Advancing Absolute Calibration for JWST and Other Applications

NASA Astrophysics Data System (ADS)

Rieke, George; Bohlin, Ralph; Boyajian, Tabetha; Carey, Sean; Casagrande, Luca; Deustua, Susana; Gordon, Karl; Kraemer, Kathleen; Marengo, Massimo; Schlawin, Everett; Su, Kate; Sloan, Greg; Volk, Kevin

2017-10-01

We propose to exploit the unique optical stability of the Spitzer telescope, along with that of IRAC, to (1) transfer the accurate absolute calibration obtained with MSX on very bright stars directly to two reference stars within the dynamic range of the JWST imagers (and of other modern instrumentation); (2) establish a second accurate absolute calibration based on the absolutely calibrated spectrum of the sun, transferred onto the astronomical system via alpha Cen A; and (3) provide accurate infrared measurements for the 11 (of 15) highest priority stars with no such data but with accurate interferometrically measured diameters, allowing us to optimize determinations of effective temperatures using the infrared flux method and thus to extend the accurate absolute calibration spectrally. This program is integral to plans for an accurate absolute calibration of JWST and will also provide a valuable Spitzer legacy.

Hematological reference values of healthy Malaysian population.

PubMed

Roshan, T M; Rosline, H; Ahmed, S A; Rapiaah, M; Wan Zaidah, A; Khattak, M N

2009-10-01

Health and disease can only be distinguished by accurate and reliable reference values of a particular laboratory test. It is now a proven fact that there is considerable variation in hematology reference intervals depending on the demographic and preanalytical variables. There are evidences that values provided by manufacturers do not have appropriate application for all populations. Moreover, reference ranges provided by different laboratory manuals and books also do not solve this problem. We are presenting here normal reference ranges of Malaysian population. These values were determined by using Sysmex XE-2100 and ACL 9000 hematology and coagulation analyzers. Results from this study showed that there were considerable differences in the reference values from manufacturers, western population or laboratory manuals compared with those from the local population.

Integrative structural annotation of de novo RNA-Seq provides an accurate reference gene set of the enormous genome of the onion (Allium cepa L.).

PubMed

Kim, Seungill; Kim, Myung-Shin; Kim, Yong-Min; Yeom, Seon-In; Cheong, Kyeongchae; Kim, Ki-Tae; Jeon, Jongbum; Kim, Sunggil; Kim, Do-Sun; Sohn, Seong-Han; Lee, Yong-Hwan; Choi, Doil

2015-02-01

The onion (Allium cepa L.) is one of the most widely cultivated and consumed vegetable crops in the world. Although a considerable amount of onion transcriptome data has been deposited into public databases, the sequences of the protein-coding genes are not accurate enough to be used, owing to non-coding sequences intermixed with the coding sequences. We generated a high-quality, annotated onion transcriptome from de novo sequence assembly and intensive structural annotation using the integrated structural gene annotation pipeline (ISGAP), which identified 54,165 protein-coding genes among 165,179 assembled transcripts totalling 203.0 Mb by eliminating the intron sequences. ISGAP performed reliable annotation, recognizing accurate gene structures based on reference proteins, and ab initio gene models of the assembled transcripts. Integrative functional annotation and gene-based SNP analysis revealed a whole biological repertoire of genes and transcriptomic variation in the onion. The method developed in this study provides a powerful tool for the construction of reference gene sets for organisms based solely on de novo transcriptome data. Furthermore, the reference genes and their variation described here for the onion represent essential tools for molecular breeding and gene cloning in Allium spp. © The Author 2014. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

SEE Action Guide for States: Guidance on Establishing and Maintaining Technical Reference Manuals for Energy Efficiency Measures

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

None

2017-06-01

The goal of this guide is to support the development, maintenance, and use of accurate and reliable Technical Reference Manuals (TRMs). TRMs provide information primarily used for estimating the energy and demand savings of end-use energy efficiency measures associated with utility customer-funded efficiency programs.

NIST TXR Validation of S-HIS radiances and a UW-SSEC Blackbody

NASA Astrophysics Data System (ADS)

Taylor, J. K.; O'Connell, J.; Rice, J. P.; Revercomb, H. E.; Best, F. A.; Tobin, D. C.; Knuteson, R. O.; Adler, D. P.; Ciganovich, N. C.; Dutcher, S. T.; Laporte, D. D.; Ellington, S. D.; Werner, M. W.; Garcia, R. K.

2007-12-01

The ability to accurately validate infrared spectral radiances measured from space by direct comparison with airborne spectrometer radiances was first demonstrated using the Scanning High-resolution Interferometer Sounder (S-HIS) aircraft instrument flown under the AIRS on the NASA Aqua spacecraft in 2002 with subsequent successful comparisons in 2004 and 2006. The comparisons span a range of conditions, including arctic and tropical atmospheres, daytime and nighttime, and ocean and land surfaces. Similar comprehensive and successful comparisons have also been conducted with S-HIS for the MODIS sensors, the Tropospheric Emission Spectrometer (TES), and most recently the MetOp Infrared Atmospheric Sounding Interferometer (IASI). These comparisons are part of a larger picture that already shows great progress toward transforming our ability to make, and verify, highly accurate spectral radiance observations from space. A key challenge, especially for climate, is to carefully define the absolute accuracy of satellite radiances. Our vision of the near-term future of spectrally resolved infrared radiance observation includes a new space-borne mission that provides benchmark observations of the emission spectrum for climate. This concept, referred to as the CLimate Absolute Radiance and REfractivity Observatory (CLARREO) in the recent NRC Decadal Survey provides more complete spectral and time-of-day coverage and would fly basic physical standards to eliminate the need to assume on-board reference stability. Therefore, the spectral radiances from this mission will also serve as benchmarks to propagate a highly accurate calibration to other space-borne IR instruments. For the current approach of calibrating infrared flight sensors, in which thermal vacuum tests are conducted before launch and stability is assumed after launch, in-flight calibration validation is essential for highly accurate applications. At present, airborne observations provide the only source of direct radiance validation with resulting traceable uncertainties approaching the level required for remote sensing and climate applications (0.1 K 3- sigma). For the calibration validation process to be accurate, repeatable, and meaningful, the reference instrument must be extremely well characterized and understood, carefully maintained, and accurately calibrated, with the calibration accuracy of the reference instrument tied to absolute standards. Tests of the S-HIS absolute calibration have been conducted using the NIST transfer radiometer (TXR). The TXR provides a more direct connection to the Blackbody reference sources maintained by NIST than the normal traceability of blackbody temperature scales and paint emissivity measurements. Two basic tests were conducted: (1) comparison of radiances measured by the S-HIS to those from the TXR, and (2) measuring the reflectivity of a UW-SSEC blackbody by using the TXR as a stable detector. Preliminary results from both tests are very promising for confirming and refining the expected absolute accuracy of the S-HIS.

Hg0 and HgCl2 Reference Gas Standards: NIST Traceability and Comparability (And EPA ALT Methods for Hg and HCl )

EPA Science Inventory

EPA and NIST have collaborated to establish the necessary procedures for establishing the required NIST traceability of commercially-provided Hg0 and HgCl2 reference generators. This presentation will discuss the approach of a joint EPA/NIST study to accurately quantify the tru...

Descriptive Drinking Norms: For Whom Does Reference Group Matter?*

PubMed Central

Larimer, Mary E.; Neighbors, Clayton; LaBrie, Joseph W.; Atkins, David C.; Lewis, Melissa A.; Lee, Christine M.; Kilmer, Jason R.; Kaysen, Debra L.; Pedersen, Eric r.; Montoya, Heidi; Hodge, Kimberley; Desai, Sruti; Hummer, Justin F.; Walter, Theresa

2011-01-01

Objective: Perceived descriptive drinking norms often differ from actual norms and are positively related to personal consumption. However, it is not clear how normative perceptions vary with specificity of the reference group. Are drinking norms more accurate and more closely related to drinking behavior as reference group specificity increases? Do these relationships vary as a function of participant demographics? The present study examined the relationship between perceived descriptive norms and drinking behavior by ethnicity (Asian or White), sex, and fraternity/sorority status. Method: Participants were 2,699 (58% female) White (75%) or Asian (25%) undergraduates from two universities who reported their own alcohol use and perceived descriptive norms for eight reference groups: "typical student"; same sex, ethnicity, or fraternity/sorority status; and all combinations of these three factors. Results: Participants generally reported the highest perceived norms for the most distal reference group (typical student), with perceptions becoming more accurate as individuals' similarity to the reference group increased. Despite increased accuracy, participants perceived that all reference groups drank more than was actually the case. Across specific subgroups (fraternity/sorority members and men) different patterns emerged. Fraternity/sorority members reliably reported higher estimates of drinking for reference groups that included fraternity/ sorority status, and, to a lesser extent, men reported higher estimates for reference groups that included men. Conclusions: The results suggest that interventions targeting normative misperceptions may need to provide feedback based on participant demography or group membership. Although reference group-specific feedback may be important for some subgroups, typical student feedback provides the largest normative discrepancy for the majority of students. PMID:21906510

Nutritional status in sick children and adolescents is not accurately reflected by BMI-SDS.

PubMed

Fusch, Gerhard; Raja, Preeya; Dung, Nguyen Quang; Karaolis-Danckert, Nadina; Barr, Ronald; Fusch, Christoph

2013-01-01

Nutritional status provides helpful information of disease severity and treatment effectiveness. Body mass index standard deviation scores (BMI-SDS) provide an approximation of body composition and thus are frequently used to classify nutritional status of sick children and adolescents. However, the accuracy of estimating body composition in this population using BMI-SDS has not been assessed. Thus, this study aims to evaluate the accuracy of nutritional status classification in sick infants and adolescents using BMI-SDS, upon comparison to classification using percentage body fat (%BF) reference charts. BMI-SDS was calculated from anthropometric measurements and %BF was measured using dual-energy x-ray absorptiometry (DXA) for 393 sick children and adolescents (5 months-18 years). Subjects were classified by nutritional status (underweight, normal weight, overweight, and obese), using 2 methods: (1) BMI-SDS, based on age- and gender-specific percentiles, and (2) %BF reference charts (standard). Linear regression and a correlation analysis were conducted to compare agreement between both methods of nutritional status classification. %BF reference value comparisons were also made between 3 independent sources based on German, Canadian, and American study populations. Correlation between nutritional status classification by BMI-SDS and %BF agreed moderately (r (2) = 0.75, 0.76 in boys and girls, respectively). The misclassification of nutritional status in sick children and adolescents using BMI-SDS was 27% when using German %BF references. Similar rates observed when using Canadian and American %BF references (24% and 23%, respectively). Using BMI-SDS to determine nutritional status in a sick population is not considered an appropriate clinical tool for identifying individual underweight or overweight children or adolescents. However, BMI-SDS may be appropriate for longitudinal measurements or for screening purposes in large field studies. When accurate nutritional status classification of a sick patient is needed for clinical purposes, nutritional status will be assessed more accurately using methods that accurately measure %BF, such as DXA.

Reweighting anthropometric data using a nearest neighbour approach.

PubMed

Kumar, Kannan Anil; Parkinson, Matthew B

2018-07-01

When designing products and environments, detailed data on body size and shape are seldom available for the specific user population. One way to mitigate this issue is to reweight available data such that they provide an accurate estimate of the target population of interest. This is done by assigning a statistical weight to each individual in the reference data, increasing or decreasing their influence on statistical models of the whole. This paper presents a new approach to reweighting these data. Instead of stratified sampling, the proposed method uses a clustering algorithm to identify relationships between the detailed and reference populations using their height, mass, and body mass index (BMI). The newly weighted data are shown to provide more accurate estimates than traditional approaches. The improved accuracy that accompanies this method provides designers with an alternative to data synthesis techniques as they seek appropriate data to guide their design practice.Practitioner Summary: Design practice is best guided by data on body size and shape that accurately represents the target user population. This research presents an alternative to data synthesis (e.g. regression or proportionality constants) for adapting data from one population for use in modelling another.

A Unified Approach to Genotype Imputation and Haplotype-Phase Inference for Large Data Sets of Trios and Unrelated Individuals

PubMed Central

Browning, Brian L.; Browning, Sharon R.

2009-01-01

We present methods for imputing data for ungenotyped markers and for inferring haplotype phase in large data sets of unrelated individuals and parent-offspring trios. Our methods make use of known haplotype phase when it is available, and our methods are computationally efficient so that the full information in large reference panels with thousands of individuals is utilized. We demonstrate that substantial gains in imputation accuracy accrue with increasingly large reference panel sizes, particularly when imputing low-frequency variants, and that unphased reference panels can provide highly accurate genotype imputation. We place our methodology in a unified framework that enables the simultaneous use of unphased and phased data from trios and unrelated individuals in a single analysis. For unrelated individuals, our imputation methods produce well-calibrated posterior genotype probabilities and highly accurate allele-frequency estimates. For trios, our haplotype-inference method is four orders of magnitude faster than the gold-standard PHASE program and has excellent accuracy. Our methods enable genotype imputation to be performed with unphased trio or unrelated reference panels, thus accounting for haplotype-phase uncertainty in the reference panel. We present a useful measure of imputation accuracy, allelic R2, and show that this measure can be estimated accurately from posterior genotype probabilities. Our methods are implemented in version 3.0 of the BEAGLE software package. PMID:19200528

Scaling laws and accurate small-amplitude stationary solution for the motion of a planar vortex filament in the Cartesian form of the local induction approximation.

PubMed

Van Gorder, Robert A

2013-04-01

We provide a formulation of the local induction approximation (LIA) for the motion of a vortex filament in the Cartesian reference frame (the extrinsic coordinate system) which allows for scaling of the reference coordinate. For general monotone scalings of the reference coordinate, we derive an equation for the planar solution to the derivative nonlinear Schrödinger equation governing the LIA. We proceed to solve this equation perturbatively in small amplitude through an application of multiple-scales analysis, which allows for accurate computation of the period of the planar vortex filament. The perturbation result is shown to agree strongly with numerical simulations, and we also relate this solution back to the solution obtained in the arclength reference frame (the intrinsic coordinate system). Finally, we discuss nonmonotone coordinate scalings and their application for finding self-intersections of vortex filaments. These self-intersecting vortex filaments are likely unstable and collapse into other structures or dissipate completely.

Selection of suitable reference genes for gene expression studies in Staphylococcus capitis during growth under erythromycin stress.

PubMed

Cui, Bintao; Smooker, Peter M; Rouch, Duncan A; Deighton, Margaret A

2016-08-01

Accurate and reproducible measurement of gene transcription requires appropriate reference genes, which are stably expressed under different experimental conditions to provide normalization. Staphylococcus capitis is a human pathogen that produces biofilm under stress, such as imposed by antimicrobial agents. In this study, a set of five commonly used staphylococcal reference genes (gyrB, sodA, recA, tuf and rpoB) were systematically evaluated in two clinical isolates of Staphylococcus capitis (S. capitis subspecies urealyticus and capitis, respectively) under erythromycin stress in mid-log and stationary phases. Two public software programs (geNorm and NormFinder) and two manual calculation methods, reference residue normalization (RRN) and relative quantitative (RQ), were applied. The potential reference genes selected by the four algorithms were further validated by comparing the expression of a well-studied biofilm gene (icaA) with phenotypic biofilm formation in S. capitis under four different experimental conditions. The four methods differed considerably in their ability to predict the most suitable reference gene or gene combination for comparing icaA expression under different conditions. Under the conditions used here, the RQ method provided better selection of reference genes than the other three algorithms; however, this finding needs to be confirmed with a larger number of isolates. This study reinforces the need to assess the stability of reference genes for analysis of target gene expression under different conditions and the use of more than one algorithm in such studies. Although this work was conducted using a specific human pathogen, it emphasizes the importance of selecting suitable reference genes for accurate normalization of gene expression more generally.

Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver.

