work, two protocols of real-time PCR (qPCR) based on SYBR Green and TaqMan were developed, and their sensitivity and specificity were evaluated. Primers and probes were designed from the o-methyltransferase gene (omt-1) involved in aflatoxin biosynthesis. Fifty-three mold strains representing aflatoxin producers and non-producers of different species, usually reported in food products, were used as references. All strains were tested for aflatoxins production by high-performance liquid chromatography-mass spectrometry (HPLC-MS). The functionality of the proposed qPCR method was demonstrated by the strong linear relationship of the standard curves constructed with the omt-1 gene copy number and Ct values for the different aflatoxin producers tested. The ability of the qPCR protocols to quantify aflatoxin-producing molds was evaluated in different artificially inoculated foods. A good linear correlation was obtained over the range 4 to 1 log cfu/g per reaction for all qPCR assays in the different food matrices (peanuts, spices and dry-fermented sausages). The detection limit in all inoculated foods ranged from 1 to 2 log cfu/g for SYBR Green and TaqMan assays. No significant effect was observed due to the different equipment, operator, and qPCR methodology used in the tests of repeatability and reproducibility for different foods. The proposed methods quantified with high efficiency the fungal load in foods. These qPCR protocols are proposed for use to quantify aflatoxin-producing molds in food products. Copyright © 2012 Elsevier Ltd. All rights reserved.

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.

Exploring the Role of Information Professionals in Improving Research Reproducibility:A Case Study in Geosciences

NASA Astrophysics Data System (ADS)

Yan, A.; West, J.

2016-12-01

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 reproduced a published study had failed at least one time in reproducing, suggesting a general lack of research reproducibility in geosciences. Although there is much enthusiasm for creation of technologies such as workflow system, literate programming, and cloud-based system to facilitate reproducibility, 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 reproducible research. Hereby we argue that LIS professionals may be well-positioned to assist researchers to make their research reproducible. In this study, we aim to answer the question: how can LIS professionals assist geoscience researchers in making their research capable of being reproduced? We first synthesize different definitions of "reproducibility" and provide a conceptual framework of "reproducibility" 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 reproducibility and

Reproducibility of UAV-based earth surface topography based on structure-from-motion algorithms.

NASA Astrophysics Data System (ADS)

Clapuyt, François; Vanacker, Veerle; Van Oost, Kristof

2014-05-01

A representation of the earth surface at very high spatial resolution is crucial to accurately 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 reproducibility 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 reproducibility of the earth surface topography. Finally, consistency between independent datasets is discussed.

High surface area calcite

NASA Astrophysics Data System (ADS)

Schultz, L. N.; Andersson, M. P.; Dalby, K. N.; Müter, D.; Okhrimenko, D. V.; Fordsmand, H.; Stipp, S. L. S.

2013-05-01

Calcite (CaCO3) is important in many fields—in nature, because it is a component of aquifers, oil reservoirs and prospective CO2 storage sites, and in industry, where it is used in products as diverse as paper, toothpaste, paint, plastic and aspirin. It is difficult to obtain high purity calcite with a high surface area but such material is necessary for industrial applications and for fundamental calcite research. Commercial powder is nearly always contaminated with growth inhibitors such as sugars, citrate or pectin and most laboratory synthesis methods deliver large precipitates, often containing vaterite or aragonite. To address this problem, we (i) adapted the method of carbonating a Ca(OH)2 slurry with CO2 gas to develop the first simple, cheap, safe and reproducible procedure using common laboratory equipment, to obtain calcite that reproducibly had a surface area of 14-17 m2/g and (ii) conducted a thorough characterization of the product. Scanning electron microscopy (SEM) revealed nanometer scale, rhombohedral crystals. X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS) and infrared spectroscopy (IR) confirmed highly crystalline, pure calcite that more closely resembles the dimensions of the biogenic calcite produced by algae in coccoliths than other methods for synthesizing calcite. We suggest that this calcite is useful when purity and high surface area are important.

Marinobacter sp. from marine sediments produce highly stable surface-active agents for combatting marine oil spills.

PubMed

Raddadi, Noura; Giacomucci, Lucia; Totaro, Grazia; Fava, Fabio

2017-11-02

The application of chemical dispersants as a response to marine oil spills is raising concerns related to their potential toxicity also towards microbes involved in oil biodegradation. Hence, oil spills occurring under marine environments necessitate the application of biodispersants that are highly active, stable and effective under marine environment context. Biosurfactants from marine bacteria could be good candidates for the development of biodispersant formulations effective in marine environment. This study aimed at establishing a collection of marine bacteria able to produce surface-active compounds and evaluating the activity and stability of the produced compounds under conditions mimicking those found under marine environment context. A total of 43 different isolates were obtained from harbor sediments. Twenty-six of them produced mainly bioemulsifiers when glucose was used as carbon source and 16 were biosurfactant/bioemulsifiers producers after growth in the presence of soybean oil. Sequencing of 16S rRNA gene classified most isolates into the genus Marinobacter. The produced emulsions were shown to be stable up to 30 months monitoring period, in the presence of 300 g/l NaCl, at 4 °C and after high temperature treatment (120 °C for 20 min). The partially purified compounds obtained after growth on soybean oil-based media exhibited low toxicity towards V. fischeri and high capability to disperse crude oil on synthetic marine water. To the best of our knowledge, stability characterization of bioemulsifiers/biosurfactants from the non-pathogenic marine bacterium Marinobacter has not been previously reported. The produced compounds were shown to have potential for different applications including the environmental sector. Indeed, their high stability in the presence of high salt concentration and low temperature, conditions characterizing the marine environment, the capability to disperse crude oil and the low ecotoxicity makes them interesting for

Reproducible Research in the Geosciences at Scale: Achievable Goal or Elusive Dream?

NASA Astrophysics Data System (ADS)

Wyborn, L. A.; Evans, B. J. K.

2016-12-01

Reproducibility is a fundamental tenant of the scientific method: it implies that any researcher, or a third party working independently, can duplicate any experiment or investigation and produce the same results. Historically computationally based research involved an individual using their own data and processing it in their own private area, often using software they wrote or inherited from close collaborators. Today, a researcher is likely to be part of a large team that will use a subset of data from an external repository and then process the data on a public or private cloud or on a large centralised supercomputer, using a mixture of their own code, third party software and libraries, or global community codes. In 'Big Geoscience' research it is common for data inputs to be extracts from externally managed dynamic data collections, where new data is being regularly appended, or existing data is revised when errors are detected and/or as processing methods are improved. New workflows increasingly use services to access data dynamically to create subsets on-the-fly from distributed sources, each of which can have a complex history. At major computational facilities, underlying systems, libraries, software and services are being constantly tuned and optimised, or as new or replacement infrastructure being installed. Likewise code used from a community repository is continually being refined, re-packaged and ported to the target platform. To achieve reproducibility, today's researcher increasingly needs to track their workflow, including querying information on the current or historical state of facilities used. Versioning methods are standard practice for software repositories or packages, but it is not common for either data repositories or data services to provide information about their state, or for systems to provide query-able access to changes in the underlying software. While a researcher can achieve transparency and describe steps in their workflow so

Differential pituitary response to GNRH and GNIH in low and high egg producing turkey hens

USDA-ARS?s Scientific Manuscript database

Turkey hens with low egg production have a negative economic impact on the industry as these hens produce fewer poults yet cost the same to maintain as their high egg-producing counterparts. Egg production begins with the secretion of gonadotropin releasing hormone (GNRH) from the hypothalamus caus...