PubMed

Wymant, Chris; Blanquart, François; Golubchik, Tanya; Gall, Astrid; Bakker, Margreet; Bezemer, Daniela; Croucher, Nicholas J; Hall, Matthew; Hillebregt, Mariska; Ong, Swee Hoe; Ratmann, Oliver; Albert, Jan; Bannert, Norbert; Fellay, Jacques; Fransen, Katrien; Gourlay, Annabelle; Grabowski, M Kate; Gunsenheimer-Bartmeyer, Barbara; Günthard, Huldrych F; Kivelä, Pia; Kouyos, Roger; Laeyendecker, Oliver; Liitsola, Kirsi; Meyer, Laurence; Porter, Kholoud; Ristola, Matti; van Sighem, Ard; Berkhout, Ben; Cornelissen, Marion; Kellam, Paul; Reiss, Peter; Fraser, Christophe

2018-01-01

Studying the evolution of viruses and their molecular epidemiology relies on accurate viral sequence data, so that small differences between similar viruses can be meaningfully interpreted. Despite its higher throughput and more detailed minority variant data, next-generation sequencing has yet to be widely adopted for HIV. The difficulty of accurately reconstructing the consensus sequence of a quasispecies from reads (short fragments of DNA) in the presence of large between- and within-host diversity, including frequent indels, may have presented a barrier. In particular, mapping (aligning) reads to a reference sequence leads to biased loss of information; this bias can distort epidemiological and evolutionary conclusions. De novo assembly avoids this bias by aligning the reads to themselves, producing a set of sequences called contigs. However contigs provide only a partial summary of the reads, misassembly may result in their having an incorrect structure, and no information is available at parts of the genome where contigs could not be assembled. To address these problems we developed the tool shiver to pre-process reads for quality and contamination, then map them to a reference tailored to the sample using corrected contigs supplemented with the user's choice of existing reference sequences. Run with two commands per sample, it can easily be used for large heterogeneous data sets. We used shiver to reconstruct the consensus sequence and minority variant information from paired-end short-read whole-genome data produced with the Illumina platform, for sixty-five existing publicly available samples and fifty new samples. We show the systematic superiority of mapping to shiver's constructed reference compared with mapping the same reads to the closest of 3,249 real references: median values of 13 bases called differently and more accurately, 0 bases called differently and less accurately, and 205 bases of missing sequence recovered. We also successfully applied shiver to whole-genome samples of Hepatitis C Virus and Respiratory Syncytial Virus. shiver is publicly available from https://github.com/ChrisHIV/shiver.

GEOdetic Data assimilation and EStimation of references for climate change InvEstigation. An overall presentation of the French GEODESIE project

NASA Astrophysics Data System (ADS)

Nahmani, S.; Coulot, D.; Biancale, R.; Bizouard, C.; Bonnefond, P.; Bouquillon, S.; Collilieux, X.; Deleflie, F.; Garayt, B.; Lambert, S. B.; Laurent-Varin, S.; Marty, J. C.; Mercier, F.; Metivier, L.; Meyssignac, B.; Pollet, A.; Rebischung, P.; Reinquin, F.; Richard, J. Y.; Tertre, F.; Woppelmann, G.

2017-12-01

Many major indicators of climate change are monitored with space observations. This monitoring is highly dependent on references that only geodesy can provide. The current accuracy of these references does not permit to fully support the challenges that the constantly evolving Earth system gives rise to, and can consequently limit the accuracy of these indicators. Thus, in the framework of the GGOS, stringent requirements are fixed to the International Terrestrial Reference Frame (ITRF) for the next decade: an accuracy at the level of 1 mm and a stability at the level of 0.1 mm/yr. This means an improvement of the current quality of ITRF by a factor of 5-10. Improving the quality of the geodetic references is an issue which requires a thorough reassessment of the methodologies involved. The most relevant and promising method to improve this quality is the direct combination of the space-geodetic measurements used to compute the official references of the IERS. The GEODESIE project aims at (i) determining highly-accurate global and consistent references and (ii) providing the geophysical and climate research communities with these references, for a better estimation of geocentric sea level rise, ice mass balance and on-going climate changes. Time series of sea levels computed from altimetric data and tide gauge records with these references will also be provided. The geodetic references will be essential bases for Earth's observation and monitoring to support the challenges of the century. The geocentric time series of sea levels will permit to better apprehend (i) the drivers of the global mean sea level rise and of regional variations of sea level and (ii) the contribution of the global climate change induced by anthropogenic greenhouse gases emissions to these drivers. All the results and computation and quality assessment reports will be available at geodesie_anr.ign.fr.This project, supported by the French Agence Nationale de la Recherche (ANR) for the period 2017-2020, will be an unprecedented opportunity to provide the French Groupe de Recherche de Géodésie Spatiale (GRGS) with complete simulation and data processing capabilities to prepare the future arrival of space missions such as the European Geodetic Reference Antenna in SPace (E-GRASP) and to significantly contribute to the GGOS with accurate references.

Radio-Optical Reference Frame Link Using the U.S. Naval Observatory Astrograph and Deep CCD Imaging

NASA Astrophysics Data System (ADS)

Zacharias, N.; Zacharias, M. I.

2014-05-01

Between 1997 and 2004 several observing runs were conducted, mainly with the CTIO 0.9 m, to image International Celestial Reference Frame (ICRF) counterparts (mostly QSOs) in order to determine accurate optical positions. Contemporary to these deep CCD images, the same fields were observed with the U.S. Naval Observatory astrograph in the same bandpass. They provide accurate positions on the Hipparcos/Tycho-2 system for stars in the 10-16 mag range used as reference stars for the deep CCD imaging data. Here we present final optical position results of 413 sources based on reference stars obtained by dedicated astrograph observations that were reduced following two different procedures. These optical positions are compared to radio very long baseline interferometry positions. The current optical system is not perfectly aligned to the ICRF radio system with rigid body rotation angles of 3-5 mas (= 3σ level) found between them for all three axes. Furthermore, statistically, the optical-radio position differences are found to exceed the total, combined, known errors in the observations. Systematic errors in the optical reference star positions and physical offsets between the centers of optical and radio emissions are both identified as likely causes. A detrimental, astrophysical, random noise component is postulated to be on about the 10 mas level. If confirmed by future observations, this could severely limit the Gaia to ICRF reference frame alignment accuracy to an error of about 0.5 mas per coordinate axis with the current number of sources envisioned to provide the link. A list of 36 ICRF sources without the detection of an optical counterpart to a limiting magnitude of about R = 22 is provided as well.

Radio-optical reference frame link using the U.S. Naval observatory astrograph and deep CCD imaging

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

Zacharias, N.; Zacharias, M. I., E-mail: nz@usno.navy.mil

2014-05-01

Between 1997 and 2004 several observing runs were conducted, mainly with the CTIO 0.9 m, to image International Celestial Reference Frame (ICRF) counterparts (mostly QSOs) in order to determine accurate optical positions. Contemporary to these deep CCD images, the same fields were observed with the U.S. Naval Observatory astrograph in the same bandpass. They provide accurate positions on the Hipparcos/Tycho-2 system for stars in the 10-16 mag range used as reference stars for the deep CCD imaging data. Here we present final optical position results of 413 sources based on reference stars obtained by dedicated astrograph observations that were reducedmore » following two different procedures. These optical positions are compared to radio very long baseline interferometry positions. The current optical system is not perfectly aligned to the ICRF radio system with rigid body rotation angles of 3-5 mas (= 3σ level) found between them for all three axes. Furthermore, statistically, the optical-radio position differences are found to exceed the total, combined, known errors in the observations. Systematic errors in the optical reference star positions and physical offsets between the centers of optical and radio emissions are both identified as likely causes. A detrimental, astrophysical, random noise component is postulated to be on about the 10 mas level. If confirmed by future observations, this could severely limit the Gaia to ICRF reference frame alignment accuracy to an error of about 0.5 mas per coordinate axis with the current number of sources envisioned to provide the link. A list of 36 ICRF sources without the detection of an optical counterpart to a limiting magnitude of about R = 22 is provided as well.« less

Mach-zehnder based optical marker/comb generator for streak camera calibration

DOEpatents

Miller, Edward Kirk

2015-03-03

This disclosure is directed to a method and apparatus for generating marker and comb indicia in an optical environment using a Mach-Zehnder (M-Z) modulator. High speed recording devices are configured to record image or other data defining a high speed event. To calibrate and establish time reference, the markers or combs are indicia which serve as timing pulses (markers) or a constant-frequency train of optical pulses (comb) to be imaged on a streak camera for accurate time based calibration and time reference. The system includes a camera, an optic signal generator which provides an optic signal to an M-Z modulator and biasing and modulation signal generators configured to provide input to the M-Z modulator. An optical reference signal is provided to the M-Z modulator. The M-Z modulator modulates the reference signal to a higher frequency optical signal which is output through a fiber coupled link to the streak camera.

Multicenter validation of the VITEK MS v2.0 MALDI-TOF mass spectrometry system for the identification of fastidious gram-negative bacteria.

PubMed

Branda, John A; Rychert, Jenna; Burnham, Carey-Ann D; Bythrow, Maureen; Garner, Omai B; Ginocchio, Christine C; Jennemann, Rebecca; Lewinski, Michael A; Manji, Ryhana; Mochon, A Brian; Procop, Gary W; Richter, Sandra S; Sercia, Linda F; Westblade, Lars F; Ferraro, Mary Jane

2014-02-01

The VITEK MS v2.0 MALDI-TOF mass spectrometry system's performance in identifying fastidious gram-negative bacteria was evaluated in a multicenter study. Compared with the reference method (DNA sequencing), the VITEK MS system provided an accurate, species-level identification for 96% of 226 isolates; an additional 1% were accurately identified to the genus level. © 2013.

Superior Cross-Species Reference Genes: A Blueberry Case Study

PubMed Central

Die, Jose V.; Rowland, Lisa J.

2013-01-01

The advent of affordable Next Generation Sequencing technologies has had major impact on studies of many crop species, where access to genomic technologies and genome-scale data sets has been extremely limited until now. The recent development of genomic resources in blueberry will enable the application of high throughput gene expression approaches that should relatively quickly increase our understanding of blueberry physiology. These studies, however, require a highly accurate and robust workflow and make necessary the identification of reference genes with high expression stability for correct target gene normalization. To create a set of superior reference genes for blueberry expression analyses, we mined a publicly available transcriptome data set from blueberry for orthologs to a set of Arabidopsis genes that showed the most stable expression in a developmental series. In total, the expression stability of 13 putative reference genes was evaluated by qPCR and a set of new references with high stability values across a developmental series in fruits and floral buds of blueberry were identified. We also demonstrated the need to use at least two, preferably three, reference genes to avoid inconsistencies in results, even when superior reference genes are used. The new references identified here provide a valuable resource for accurate normalization of gene expression in Vaccinium spp. and may be useful for other members of the Ericaceae family as well. PMID:24058469

Accuracy of Referring Provider and Endoscopist Impressions of Colonoscopy Indication.

PubMed

Naveed, Mariam; Clary, Meredith; Ahn, Chul; Kubiliun, Nisa; Agrawal, Deepak; Cryer, Byron; Murphy, Caitlin; Singal, Amit G

2017-07-01

Background: Referring provider and endoscopist impressions of colonoscopy indication are used for clinical care, reimbursement, and quality reporting decisions; however, the accuracy of these impressions is unknown. This study assessed the sensitivity, specificity, positive and negative predictive value, and overall accuracy of methods to classify colonoscopy indication, including referring provider impression, endoscopist impression, and administrative algorithm compared with gold standard chart review. Methods: We randomly sampled 400 patients undergoing a colonoscopy at a Veterans Affairs health system between January 2010 and December 2010. Referring provider and endoscopist impressions of colonoscopy indication were compared with gold-standard chart review. Indications were classified into 4 mutually exclusive categories: diagnostic, surveillance, high-risk screening, or average-risk screening. Results: Of 400 colonoscopies, 26% were performed for average-risk screening, 7% for high-risk screening, 26% for surveillance, and 41% for diagnostic indications. Accuracy of referring provider and endoscopist impressions of colonoscopy indication were 87% and 84%, respectively, which were significantly higher than that of the administrative algorithm (45%; P <.001 for both). There was substantial agreement between endoscopist and referring provider impressions (κ=0.76). All 3 methods showed high sensitivity (>90%) for determining screening (vs nonscreening) indication, but specificity of the administrative algorithm was lower (40.3%) compared with referring provider (93.7%) and endoscopist (84.0%) impressions. Accuracy of endoscopist, but not referring provider, impression was lower in patients with a family history of colon cancer than in those without (65% vs 84%; P =.001). Conclusions: Referring provider and endoscopist impressions of colonoscopy indication are both accurate and may be useful data to incorporate into algorithms classifying colonoscopy indication. Copyright © 2017 by the National Comprehensive Cancer Network.

Evaluation of Suitable Reference Genes for Normalization of qPCR Gene Expression Studies in Brinjal (Solanum melongena L.) During Fruit Developmental Stages.

PubMed

Kanakachari, Mogilicherla; Solanke, Amolkumar U; Prabhakaran, Narayanasamy; Ahmad, Israr; Dhandapani, Gurusamy; Jayabalan, Narayanasamy; Kumar, Polumetla Ananda

2016-02-01

Brinjal/eggplant/aubergine is one of the major solanaceous vegetable crops. Recent availability of genome information greatly facilitates the fundamental research on brinjal. Gene expression patterns during different stages of fruit development can provide clues towards the understanding of its biological functions. Quantitative real-time PCR (qPCR) has become one of the most widely used methods for rapid and accurate quantification of gene expression. However, its success depends on the use of a suitable reference gene for data normalization. For qPCR analysis, a single reference gene is not universally suitable for all experiments. Therefore, reference gene validation is a crucial step. Suitable reference genes for qPCR analysis of brinjal fruit development have not been investigated so far. In this study, we have selected 21 candidate reference genes from the Brinjal (Solanum melongena) Plant Gene Indices database (compbio.dfci.harvard.edu/tgi/plant.html) and studied their expression profiles by qPCR during six different fruit developmental stages (0, 5, 10, 20, 30, and 50 days post anthesis) along with leaf samples of the Pusa Purple Long (PPL) variety. To evaluate the stability of gene expression, geNorm and NormFinder analytical softwares were used. geNorm identified SAND (SAND family protein) and TBP (TATA binding protein) as the best pairs of reference genes in brinjal fruit development. The results showed that for brinjal fruit development, individual or a combination of reference genes should be selected for data normalization. NormFinder identified Expressed gene (expressed sequence) as the best single reference gene in brinjal fruit development. In this study, we have identified and validated for the first time reference genes to provide accurate transcript normalization and quantification at various fruit developmental stages of brinjal which can also be useful for gene expression studies in other Solanaceae plant species.

Identification and evaluation of new reference genes in Gossypium hirsutum for accurate normalization of real-time quantitative RT-PCR data.

PubMed

Artico, Sinara; Nardeli, Sarah M; Brilhante, Osmundo; Grossi-de-Sa, Maria Fátima; Alves-Ferreira, Marcio

2010-03-21

Normalizing through reference genes, or housekeeping genes, can make more accurate and reliable results from reverse transcription real-time quantitative polymerase chain reaction (qPCR). Recent studies have shown that no single housekeeping gene is universal for all experiments. Thus, suitable reference genes should be the first step of any qPCR analysis. Only a few studies on the identification of housekeeping gene have been carried on plants. Therefore qPCR studies on important crops such as cotton has been hampered by the lack of suitable reference genes. By the use of two distinct algorithms, implemented by geNorm and NormFinder, we have assessed the gene expression of nine candidate reference genes in cotton: GhACT4, GhEF1alpha5, GhFBX6, GhPP2A1, GhMZA, GhPTB, GhGAPC2, GhbetaTUB3 and GhUBQ14. The candidate reference genes were evaluated in 23 experimental samples consisting of six distinct plant organs, eight stages of flower development, four stages of fruit development and in flower verticils. The expression of GhPP2A1 and GhUBQ14 genes were the most stable across all samples and also when distinct plants organs are examined. GhACT4 and GhUBQ14 present more stable expression during flower development, GhACT4 and GhFBX6 in the floral verticils and GhMZA and GhPTB during fruit development. Our analysis provided the most suitable combination of reference genes for each experimental set tested as internal control for reliable qPCR data normalization. In addition, to illustrate the use of cotton reference genes we checked the expression of two cotton MADS-box genes in distinct plant and floral organs and also during flower development. We have tested the expression stabilities of nine candidate genes in a set of 23 tissue samples from cotton plants divided into five different experimental sets. As a result of this evaluation, we recommend the use of GhUBQ14 and GhPP2A1 housekeeping genes as superior references for normalization of gene expression measures in different cotton plant organs; GhACT4 and GhUBQ14 for flower development, GhACT4 and GhFBX6 for the floral organs and GhMZA and GhPTB for fruit development. We also provide the primer sequences whose performance in qPCR experiments is demonstrated. These genes will enable more accurate and reliable normalization of qPCR results for gene expression studies in this important crop, the major source of natural fiber and also an important source of edible oil. The use of bona fide reference genes allowed a detailed and accurate characterization of the temporal and spatial expression pattern of two MADS-box genes in cotton.

Identification and evaluation of new reference genes in Gossypium hirsutum for accurate normalization of real-time quantitative RT-PCR data

PubMed Central

2010-01-01

Background Normalizing through reference genes, or housekeeping genes, can make more accurate and reliable results from reverse transcription real-time quantitative polymerase chain reaction (qPCR). Recent studies have shown that no single housekeeping gene is universal for all experiments. Thus, suitable reference genes should be the first step of any qPCR analysis. Only a few studies on the identification of housekeeping gene have been carried on plants. Therefore qPCR studies on important crops such as cotton has been hampered by the lack of suitable reference genes. Results By the use of two distinct algorithms, implemented by geNorm and NormFinder, we have assessed the gene expression of nine candidate reference genes in cotton: GhACT4, GhEF1α5, GhFBX6, GhPP2A1, GhMZA, GhPTB, GhGAPC2, GhβTUB3 and GhUBQ14. The candidate reference genes were evaluated in 23 experimental samples consisting of six distinct plant organs, eight stages of flower development, four stages of fruit development and in flower verticils. The expression of GhPP2A1 and GhUBQ14 genes were the most stable across all samples and also when distinct plants organs are examined. GhACT4 and GhUBQ14 present more stable expression during flower development, GhACT4 and GhFBX6 in the floral verticils and GhMZA and GhPTB during fruit development. Our analysis provided the most suitable combination of reference genes for each experimental set tested as internal control for reliable qPCR data normalization. In addition, to illustrate the use of cotton reference genes we checked the expression of two cotton MADS-box genes in distinct plant and floral organs and also during flower development. Conclusion We have tested the expression stabilities of nine candidate genes in a set of 23 tissue samples from cotton plants divided into five different experimental sets. As a result of this evaluation, we recommend the use of GhUBQ14 and GhPP2A1 housekeeping genes as superior references for normalization of gene expression measures in different cotton plant organs; GhACT4 and GhUBQ14 for flower development, GhACT4 and GhFBX6 for the floral organs and GhMZA and GhPTB for fruit development. We also provide the primer sequences whose performance in qPCR experiments is demonstrated. These genes will enable more accurate and reliable normalization of qPCR results for gene expression studies in this important crop, the major source of natural fiber and also an important source of edible oil. The use of bona fide reference genes allowed a detailed and accurate characterization of the temporal and spatial expression pattern of two MADS-box genes in cotton. PMID:20302670

Development of an extended straightness measurement reference

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

Schenz, R.F.; Griffith, L.V.; Sommargren, G.E.

1988-09-06

The most accurate diamond turning machines have used physical straightness references. These references commonly are made of optical materials, such as Zerodur, and are flat enough to permit straightness measurements with an accuracy of 100--150 nm (4--6 microinches) p-v. In most cases, the flatness error is stable and can be accommodated by using a calibration table. The straightedges for the Large Optics Diamond Turning Machine (LODTM) at Lawrence Livermore National Laboratory (LLNL) are 1.1 meters in length and allow a straightness reference accuracy of 25--50 nm (1--2 microinches) p-v after calibration. Fabrication problems become insurmountable when a straightness reference formore » a length of up to 4 meters is desired. Moreover, the method of calibration by straightedge reversal does not account for gravitational sag when the sensing direction is vertical. Vertical sensing would be required in a four meter system and sag would become unacceptably large. Recent developments published in the literature suggest that the use of a laser beam for a reference may be feasible. Workers at Osaka University have reported a laser beam straightness reference that has a resolution of 3.5 nm, although tests were done only over a 200 mm length. LLNL has begun an investigation on the use of a directionally stabilized laser beam as a straightness measurement reference. The goal of the investigation is to provide a reference that is accurate to 25 nm (1 microinch) over a four meter distance. 3 refs., 2 figs.« less

Genetics on the World Wide Web.

PubMed

Trangenstein, P A; Hetteberg, C

1998-11-01

Since 1990, when the Human Genome Project was initiated, the amount of genetic information on the World Wide Web (WWW) has grown substantially. The WWW has become an important resource for current, accurate, and reliable genetic information for health care professionals and the general public. The purpose of this article is to provide a variety of genetics-related WWW sites that are useful for all levels of practitioners interested in genetics. In selecting sites to be included in this article, a number of evaluation tools were reviewed. The primary concern was that these sites be reputable and provide accurate, timely information. A table of the WWW sites is included for quick easy reference.

Entomopathogen ID: a curated sequence resource for entomopathogenic fungi

USDA-ARS?s Scientific Manuscript database

We report the development of a publicly accessible, curated database of Hypocrealean entomopathogenic fungi sequence data. The goal is to provide a platform for users to easily access sequence data from reference strains. The database can be used to accurately identify unknown entomopathogenic fungi...

The Global GNSS, SLR, VLBI, and DORIS Networks and their Support of GGOS: IGS+ILRS+IVS+IDS

NASA Technical Reports Server (NTRS)

Noll, Carey

2008-01-01

The global network of the International GNSS Service (IGS), the International Laser Ranging Service (ILRS), the International VLBI Service for Geodesy and Astrometry (IVS), and the International DORIS Service (IDS) are part of the ground-based infrastructure for GGOS. The observations obtained from these global networks provide for the determination and maintenance of the International Terrestrial Reference Frame (ITRF), an accurate set of positions and velocities that provides a stable coordinate system allowing scientists ts to link measurements over space and time. Many of these sites offer co-location of two or more techniques. Co-location provides integration of technique-specific networks into the ITRF as well as an assessment/validation of the quality and accuracy of the resulting measurements. As of fall 2008, these networks consisted of 410 GNSS sites, 42 laser ranging sites, 45 VLBI sites, and 58 DORIS sites. This poster will illustrate the global coverage of these networks, highlighting inter-technique co-locations, and show the importance of these networks 60 the underlying goals of GGOS including providing the observational basis to maintain a stable, accurate, global reference frame.

Pyramid beam splitter

DOEpatents

McKeown, Mark H.; Beason, Steven C.; Fairer, George

1992-01-01

The apparatus of the present invention provides means for obtaining accurate, dependable, measurement of bearings and directions for geologic mapping in subterranean shafts, such as, for example, nuclear waste storage investigations. In operation, a laser beam is projected along a reference bearing. A pyramid is mounted such that the laser beam is parallel to the pyramid axis and can impinge on the apex of the pyramid thus splitting the beam several ways into several beams at right angles to each other and at right angles to the reference beam. The pyramid is also translatable and rotatable in a plane perpendicular to the reference beam.

Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver

PubMed Central

Blanquart, François; Golubchik, Tanya; Gall, Astrid; Bakker, Margreet; Bezemer, Daniela; Croucher, Nicholas J; Hall, Matthew; Hillebregt, Mariska; Ratmann, Oliver; Albert, Jan; Bannert, Norbert; Fellay, Jacques; Fransen, Katrien; Gourlay, Annabelle; Grabowski, M Kate; Gunsenheimer-Bartmeyer, Barbara; Günthard, Huldrych F; Kivelä, Pia; Kouyos, Roger; Laeyendecker, Oliver; Liitsola, Kirsi; Meyer, Laurence; Porter, Kholoud; Ristola, Matti; van Sighem, Ard; Cornelissen, Marion; Kellam, Paul; Reiss, Peter

2018-01-01

Abstract Studying the evolution of viruses and their molecular epidemiology relies on accurate viral sequence data, so that small differences between similar viruses can be meaningfully interpreted. Despite its higher throughput and more detailed minority variant data, next-generation sequencing has yet to be widely adopted for HIV. The difficulty of accurately reconstructing the consensus sequence of a quasispecies from reads (short fragments of DNA) in the presence of large between- and within-host diversity, including frequent indels, may have presented a barrier. In particular, mapping (aligning) reads to a reference sequence leads to biased loss of information; this bias can distort epidemiological and evolutionary conclusions. De novo assembly avoids this bias by aligning the reads to themselves, producing a set of sequences called contigs. However contigs provide only a partial summary of the reads, misassembly may result in their having an incorrect structure, and no information is available at parts of the genome where contigs could not be assembled. To address these problems we developed the tool shiver to pre-process reads for quality and contamination, then map them to a reference tailored to the sample using corrected contigs supplemented with the user’s choice of existing reference sequences. Run with two commands per sample, it can easily be used for large heterogeneous data sets. We used shiver to reconstruct the consensus sequence and minority variant information from paired-end short-read whole-genome data produced with the Illumina platform, for sixty-five existing publicly available samples and fifty new samples. We show the systematic superiority of mapping to shiver’s constructed reference compared with mapping the same reads to the closest of 3,249 real references: median values of 13 bases called differently and more accurately, 0 bases called differently and less accurately, and 205 bases of missing sequence recovered. We also successfully applied shiver to whole-genome samples of Hepatitis C Virus and Respiratory Syncytial Virus. shiver is publicly available from https://github.com/ChrisHIV/shiver. PMID:29876136

Identification of a chicken (Gallus gallus) endogenous reference gene (Actb) and its application in meat adulteration.

PubMed

Xiang, Wenjin; Shang, Ying; Wang, Qin; Xu, Yuancong; Zhu, Pengyu; Huang, Kunlun; Xu, Wentao

2017-11-01

The genes commonly used to determine meat species are mainly mitochondrial, but the copy numbers of such genes are high, meaning they cannot be accurately quantified. In this paper, for the first time, the chromosomal gene Actb was selected as an endogenous reference gene for chicken species. It was assayed in four different chicken varieties and 16 other species using both qualitative and quantitative PCR. No amplification of the Actb gene was found in species other than chicken and no allelic variations were detected in chicken. Southern blot and digital-PCR confirmed the Actb gene was present as a single copy in the chicken genome. The quantitative detection limit was 10pg of DNA, which is equivalent to eight copies. All experiments indicated that the Actb gene is a useful endogenous reference gene for chicken, and provides a convenient and accurate approach for detection of chicken in feed and food. Copyright © 2017 Elsevier Ltd. All rights reserved.

Handbook of the Economics of Education. Volume 1

ERIC Educational Resources Information Center

Hanushek, Erik A., Ed.; Welch, F., Ed.

2006-01-01

The Handbooks in Economics series continues to provide the various branches of economics with handbooks which are definitive reference sources, suitable for use by professional researchers, advanced graduate students, or by those seeking a teaching supplement. With contributions from leading researchers, each Handbook presents an accurate,…

Handbook of the Economics of Education. Volume 2

ERIC Educational Resources Information Center

Hanushek, Erik A., Ed.; Welch, F., Ed.

2006-01-01

The Handbooks in Economics series continues to provide the various branches of economics with handbooks which are definitive reference sources, suitable for use by professional researchers, advanced graduate students, or by those seeking a teaching supplement. With contributions from leading researchers, each Handbook presents an accurate,…

The visible ground surface as a reference frame for scaling binocular depth of a target in midair

PubMed Central

WU, JUN; ZHOU, LIU; SHI, PAN; HE, ZIJIANG J; OOI, TENG LENG

2014-01-01

The natural ground surface carries texture information that extends continuously from one’s feet to the horizon, providing a rich depth resource for accurately locating an object resting on it. Here, we showed that the ground surface’s role as a reference frame also aids in locating a target suspended in midair based on relative binocular disparity. Using real world setup in our experiments, we first found that a suspended target is more accurately localized when the ground surface is visible and the observer views the scene binocularly. In addition, the increased accuracy occurs only when the scene is viewed for 5 sec rather than 0.15 sec, suggesting that the binocular depth process takes time. Second, we found that manipulation of the configurations of the texture-gradient and/or linear-perspective cues on the visible ground surface affects the perceived distance of the suspended target in midair. Third, we found that a suspended target is more accurately localized against a ground texture surface than a ceiling texture surface. This suggests that our visual system usesthe ground surface as the preferred reference frame to scale the distance of a suspended target according to its relative binocular disparity. PMID:25384237

Thermal radiation transfer calculations in combustion fields using the SLW model coupled with a modified reference approach

NASA Astrophysics Data System (ADS)

Darbandi, Masoud; Abrar, Bagher

2018-01-01

The spectral-line weighted-sum-of-gray-gases (SLW) model is considered as a modern global model, which can be used in predicting the thermal radiation heat transfer within the combustion fields. The past SLW model users have mostly employed the reference approach to calculate the local values of gray gases' absorption coefficient. This classical reference approach assumes that the absorption spectra of gases at different thermodynamic conditions are scalable with the absorption spectrum of gas at a reference thermodynamic state in the domain. However, this assumption cannot be reasonable in combustion fields, where the gas temperature is very different from the reference temperature. Consequently, the results of SLW model incorporated with the classical reference approach, say the classical SLW method, are highly sensitive to the reference temperature magnitude in non-isothermal combustion fields. To lessen this sensitivity, the current work combines the SLW model with a modified reference approach, which is a particular one among the eight possible reference approach forms reported recently by Solovjov, et al. [DOI: 10.1016/j.jqsrt.2017.01.034, 2017]. The combination is called "modified SLW method". This work shows that the modified reference approach can provide more accurate total emissivity calculation than the classical reference approach if it is coupled with the SLW method. This would be particularly helpful for more accurate calculation of radiation transfer in highly non-isothermal combustion fields. To approve this, we use both the classical and modified SLW methods and calculate the radiation transfer in such fields. It is shown that the modified SLW method can almost eliminate the sensitivity of achieved results to the chosen reference temperature in treating highly non-isothermal combustion fields.

Role of orientation reference selection in motion sickness

NASA Technical Reports Server (NTRS)

Peterka, Robert J.; Black, F. Owen

1990-01-01

Three areas related to human orientation control are investigated: (1) reflexes associated with the control of eye movements and posture; (2) the perception of body rotation and position with respect to gravity; and (3) the strategies used to resolve sensory conflict situations which arise when different sensory systems provide orientation cues which are not consistent with one another or with previous experience. Of particular interest is the possibility that a subject may be able to ignore an inaccurate sensory modality in favor of one or more other sensory modalities which do provide accurate orientation reference information. This process is referred as sensory selection. This proposal will attempt to quantify subject's sensory selection abilities and determine if this ability confers some immunity to the development of motion sickness symptoms.

Towards ontology-based decision support systems for complex ultrasound diagnosis in obstetrics and gynecology.

PubMed

Maurice, P; Dhombres, F; Blondiaux, E; Friszer, S; Guilbaud, L; Lelong, N; Khoshnood, B; Charlet, J; Perrot, N; Jauniaux, E; Jurkovic, D; Jouannic, J-M

2017-05-01

We have developed a new knowledge base intelligent system for obstetrics and gynecology ultrasound imaging, based on an ontology and a reference image collection. This study evaluates the new system to support accurate annotations of ultrasound images. We have used the early ultrasound diagnosis of ectopic pregnancies as a model clinical issue. The ectopic pregnancy ontology was derived from medical texts (4260 ultrasound reports of ectopic pregnancy from a specialist center in the UK and 2795 Pubmed abstracts indexed with the MeSH term "Pregnancy, Ectopic") and the reference image collection was built on a selection from 106 publications. We conducted a retrospective analysis of the signs in 35 scans of ectopic pregnancy by six observers using the new system. The resulting ectopic pregnancy ontology consisted of 1395 terms, and 80 images were collected for the reference collection. The observers used the knowledge base intelligent system to provide a total of 1486 sign annotations. The precision, recall and F-measure for the annotations were 0.83, 0.62 and 0.71, respectively. The global proportion of agreement was 40.35% 95% CI [38.64-42.05]. The ontology-based intelligent system provides accurate annotations of ultrasound images and suggests that it may benefit non-expert operators. The precision rate is appropriate for accurate input of a computer-based clinical decision support and could be used to support medical imaging diagnosis of complex conditions in obstetrics and gynecology. Copyright © 2017. Published by Elsevier Masson SAS.

International Laser Ranging Service (ILRS): Terms of Reference

NASA Technical Reports Server (NTRS)

Husson, Van; Noll, Carey

2000-01-01

The International Laser Ranging Service (ILRS) is an established Service within Section II , Advanced Space Technology, of the International Association of Geodesy (IAG). The primary objective of the ILRS is to provide a service to support, through Satellite and Lunar Laser Ranging data and related products, geodetic and geophysical research activities as well as International Earth Rotation Service (IERS) products important to the maintenance of an accurate International Terrestrial Reference Frame (ITRF). The service also develops the necessary standards/specifications and encourages international adherence to its conventions.

Determination of the extragalactic-planetary frame tie from joint analysis of radio interferometric and lunar laser ranging measurements

NASA Technical Reports Server (NTRS)

Folkner, W. M.; Charlot, P.; Finger, M. H.; Williams, J. G.; Sovers, O. J.; Newhall, XX; Standish, E. M., Jr.