Methods for Producing High-Performance Silicon Carbide Fibers, Architectural Preforms, and High-Temperature Composite Structures

NASA Technical Reports Server (NTRS)

Yun, Hee-Mann (Inventor); DiCarlo, James A. (Inventor)

2014-01-01

Methods are disclosed for producing architectural preforms and high-temperature composite structures containing high-strength ceramic fibers with reduced preforming stresses within each fiber, with an in-situ grown coating on each fiber surface, with reduced boron within the bulk of each fiber, and with improved tensile creep and rupture resistance properties tier each fiber. The methods include the steps of preparing an original sample of a preform formed from a pre-selected high-strength silicon carbide ceramic fiber type, placing the original sample in a processing furnace under a pre-selected preforming stress state and thermally treating the sample in the processing furnace at a pre-selected processing temperature and hold time in a processing gas having a pre-selected composition, pressure, and flow rate. For the high-temperature composite structures, the method includes additional steps of depositing a thin interphase coating on the surface of each fiber and forming a ceramic or carbon-based matrix within the sample.

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.

Diagnostic performance of reproducible chest wall tenderness to rule out acute coronary syndrome in acute chest pain: a prospective diagnostic study

PubMed Central

Gräni, Christoph; Senn, Oliver; Bischof, Manuel; Cippà, Pietro E; Hauffe, Till; Zimmerli, Lukas; Battegay, Edouard; Franzen, Daniel

2015-01-01

Objectives Acute chest pain (ACP) is a leading cause of hospital emergency unit consultation. As there are various underlying conditions, ranging from musculoskeletal disorders to acute coronary syndrome (ACS), thorough clinical diagnostics are warranted. The aim of this prospective study was to assess whether reproducible chest wall tenderness (CWT) on palpation in patients with ACP can help to rule out ACS. Methods In this prospective, double-blinded diagnostic study, all consecutive patients assessed in the emergency unit at the University Hospital Zurich because of ACP between July 2012 and December 2013 were included when a member of the study team was present. Reproducible CWT on palpation was the initial step and was recorded before further examinations were initiated. The final diagnosis was adjudicated by a study-independent physician. Results 121 patients (60.3% male, median age 47 years, IQR 34–66.5 years) were included. The prevalence of ACS was 11.6%. Non-reproducible CWT had a high sensitivity of 92.9% (95% CI 66.1% to 98.8%) for ACS and the presence of reproducible CWT ruled out ACS (p=0.003) with a high negative predictive value (98.1%, 95% CI 89.9% to 99.7%). Conversely non-reproducible CWT ruled in ACS with low specificity (48.6%, 95% CI 38.8% to 58.5%) and low positive predictive value (19.1%, 95% CI 10.6% to 30.5%). Conclusions This prospective diagnostic study supports the concept that reproducible CWT helps to rule out ACS in patients with ACP in an early stage of the evaluation process. However, ACS and other diagnoses should be considered in patients with a negative CWT test. Trial registration number ClinicalTrial.gov: NCT01724996. PMID:25631316

Diagnostic performance of reproducible chest wall tenderness to rule out acute coronary syndrome in acute chest pain: a prospective diagnostic study.

PubMed

Gräni, Christoph; Senn, Oliver; Bischof, Manuel; Cippà, Pietro E; Hauffe, Till; Zimmerli, Lukas; Battegay, Edouard; Franzen, Daniel

2015-01-28

Acute chest pain (ACP) is a leading cause of hospital emergency unit consultation. As there are various underlying conditions, ranging from musculoskeletal disorders to acute coronary syndrome (ACS), thorough clinical diagnostics are warranted. The aim of this prospective study was to assess whether reproducible chest wall tenderness (CWT) on palpation in patients with ACP can help to rule out ACS. In this prospective, double-blinded diagnostic study, all consecutive patients assessed in the emergency unit at the University Hospital Zurich because of ACP between July 2012 and December 2013 were included when a member of the study team was present. Reproducible CWT on palpation was the initial step and was recorded before further examinations were initiated. The final diagnosis was adjudicated by a study-independent physician. 121 patients (60.3% male, median age 47 years, IQR 34-66.5 years) were included. The prevalence of ACS was 11.6%. Non-reproducible CWT had a high sensitivity of 92.9% (95% CI 66.1% to 98.8%) for ACS and the presence of reproducible CWT ruled out ACS (p=0.003) with a high negative predictive value (98.1%, 95% CI 89.9% to 99.7%). Conversely non-reproducible CWT ruled in ACS with low specificity (48.6%, 95% CI 38.8% to 58.5%) and low positive predictive value (19.1%, 95% CI 10.6% to 30.5%). This prospective diagnostic study supports the concept that reproducible CWT helps to rule out ACS in patients with ACP in an early stage of the evaluation process. However, ACS and other diagnoses should be considered in patients with a negative CWT test. ClinicalTrial.gov: NCT01724996. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

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.

Genome sequence and annotation of Trichoderma parareesei, the ancestor of the cellulase producer Trichoderma reesei

DOE PAGES

Yang, Dongqing; Pomraning, Kyle; Kopchinskiy, Alexey; ...

2015-08-13

The filamentous fungus Trichoderma parareesei is the asexually reproducing ancestor of Trichoderma reesei, the holomorphic industrial producer of cellulase and hemicellulase. Here, we present the genome sequence of the T. parareesei type strain CBS 125925, which contains genes for 9,318 proteins.

Highly-controlled, reproducible measurements of aerosol emissions from African biomass combustion

NASA Astrophysics Data System (ADS)

Haslett, Sophie; Thomas, J. Chris; Morgan, William; Hadden, Rory; Liu, Dantong; Allan, James; Williams, Paul; Sekou, Keïta; Liousse, Catherine; Coe, Hugh

2017-04-01

Particulate emissions from biomass burning can alter the atmosphere's radiative balance and cause significant harm to human health. However, the relationship between these emissions and fundamental combustion processes is, to date, poorly characterised. In atmospheric models, aerosol emissions are represented by emission factors based on mass loss, which are averaged over an entire combustion event for each particulate species. This approach, however, masks huge variability in emissions during different phases of the combustion period. Laboratory tests have shown that even small changes to the burning environment can lead to huge variation in observed aerosol emission factors (Akagi et al., 2011). In order to address this gap in understanding, in this study, small wood samples sourced from Côte D'Ivoire were burned in a highly-controlled laboratory environment. The shape and mass of samples, available airflow and surrounding heat were carefully regulated. Organic aerosol and refractory black carbon emissions were measured in real-time using an Aerosol Mass Spectrometer and a Single Particle Soot Photometer, respectively. Both of these instruments are used regularly to measure aerosol concentrations in the field. This methodology produced remarkably repeatable results, allowing three different phases of combustion to be identified by their emissions. Black carbon was emitted predominantly during flaming combustion; organic aerosols were emitted during pyrolysis before ignition and from smouldering-dominated behaviour near the end of combustion. During the flaming period, there was a strong correlation between the emission of black carbon and the rate of mass loss, which suggests there is value in employing a mass-based emission factor for this species. However, very little correlation was seen between organic aerosol and mass loss throughout the tests. As such, results here suggest that emission factors averaged over an entire combustion event are unlikely to be

Single image super-resolution via an iterative reproducing kernel Hilbert space method.