1994-01-01

Very Long Baseline Interferometry (VLBI) observations of extragalactic radio sources provide the basis for defining an accurate non-rotating reference frame in terms of angular positions of the sources. Measurements of the distance from the Earth to the Moon and to the inner planets provide the basis for defining an inertial planetary ephemeris reference frame. The relative orientation, or frame tie, between these two reference frames is of interest for combining Earth orientation measurements, for comparing Earth orientation results with theories referred to the mean equator and equinox, and for determining the positions of the planets with respect to the extragalactic reference frame. This work presents an indirect determination of the extragalactic-planetary frame tie from a combined reduction of VLBI and Lunar Laser Ranging (LLR) observations. For this determination, data acquired by LLR tracking stations since 1969 have been analyzed and combined with 14 years of VLBI data acquired by NASA's Deep Space Network since 1978. The frame tie derived from this joint analysis, with an accuracy of 0.003 sec, is the most accurate determination obtained so far. This result, combined with a determination of the mean ecliptic (defined in the rotating sense), shows that the mean equinox of epoch J2000 is offset from the x-axis of the extragalactic frame adopted by the International Earth Rotation Service for astrometric and geodetic applications by 0.078 sec +/- 0.010 sec along the y-direction and y 0.019 sec +/- 0.001 sec. along the z-direction.

To amend title 13, United States Code, to provide for the more accurate and complete enumeration of certain overseas Americans in the decennial census.

THOMAS, 111th Congress

Rep. Bishop, Rob [R-UT-1

2009-06-24

House - 10/23/2009 Referred to the Subcommittee on Information Policy, Census, and National Archives. (All Actions) Tracker: This bill has the status IntroducedHere are the steps for Status of Legislation:

Development and applications of the EntomopathogenID MLSA database for use in agricultural systems

USDA-ARS?s Scientific Manuscript database

The current study reports the development and application of a publicly accessible, curated database of Hypocrealean entomopathogenic fungi sequence data. The goal was to provide a platform for users to easily access sequence data from reference strains. The database can be used to accurately identi...

Perturbation theory for water with an associating reference fluid

NASA Astrophysics Data System (ADS)

Marshall, Bennett D.

2017-11-01

The theoretical description of the thermodynamics of water is challenged by the structural transition towards tetrahedral symmetry at ambient conditions. As perturbation theories typically assume a spherically symmetric reference fluid, they are incapable of accurately describing the liquid properties of water at ambient conditions. In this paper we address this problem by introducing the concept of an associated reference perturbation theory (APT). In APT we treat the reference fluid as an associating hard sphere fluid which transitions to tetrahedral symmetry in the fully hydrogen bonded limit. We calculate this transition in a theoretically self-consistent manner without appealing to molecular simulations. This associated reference provides the reference fluid for a second order Barker-Henderson perturbative treatment of the long-range attractions. We demonstrate that this approach gives a significantly improved description of water as compared to standard perturbation theories.

GEOdetic Data assimilation and EStimation of references for climate change InvEstigation. An overall presentation of the French GEODESIE project

NASA Astrophysics Data System (ADS)

Coulot, David; Richard, Jean-Yves

2017-04-01

Many major indicators of climate change are monitored with space observations (sea level rise from satellite altimetry, ice melting from dedicated satellites, etc.). This monitoring is highly dependent on references (positions and velocities of ground observing instruments, orbits of satellites, etc.) that only geodesy can provide. The current accuracy of these references does not permit to fully support the challenges that the constantly evolving Earth system gives rise to, and can consequently limit the accuracy of these indicators. For this reason, in the framework of the Global Geodetic Observing System (GGOS), stringent requirements are fixed to the International Terrestrial Reference Frame (ITRF) for the next decade: an accuracy at the level of 1 mm and a stability at the level of 0.1 mm/yr. This means an improvement of the current quality of ITRF by a factor of 5-10. Improving the quality of the geodetic references is an issue which requires a thorough reassessment of the methodologies involved. The most relevant and promising method to improve this quality is the direct combination (Combination at Observation Level - COL) of the space-geodetic measurements used to compute the official references of the International Earth Rotation and Reference Systems Service (IERS). The GEODESIE project aims at (i) determining highly-accurate global and consistent references (time series of Terrestrial Reference Frames and Celestial Reference Frames, of Earth's Orientation Parameters, and orbits of Earth's observation satellites) and (ii) providing the geophysical and climate research communities with these references, for a better estimation of geocentric sea level rise, ice mass balance and on-going climate changes. Time series of sea levels computed from altimetric data and tide gauge records with these references (orbits of satellite altimeters, Terrestrial Reference Frames and related vertical velocities of stations) will also be provided. The geodetic references will be essential bases for Earth's observation and monitoring to support the challenges of the century. The geocentric time series of sea levels will permit to better apprehend (i) the drivers of the global mean sea level rise and of regional variations of sea level and (ii) the contribution of the global climate change induced by anthropogenic greenhouse gases emissions to these drivers. All the results and computation and quality assessment reports will be available on a Website designed and opened in the Summer of 2017. This project, supported by the French Agence Nationale de la Recherche (ANR) for the period 2017-2020, will be an unprecedented opportunity to provide the French Groupe de Recherche de Géodésie Spatiale (GRGS) with complete simulation and data processing capabilities to prepare the future arrival of space missions such as the European Geodetic Reference Antenna in SPace (E-GRASP) and to significantly contribute to the GGOS with accurate references.

Establishing Accurate and Sustainable Geospatial Reference Layers in Developing Countries

NASA Astrophysics Data System (ADS)

Seaman, V. Y.

2017-12-01

Accurate geospatial reference layers (settlement names & locations, administrative boundaries, and population) are not readily available for most developing countries. This critical information gap makes it challenging for governments to efficiently plan, allocate resources, and provide basic services. It also hampers international agencies' response to natural disasters, humanitarian crises, and other emergencies. The current work involves a recent successful effort, led by the Bill & Melinda Gates Foundation and the Government of Nigeria, to obtain such data. The data collection began in 2013, with local teams collecting names, coordinates, and administrative attributes for over 100,000 settlements using ODK-enabled smartphones. A settlement feature layer extracted from satellite imagery was used to ensure all settlements were included. Administrative boundaries (Ward, LGA) were created using the settlement attributes. These "new" boundary layers were much more accurate than existing shapefiles used by the government and international organizations. The resulting data sets helped Nigeria eradicate polio from all areas except in the extreme northeast, where security issues limited access and vaccination activities. In addition to the settlement and boundary layers, a GIS-based population model was developed, in partnership with Oak Ridge National Laboratories and Flowminder), that used the extracted settlement areas and characteristics, along with targeted microcensus data. This model provides population and demographics estimates independent of census or other administrative data, at a resolution of 90 meters. These robust geospatial data layers found many other uses, including establishing catchment area settlements and populations for health facilities, validating denominators for population-based surveys, and applications across a variety of government sectors. Based on the success of the Nigeria effort, a partnership between DfID and the Bill & Melinda Gates Foundation was formed in 2017 to help other developing countries collect these geospatial reference layers, and to build capacity within the host governments to manage, use, and sustain them. This work will support, wherever possible, a national geo-referenced census, from which the reference layers can be extracted.

International Laser Ranging Service (ILRS) 2003-2004 Annual Report

NASA Technical Reports Server (NTRS)

Pearlman, Michael (Editor); Noll, Carey (Editor)

2005-01-01

The International Laser Ranging Service (ILRS) organizes and coordinates Satellite Laser Ranging (SLR) and Lunar Laser Ranging (LLR) to support programs in geodetic, geophysical, and lunar research activities and provides the International Earth Rotation and Reference Systems Service (IERS) with products important to the maintenance of an accurate International Terrestrial Reference Frame (ITRF). This reference frame provides the stability through which systematic measurements of the Earth can be made over thousands of kilometers, decades of time, and evolution of measurement technology. This 2003-2004 ILRS annual report is comprised of individual contributions from ILRS components within the international geodetic community for the years 2003-2004. The report documents changes and progress of the ILRS and is also available on the ILRS Web site at http://ilrs.gsfc.nasa.gov/reports/ilrs_reports/ilrsar_2003.html.

Genotype imputation in the domestic dog

PubMed Central

Meurs, K. M.

2016-01-01

Application of imputation methods to accurately predict a dense array of SNP genotypes in the dog could provide an important supplement to current analyses of array-based genotyping data. Here, we developed a reference panel of 4,885,283 SNPs in 83 dogs across 15 breeds using whole genome sequencing. We used this panel to predict the genotypes of 268 dogs across three breeds with 84,193 SNP array-derived genotypes as inputs. We then (1) performed breed clustering of the actual and imputed data; (2) evaluated several reference panel breed combinations to determine an optimal reference panel composition; and (3) compared the accuracy of two commonly used software algorithms (Beagle and IMPUTE2). Breed clustering was well preserved in the imputation process across eigenvalues representing 75 % of the variation in the imputed data. Using Beagle with a target panel from a single breed, genotype concordance was highest using a multi-breed reference panel (92.4 %) compared to a breed-specific reference panel (87.0 %) or a reference panel containing no breeds overlapping with the target panel (74.9 %). This finding was confirmed using target panels derived from two other breeds. Additionally, using the multi-breed reference panel, genotype concordance was slightly higher with IMPUTE2 (94.1 %) compared to Beagle; Pearson correlation coefficients were slightly higher for both software packages (0.946 for Beagle, 0.961 for IMPUTE2). Our findings demonstrate that genotype imputation from SNP array-derived data to whole genome-level genotypes is both feasible and accurate in the dog with appropriate breed overlap between the target and reference panels. PMID:27129452

To amend title 13, United States Code, to provide for the more accurate and complete enumeration of certain overseas Americans in the decennial census.

THOMAS, 112th Congress

Rep. Bishop, Rob [R-UT-1

2011-03-02

House - 03/18/2011 Referred to the Subcommittee on Health Care, District of Columbia, Census and the National Archives. (All Actions) Tracker: This bill has the status IntroducedHere are the steps for Status of Legislation:

Water--1970. Chemical Engineering Progress Symposium Series No. 107, Volume 67, 1971.

ERIC Educational Resources Information Center

Cecil, Lawrence K., Ed.

Due to the tremendous interest in all phases of environmental control, particularly with reference to water pollution control, the American Institute of Chemical Engineers (AIChE) is attempting to provide the lay public with accurate information about water resources so they may react with proper knowledge and constructive activity. This anthology…

Automatic readout micrometer

DOEpatents

Lauritzen, Ted

1982-01-01

A measuring system is disclosed for surveying and very accurately positioning objects with respect to a reference line. A principal use of this surveying system is for accurately aligning the electromagnets which direct a particle beam emitted from a particle accelerator. Prior art surveying systems require highly skilled surveyors. Prior art systems include, for example, optical surveying systems which are susceptible to operator reading errors, and celestial navigation-type surveying systems, with their inherent complexities. The present invention provides an automatic readout micrometer which can very accurately measure distances. The invention has a simplicity of operation which practically eliminates the possibilities of operator optical reading error, owning to the elimination of traditional optical alignments for making measurements. The invention has an extendable arm which carries a laser surveying target. The extendable arm can be continuously positioned over its entire length of travel by either a coarse or fine adjustment without having the fine adjustment outrun the coarse adjustment until a reference laser beam is centered on the target as indicated by a digital readout. The length of the micrometer can then be accurately and automatically read by a computer and compared with a standardized set of alignment measurements. Due to its construction, the micrometer eliminates any errors due to temperature changes when the system is operated within a standard operating temperature range.

Automatic readout micrometer

DOEpatents

Lauritzen, T.

A measuring system is described for surveying and very accurately positioning objects with respect to a reference line. A principle use of this surveying system is for accurately aligning the electromagnets which direct a particle beam emitted from a particle accelerator. Prior art surveying systems require highly skilled surveyors. Prior art systems include, for example, optical surveying systems which are susceptible to operator reading errors, and celestial navigation-type surveying systems, with their inherent complexities. The present invention provides an automatic readout micrometer which can very accurately measure distances. The invention has a simplicity of operation which practically eliminates the possibilities of operator optical reading error, owning to the elimination of traditional optical alignments for making measurements. The invention has an extendable arm which carries a laser surveying target. The extendable arm can be continuously positioned over its entire length of travel by either a coarse of fine adjustment without having the fine adjustment outrun the coarse adjustment until a reference laser beam is centered on the target as indicated by a digital readout. The length of the micrometer can then be accurately and automatically read by a computer and compared with a standardized set of alignment measurements. Due to its construction, the micrometer eliminates any errors due to temperature changes when the system is operated within a standard operating temperature range.

DNA barcode data accurately assign higher spider taxa

PubMed Central

Coddington, Jonathan A.; Agnarsson, Ingi; Cheng, Ren-Chung; Čandek, Klemen; Driskell, Amy; Frick, Holger; Gregorič, Matjaž; Kostanjšek, Rok; Kropf, Christian; Kweskin, Matthew; Lokovšek, Tjaša; Pipan, Miha; Vidergar, Nina

2016-01-01

The use of unique DNA sequences as a method for taxonomic identification is no longer fundamentally controversial, even though debate continues on the best markers, methods, and technology to use. Although both existing databanks such as GenBank and BOLD, as well as reference taxonomies, are imperfect, in best case scenarios “barcodes” (whether single or multiple, organelle or nuclear, loci) clearly are an increasingly fast and inexpensive method of identification, especially as compared to manual identification of unknowns by increasingly rare expert taxonomists. Because most species on Earth are undescribed, a complete reference database at the species level is impractical in the near term. The question therefore arises whether unidentified species can, using DNA barcodes, be accurately assigned to more inclusive groups such as genera and families—taxonomic ranks of putatively monophyletic groups for which the global inventory is more complete and stable. We used a carefully chosen test library of CO1 sequences from 49 families, 313 genera, and 816 species of spiders to assess the accuracy of genus and family-level assignment. We used BLAST queries of each sequence against the entire library and got the top ten hits. The percent sequence identity was reported from these hits (PIdent, range 75–100%). Accurate assignment of higher taxa (PIdent above which errors totaled less than 5%) occurred for genera at PIdent values >95 and families at PIdent values ≥ 91, suggesting these as heuristic thresholds for accurate generic and familial identifications in spiders. Accuracy of identification increases with numbers of species/genus and genera/family in the library; above five genera per family and fifteen species per genus all higher taxon assignments were correct. We propose that using percent sequence identity between conventional barcode sequences may be a feasible and reasonably accurate method to identify animals to family/genus. However, the quality of the underlying database impacts accuracy of results; many outliers in our dataset could be attributed to taxonomic and/or sequencing errors in BOLD and GenBank. It seems that an accurate and complete reference library of families and genera of life could provide accurate higher level taxonomic identifications cheaply and accessibly, within years rather than decades. PMID:27547527

Digital antimicrobial susceptibility testing using the MilliDrop technology.

PubMed

Jiang, L; Boitard, L; Broyer, P; Chareire, A-C; Bourne-Branchu, P; Mahé, P; Tournoud, M; Franceschi, C; Zambardi, G; Baudry, J; Bibette, J

2016-03-01

We present the MilliDrop Analyzer (MDA), a droplet-based millifluidic system for digital antimicrobial susceptibility testing (D-AST), which enables us to determine minimum inhibitory concentrations (MICs) precisely and accurately. The MilliDrop technology was validated by using resazurin for fluorescence readout, for comparison with standard methodology, and for conducting reproducibility studies. In this first assessment, the susceptibility of a reference Gram-negative strain Escherichia coli ATCC 25922 to gentamicin, chloramphenicol, and nalidixic acid were tested by the MDA, VITEK®2, and broth microdilution as a reference standard. We measured the susceptibility of clinically relevant Gram-positive strains of Staphylococcus aureus to vancomycin, including vancomycin-intermediate S. aureus (VISA), heterogeneous vancomycin-intermediate S. aureus (hVISA), and vancomycin-susceptible S. aureus (VSSA) strains. The MDA provided results which were much more accurate than those of VITEK®2 and standard broth microdilution. The enhanced accuracy enabled us to reliably discriminate between VSSA and hVISA strains.

Test of simple fluid theories for the Lennard-Jones system

NASA Astrophysics Data System (ADS)

Malijevský, A.; Labik, S.

1988-03-01

A test is made of a new version of the reference-hypernetted chain approximation (RHNC) with minimized free energy proposed by Lado, Foiles and Ashcroft. An accurate relationship is used for the bridge function of the reference hard spheres. The calculated values of the compressibility factor and the internal energy are compared with simulation data, with results of the exponential approximation of Andersen et al., and with results of the Madden-Fitts approximation. The RHNC provides the most reliable results over wide ranges of reduced temperatures and densities.

Seshat: A Web service for accurate annotation, validation, and analysis of TP53 variants generated by conventional and next-generation sequencing.

PubMed

Tikkanen, Tuomas; Leroy, Bernard; Fournier, Jean Louis; Risques, Rosa Ana; Malcikova, Jitka; Soussi, Thierry

2018-07-01

Accurate annotation of genomic variants in human diseases is essential to allow personalized medicine. Assessment of somatic and germline TP53 alterations has now reached the clinic and is required in several circumstances such as the identification of the most effective cancer therapy for patients with chronic lymphocytic leukemia (CLL). Here, we present Seshat, a Web service for annotating TP53 information derived from sequencing data. A flexible framework allows the use of standard file formats such as Mutation Annotation Format (MAF) or Variant Call Format (VCF), as well as common TXT files. Seshat performs accurate variant annotations using the Human Genome Variation Society (HGVS) nomenclature and the stable TP53 genomic reference provided by the Locus Reference Genomic (LRG). In addition, using the 2017 release of the UMD_TP53 database, Seshat provides multiple statistical information for each TP53 variant including database frequency, functional activity, or pathogenicity. The information is delivered in standardized output tables that minimize errors and facilitate comparison of mutational data across studies. Seshat is a beneficial tool to interpret the ever-growing TP53 sequencing data generated by multiple sequencing platforms and it is freely available via the TP53 Website, http://p53.fr or directly at http://vps338341.ovh.net/. © 2018 Wiley Periodicals, Inc.

Quantification of methionine and selenomethionine in biological samples using multiple reaction monitoring high performance liquid chromatography tandem mass spectrometry (MRM-HPLC-MS/MS).

PubMed

Vu, Dai Long; Ranglová, Karolína; Hájek, Jan; Hrouzek, Pavel

2018-05-01

Quantification of selenated amino-acids currently relies on methods employing inductively coupled plasma mass spectrometry (ICP-MS). Although very accurate, these methods do not allow the simultaneous determination of standard amino-acids, hampering the comparison of the content of selenated versus non-selenated species such as methionine (Met) and selenomethionine (SeMet). This paper reports two approaches for the simultaneous quantification of Met and SeMet. In the first approach, standard enzymatic hydrolysis employing Protease XIV was applied for the preparation of samples. The second approach utilized methanesulfonic acid (MA) for the hydrolysis of samples, either in a reflux system or in a microwave oven, followed by derivatization with diethyl ethoxymethylenemalonate. The prepared samples were then analyzed by multiple reaction monitoring high performance liquid chromatography tandem mass spectrometry (MRM-HPLC-MS/MS). Both approaches provided platforms for the accurate determination of selenium/sulfur substitution rate in Met. Moreover the second approach also provided accurate simultaneous quantification of Met and SeMet with a low limit of detection, low limit of quantification and wide linearity range, comparable to the commonly used gas chromatography mass spectrometry (GC-MS) method or ICP-MS. The novel method was validated using certified reference material in conjunction with the GC-MS reference method. Copyright © 2018. Published by Elsevier B.V.

Pathway to 2022: The Ongoing Modernization of the United States National Spatial Reference System

NASA Astrophysics Data System (ADS)

Stone, W. A.; Caccamise, D.

2017-12-01

The National Oceanic and Atmospheric Administration's National Geodetic Survey (NGS) mission is "to define, maintain and provide access to the National Spatial Reference System (NSRS) to meet our nation's economic, social, and environmental needs." The NSRS is an assemblage of geophysical and geodetic models, tools, and data, with the most-visible components being the North American Datum of 1983 (NAD83) and the North American Vertical Datum of 1988 (NAVD88), which together provide a consistent spatial reference framework for myriad geospatial applications and positioning requirements throughout the United States. The NGS is engaged in an ongoing and comprehensive multi-year project of modernizing the NSRS, a makeover necessitated by technological developments and user accuracy requirements, all with a goal of providing a modern, accurate, accessible, and globally aligned national positioning framework exploiting the substantial power and utility of the Global Navigation Satellite System - of both today and tomorrow. The modernized NSRS will include four new-generation geometric terrestrial reference frames (replacing NAD83) and a technically unprecedented geopotential datum (replacing NAVD88), all to be released in 2022 (anticipated). This poster/presentation will describe the justification for this modernization effort and will update the status and planned evolution of the NSRS as 2022 draws ever closer. Also discussed will be recent developments, including the publication of "blueprint" documents addressing technical details of various facets of the modernized NSRS and a continued series of public Geospatial Summits. Supporting/ancillary projects such as Gravity for the Redefinition of the American Vertical Datum (GRAV-D), which will result in the generation of a highly accurate gravimetric geoid - or definitional reference surface (zero elevation) - for the future geopotential datum, and Geoid Slope Validation Surveys (GSVS), which are exploring the achievable accuracy of the new geopotential datum, will be summarized. Also included will be suggestions of user preparation for transition to the NSRS of tomorrow.

Speckle interferometry using fiber optic phase stepping

NASA Technical Reports Server (NTRS)

Mercer, Carolyn R.; Beheim, Glenn

1989-01-01

A system employing closed-loop phase-stepping is used to measure the out-of-plane deformation of a diffusely reflecting object. Optical fibers are used to provide reference and object beam illumination for a standard two-beam speckle interferometer, providing set-up flexibility and ease of alignment. Piezoelectric fiber-stretchers and a phase-measurement/servo system are used to provide highly accurate phase steps. Intensity data is captured with a charge-injection-device camera, and is converted into a phase map using a desktop computer. The closed-loop phase-stepping system provides 90 deg phase steps which are accurate to 0.02 deg, greatly improving this system relative to open-loop interferometers. The system is demonstrated on a speckle interferometer, measuring the rigid-body translation of a diffusely reflecting object with an accuracy + or - 10 deg, or roughly + or - 15 nanometers. This accuracy is achieved without the use of a pneumatically mounted optics table.

A bill to amend title 13, United States Code, to provide for the more accurate and complete enumeration of certain overseas Americans in the decennial census, and for other purposes.

THOMAS, 112th Congress

Sen. Hatch, Orrin G. [R-UT

2011-03-30

Senate - 03/30/2011 Read twice and referred to the Committee on Homeland Security and Governmental Affairs. (All Actions) Tracker: This bill has the status IntroducedHere are the steps for Status of Legislation:

Impact of Dysphoria and Self-Consciousness on Perceptions of Social Competence: Test of the Depressive Realism Hypothesis

ERIC Educational Resources Information Center

Chau, Phuong M.; Milling, Leonard S.

2006-01-01

Depressive realism refers to a cognitive style wherein depressed people sometimes have more accurate perceptions of reality than nondepressed people. The notion of depressives being "sadder yet wiser" was controversial when first presented, and continues to be heavily debated. Self-perception studies provide maximum external validity,…

Benchmarking Attosecond Physics with Atomic Hydrogen

DTIC Science & Technology

2015-05-25

theoretical simulations are available in this regime. We provided accurate reference data on the photoionization yield and the CEP-dependent...this difficulty. This experiment claimed to show that, contrary to current understanding, the photoionization of an atomic electron is not an... photoion yield and transferrable intensity calibration. The dependence of photoionization probability on laser intensity is one of the most

An Interactive, Versatile, Three-Dimensional Display, Manipulation and Plotting System for Biomedical Research

ERIC Educational Resources Information Center

Feldmann, Richard J.; And Others

1972-01-01

Computer graphics provides a valuable tool for the representation and a better understanding of structures, both small and large. Accurate and rapid construction, manipulation, and plotting of structures, such as macromolecules as complex as hemoglobin, are performed by a collection of computer programs and a time-sharing computer. (21 references)…

Light detection and ranging (LIDAR): an emerging tool for multiple resource inventory.

Treesearch

Stephen E. Reutebuch; Hans-Erik Andersen; Robert J. McGaughey

2005-01-01

Airborne laser scanning of forests has been shown to provide accurate terrain models and, at the same time, estimates of multiple resource inventory variables through active sensing of three-dimensional (3D) forest vegetation. Brief overviews of airborne laser scanning technology [often referred to as "light detection and ranging" (LIDAR)] and research...

Bounded Linear Stability Analysis - A Time Delay Margin Estimation Approach for Adaptive Control

NASA Technical Reports Server (NTRS)

Nguyen, Nhan T.; Ishihara, Abraham K.; Krishnakumar, Kalmanje Srinlvas; Bakhtiari-Nejad, Maryam

2009-01-01

This paper presents a method for estimating time delay margin for model-reference adaptive control of systems with almost linear structured uncertainty. The bounded linear stability analysis method seeks to represent the conventional model-reference adaptive law by a locally bounded linear approximation within a small time window using the comparison lemma. The locally bounded linear approximation of the combined adaptive system is cast in a form of an input-time-delay differential equation over a small time window. The time delay margin of this system represents a local stability measure and is computed analytically by a matrix measure method, which provides a simple analytical technique for estimating an upper bound of time delay margin. Based on simulation results for a scalar model-reference adaptive control system, both the bounded linear stability method and the matrix measure method are seen to provide a reasonably accurate and yet not too conservative time delay margin estimation.

Using pseudoalignment and base quality to accurately quantify microbial community composition

PubMed Central

Novembre, John

2018-01-01

Pooled DNA from multiple unknown organisms arises in a variety of contexts, for example microbial samples from ecological or human health research. Determining the composition of pooled samples can be difficult, especially at the scale of modern sequencing data and reference databases. Here we propose a novel method for taxonomic profiling in pooled DNA that combines the speed and low-memory requirements of k-mer based pseudoalignment with a likelihood framework that uses base quality information to better resolve multiply mapped reads. We apply the method to the problem of classifying 16S rRNA reads using a reference database of known organisms, a common challenge in microbiome research. Using simulations, we show the method is accurate across a variety of read lengths, with different length reference sequences, at different sample depths, and when samples contain reads originating from organisms absent from the reference. We also assess performance in real 16S data, where we reanalyze previous genetic association data to show our method discovers a larger number of quantitative trait associations than other widely used methods. We implement our method in the software Karp, for k-mer based analysis of read pools, to provide a novel combination of speed and accuracy that is uniquely suited for enhancing discoveries in microbial studies. PMID:29659582

Skinfold reference curves and their use in predicting metabolic syndrome risk in children.

PubMed

Andaki, Alynne C R; Quadros, Teresa M B de; Gordia, Alex P; Mota, Jorge; Tinôco, Adelson L A; Mendes, Edmar L

To draw skinfold (SF) reference curves (subscapular, suprailiac, biceps, triceps) and to determine SF cutoff points for predicting the risk of metabolic syndrome (MetS) in children aged 6-10 years old. This was a cross-sectional study with a random sample of 1480 children aged 6-10 years old, 52.2% females, from public and private schools located in the urban and rural areas of the municipality of Uberaba (MG). Anthropometry, blood pressure, and fasting blood samples were taken at school, following specific protocols. The LMS method was used to draw the reference curves and ROC curve analysis to determine the accuracy and cutoff points for the evaluated skinfolds. The four SF evaluated (subscapular, suprailiac, biceps, and triceps) and their sum (∑4SF) were accurate in predicting MetS for both girls and boys. Additionally, cutoffs have been proposed and percentile curves (p5, p10, p25, p50, p75, p90, and p95) were outlined for the four SF and ∑4SF, for both genders. SF measurements were accurate in predicting metabolic syndrome in children aged 6-10 years old. Age- and gender-specific smoothed percentiles curves of SF provide a reference for the detection of risk for MetS in children. Copyright © 2017. Published by Elsevier Editora Ltda.

Identification of Reference Genes for Normalizing Quantitative Real-Time PCR in Urechis unicinctus

NASA Astrophysics Data System (ADS)

Bai, Yajiao; Zhou, Di; Wei, Maokai; Xie, Yueyang; Gao, Beibei; Qin, Zhenkui; Zhang, Zhifeng

2018-06-01

The reverse transcription quantitative real-time PCR (RT-qPCR) has become one of the most important techniques of studying gene expression. A set of valid reference genes are essential for the accurate normalization of data. In this study, five candidate genes were analyzed with geNorm, NormFinder, BestKeeper and ΔCt methods to identify the genes stably expressed in echiuran Urechis unicinctus, an important commercial marine benthic worm, under abiotic (sulfide stress) and normal (adult tissues, embryos and larvae at different development stages) conditions. The comprehensive results indicated that the expression of TBP was the most stable at sulfide stress and in developmental process, while the expression of EF- 1- α was the most stable at sulfide stress and in various tissues. TBP and EF- 1- α were recommended as a suitable reference gene combination to accurately normalize the expression of target genes at sulfide stress; and EF- 1- α, TBP and TUB were considered as a potential reference gene combination for normalizing the expression of target genes in different tissues. No suitable gene combination was obtained among these five candidate genes for normalizing the expression of target genes for developmental process of U. unicinctus. Our results provided a valuable support for quantifying gene expression using RT-qPCR in U. unicinctus.

Shortwave Radiometer Calibration Methods Comparison and Resulting Solar Irradiance Measurement Differences: A User Perspective

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

Habte, Aron; Sengupta, Manajit; Andreas, Afshin

Banks financing solar energy projects require assurance that these systems will produce the energy predicted. Furthermore, utility planners and grid system operators need to understand the impact of the variable solar resource on solar energy conversion system performance. Accurate solar radiation data sets reduce the expense associated with mitigating performance risk and assist in understanding the impacts of solar resource variability. The accuracy of solar radiation measured by radiometers depends on the instrument performance specification, installation method, calibration procedure, measurement conditions, maintenance practices, location, and environmental conditions. This study addresses the effect of different calibration methods provided by radiometric calibrationmore » service providers, such as NREL and manufacturers of radiometers, on the resulting calibration responsivity. Some of these radiometers are calibrated indoors and some outdoors. To establish or understand the differences in calibration methodology, we processed and analyzed field-measured data from these radiometers. This study investigates calibration responsivities provided by NREL's broadband outdoor radiometer calibration (BORCAL) and a few prominent manufacturers. The BORCAL method provides the outdoor calibration responsivity of pyranometers and pyrheliometers at 45 degree solar zenith angle, and as a function of solar zenith angle determined by clear-sky comparisons with reference irradiance. The BORCAL method also employs a thermal offset correction to the calibration responsivity of single-black thermopile detectors used in pyranometers. Indoor calibrations of radiometers by their manufacturers are performed using a stable artificial light source in a side-by-side comparison between the test radiometer under calibration and a reference radiometer of the same type. In both methods, the reference radiometer calibrations are traceable to the World Radiometric Reference (WRR). These different methods of calibration demonstrated +1% to +2% differences in solar irradiance measurement. Analyzing these differences will ultimately help determine the uncertainty of the field radiometer data and guide the development of a consensus standard for calibration. Further advancing procedures for precisely calibrating radiometers to world reference standards that reduce measurement uncertainty will allow more accurate prediction of solar output and improve the bankability of solar projects.« less

A convenient method for X-ray analysis in TEM that measures mass thickness and composition

NASA Astrophysics Data System (ADS)

Statham, P.; Sagar, J.; Holland, J.; Pinard, P.; Lozano-Perez, S.

2018-01-01

We consider a new approach for quantitative analysis in transmission electron microscopy (TEM) that offers the same convenience as single-standard quantitative analysis in scanning electron microscopy (SEM). Instead of a bulk standard, a thin film with known mass thickness is used as a reference. The procedure involves recording an X-ray spectrum from the reference film for each session of acquisitions on real specimens. There is no need to measure the beam current; the current only needs to be stable for the duration of the session. A new reference standard with a large (1 mm x 1 mm) area of uniform thickness of 100 nm silicon nitride is used to reveal regions of X-ray detector occlusion that would give misleading results for any X-ray method that measures thickness. Unlike previous methods, the new X-ray method does not require an accurate beam current monitor but delivers equivalent accuracy in mass thickness measurement. Quantitative compositional results are also automatically corrected for specimen self-absorption. The new method is tested using a wedge specimen of Inconel 600 that is used to calibrate the high angle angular dark field (HAADF) signal to provide a thickness reference and results are compared with electron energy-loss spectrometry (EELS) measurements. For the new X-ray method, element composition results are consistent with the expected composition for the alloy and the mass thickness measurement is shown to provide an accurate alternative to EELS for thickness determination in TEM without the uncertainty associated with mean free path estimates.

Mobile Applications for Women's Health and Midwifery Care: A Pocket Reference for the 21st Century.