PubMed

Deng, Liang-Jian; Guo, Weihong; Huang, Ting-Zhu

2016-11-01

Image super-resolution, a process to enhance image resolution, has important applications in satellite imaging, high definition television, medical imaging, etc. Many existing approaches use multiple low-resolution images to recover one high-resolution image. In this paper, we present an iterative scheme to solve single image super-resolution problems. It recovers a high quality high-resolution image from solely one low-resolution image without using a training data set. We solve the problem from image intensity function estimation perspective and assume the image contains smooth and edge components. We model the smooth components of an image using a thin-plate reproducing kernel Hilbert space (RKHS) and the edges using approximated Heaviside functions. The proposed method is applied to image patches, aiming to reduce computation and storage. Visual and quantitative comparisons with some competitive approaches show the effectiveness of the proposed method.

Reproducibility of Clathromorphum compactum coralline algal Mg/Ca ratios and comparison to high-resolution sea surface temperature data

NASA Astrophysics Data System (ADS)

Hetzinger, S.; Halfar, J.; Kronz, A.; Simon, K.; Adey, W. H.; Steneck, R. S.

2018-01-01

The potential of crustose coralline algae as high-resolution archives of past ocean variability in mid- to high-latitudes has only recently been recognized. Few comparisons of coralline algal proxies, such as temperature-dependent algal magnesium to calcium (Mg/Ca) ratios, with in situ-measured surface ocean data exist, even rarer are well replicated records from individual sites. We present Mg/Ca records from nine coralline algal specimens (Clathromorphum compactum) from a single site in the Gulf of Maine, North Atlantic. Sections from algal mounds were analyzed using Laser Ablation-Inductively Coupled Plasma Mass Spectrometry (LA-ICP-MS) yielding individual Mg/Ca records of up to 30 years in length. We first test intra- and intersample signal replication and show that algal Mg/Ca ratios are reproducible along several transects within individual sample specimens and between different samples from the same study site. In addition, LA-ICP-MS-derived Mg/Ca ratios are compared to electron microprobe (EMP) analyzed data on the longest-lived specimens and were found to be statistically commensurable. Second, we evaluate whether relationships between algal-based SST reconstructions and in situ temperature data can be improved by averaging Mg/Ca records from multiple algal specimens (intersample averages). We found that intersample averages yield stronger relationships to sea surface temperature (SST) data than Mg/Ca records derived from individual samples alone. Thus, Mg/Ca-based paleotemperature reconstructions from coralline algae can benefit from using multiple samples per site, and can expand temperature proxy precision from seasonal to monthly.

Reproducibility of cervical range of motion in patients with neck pain

PubMed Central

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

2005-01-01

Background Reproducibility 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 reproducibility 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 reproducibility and the inter-rater reproducibility were good. We recommend to compare the reproducibility and clinical applicability of the EDI-320 inclinometer with other cervical ROM measures in symptomatic patients. PMID:16351719

A Reproducible Approach of Preparing High-Quality Overdoped Bi 2 Sr 2 CaCu 2 O 8+δ Single Crystals by Oxygen Annealing and Quenching Method

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

Zhang, Yu-Xiao; Zhao, Lin; Gu, Gen-Da

2016-06-01

Here, we report a reproducible approach in preparing high-quality overdoped Bi 2Sr 2 CaCu 2 O 8+δ (Bi2212) single crystals by annealing Bi2212 crystals in high oxygen pressure followed by a fast quenching. High-quality overdoped and heavily overdoped Bi2212 single crystals are obtained by controlling the annealing oxygen pressure. Furthermore, we find that, beyond a limit of oxygen pressure that can achieve most heavily overdoped Bi2212 with a T c ~63 K, the annealed Bi2212 begins to decompose. This accounts for the existence of the hole-doping limit and thus the T c limit in the heavily overdoped region of Bi2212more » by the oxygen annealing process. Our results provide a reliable way in preparing high-quality overdoped and heavily overdoped Bi2212 crystals that are important for studies of the physical properties, electronic structure and superconductivity mechanism of the cuprate superconductors.« less

High average power, highly brilliant laser-produced plasma source for soft X-ray spectroscopy.

PubMed

Mantouvalou, Ioanna; Witte, Katharina; Grötzsch, Daniel; Neitzel, Michael; Günther, Sabrina; Baumann, Jonas; Jung, Robert; Stiel, Holger; Kanngiesser, Birgit; Sandner, Wolfgang

2015-03-01

In this work, a novel laser-produced plasma source is presented which delivers pulsed broadband soft X-radiation in the range between 100 and 1200 eV. The source was designed in view of long operating hours, high stability, and cost effectiveness. It relies on a rotating and translating metal target and achieves high stability through an on-line monitoring device using a four quadrant extreme ultraviolet diode in a pinhole camera arrangement. The source can be operated with three different laser pulse durations and various target materials and is equipped with two beamlines for simultaneous experiments. Characterization measurements are presented with special emphasis on the source position and emission stability of the source. As a first application, a near edge X-ray absorption fine structure measurement on a thin polyimide foil shows the potential of the source for soft X-ray spectroscopy.

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.

Energy deposition at the bone-tissue interface from nuclear fragments produced by high-energy nucleons

NASA Technical Reports Server (NTRS)

Cucinotta, Francis A.; Hajnal, Ferenc; Wilson, John W.

1990-01-01

The transport of nuclear fragmentation recoils produced by high-energy nucleons in the region of the bone-tissue interface is considered. Results for the different flux and absorbed dose for recoils produced by 1 GeV protons are presented in a bidirectional transport model. The energy deposition in marrow cavities is seen to be enhanced by recoils produced in bone. Approximate analytic formulae for absorbed dose near the interface region are also presented for a simplified range-energy model.

Reproducibility and Transparency in Ocean-Climate Modeling

NASA Astrophysics Data System (ADS)

Hannah, N.; Adcroft, A.; Hallberg, R.; Griffies, S. M.

2015-12-01

Reproducibility is a cornerstone of the scientific method. Within geophysical modeling and simulation achieving reproducibility 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 reproducibility 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.

Social smile reproducibility using 3-D stereophotogrammetry and reverse engineering technology.

PubMed

Dindaroğlu, Furkan; Duran, Gökhan Serhat; Görgülü, Serkan; Yetkiner, Enver

2016-05-01

To assess the range of social smile reproducibility using 3-D stereophotogrammetry and reverse engineering technology. Social smile images of white adolescents (N  =  15, mean age  =  15.4 ±1.5 years; range  =  14-17 years) were obtained using 3dMDFlex (3dMD, Atlanta, Ga). Each participant was asked to produce 16 social smiles at 3-minute intervals. All images were obtained in natural head position. Alignment of images, segmentation of smile area, and 3-D deviation analysis were carried out using Geomagic Control software (3D Systems Inc, Cary, NC). A single image was taken as a reference, and the remaining 15 images were compared with the reference image to evaluate positive and negative deviations. The differences between the mean deviation limits of participants with the highest and the lowest deviations and the total mean deviations were evaluated using Bland-Altman Plots. Minimum and maximum deviations of a single image from the reference image were 0.34 and 2.69 mm, respectively. Lowest deviation between two images was within 0.5 mm and 1.54 mm among all participants (mean, 0.96 ± 0.21 mm), and the highest deviation was between 0.41 mm and 2.69 mm (mean, 1.53 ± 0.46 mm). For a single patient, when all alignments were considered together, the mean deviation was between 0.32 ± 0.10 mm and 0.59 ± 0.24 mm. Mean deviation for one image was between 0.14 and 1.21 mm. The range of reproducibility of the social smile presented individual variability, but this variation was not clinically significant or detectable under routine clinical observation.