PubMed

Arbour, Megan W; Stec, Melissa A

2018-05-01

Midwives and other women's health care providers are charged with providing high-quality care to women based on the most current available evidence. Quick, reliable, and accurate access to evidence-based information is essential. Numerous smartphone and mobile device applications (apps) are available to assist clinicians in providing care for women. This article discusses clinical reference apps, including those for evidence-based care guidelines, women's health care, pharmacologic reference, laboratory and diagnostic guides, as well as apps for information storage and management, electronic health records, and client education. Midwives and other clinicians are encouraged to thoughtfully integrate mobile apps into their clinical practices to improve client outcomes and clinician and client satisfaction. Although the thousands of health care apps that are available may seem daunting, this article highlights key apps that may help clinicians improve their care of women. By adding one app at a time, midwives and other women's health care providers can successfully integrate mobile apps into clinical practice. © 2018 by the American College of Nurse-Midwives.

Construction and application of a new dual-hybrid random phase approximation.

PubMed

Mezei, Pál D; Csonka, Gábor I; Ruzsinszky, Adrienn; Kállay, Mihály

2015-10-13

The direct random phase approximation (dRPA) combined with Kohn-Sham reference orbitals is among the most promising tools in computational chemistry and applicable in many areas of chemistry and physics. The reason for this is that it scales as N(4) with the system size, which is a considerable advantage over the accurate ab initio wave function methods like standard coupled-cluster. dRPA also yields a considerably more accurate description of thermodynamic and electronic properties than standard density-functional theory methods. It is also able to describe strong static electron correlation effects even in large systems with a small or vanishing band gap missed by common single-reference methods. However, dRPA has several flaws due to its self-correlation error. In order to obtain accurate and precise reaction energies, barriers and noncovalent intra- and intermolecular interactions, we construct a new dual-hybrid dRPA (hybridization of exact and semilocal exchange in both the energy and the orbitals) and test the performance of this new functional on isogyric, isodesmic, hypohomodesmotic, homodesmotic, and hyperhomodesmotic reaction classes. We also use a test set of 14 Diels-Alder reactions, six atomization energies (AE6), 38 hydrocarbon atomization energies, and 100 reaction barrier heights (DBH24, HT-BH38, and NHT-BH38). For noncovalent complexes, we use the NCCE31 and S22 test sets. To test the intramolecular interactions, we use a set of alkane, cysteine, phenylalanine-glycine-glycine tripeptide, and monosaccharide conformers. We also discuss the delocalization and static correlation errors. We show that a universally accurate description of chemical properties can be provided by a large, 75% exact exchange mixing both in the calculation of the reference orbitals and the final energy.

Monitoring for airborne allergens

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

Burge, H.A.

1992-07-01

Monitoring for allergens can provide some information on the kinds and levels of exposure experienced by local patient populations, providing volumetric methods are used for sample collection and analysis is accurate and consistent. Such data can also be used to develop standards for the specific environment and to begin to develop predictive models. Comparing outdoor allergen aerosols between different monitoring sites requires identical collection and analysis methods and some kind of rational standard, whether arbitrary, or based on recognized health effects.32 references.

Effects of spatial coherence in diffraction phase microscopy.

PubMed

Edwards, Chris; Bhaduri, Basanta; Nguyen, Tan; Griffin, Benjamin G; Pham, Hoa; Kim, Taewoo; Popescu, Gabriel; Goddard, Lynford L

2014-03-10

Quantitative phase imaging systems using white light illumination can exhibit lower noise figures than laser-based systems. However, they can also suffer from object-dependent artifacts, such as halos, which prevent accurate reconstruction of the surface topography. In this work, we show that white light diffraction phase microscopy using a standard halogen lamp can produce accurate height maps of even the most challenging structures provided that there is proper spatial filtering at: 1) the condenser to ensure adequate spatial coherence and 2) the output Fourier plane to produce a uniform reference beam. We explain that these object-dependent artifacts are a high-pass filtering phenomenon, establish design guidelines to reduce the artifacts, and then apply these guidelines to eliminate the halo effect. Since a spatially incoherent source requires significant spatial filtering, the irradiance is lower and proportionally longer exposure times are needed. To circumvent this tradeoff, we demonstrate that a supercontinuum laser, due to its high radiance, can provide accurate measurements with reduced exposure times, allowing for fast dynamic measurements.

LipidQC: Method Validation Tool for Visual Comparison to SRM 1950 Using NIST Interlaboratory Comparison Exercise Lipid Consensus Mean Estimate Values.

PubMed

Ulmer, Candice Z; Ragland, Jared M; Koelmel, Jeremy P; Heckert, Alan; Jones, Christina M; Garrett, Timothy J; Yost, Richard A; Bowden, John A

2017-12-19

As advances in analytical separation techniques, mass spectrometry instrumentation, and data processing platforms continue to spur growth in the lipidomics field, more structurally unique lipid species are detected and annotated. The lipidomics community is in need of benchmark reference values to assess the validity of various lipidomics workflows in providing accurate quantitative measurements across the diverse lipidome. LipidQC addresses the harmonization challenge in lipid quantitation by providing a semiautomated process, independent of analytical platform, for visual comparison of experimental results of National Institute of Standards and Technology Standard Reference Material (SRM) 1950, "Metabolites in Frozen Human Plasma", against benchmark consensus mean concentrations derived from the NIST Lipidomics Interlaboratory Comparison Exercise.

Muscle parameters estimation based on biplanar radiography.

PubMed

Dubois, G; Rouch, P; Bonneau, D; Gennisson, J L; Skalli, W

2016-11-01

The evaluation of muscle and joint forces in vivo is still a challenge. Musculo-Skeletal (musculo-skeletal) models are used to compute forces based on movement analysis. Most of them are built from a scaled-generic model based on cadaver measurements, which provides a low level of personalization, or from Magnetic Resonance Images, which provide a personalized model in lying position. This study proposed an original two steps method to access a subject-specific musculo-skeletal model in 30 min, which is based solely on biplanar X-Rays. First, the subject-specific 3D geometry of bones and skin envelopes were reconstructed from biplanar X-Rays radiography. Then, 2200 corresponding control points were identified between a reference model and the subject-specific X-Rays model. Finally, the shape of 21 lower limb muscles was estimated using a non-linear transformation between the control points in order to fit the muscle shape of the reference model to the X-Rays model. Twelfth musculo-skeletal models were reconstructed and compared to their reference. The muscle volume was not accurately estimated with a standard deviation (SD) ranging from 10 to 68%. However, this method provided an accurate estimation the muscle line of action with a SD of the length difference lower than 2% and a positioning error lower than 20 mm. The moment arm was also well estimated with SD lower than 15% for most muscle, which was significantly better than scaled-generic model for most muscle. This method open the way to a quick modeling method for gait analysis based on biplanar radiography.

Talbot-Lau x-ray deflectometry phase-retrieval methods for electron density diagnostics in high-energy density experiments.

PubMed

Valdivia, Maria Pia; Stutman, Dan; Stoeckl, Christian; Mileham, Chad; Begishev, Ildar A; Bromage, Jake; Regan, Sean P

2018-01-10

Talbot-Lau x-ray interferometry uses incoherent x-ray sources to measure refraction index changes in matter. These measurements can provide accurate electron density mapping through phase retrieval. An adaptation of the interferometer has been developed in order to meet the specific requirements of high-energy density experiments. This adaptation is known as a moiré deflectometer, which allows for single-shot capabilities in the form of interferometric fringe patterns. The moiré x-ray deflectometry technique requires a set of object and reference images in order to provide electron density maps, which can be costly in the high-energy density environment. In particular, synthetic reference phase images obtained ex situ through a phase-scan procedure, can provide a feasible solution. To test this procedure, an object phase map was retrieved from a single-shot moiré image obtained from a plasma-produced x-ray source. A reference phase map was then obtained from phase-stepping measurements using a continuous x-ray tube source in a small laboratory setting. The two phase maps were used to retrieve an electron density map. A comparison of the moiré and phase-stepping phase-retrieval methods was performed to evaluate single-exposure plasma electron density mapping for high-energy density and other transient plasma experiments. It was found that a combination of phase-retrieval methods can deliver accurate refraction angle mapping. Once x-ray backlighter quality is optimized, the ex situ method is expected to deliver electron density mapping with improved resolution. The steps necessary for improved diagnostic performance are discussed.

Surgical management of patients with primary brain tumors.

PubMed

Bohan, Eileen; Glass-Macenka, Deanna

2004-11-01

To provide an overview of the diagnostic work-up, intraoperative technologies, postoperative treatment options, and investigational new therapies in patients with malignant brain tumors. Published textbooks and articles and other reference materials. Recent improvements in diagnostic and surgical equipment have influenced outcomes and overall quality of life for patients with central nervous system tumors. The ability to more accurately target and more safely remove brain tumors has enhanced the postoperative period and decreased hospital stays. However, malignant neoplasms continue to be refractory to current treatments, necessitating innovative surgical approaches at the time of initial diagnosis and at tumor recurrence. Nurses with an understanding of current diagnostic and surgical treatment modalities for brain tumors are able to provide accurate patient education and comprehensive care, enhancing the overall hospital and outpatient experience.

Monthly AOD maps combining strengths of remote sensing products

NASA Astrophysics Data System (ADS)

Kinne, Stefan

2010-05-01

The mid-visible aerosol optical depth (AOD) is the most prominent property to quantify aerosol amount the atmospheric column. Almost all aerosol retrievals of satellite sensors provide estimates for this property, however, often with limited success. As sensors differ in capabilities individual retrievals have local and regional strengths and weaknesses. Focusing on individual retrieval strengths a satellite based AOD composite has been constructed. Hereby, every retrieval performance has been assessed in statistical comparisons to ground-based sun-photometry, which provide highly accurate references though only at few globally distributed monitoring sites. Based on these comparisons, which consider bias as well as spatial patterns and seasonality, the regionally best performing satellite AOD products are combined. The resulting remote sensing AOD composite provide a general reference for the spatial and temporal AOD distribution on an (almost) global basis - solely tied to sensor data.

A Simple Plasma Retinol Isotope Ratio Method for Estimating β-Carotene Relative Bioefficacy in Humans: Validation with the Use of Model-Based Compartmental Analysis.

PubMed

Ford, Jennifer Lynn; Green, Joanne Balmer; Lietz, Georg; Oxley, Anthony; Green, Michael H

2017-09-01

Background: Provitamin A carotenoids are an important source of dietary vitamin A for many populations. Thus, accurate and simple methods for estimating carotenoid bioefficacy are needed to evaluate the vitamin A value of test solutions and plant sources. β-Carotene bioefficacy is often estimated from the ratio of the areas under plasma isotope response curves after subjects ingest labeled β-carotene and a labeled retinyl acetate reference dose [isotope reference method (IRM)], but to our knowledge, the method has not yet been evaluated for accuracy. Objectives: Our objectives were to develop and test a physiologically based compartmental model that includes both absorptive and postabsorptive β-carotene bioconversion and to use the model to evaluate the accuracy of the IRM and a simple plasma retinol isotope ratio [(RIR), labeled β-carotene-derived retinol/labeled reference-dose-derived retinol in one plasma sample] for estimating relative bioefficacy. Methods: We used model-based compartmental analysis (Simulation, Analysis and Modeling software) to develop and apply a model that provided known values for β-carotene bioefficacy. Theoretical data for 10 subjects were generated by the model and used to determine bioefficacy by RIR and IRM; predictions were compared with known values. We also applied RIR and IRM to previously published data. Results: Plasma RIR accurately predicted β-carotene relative bioefficacy at 14 d or later. IRM also accurately predicted bioefficacy by 14 d, except that, when there was substantial postabsorptive bioconversion, IRM underestimated bioefficacy. Based on our model, 1-d predictions of relative bioefficacy include absorptive plus a portion of early postabsorptive conversion. Conclusion: The plasma RIR is a simple tracer method that accurately predicts β-carotene relative bioefficacy based on analysis of one blood sample obtained at ≥14 d after co-ingestion of labeled β-carotene and retinyl acetate. The method also provides information about the contributions of absorptive and postabsorptive conversion to total bioefficacy if an additional sample is taken at 1 d. © 2017 American Society for Nutrition.

Technology in nursing scholarship: use of citation reference managers.

PubMed

Smith, Cheryl M; Baker, Bradford

2007-06-01

Nurses, especially those in academia, feel the pressure to publish but have a limited time to write. One of the more time-consuming and frustrating tasks of research, and subsequent publications, is the collection and organization of accurate citations of sources of information. The purpose of this article is to discuss three types of citation reference managers (personal bibliographic software) and how their use can provide consistency and accuracy in recording all the information needed for the research and writing process. The advantages and disadvantages of three software programs, EndNote, Reference Manager, and ProCite, are discussed. These three software products have a variety of options that can be used in personal data management to assist researchers in becoming published authors.

Characterization of reference genes for qPCR analysis in various tissues of the Fujian oyster Crassostrea angulata

NASA Astrophysics Data System (ADS)

Pu, Fei; Yang, Bingye; Ke, Caihuan

2015-07-01

Accurate quantification of transcripts using quantitative real-time polymerase chain reaction (qPCR) depends on the identification of reliable reference genes for normalization. This study aimed to identify and validate seven reference genes, including actin-2 ( ACT-2), elongation factor 1 alpha ( EF-1α), elongation factor 1 beta ( EF-1β), glyceraldehyde-3-phosphate dehydrogenase ( GAPDH), ubiquitin ( UBQ), β-tubulin ( β-TUB), and 18S ribosomal RNA, from Crassostrea angulata, a valuable marine bivalve cultured worldwide. Transcript levels of the candidate reference genes were examined using qPCR analysis and showed differential expression patterns in the mantle, gill, adductor muscle, labial palp, visceral mass, hemolymph and gonad tissues. Quantitative data were analyzed using the geNorm software to assess the expression stability of the candidate reference genes, revealing that β-TUB and UBQ were the most stable genes. The commonly used GAPDH and 18S rRNA showed low stability, making them unsuitable candidates in this system. The expression pattern of the G protein β-subunit gene ( Gβ) across tissue types was also examined and normalized to the expression of each or both of UBQ and β-TUB as internal controls. This revealed consistent trends with all three normalization approaches, thus validating the reliability of UBQ and β-TUB as optimal internal controls. The study provides the first validated reference genes for accurate data normalization in transcript profiling in Crassostrea angulata, which will be indispensable for further functional genomics studies in this economically valuable marine bivalve.

Identification of reference genes for RT-qPCR analysis in peach genotypes with contrasting chilling requirements.

PubMed

Marini, N; Bevilacqua, C B; Büttow, M V; Raseira, M C B; Bonow, S

2017-05-25

Selecting and validating reference genes are the first steps in studying gene expression by reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR). The present study aimed to evaluate the stability of five reference genes for the purpose of normalization when studying gene expression in various cultivars of Prunus persica with different chilling requirements. Flower bud tissues of nine peach genotypes from Embrapa's peach breeding program with different chilling requirements were used, and five candidate reference genes based on the RT-qPCR that were useful for studying the relative quantitative gene expression and stability were evaluated using geNorm, NormFinder, and bestKeeper software packages. The results indicated that among the genes tested, the most stable genes to be used as reference genes are Act and UBQ10. This study is the first survey of the stability of reference genes in peaches under chilling stress and provides guidelines for more accurate RT-qPCR results.

Identification of "Known Unknowns" Utilizing Accurate Mass Data and ChemSpider

NASA Astrophysics Data System (ADS)

Little, James L.; Williams, Antony J.; Pshenichnov, Alexey; Tkachenko, Valery

2012-01-01

In many cases, an unknown to an investigator is actually known in the chemical literature, a reference database, or an internet resource. We refer to these types of compounds as "known unknowns." ChemSpider is a very valuable internet database of known compounds useful in the identification of these types of compounds in commercial, environmental, forensic, and natural product samples. The database contains over 26 million entries from hundreds of data sources and is provided as a free resource to the community. Accurate mass mass spectrometry data is used to query the database by either elemental composition or a monoisotopic mass. Searching by elemental composition is the preferred approach. However, it is often difficult to determine a unique elemental composition for compounds with molecular weights greater than 600 Da. In these cases, searching by the monoisotopic mass is advantageous. In either case, the search results are refined by sorting the number of references associated with each compound in descending order. This raises the most useful candidates to the top of the list for further evaluation. These approaches were shown to be successful in identifying "known unknowns" noted in our laboratory and for compounds of interest to others.

Hg0 and HgCl2 Reference Gas Standards: ?NIST Traceability ...