Reproducibility Issues: Avoiding Pitfalls in Animal Inflammation Models.

PubMed

Laman, Jon D; Kooistra, Susanne M; Clausen, Björn E

2017-01-01

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) reproducibility 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 reproducibility 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.

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.

A reproducible accelerated in vitro release testing method for PLGA microspheres.

PubMed

Shen, Jie; Lee, Kyulim; Choi, Stephanie; Qu, Wen; Wang, Yan; Burgess, Diane J

2016-02-10

The objective of the present study was to develop a discriminatory and reproducible accelerated in vitro release method for long-acting PLGA microspheres with inner structure/porosity differences. Risperidone was chosen as a model drug. Qualitatively and quantitatively equivalent PLGA microspheres with different inner structure/porosity were obtained using different manufacturing processes. Physicochemical properties as well as degradation profiles of the prepared microspheres were investigated. Furthermore, in vitro release testing of the prepared risperidone microspheres was performed using the most common in vitro release methods (i.e., sample-and-separate and flow through) for this type of product. The obtained compositionally equivalent risperidone microspheres had similar drug loading but different inner structure/porosity. When microsphere particle size appeared similar, porous risperidone microspheres showed faster microsphere degradation and drug release compared with less porous microspheres. Both in vitro release methods investigated were able to differentiate risperidone microsphere formulations with differences in porosity under real-time (37 °C) and accelerated (45 °C) testing conditions. Notably, only the accelerated USP apparatus 4 method showed good reproducibility for highly porous risperidone microspheres. These results indicated that the accelerated USP apparatus 4 method is an appropriate fast quality control tool for long-acting PLGA microspheres (even with porous structures). Copyright © 2015 Elsevier B.V. All rights reserved.

Test-Retest Reproducibility of the Microperimeter MP3 With Fundus Image Tracking in Healthy Subjects and Patients With Macular Disease.

PubMed

Palkovits, Stefan; Hirnschall, Nino; Georgiev, Stefan; Leisser, Christoph; Findl, Oliver

2018-02-01

To evaluate the test-retest reproducibility of a novel microperimeter with fundus image tracking (MP3, Nidek Co, Japan) in healthy subjects and patients with macular disease. Ten healthy subjects and 20 patients suffering from range of macular diseases were included. After training measurements, two additional microperimetry measurements were scheduled. Test-retest reproducibility was assessed for mean retinal sensitivity, pointwise sensitivity, and deep scotoma size using the coefficient of repeatability and Bland-Altman diagrams. In addition, in a subgroup of patients microperimetry was compared with conventional perimetry. Average differences in mean retinal sensitivity between the two study measurements were 0.26 ± 1.7 dB (median 0 dB; interquartile range [IQR] -1 to 1) for the healthy and 0.36 ± 2.5 dB (median 0 dB; IQR -1 to 2) for the macular patient group. Coefficients of repeatability for mean retinal sensitivity and pointwise retinal sensitivity were 1.2 and 3.3 dB for the healthy subjects and 1.6 and 5.0 dB for the macular disease patients, respectively. Absolute agreement in deep scotoma size between both study days was found in 79.9% of the test loci. The microperimeter MP3 shows an adequate test-retest reproducibility for mean retinal sensitivity, pointwise retinal sensitivity, and deep scotoma size in healthy subjects and patients suffering from macular disease. Furthermore, reproducibility of microperimetry is higher than conventional perimetry. Reproducibility is an important measure for each diagnostic device. Especially in a clinical setting high reproducibility set the basis to achieve reliable results using the specific device. Therefore, assessment of the reproducibility is of eminent importance to interpret the findings of future studies.

Regulating Ultrasound Cavitation in order to Induce Reproducible Sonoporation

NASA Astrophysics Data System (ADS)

Mestas, J.-L.; Alberti, L.; El Maalouf, J.; Béra, J.-C.; Gilles, B.

2010-03-01

Sonoporation would be linked to cavitation, which generally appears to be a non reproducible 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 reproducible 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 reproducibility. This device was implemented for study of sonodynamic effect. The regulation provides more reproducible 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

Extractive Fermentation of Sugarcane Juice to Produce High Yield and Productivity of Bioethanol

NASA Astrophysics Data System (ADS)

Rofiqah, U.; Widjaja, T.; Altway, A.; Bramantyo, A.

2017-04-01

Ethanol production by batch fermentation requires a simple process and it is widely used. Batch fermentation produces ethanol with low yield and productivity due to the accumulation of ethanol in which poisons microorganisms in the fermenter. Extractive fermentation technique is applied to solve the microorganism inhibition problem by ethanol. Extractive fermentation technique can produce ethanol with high yield and productivity. In this process raffinate still, contains much sugar because conversion in the fermentation process is not perfect. Thus, to enhance ethanol yield and productivity, recycle system is applied by returning the raffinate from the extraction process to the fermentation process. This raffinate also contains ethanol which would inhibit the performance of microorganisms in producing ethanol during the fermentation process. Therefore, this study aims to find the optimum condition for the amount of solvent to broth ratio (S: B) and recycle to fresh feed ratio (R: F) which enter the fermenter to produce high yield and productivity. This research was carried out by experiment. In the experiment, sugarcane juice was fermented using Zymomonasmobilis mutant. The fermentation broth was extracted using amyl alcohol. The process was integrated with the recycle system by varying the recycle ratio. The highest yield and productivity is 22.3901% and 103.115 g / L.h respectively, obtained in a process that uses recycle to fresh feed ratio (R: F) of 50:50 and solvents to both ratio of 1.

Reproducible high-resolution multispectral image acquisition in dermatology

NASA Astrophysics Data System (ADS)

Duliu, Alexandru; Gardiazabal, José; Lasser, Tobias; Navab, Nassir

2015-07-01

Multispectral image acquisitions are increasingly popular in dermatology, due to their improved spectral resolution which enables better tissue discrimination. Most applications however focus on restricted regions of interest, imaging only small lesions. In this work we present and discuss an imaging framework for high-resolution multispectral imaging on large regions of interest.

Reproducibility of the serum lipid response to coffee oil in healthy volunteers

PubMed Central

Boekschoten, Mark V; Engberink, Mariëlle F; Katan, Martijn B; Schouten, Evert G

2003-01-01

Background Humans and animals show a certain consistency in the response of their serum lipids to fat-modified diets. This may indicate a genetic basis underlying this response. Coffee oil might be used as a model substance to investigate which genes determine differences in the serum lipid response. Before carrying out such studies our objective was to investigate to what extent the effect of coffee oil on serum lipid concentrations is reproducible within subjects. Methods The serum lipid response of 32 healthy volunteers was measured twice in separate five-week periods in which coffee oil was administered (69 mg cafestol / day). Results Total cholesterol levels increased by 24% in period 1 (range:0;52%) and 18% in period 2 (1;48%), LDL cholesterol by 29 % (-9;71%) and 20% (-12;57%), triglycerides by 66% (16;175%) and 58% (-13;202%), and HDL cholesterol did not change significantly: The range of the HDL response was -19;25% in period 1 and -20;33% in period 2. The correlation between the two responses was 0.20 (95%CI -0.16, 0.51) for total cholesterol, 0.16 (95%CI -0.20, 0.48) for LDL, 0.67 (95%CI 0.42, 0.83) for HDL, and 0.77 (95%CI 0.56, 0.88) for triglycerides. Conclusions The responses of total and LDL cholesterol to coffee oil were poorly reproducible within subjects. The responses of HDL and triglycerides, however, appeared to be highly reproducible. Therefore, investigating the genetic sources of the variation in the serum-lipid response to coffee oil is more promising for HDL and triglycerides. PMID:14613505

Reproducibility of the kinematics and kinetics of the lower extremity during normal stair-climbing.

PubMed

Yu, B; Kienbacher, T; Growney, E S; Johnson, M E; An, K N

1997-05-01

The purpose of this study was to examine the intrasubject reproducibility 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 reproducibility 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 reproducible; (b) the kinetic measures during the transition steps from level walking to ascending and from descending to level walking were significantly less reproducible than those during the other steps; (c) the data from the sagittal plane were more reproducible than those from the other two planes; and (d) the kinetic measures were more reproducible than the kinematic measures, especially for abduction-adduction and internal-external rotation.

Multi-site assessment of the precision and reproducibility of multiple reaction monitoring–based measurements of proteins in plasma

PubMed Central

Addona, Terri A; Abbatiello, Susan E; Schilling, Birgit; Skates, Steven J; Mani, D R; Bunk, David M; Spiegelman, Clifford H; Zimmerman, Lisa J; Ham, Amy-Joan L; Keshishian, Hasmik; Hall, Steven C; Allen, Simon; Blackman, Ronald K; Borchers, Christoph H; Buck, Charles; Cardasis, Helene L; Cusack, Michael P; Dodder, Nathan G; Gibson, Bradford W; Held, Jason M; Hiltke, Tara; Jackson, Angela; Johansen, Eric B; Kinsinger, Christopher R; Li, Jing; Mesri, Mehdi; Neubert, Thomas A; Niles, Richard K; Pulsipher, Trenton C; Ransohoff, David; Rodriguez, Henry; Rudnick, Paul A; Smith, Derek; Tabb, David L; Tegeler, Tony J; Variyath, Asokan M; Vega-Montoto, Lorenzo J; Wahlander, Åsa; Waldemarson, Sofia; Wang, Mu; Whiteaker, Jeffrey R; Zhao, Lei; Anderson, N Leigh; Fisher, Susan J; Liebler, Daniel C; Paulovich, Amanda G; Regnier, Fred E; Tempst, Paul; Carr, Steven A

2010-01-01

Verification of candidate biomarkers relies upon specific, quantitative assays optimized for selective detection of target proteins, and is increasingly viewed as a critical step in the discovery pipeline that bridges unbiased biomarker discovery to preclinical validation. Although individual laboratories have demonstrated that multiple reaction monitoring (MRM) coupled with isotope dilution mass spectrometry can quantify candidate protein biomarkers in plasma, reproducibility and transferability of these assays between laboratories have not been demonstrated. We describe a multilaboratory study to assess reproducibility, recovery, linear dynamic range and limits of detection and quantification of multiplexed, MRM-based assays, conducted by NCI-CPTAC. Using common materials and standardized protocols, we demonstrate that these assays can be highly reproducible within and across laboratories and instrument platforms, and are sensitive to low µg/ml protein concentrations in unfractionated plasma. We provide data and benchmarks against which individual laboratories can compare their performance and evaluate new technologies for biomarker verification in plasma. PMID:19561596

Effects produced by iodine irradiation on high resistivity silicon

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

Lazanu, S.; Slav, A.; Lepadatu, A.-M.

2012-12-10

The effects of 5 Multiplication-Sign 10{sup 11} cm{sup -26+}I{sup 127} ions of 28 MeV kinetic energy on high resistivity (100) Si were studied. The profile of primary defects was simulated. The defects produced by irradiation which act as traps were investigated. Thermally stimulated current measurements without externally applied bias were used, and for this the traps were charged by illuminating samples with 1000, 800, and 400 nm wavelengths. The discharge currents were recorded and modeled, and therefore the parameters of the traps were determined. The presence of I ions, heavier than Si, stopped into the target was modeled as amore » temperature independent electric field.« less

Discovery of Alternative Producers of the Enediyne Antitumor Antibiotic C-1027 with High Titers.

PubMed

Yan, Xiaohui; Hindra; Ge, Huiming; Yang, Dong; Huang, Tingting; Crnovcic, Ivana; Chang, Chin-Yuan; Fang, Shi-Ming; Annaval, Thibault; Zhu, Xiangcheng; Huang, Yong; Zhao, Li-Xing; Jiang, Yi; Duan, Yanwen; Shen, Ben

2018-03-23

The potent cytotoxicity and unique mode of action make the enediyne antitumor antibiotic C-1027 an exquisite drug candidate for anticancer chemotherapy. However, clinical development of C-1027 has been hampered by its low titer from the original producer Streptomyces globisporus C-1027. Here we report three new C-1027 alternative producers, Streptomyces sp. CB00657, CB02329, and CB03608, from The Scripps Research Institute actinomycetes strain collection. Together with the previously disclosed Streptomyces sp. CB02366 strain, four C-1027 alternative producers with C-1027 titers of up to 11-fold higher than the original producer have been discovered. The five C-1027 producers, isolated from distant geographic locations, are distinct Streptomyces strains based on morphology and taxonomy. Pulsed-field gel electrophoresis and Southern analysis of the five C-1027 producers reveal that their C-1027 biosynthetic gene clusters (BGCs) are all located on giant plasmids of varying sizes. The high nucleotide sequence similarity among the five C-1027 BGCs implies that they most likely have evolved from a common ancestor.

Repeatability and reproducibility of ocular biometry using a new noncontact optical low-coherence interferometer.

PubMed

Huang, Jinhai; Savini, Giacomo; Wu, Fan; Yu, Xinxin; Yang, Jing; Yu, Ayong; Yu, Ye; Wang, Qinmei

2015-10-01

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. Observational 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 reproducibility. 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 reproducible 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 observed 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 reproducibility 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.

Reproducible automated breast density measure with no ionizing radiation using fat-water decomposition MRI.