EPA Pesticide Factsheets

EPA and NIST have collaborated to establish the necessary procedures for establishing the required NIST traceability of commercially-provided Hg0 and HgCl2 reference generators. This presentation will discuss the approach of a joint EPA/NIST study to accurately quantify the true concentrations of Hg0 and HgCl2 reference gases produced from high quality, NIST-traceable, commercial Hg0 and HgCl2 generators. This presentation will also discuss the availability of HCl and Hg0 compressed reference gas standards as a result of EPA's recently approved Alternative Methods 114 and 118. Gaseous elemental mercury (Hg0) and oxidized mercury (HgCl2) reference standards are integral to the use of mercury continuous emissions monitoring systems (Hg CEMS) for regulatory compliance emissions monitoring. However, a quantitative disparity of approximately 7-10% has been observed between commercial Hg0 and HgCl2 reference gases which currently limits the use of (HgCl2) reference gas standards. Resolving this disparity would enable the expanded use of (HgCl2) reference gas standards for regulatory compliance purposes.

A Circular Dichroism Reference Database for Membrane Proteins

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

Wallace,B.; Wien, F.; Stone, T.

2006-01-01

Membrane proteins are a major product of most genomes and the target of a large number of current pharmaceuticals, yet little information exists on their structures because of the difficulty of crystallising them; hence for the most part they have been excluded from structural genomics programme targets. Furthermore, even methods such as circular dichroism (CD) spectroscopy which seek to define secondary structure have not been fully exploited because of technical limitations to their interpretation for membrane embedded proteins. Empirical analyses of circular dichroism (CD) spectra are valuable for providing information on secondary structures of proteins. However, the accuracy of themore » results depends on the appropriateness of the reference databases used in the analyses. Membrane proteins have different spectral characteristics than do soluble proteins as a result of the low dielectric constants of membrane bilayers relative to those of aqueous solutions (Chen & Wallace (1997) Biophys. Chem. 65:65-74). To date, no CD reference database exists exclusively for the analysis of membrane proteins, and hence empirical analyses based on current reference databases derived from soluble proteins are not adequate for accurate analyses of membrane protein secondary structures (Wallace et al (2003) Prot. Sci. 12:875-884). We have therefore created a new reference database of CD spectra of integral membrane proteins whose crystal structures have been determined. To date it contains more than 20 proteins, and spans the range of secondary structures from mostly helical to mostly sheet proteins. This reference database should enable more accurate secondary structure determinations of membrane embedded proteins and will become one of the reference database options in the CD calculation server DICHROWEB (Whitmore & Wallace (2004) NAR 32:W668-673).« less

Novel blood pressure and pulse pressure estimation based on pulse transit time and stroke volume approximation.

PubMed

Lee, Joonnyong; Sohn, JangJay; Park, Jonghyun; Yang, SeungMan; Lee, Saram; Kim, Hee Chan

2018-06-18

Non-invasive continuous blood pressure monitors are of great interest to the medical community due to their value in hypertension management. Recently, studies have shown the potential of pulse pressure as a therapeutic target for hypertension, but not enough attention has been given to non-invasive continuous monitoring of pulse pressure. Although accurate pulse pressure estimation can be of direct value to hypertension management and indirectly to the estimation of systolic blood pressure, as it is the sum of pulse pressure and diastolic blood pressure, only a few inadequate methods of pulse pressure estimation have been proposed. We present a novel, non-invasive blood pressure and pulse pressure estimation method based on pulse transit time and pre-ejection period. Pre-ejection period and pulse transit time were measured non-invasively using electrocardiogram, seismocardiogram, and photoplethysmogram measured from the torso. The proposed method used the 2-element Windkessel model to model pulse pressure with the ratio of stroke volume, approximated by pre-ejection period, and arterial compliance, estimated by pulse transit time. Diastolic blood pressure was estimated using pulse transit time, and systolic blood pressure was estimated as the sum of the two estimates. The estimation method was verified in 11 subjects in two separate conditions with induced cardiovascular response and the results were compared against a reference measurement and values obtained from a previously proposed method. The proposed method yielded high agreement with the reference (pulse pressure correlation with reference R ≥ 0.927, diastolic blood pressure correlation with reference R ≥ 0.854, systolic blood pressure correlation with reference R ≥ 0.914) and high estimation accuracy in pulse pressure (mean root-mean-squared error ≤ 3.46 mmHg) and blood pressure (mean root-mean-squared error ≤ 6.31 mmHg for diastolic blood pressure and ≤ 8.41 mmHg for systolic blood pressure) over a wide range of hemodynamic changes. The proposed pulse pressure estimation method provides accurate estimates in situations with and without significant changes in stroke volume. The proposed method improves upon the currently available systolic blood pressure estimation methods by providing accurate pulse pressure estimates.

Modified fast frequency acquisition via adaptive least squares algorithm

NASA Technical Reports Server (NTRS)

Kumar, Rajendra (Inventor)

1992-01-01

A method and the associated apparatus for estimating the amplitude, frequency, and phase of a signal of interest are presented. The method comprises the following steps: (1) inputting the signal of interest; (2) generating a reference signal with adjustable amplitude, frequency and phase at an output thereof; (3) mixing the signal of interest with the reference signal and a signal 90 deg out of phase with the reference signal to provide a pair of quadrature sample signals comprising respectively a difference between the signal of interest and the reference signal and a difference between the signal of interest and the signal 90 deg out of phase with the reference signal; (4) using the pair of quadrature sample signals to compute estimates of the amplitude, frequency, and phase of an error signal comprising the difference between the signal of interest and the reference signal employing a least squares estimation; (5) adjusting the amplitude, frequency, and phase of the reference signal from the numerically controlled oscillator in a manner which drives the error signal towards zero; and (6) outputting the estimates of the amplitude, frequency, and phase of the error signal in combination with the reference signal to produce a best estimate of the amplitude, frequency, and phase of the signal of interest. The preferred method includes the step of providing the error signal as a real time confidence measure as to the accuracy of the estimates wherein the closer the error signal is to zero, the higher the probability that the estimates are accurate. A matrix in the estimation algorithm provides an estimate of the variance of the estimation error.

GPS inferred geocentric reference frame for satellite positioning and navigation

NASA Technical Reports Server (NTRS)

Malla, Rajendra P.; Wu, Sien-Chong

1989-01-01

Accurate geocentric three-dimensional positioning is of great importance for various geodetic and oceanographic applications. While relative positioning accuracy of a few centimeters has become a reality using Very Long Baseline Interferometry (VLBI), the uncertainty in the offset of the adopted coordinate system origin from the geocenter is still believed to be of the order of one meter. Satellite Laser Ranging (SLR) is capable of determining this offset to better than 10 cm, though, because of the limited number of satellites, this requires a long arc of data. The Global Positioning System (GPS) measurements provide a powerful alternative for an accurate determination of this origin offset in relatively short period of time. Two strategies are discussed, the first utilizes the precise relative positions predetermined by VLBI, whereas the second establishes a reference frame by holding only one of the tracking sites longitude fixed. Covariance analysis studies indicate that geocentric positioning to an accuracy of a few centimeters can be achieved with just one day of precise GPS pseudorange and carrier phase data.

Superior cognitive mapping through single landmark-related learning than through boundary-related learning.

PubMed

Zhou, Ruojing; Mou, Weimin

2016-08-01

Cognitive mapping is assumed to be through hippocampus-dependent place learning rather than striatum-dependent response learning. However, we proposed that either type of spatial learning, as long as it involves encoding metric relations between locations and reference points, could lead to a cognitive map. Furthermore, the fewer reference points to specify individual locations, the more accurate a cognitive map of these locations will be. We demonstrated that participants have more accurate representations of vectors between 2 locations and of configurations among 3 locations when locations are individually encoded in terms of a single landmark than when locations are encoded in terms of a boundary. Previous findings have shown that learning locations relative to a boundary involve stronger place learning and higher hippocampal activation whereas learning relative to a single landmark involves stronger response learning and higher striatal activation. Recognizing this, we have provided evidence challenging the cognitive map theory but favoring our proposal. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Validation of a T1 and T2* leakage correction method based on multi-echo DSC-MRI using MION as a reference standard

PubMed Central

Stokes, Ashley M.; Semmineh, Natenael; Quarles, C. Chad

2015-01-01

Purpose A combined biophysical- and pharmacokinetic-based method is proposed to separate, quantify, and correct for both T1 and T2* leakage effects using dual-echo DSC acquisitions to provide more accurate hemodynamic measures, as validated by a reference intravascular contrast agent (CA). Methods Dual-echo DSC-MRI data were acquired in two rodent glioma models. The T1 leakage effects were removed and also quantified in order to subsequently correct for the remaining T2* leakage effects. Pharmacokinetic, biophysical, and combined biophysical and pharmacokinetic models were used to obtain corrected cerebral blood volume (CBV) and cerebral blood flow (CBF), and these were compared with CBV and CBF from an intravascular CA. Results T1-corrected CBV was significantly overestimated compared to MION CBV, while T1+T2*-correction yielded CBV values closer to the reference values. The pharmacokinetic and simplified biophysical methods showed similar results and underestimated CBV in tumors exhibiting strong T2* leakage effects. The combined method was effective for correcting T1 and T2* leakage effects across tumor types. Conclusions Correcting for both T1 and T2* leakage effects yielded more accurate measures of CBV. The combined correction method yields more reliable CBV measures than either correction method alone, but for certain brain tumor types (e.g., gliomas) the simplified biophysical method may provide a robust and computationally efficient alternative. PMID:26362714

Reverse transcription quantitative real-time polymerase chain reaction reference genes in the spared nerve injury model of neuropathic pain: validation and literature search.

PubMed

Piller, Nicolas; Decosterd, Isabelle; Suter, Marc R

2013-07-10

The reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) is a widely used, highly sensitive laboratory technique to rapidly and easily detect, identify and quantify gene expression. Reliable RT-qPCR data necessitates accurate normalization with validated control genes (reference genes) whose expression is constant in all studied conditions. This stability has to be demonstrated.We performed a literature search for studies using quantitative or semi-quantitative PCR in the rat spared nerve injury (SNI) model of neuropathic pain to verify whether any reference genes had previously been validated. We then analyzed the stability over time of 7 commonly used reference genes in the nervous system - specifically in the spinal cord dorsal horn and the dorsal root ganglion (DRG). These were: Actin beta (Actb), Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), ribosomal proteins 18S (18S), L13a (RPL13a) and L29 (RPL29), hypoxanthine phosphoribosyltransferase 1 (HPRT1) and hydroxymethylbilane synthase (HMBS). We compared the candidate genes and established a stability ranking using the geNorm algorithm. Finally, we assessed the number of reference genes necessary for accurate normalization in this neuropathic pain model. We found GAPDH, HMBS, Actb, HPRT1 and 18S cited as reference genes in literature on studies using the SNI model. Only HPRT1 and 18S had been once previously demonstrated as stable in RT-qPCR arrays. All the genes tested in this study, using the geNorm algorithm, presented gene stability values (M-value) acceptable enough for them to qualify as potential reference genes in both DRG and spinal cord. Using the coefficient of variation, 18S failed the 50% cut-off with a value of 61% in the DRG. The two most stable genes in the dorsal horn were RPL29 and RPL13a; in the DRG they were HPRT1 and Actb. Using a 0.15 cut-off for pairwise variations we found that any pair of stable reference gene was sufficient for the normalization process. In the rat SNI model, we validated and ranked Actb, RPL29, RPL13a, HMBS, GAPDH, HPRT1 and 18S as good reference genes in the spinal cord. In the DRG, 18S did not fulfill stability criteria. The combination of any two stable reference genes was sufficient to provide an accurate normalization.

Accurate reconstruction of 3D cardiac geometry from coarsely-sliced MRI.

PubMed

Ringenberg, Jordan; Deo, Makarand; Devabhaktuni, Vijay; Berenfeld, Omer; Snyder, Brett; Boyers, Pamela; Gold, Jeffrey

2014-02-01

We present a comprehensive validation analysis to assess the geometric impact of using coarsely-sliced short-axis images to reconstruct patient-specific cardiac geometry. The methods utilize high-resolution diffusion tensor MRI (DTMRI) datasets as reference geometries from which synthesized coarsely-sliced datasets simulating in vivo MRI were produced. 3D models are reconstructed from the coarse data using variational implicit surfaces through a commonly used modeling tool, CardioViz3D. The resulting geometries were then compared to the reference DTMRI models from which they were derived to analyze how well the synthesized geometries approximate the reference anatomy. Averaged over seven hearts, 95% spatial overlap, less than 3% volume variability, and normal-to-surface distance of 0.32 mm was observed between the synthesized myocardial geometries reconstructed from 8 mm sliced images and the reference data. The results provide strong supportive evidence to validate the hypothesis that coarsely-sliced MRI may be used to accurately reconstruct geometric ventricular models. Furthermore, the use of DTMRI for validation of in vivo MRI presents a novel benchmark procedure for studies which aim to substantiate their modeling and simulation methods using coarsely-sliced cardiac data. In addition, the paper outlines a suggested original procedure for deriving image-based ventricular models using the CardioViz3D software. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Getting DNA copy numbers without control samples

PubMed Central

2012-01-01

Background The selection of the reference to scale the data in a copy number analysis has paramount importance to achieve accurate estimates. Usually this reference is generated using control samples included in the study. However, these control samples are not always available and in these cases, an artificial reference must be created. A proper generation of this signal is crucial in terms of both noise and bias. We propose NSA (Normality Search Algorithm), a scaling method that works with and without control samples. It is based on the assumption that genomic regions enriched in SNPs with identical copy numbers in both alleles are likely to be normal. These normal regions are predicted for each sample individually and used to calculate the final reference signal. NSA can be applied to any CN data regardless the microarray technology and preprocessing method. It also finds an optimal weighting of the samples minimizing possible batch effects. Results Five human datasets (a subset of HapMap samples, Glioblastoma Multiforme (GBM), Ovarian, Prostate and Lung Cancer experiments) have been analyzed. It is shown that using only tumoral samples, NSA is able to remove the bias in the copy number estimation, to reduce the noise and therefore, to increase the ability to detect copy number aberrations (CNAs). These improvements allow NSA to also detect recurrent aberrations more accurately than other state of the art methods. Conclusions NSA provides a robust and accurate reference for scaling probe signals data to CN values without the need of control samples. It minimizes the problems of bias, noise and batch effects in the estimation of CNs. Therefore, NSA scaling approach helps to better detect recurrent CNAs than current methods. The automatic selection of references makes it useful to perform bulk analysis of many GEO or ArrayExpress experiments without the need of developing a parser to find the normal samples or possible batches within the data. The method is available in the open-source R package NSA, which is an add-on to the aroma.cn framework. http://www.aroma-project.org/addons. PMID:22898240

Getting DNA copy numbers without control samples.

PubMed

Ortiz-Estevez, Maria; Aramburu, Ander; Rubio, Angel

2012-08-16

The selection of the reference to scale the data in a copy number analysis has paramount importance to achieve accurate estimates. Usually this reference is generated using control samples included in the study. However, these control samples are not always available and in these cases, an artificial reference must be created. A proper generation of this signal is crucial in terms of both noise and bias.We propose NSA (Normality Search Algorithm), a scaling method that works with and without control samples. It is based on the assumption that genomic regions enriched in SNPs with identical copy numbers in both alleles are likely to be normal. These normal regions are predicted for each sample individually and used to calculate the final reference signal. NSA can be applied to any CN data regardless the microarray technology and preprocessing method. It also finds an optimal weighting of the samples minimizing possible batch effects. Five human datasets (a subset of HapMap samples, Glioblastoma Multiforme (GBM), Ovarian, Prostate and Lung Cancer experiments) have been analyzed. It is shown that using only tumoral samples, NSA is able to remove the bias in the copy number estimation, to reduce the noise and therefore, to increase the ability to detect copy number aberrations (CNAs). These improvements allow NSA to also detect recurrent aberrations more accurately than other state of the art methods. NSA provides a robust and accurate reference for scaling probe signals data to CN values without the need of control samples. It minimizes the problems of bias, noise and batch effects in the estimation of CNs. Therefore, NSA scaling approach helps to better detect recurrent CNAs than current methods. The automatic selection of references makes it useful to perform bulk analysis of many GEO or ArrayExpress experiments without the need of developing a parser to find the normal samples or possible batches within the data. The method is available in the open-source R package NSA, which is an add-on to the aroma.cn framework. http://www.aroma-project.org/addons.

Validation of reference genes for quantitative gene expression analysis in experimental epilepsy.