PubMed

Ding, Jie; Stopeck, Alison T; Gao, Yi; Marron, Marilyn T; Wertheim, Betsy C; Altbach, Maria I; Galons, Jean-Philippe; Roe, Denise J; Wang, Fang; Maskarinec, Gertraud; Thomson, Cynthia A; Thompson, Patricia A; Huang, Chuan

2018-04-06

Increased breast density is a significant independent risk factor for breast cancer, and recent studies show that this risk is modifiable. Hence, breast density measures sensitive to small changes are desired. Utilizing fat-water decomposition MRI, we propose an automated, reproducible breast density measurement, which is nonionizing and directly comparable to mammographic density (MD). Retrospective study. The study included two sample sets of breast cancer patients enrolled in a clinical trial, for concordance analysis with MD (40 patients) and reproducibility analysis (10 patients). The majority of MRI scans (59 scans) were performed with a 1.5T GE Signa scanner using radial IDEAL-GRASE sequence, while the remaining (seven scans) were performed with a 3T Siemens Skyra using 3D Cartesian 6-echo GRE sequence with a similar fat-water separation technique. After automated breast segmentation, breast density was calculated using FraGW, a new measure developed to reliably reflect the amount of fibroglandular tissue and total water content in the entire breast. Based on its concordance with MD, FraGW was calibrated to MR-based breast density (MRD) to be comparable to MD. A previous breast density measurement, Fra80-the ratio of breast voxels with <80% fat fraction-was also calculated for comparison with FraGW. Pearson correlation was performed between MD (reference standard) and FraGW (and Fra80). Test-retest reproducibility of MRD was evaluated using the difference between test-retest measures (Δ 1-2 ) and intraclass correlation coefficient (ICC). Both FraGW and Fra80 were strongly correlated with MD (Pearson ρ: 0.96 vs. 0.90, both P < 0.0001). MRD converted from FraGW showed higher test-retest reproducibility (Δ 1-2 variation: 1.1% ± 1.2%; ICC: 0.99) compared to MD itself (literature intrareader ICC ≤0.96) and Fra80. The proposed MRD is directly comparable with MD and highly reproducible, which enables the early detection of small breast density changes

Reliability, repeatability, and reproducibility of pulmonary transit time assessment by contrast enhanced echocardiography.

PubMed

Herold, Ingeborg H F; Saporito, Salvatore; Bouwman, R Arthur; Houthuizen, Patrick; van Assen, Hans C; Mischi, Massimo; Korsten, Hendrikus H M

2016-01-05

The aim of this study is to investigate the inter and intra-rater reliability, repeatability, and reproducibility of pulmonary transit time (PTT) measurement in patients using contrast enhanced ultrasound (CEUS), as an indirect measure of preload and left ventricular function. Mean transit times (MTT) were measured by drawing a region of interest (ROI) in right and left cardiac ventricle in the CEUS loops. Acoustic intensity dilution curves were obtained from the ROIs. MTTs were calculated by applying model-based fitting on the dilution curves. PTT was calculated as the difference of the MTTs. Eight raters with different levels of experience measured the PTT (time moment 1) and repeated the measurement within a week (time moment 2). Reliability and agreement were assessed using intra-class correlations (ICC) and Bland-Altman analysis. Repeatability was tested by estimating the variance of means (ANOVA) of three injections in each patient at different doses. Reproducibility was tested by the ICC of the two time moments. Fifteen patients with heart failure were included. The mean PTT was 11.8 ± 3.1 s at time moment 1 and 11.7 ± 2.9 s at time moment 2. The inter-rater reliability for PTT was excellent (ICC = 0.94). The intra-rater reliability per rater was between 0.81-0.99. Bland-Altman analysis revealed a bias of 0.10 s within the rater groups. Reproducibility for PTT showed an ICC = 0.94 between the two time moments. ANOVA showed no significant difference between the means of the three different doses F = 0.048 (P = 0.95). The mean and standard deviation for PTT estimates at three different doses was 11.6 ± 3.3 s. PTT estimation using CEUS shows a high inter- and intra-rater reliability, repeatability at three different doses, and reproducibility by ROI drawing. This makes the minimally invasive PTT measurement using contrast echocardiography ready for clinical evaluation in patients with heart failure and for preload estimation.

Evaluation of the reproducibility of amplicon sequencing with Illumina MiSeq platform

PubMed Central

Van Nostrand, Joy D.; Ning, Daliang; Sun, Bo; Xue, Kai; Liu, Feifei; Deng, Ye; Liang, Yuting; Zhou, Jizhong

2017-01-01

and with caution. For example, including technical replicates, removing spurious sequences and unrepresentative OTUs, using a clustering method with a high stringency for OTU generation, estimating treatment effects at higher taxonomic levels, and adapting the unique molecular identifier (UMI) and other newly developed methods to lower PCR and sequencing error and to identify true low abundance rare species all can increase reproducibility. PMID:28453559

Evaluation of the reproducibility of amplicon sequencing with Illumina MiSeq platform.

PubMed

Wen, Chongqing; Wu, Liyou; Qin, Yujia; Van Nostrand, Joy D; Ning, Daliang; Sun, Bo; Xue, Kai; Liu, Feifei; Deng, Ye; Liang, Yuting; Zhou, Jizhong

2017-01-01

with caution. For example, including technical replicates, removing spurious sequences and unrepresentative OTUs, using a clustering method with a high stringency for OTU generation, estimating treatment effects at higher taxonomic levels, and adapting the unique molecular identifier (UMI) and other newly developed methods to lower PCR and sequencing error and to identify true low abundance rare species all can increase reproducibility.

A stepwise approach for the reproducible optimization of PAMO expression in Escherichia coli for whole-cell biocatalysis

PubMed Central

2012-01-01

Background Baeyer-Villiger monooxygenases (BVMOs) represent a group of enzymes of considerable biotechnological relevance as illustrated by their growing use as biocatalyst in a variety of synthetic applications. However, due to their increased use the reproducible expression of BVMOs and other biotechnologically relevant enzymes has become a pressing matter while knowledge about the factors governing their reproducible expression is scattered. Results Here, we have used phenylacetone monooxygenase (PAMO) from Thermobifida fusca, a prototype Type I BVMO, as a model enzyme to develop a stepwise strategy to optimize the biotransformation performance of recombinant E. coli expressing PAMO in 96-well microtiter plates in a reproducible fashion. Using this system, the best expression conditions of PAMO were investigated first, including different host strains, temperature as well as time and induction period for PAMO expression. This optimized system was used next to improve biotransformation conditions, the PAMO-catalyzed conversion of phenylacetone, by evaluating the best electron donor, substrate concentration, and the temperature and length of biotransformation. Combining all optimized parameters resulted in a more than four-fold enhancement of the biocatalytic performance and, importantly, this was highly reproducible as indicated by the relative standard deviation of 1% for non-washed cells and 3% for washed cells. Furthermore, the optimized procedure was successfully adapted for activity-based mutant screening. Conclusions Our optimized procedure, which provides a comprehensive overview of the key factors influencing the reproducible expression and performance of a biocatalyst, is expected to form a rational basis for the optimization of miniaturized biotransformations and for the design of novel activity-based screening procedures suitable for BVMOs and other NAD(P)H-dependent enzymes as well. PMID:22720747

Reproducibility of Nordic Sleep Questionnaire in spinal cord injured.

PubMed

Biering-Sørensen, F; Biering-Sørensen, M; Hilden, J

1994-11-01

A recently proposed Nordic Sleep Questionnaire (NSQ) comprises 26 questions concerning qualitative and quantitative aspects of the respondent's sleep habits. Its reproducibility 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 reproducibility, although they had more 'pathology' to report and thus more scope for contradicting themselves. The questions in the NSQ generally were satisfactorily reproducible. 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.

Device Engineering Towards Improved Tin Sulfide Solar Cell Performance and Performance Reproducibility

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

Steinmann, Vera; Chakraborty, Rupak; Rekemeyer, Paul

2016-11-21

As novel absorber materials are developed and screened for their photovoltaic (PV) properties, the challenge remains to rapidly test promising candidates in high-performing PV devices. There is a need to engineer new compatible device architectures, including the development of novel transparent conductive oxides and buffer layers. Here, we consider the two approaches of a substrate-style and a superstrate-style device architecture for novel thin-film solar cells. We use tin sulfide as a test absorber material. Upon device engineering, we demonstrate new approaches to improve device performance and performance reproducibility.

Inter-study reproducibility of cardiovascular magnetic resonance tagging

PubMed Central

2013-01-01

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 reproducibility. Torsion rates had superior intra-, interobserver, and inter-study reproducibility 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 reproducibility of all strain and torsion parameters was excellent. Inter-study reproducibility 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

46 CFR 56.97-38 - Initial service leak test (reproduces 137.7).

Code of Federal Regulations, 2010 CFR

2010-10-01

... 46 Shipping 2 2010-10-01 2010-10-01 false Initial service leak test (reproduces 137.7). 56.97-38... PIPING SYSTEMS AND APPURTENANCES Pressure Tests § 56.97-38 Initial service leak test (reproduces 137.7). (a) An initial service leak test and inspection is acceptable when other types of test are not...

46 CFR 54.10-5 - Maximum allowable working pressure (reproduces UG-98).

Code of Federal Regulations, 2013 CFR

2013-10-01

... 46 Shipping 2 2013-10-01 2013-10-01 false Maximum allowable working pressure (reproduces 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 (reproduces UG-98). (a) The maximum allowable...

46 CFR 54.10-5 - Maximum allowable working pressure (reproduces UG-98).

Code of Federal Regulations, 2011 CFR

2011-10-01

... 46 Shipping 2 2011-10-01 2011-10-01 false Maximum allowable working pressure (reproduces 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 (reproduces UG-98). (a) The maximum allowable...

46 CFR 54.10-5 - Maximum allowable working pressure (reproduces UG-98).

Code of Federal Regulations, 2014 CFR

2014-10-01

... 46 Shipping 2 2014-10-01 2014-10-01 false Maximum allowable working pressure (reproduces 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 (reproduces UG-98). (a) The maximum allowable...

46 CFR 54.10-5 - Maximum allowable working pressure (reproduces UG-98).

Code of Federal Regulations, 2012 CFR

2012-10-01

... 46 Shipping 2 2012-10-01 2012-10-01 false Maximum allowable working pressure (reproduces 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 (reproduces UG-98). (a) The maximum allowable...

Producing Gestures Facilitates Route Learning

PubMed Central

So, Wing Chee; Ching, Terence Han-Wei; Lim, Phoebe Elizabeth; Cheng, Xiaoqin; Ip, Kit Yee

2014-01-01

The present study investigates whether producing gestures would facilitate route learning in a navigation task and whether its facilitation effect is comparable to that of hand movements that leave physical visible traces. In two experiments, we focused on gestures produced without accompanying speech, i.e., co-thought gestures (e.g., an index finger traces the spatial sequence of a route in the air). Adult participants were asked to study routes shown in four diagrams, one at a time. Participants reproduced the routes (verbally in Experiment 1 and non-verbally in Experiment 2) without rehearsal or after rehearsal by mentally simulating the route, by drawing it, or by gesturing (either in the air or on paper). Participants who moved their hands (either in the form of gestures or drawing) recalled better than those who mentally simulated the routes and those who did not rehearse, suggesting that hand movements produced during rehearsal facilitate route learning. Interestingly, participants who gestured the routes in the air or on paper recalled better than those who drew them on paper in both experiments, suggesting that the facilitation effect of co-thought gesture holds for both verbal and nonverbal recall modalities. It is possibly because, co-thought gesture, as a kind of representational action, consolidates spatial sequence better than drawing and thus exerting more powerful influence on spatial representation. PMID:25426624

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

Spatial mapping and statistical reproducibility of an array of 256 one-dimensional quantum wires

NASA Astrophysics Data System (ADS)

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.

2015-08-01

We utilize a multiplexing architecture to measure the conductance properties of an array of 256 split gates. We investigate the reproducibility 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 reproducibility 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 observed 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.

Multispectral Image Compression for Improvement of Colorimetric and Spectral Reproducibility by Nonlinear Spectral Transform

NASA Astrophysics Data System (ADS)

Yu, Shanshan; Murakami, Yuri; Obi, Takashi; Yamaguchi, Masahiro; Ohyama, Nagaaki

2006-09-01

The article proposes a multispectral image compression scheme using nonlinear spectral transform for better colorimetric and spectral reproducibility. In the method, we show the reduction of colorimetric error under a defined viewing illuminant and also that spectral accuracy can be improved simultaneously using a nonlinear spectral transform called Labplus, which takes into account the nonlinearity of human color vision. Moreover, we show that the addition of diagonal matrices to Labplus can further preserve the spectral accuracy and has a generalized effect of improving the colorimetric accuracy under other viewing illuminants than the defined one. Finally, we discuss the usage of the first-order Markov model to form the analysis vectors for the higher order channels in Labplus to reduce the computational complexity. We implement a multispectral image compression system that integrates Labplus with JPEG2000 for high colorimetric and spectral reproducibility. Experimental results for a 16-band multispectral image show the effectiveness of the proposed scheme.

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.;

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.

Validation of the manufacturing process used to produce long-acting recombinant factor IX Fc fusion protein

PubMed Central

McCue, J; Osborne, D; Dumont, J; Peters, R; Mei, B; Pierce, G F; Kobayashi, K; Euwart, D

2014-01-01

Recombinant factor IX Fc (rFIXFc) fusion protein is the first of a new class of bioengineered long-acting factors approved for the treatment and prevention of bleeding episodes in haemophilia B. The aim of this work was to describe the manufacturing process for rFIXFc, to assess product quality and to evaluate the capacity of the process to remove impurities and viruses. This manufacturing process utilized a transferable and scalable platform approach established for therapeutic antibody manufacturing and adapted for production of the rFIXFc molecule. rFIXFc was produced using a process free of human- and animal-derived raw materials and a host cell line derived from human embryonic kidney (HEK) 293H cells. The process employed multi-step purification and viral clearance processing, including use of a protein A affinity capture chromatography step, which binds to the Fc portion of the rFIXFc molecule with high affinity and specificity, and a 15 nm pore size virus removal nanofilter. Process validation studies were performed to evaluate identity, purity, activity and safety. The manufacturing process produced rFIXFc with consistent product quality and high purity. Impurity clearance validation studies demonstrated robust and reproducible removal of process-related impurities and adventitious viruses. The rFIXFc manufacturing process produces a highly pure product, free of non-human glycan structures. Validation studies demonstrate that this product is produced with consistent quality and purity. In addition, the scalability and transferability of this process are key attributes to ensure consistent and continuous supply of rFIXFc. PMID:24811361

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.

Evaluation of guidewire path reproducibility

PubMed Central

Schafer, Sebastian; Hoffmann, Kenneth R.; Noël, Peter B.; Ionita, Ciprian N.; Dmochowski, Jacek

2008-01-01

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 reproducibility 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 reproducible in shape and position. PMID:18561663

Improved quantitation and reproducibility in multi-PET/CT lung studies by combining CT information.

PubMed

Holman, Beverley F; Cuplov, Vesna; Millner, Lynn; Endozo, Raymond; Maher, Toby M; Groves, Ashley M; Hutton, Brian F; Thielemans, Kris

2018-06-05

Matched attenuation maps are vital for obtaining accurate and reproducible kinetic and static parameter estimates from PET data. With increased interest in PET/CT imaging of diffuse lung diseases for assessing disease progression and treatment effectiveness, understanding the extent of the effect of respiratory motion and establishing methods for correction are becoming more important. In a previous study, we have shown that using the wrong attenuation map leads to large errors due to density mismatches in the lung, especially in dynamic PET scans. Here, we extend this work to the case where the study is sub-divided into several scans, e.g. for patient comfort, each with its own CT (cine-CT and 'snap shot' CT). A method to combine multi-CT information into a combined-CT has then been developed, which averages the CT information from each study section to produce composite CT images with the lung density more representative of that in the PET data. This combined-CT was applied to nine patients with idiopathic pulmonary fibrosis, imaged with dynamic 18 F-FDG PET/CT to determine the improvement in the precision of the parameter estimates. Using XCAT simulations, errors in the influx rate constant were found to be as high as 60% in multi-PET/CT studies. Analysis of patient data identified displacements between study sections in the time activity curves, which led to an average standard error in the estimates of the influx rate constant of 53% with conventional methods. This reduced to within 5% after use of combined-CTs for attenuation correction of the study sections. Use of combined-CTs to reconstruct the sections of a multi-PET/CT study, as opposed to using the individually acquired CTs at each study stage, produces more precise parameter estimates and may improve discrimination between diseased and normal lung.

Reproducing American Sign Language sentences: cognitive scaffolding in working memory

PubMed Central

Supalla, Ted; Hauser, Peter C.; Bavelier, Daphne

2014-01-01

The American Sign Language Sentence Reproduction Test (ASL-SRT) requires the precise reproduction of a series of ASL sentences increasing in complexity and length. Error analyses of such tasks provides insight into working memory and scaffolding processes. Data was collected from three groups expected to differ in fluency: deaf children, deaf adults and hearing adults, all users of ASL. Quantitative (correct/incorrect recall) and qualitative error analyses were performed. Percent correct on the reproduction task supports its sensitivity to fluency as test performance clearly differed across the three groups studied. A linguistic analysis of errors further documented differing strategies and bias across groups. Subjects' recall projected the affordance and constraints of deep linguistic representations to differing degrees, with subjects resorting to alternate processing strategies when they failed to recall the sentence correctly. A qualitative error analysis allows us to capture generalizations about the relationship between error pattern and the cognitive scaffolding, which governs the sentence reproduction process. Highly fluent signers and less-fluent signers share common chokepoints on particular words in sentences. However, they diverge in heuristic strategy. Fluent signers, when they make an error, tend to preserve semantic details while altering morpho-syntactic domains. They produce syntactically correct sentences with equivalent meaning to the to-be-reproduced one, but these are not verbatim reproductions of the original sentence. In contrast, less-fluent signers tend to use a more linear strategy, preserving lexical status and word ordering while omitting local inflections, and occasionally resorting to visuo-motoric imitation. Thus, whereas fluent signers readily use top-down scaffolding in their working memory, less fluent signers fail to do so. Implications for current models of working memory across spoken and signed modalities are considered. PMID

Demonstration of radiation pulse shaping with nested-tungsten-wire-array pinches for high-yield inertial confinement fusion.

PubMed

Cuneo, M E; Vesey, R A; Sinars, D B; Chittenden, J P; Waisman, E M; Lemke, R W; Lebedev, S V; Bliss, D E; Stygar, W A; Porter, J L; Schroen, D G; Mazarakis, M G; Chandler, G A; Mehlhorn, T A

2005-10-28

Nested wire-array pinches are shown to generate soft x-ray radiation pulse shapes required for three-shock isentropic compression and hot-spot ignition of high-yield inertial confinement fusion capsules. We demonstrate a reproducible and tunable foot pulse (first shock) produced by interaction of the outer and inner arrays. A first-step pulse (second shock) is produced by inner array collision with a central CH2 foam target. Stagnation of the inner array at the axis produces the third shock. Capsules optimized for several of these shapes produce 290-900 MJ fusion yields in 1D simulations.

Test–Retest Reproducibility of the Microperimeter MP3 With Fundus Image Tracking in Healthy Subjects and Patients With Macular Disease

PubMed Central

Palkovits, Stefan; Hirnschall, Nino; Georgiev, Stefan; Leisser, Christoph

2018-01-01

Purpose To evaluate the test–retest reproducibility of a novel microperimeter with fundus image tracking (MP3, Nidek Co, Japan) in healthy subjects and patients with macular disease. Methods Ten healthy subjects and 20 patients suffering from range of macular diseases were included. After training measurements, two additional microperimetry measurements were scheduled. Test–retest reproducibility was assessed for mean retinal sensitivity, pointwise sensitivity, and deep scotoma size using the coefficient of repeatability and Bland-Altman diagrams. In addition, in a subgroup of patients microperimetry was compared with conventional perimetry. Results Average differences in mean retinal sensitivity between the two study measurements were 0.26 ± 1.7 dB (median 0 dB; interquartile range [IQR] −1 to 1) for the healthy and 0.36 ± 2.5 dB (median 0 dB; IQR −1 to 2) for the macular patient group. Coefficients of repeatability for mean retinal sensitivity and pointwise retinal sensitivity were 1.2 and 3.3 dB for the healthy subjects and 1.6 and 5.0 dB for the macular disease patients, respectively. Absolute agreement in deep scotoma size between both study days was found in 79.9% of the test loci. Conclusion The microperimeter MP3 shows an adequate test–retest reproducibility for mean retinal sensitivity, pointwise retinal sensitivity, and deep scotoma size in healthy subjects and patients suffering from macular disease. Furthermore, reproducibility of microperimetry is higher than conventional perimetry. Translational Relevance Reproducibility is an important measure for each diagnostic device. Especially in a clinical setting high reproducibility set the basis to achieve reliable results using the specific device. Therefore, assessment of the reproducibility is of eminent importance to interpret the findings of future studies. PMID:29430338

Within-subject reproducibility of near-infrared spectroscopy signals in sensorimotor activation after 6 months

NASA Astrophysics Data System (ADS)

Sato, Hiroki; Kiguchi, Masashi; Maki, Atsushi; Fuchino, Yutaka; Obata, Akiko; Yoro, Takeshi; Koizumi, Hideaki

2006-01-01

Near-infrared spectroscopy (NIRS) can measure the product of the optical path length and the concentration change in oxygenated hemoglobin (ΔC‧oxy), deoxygenated hemoglobin (ΔC‧deoxy), and their sum (ΔC‧total) in the human cerebral cortex, and it has been used for noninvasive investigation of human brain functions. We evaluate the within-subject reproducibility of the NIRS signals by repeated measurement of the sensorimotor cortex in healthy adults taken over a period of about 6 months using near-infrared (NIR) topography. The maximum signal amplitudes and the location of activation centers are compared between two sessions for each subject. The signal amplitudes vary between sessions and no consistent tendency in the changes is found among subjects. However, the distance between the activation centers identified in two sessions is relatively small, within 20 mm on average across subjects, which is comparable to the smallest distance between measurement positions in the NIR topography (21 mm). Moreover, within-subject comparisons of signal time courses show high correlation coefficients (>0.8) between the two sessions. This result, demonstrating a high within-subject reproducibility of the temporal information in NIRS signals, particularly contributes to the development of a new application of NIRS.