PubMed

Sadangi, Chinmaya; Rosenow, Felix; Norwood, Braxton A

2017-12-01

To grasp the molecular mechanisms and pathophysiology underlying epilepsy development (epileptogenesis) and epilepsy itself, it is important to understand the gene expression changes that occur during these phases. Quantitative real-time polymerase chain reaction (qPCR) is a technique that rapidly and accurately determines gene expression changes. It is crucial, however, that stable reference genes are selected for each experimental condition to ensure that accurate values are obtained for genes of interest. If reference genes are unstably expressed, this can lead to inaccurate data and erroneous conclusions. To date, epilepsy studies have used mostly single, nonvalidated reference genes. This is the first study to systematically evaluate reference genes in male Sprague-Dawley rat models of epilepsy. We assessed 15 potential reference genes in hippocampal tissue obtained from 2 different models during epileptogenesis, 1 model during chronic epilepsy, and a model of noninjurious seizures. Reference gene ranking varied between models and also differed between epileptogenesis and chronic epilepsy time points. There was also some variance between the four mathematical models used to rank reference genes. Notably, we found novel reference genes to be more stably expressed than those most often used in experimental epilepsy studies. The consequence of these findings is that reference genes suitable for one epilepsy model may not be appropriate for others and that reference genes can change over time. It is, therefore, critically important to validate potential reference genes before using them as normalizing factors in expression analysis in order to ensure accurate, valid results. © 2017 Wiley Periodicals, Inc.

QuickBird and OrbView-3 Geopositional Accuracy Assessment

NASA Technical Reports Server (NTRS)

Helder, Dennis; Ross, Kenton

2006-01-01

Objective: Compare vendor-provided image coordinates with known references visible in the imagery. Approach: Use multiple, well-characterized sites with >40 ground control points (GCPs); sites that are a) Well distributed; b) Accurately surveyed; and c) Easily found in imagery. Perform independent assessments with independent teams. Each team has slightly different measurement techniques and data processing methods. NASA Stennis Space Center. South Dakota State University.

Rapid Bacterial Whole-Genome Sequencing to Enhance Diagnostic and Public Health Microbiology

PubMed Central

Reuter, Sandra; Ellington, Matthew J.; Cartwright, Edward J. P.; Köser, Claudio U.; Török, M. Estée; Gouliouris, Theodore; Harris, Simon R.; Brown, Nicholas M.; Holden, Matthew T. G.; Quail, Mike; Parkhill, Julian; Smith, Geoffrey P.; Bentley, Stephen D.; Peacock, Sharon J.

2014-01-01

IMPORTANCE The latest generation of benchtop DNA sequencing platforms can provide an accurate whole-genome sequence (WGS) for a broad range of bacteria in less than a day. These could be used to more effectively contain the spread of multidrug-resistant pathogens. OBJECTIVE To compare WGS with standard clinical microbiology practice for the investigation of nosocomial outbreaks caused by multidrug-resistant bacteria, the identification of genetic determinants of antimicrobial resistance, and typing of other clinically important pathogens. DESIGN, SETTING, AND PARTICIPANTS A laboratory-based study of hospital inpatients with a range of bacterial infections at Cambridge University Hospitals NHS Foundation Trust, a secondary and tertiary referral center in England, comparing WGS with standard diagnostic microbiology using stored bacterial isolates and clinical information. MAIN OUTCOMES AND MEASURES Specimens were taken and processed as part of routine clinical care, and cultured isolates stored and referred for additional reference laboratory testing as necessary. Isolates underwent DNA extraction and library preparation prior to sequencing on the Illumina MiSeq platform. Bioinformatic analyses were performed by persons blinded to the clinical, epidemiologic, and antimicrobial susceptibility data. RESULTS We investigated 2 putative nosocomial outbreaks, one caused by vancomycin-resistant Enterococcus faecium and the other by carbapenem-resistant Enterobacter cloacae; WGS accurately discriminated between outbreak and nonoutbreak isolates and was superior to conventional typing methods. We compared WGS with standard methods for the identification of the mechanism of carbapenem resistance in a range of gram-negative bacteria (Acinetobacter baumannii, E cloacae, Escherichia coli, and Klebsiella pneumoniae). This demonstrated concordance between phenotypic and genotypic results, and the ability to determine whether resistance was attributable to the presence of carbapenemases or other resistance mechanisms. Whole-genome sequencing was used to recapitulate reference laboratory typing of clinical isolates of Neisseria meningitidis and to provide extended phylogenetic analyses of these. CONCLUSIONS AND RELEVANCE The speed, accuracy, and depth of information provided by WGS platforms to confirm or refute outbreaks in hospitals and the community, and to accurately define transmission of multidrug-resistant and other organisms, represents an important advance. PMID:23857503

Reference Intervals of Alpha-Fetoprotein and Carcinoembryonic Antigen in the Apparently Healthy Population.

PubMed

Zhang, Gao-Ming; Guo, Xu-Xiao; Ma, Xiao-Bo; Zhang, Guo-Ming

2016-12-12

BACKGROUND The aim of this study was to calculate 95% reference intervals and double-sided limits of serum alpha-fetoprotein (AFP) and carcinoembryonic antigen (CEA) according to the CLSI EP28-A3 guideline. MATERIAL AND METHODS Serum AFP and CEA values were measured in samples from 26 000 healthy subjects in the Shuyang area receiving general health checkups. The 95% reference intervals and upper limits were calculated by using MedCalc. RESULTS We provided continuous reference intervals from 20 years old to 90 years old for AFP and CEA. The reference intervals were: AFP, 1.31-7.89 ng/ml (males) and 1.01-7.10 ng/ml (females); CEA, 0.51-4.86 ng/ml (males) and 0.35-3.45ng/ml (females). AFP and CEA were significantly positively correlated with age in both males (r=0.196 and r=0.198) and females (r=0.121 and r=0.197). CONCLUSIONS Different races or populations and different detection systems may result in different reference intervals for AFP and CEA. Continuous reference intervals of age changes are more accurate than age groups.

National Athletic Trainers' Association Position Statement: Anabolic-Androgenic Steroids

PubMed Central

Kersey, Robert D.; Elliot, Diane L.; Goldberg, Linn; Kanayama, Gen; Leone, James E.; Pavlovich, Mike; Pope, Harrison G.

2012-01-01

This NATA position statement was developed by the NATA Research & Education Foundation. Objective This manuscript summarizes the best available scholarly evidence related to anabolic-androgenic steroids (AAS) as a reference for health care professionals, including athletic trainers, educators, and interested others. Background Health care professionals associated with sports or exercise should understand and be prepared to educate others about AAS. These synthetic, testosterone-based derivatives are widely abused by athletes and nonathletes to gain athletic performance advantages, develop their physiques, and improve their body image. Although AAS can be ergogenic, their abuse may lead to numerous negative health effects. Recommendations Abusers of AAS often rely on questionable information sources. Sports medicine professionals can therefore serve an important role by providing accurate, reliable information. The recommendations provide health care professionals with a current and accurate synopsis of the AAS-related research. PMID:23068595

MALDI-TOF MS versus VITEK 2 ANC card for identification of anaerobic bacteria.

PubMed

Li, Yang; Gu, Bing; Liu, Genyan; Xia, Wenying; Fan, Kun; Mei, Yaning; Huang, Peijun; Pan, Shiyang

2014-05-01

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is an accurate, rapid and inexpensive technique that has initiated a revolution in the clinical microbiology laboratory for identification of pathogens. The Vitek 2 anaerobe and Corynebacterium (ANC) identification card is a newly developed method for identification of corynebacteria and anaerobic species. The aim of this study was to evaluate the effectiveness of the ANC card and MALDI-TOF MS techniques for identification of clinical anaerobic isolates. Five reference strains and a total of 50 anaerobic bacteria clinical isolates comprising ten different genera and 14 species were identified and analyzed by the ANC card together with Vitek 2 identification system and Vitek MS together with version 2.0 database respectively. 16S rRNA gene sequencing was used as reference method for accuracy in the identification. Vitek 2 ANC card and Vitek MS provided comparable results at species level for the five reference strains. Of 50 clinical strains, the Vitek MS provided identification for 46 strains (92%) to the species level, 47 (94%) to genus level, one (2%) low discrimination, two (4%) no identification and one (2%) misidentification. The Vitek 2 ANC card provided identification for 43 strains (86%) correct to the species level, 47 (94%) correct to the genus level, three (6%) low discrimination, three (6%) no identification and one (2%) misidentification. Both Vitek MS and Vitek 2 ANC card can be used for accurate routine clinical anaerobe identification. Comparing to the Vitek 2 ANC card, Vitek MS is easier, faster and more economic for each test. The databases currently available for both systems should be updated and further developed to enhance performance.

Subsidence at the Fairport Harbor Water Level Gauge

NASA Astrophysics Data System (ADS)

Conner, D. A.

2014-12-01

SUBSIDENCE AT THE FAIRPORT HARBOR WATER LEVEL GAUGE I will provide information on methods being used to monitor Lake Erie water levels and earth movement at Fairport Harbor, Ohio. Glacial Isostatic Adjustment (GIA) is responsible for vertical movement throughout the Great Lakes region. Fairport Harbor is also experiencing vertical movement due to salt mining, so the nearby water level gauge operated by the National Oceanic and Atmospheric Administration (NOAA) is affected by both GIA and mining. NOAA's National Geodetic Survey (NGS) defines and maintains the National Spatial Reference System (NSRS). The NSRS includes a network of permanently marked points; a consistent, accurate, and up-to-date national shoreline; a network of Continuously Operating Reference Stations (CORS) which supports three-dimensional positioning activities; and a set of accurate models describing dynamic, geophysical processes that affect spatial measurements. The NSRS provides the spatial reference foundation for transportation, mapping, charting and a multitude of scientific and engineering applications. Fundamental elements of geodetic infrastructure include GPS CORS (3-D), water level and tide gauges (height) and a system of vertical bench marks (height). When two or more of these elements converge they may provide an independent determination of position and vertical stability as is the case here at the Fairport Harbor water level gauge. Analysis of GPS, leveling and water level data reveal that this gauge is subsiding at about 2-3 mm/year, independent of the effects of GIA. Analysis of data from the nearby OHLA GPS CORS shows it subsiding at about 4 mm/yr, four times faster than expected due to GIA alone. A long history of salt mine activity in the area is known to geologists but it came as a surprise to other scientists.

Modeling and Implementation of Multi-Position Non-Continuous Rotation Gyroscope North Finder.

PubMed

Luo, Jun; Wang, Zhiqian; Shen, Chengwu; Kuijper, Arjan; Wen, Zhuoman; Liu, Shaojin

2016-09-20

Even when the Global Positioning System (GPS) signal is blocked, a rate gyroscope (gyro) north finder is capable of providing the required azimuth reference information to a certain extent. In order to measure the azimuth between the observer and the north direction very accurately, we propose a multi-position non-continuous rotation gyro north finding scheme. Our new generalized mathematical model analyzes the elements that affect the azimuth measurement precision and can thus provide high precision azimuth reference information. Based on the gyro's principle of detecting a projection of the earth rotation rate on its sensitive axis and the proposed north finding scheme, we are able to deduct an accurate mathematical model of the gyro outputs against azimuth with the gyro and shaft misalignments. Combining the gyro outputs model and the theory of propagation of uncertainty, some approaches to optimize north finding are provided, including reducing the gyro bias error, constraining the gyro random error, increasing the number of rotation points, improving rotation angle measurement precision, decreasing the gyro and the shaft misalignment angles. According them, a north finder setup is built and the azimuth uncertainty of 18" is obtained. This paper provides systematic theory for analyzing the details of the gyro north finder scheme from simulation to implementation. The proposed theory can guide both applied researchers in academia and advanced practitioners in industry for designing high precision robust north finder based on different types of rate gyroscopes.

A global dataset of crowdsourced land cover and land use reference data.

PubMed

Fritz, Steffen; See, Linda; Perger, Christoph; McCallum, Ian; Schill, Christian; Schepaschenko, Dmitry; Duerauer, Martina; Karner, Mathias; Dresel, Christopher; Laso-Bayas, Juan-Carlos; Lesiv, Myroslava; Moorthy, Inian; Salk, Carl F; Danylo, Olha; Sturn, Tobias; Albrecht, Franziska; You, Liangzhi; Kraxner, Florian; Obersteiner, Michael

2017-06-13

Global land cover is an essential climate variable and a key biophysical driver for earth system models. While remote sensing technology, particularly satellites, have played a key role in providing land cover datasets, large discrepancies have been noted among the available products. Global land use is typically more difficult to map and in many cases cannot be remotely sensed. In-situ or ground-based data and high resolution imagery are thus an important requirement for producing accurate land cover and land use datasets and this is precisely what is lacking. Here we describe the global land cover and land use reference data derived from the Geo-Wiki crowdsourcing platform via four campaigns. These global datasets provide information on human impact, land cover disagreement, wilderness and land cover and land use. Hence, they are relevant for the scientific community that requires reference data for global satellite-derived products, as well as those interested in monitoring global terrestrial ecosystems in general.

A global dataset of crowdsourced land cover and land use reference data

PubMed Central

Fritz, Steffen; See, Linda; Perger, Christoph; McCallum, Ian; Schill, Christian; Schepaschenko, Dmitry; Duerauer, Martina; Karner, Mathias; Dresel, Christopher; Laso-Bayas, Juan-Carlos; Lesiv, Myroslava; Moorthy, Inian; Salk, Carl F.; Danylo, Olha; Sturn, Tobias; Albrecht, Franziska; You, Liangzhi; Kraxner, Florian; Obersteiner, Michael

2017-01-01

Global land cover is an essential climate variable and a key biophysical driver for earth system models. While remote sensing technology, particularly satellites, have played a key role in providing land cover datasets, large discrepancies have been noted among the available products. Global land use is typically more difficult to map and in many cases cannot be remotely sensed. In-situ or ground-based data and high resolution imagery are thus an important requirement for producing accurate land cover and land use datasets and this is precisely what is lacking. Here we describe the global land cover and land use reference data derived from the Geo-Wiki crowdsourcing platform via four campaigns. These global datasets provide information on human impact, land cover disagreement, wilderness and land cover and land use. Hence, they are relevant for the scientific community that requires reference data for global satellite-derived products, as well as those interested in monitoring global terrestrial ecosystems in general. PMID:28608851

SENIORLAB: a prospective observational study investigating laboratory parameters and their reference intervals in the elderly.

PubMed

Risch, Martin; Nydegger, Urs; Risch, Lorenz

2017-01-01

In clinical practice, laboratory results are often important for making diagnostic, therapeutic, and prognostic decisions. Interpreting individual results relies on accurate reference intervals and decision limits. Despite the considerable amount of resources in clinical medicine spent on elderly patients, accurate reference intervals for the elderly are rarely available. The SENIORLAB study set out to determine reference intervals in the elderly by investigating a large variety of laboratory parameters in clinical chemistry, hematology, and immunology. The SENIORLAB study is an observational, prospective cohort study. Subjectively healthy residents of Switzerland aged 60 years and older were included for baseline examination (n = 1467), where anthropometric measurements were taken, medical history was reviewed, and a fasting blood sample was drawn under optimal preanalytical conditions. More than 110 laboratory parameters were measured, and a biobank was set up. The study participants are followed up every 3 to 5 years for quality of life, morbidity, and mortality. The primary aim is to evaluate different laboratory parameters at age-related reference intervals. The secondary aims of this study include the following: identify associations between different parameters, identify diagnostic characteristics to diagnose different circumstances, identify the prevalence of occult disease in subjectively healthy individuals, and identify the prognostic factors for the investigated outcomes, including mortality. To obtain better grounds to justify clinical decisions, specific reference intervals for laboratory parameters of the elderly are needed. Reference intervals are obtained from healthy individuals. A major obstacle when obtaining reference intervals in the elderly is the definition of health in seniors because individuals without any medical condition and any medication are rare in older adulthood. Reference intervals obtained from such individuals cannot be considered representative for seniors in a status of age-specific normal health. In addition to the established methods for determining reference intervals, this longitudinal study utilizes a unique approach, in that survival and long-term well-being are taken as indicators of health in seniors. This approach is expected to provide robust and representative reference intervals that are obtained from an adequate reference population and not a collective of highly selected individuals. The present study was registered under International Standard Randomized Controlled Trial Number registry: ISRCTN53778569.

Reference Gauging System for a Small-Scale Liquid Hydrogen Tank

NASA Technical Reports Server (NTRS)

VanDresar, Neil T.; Siegwarth, James D.

2003-01-01

A system to accurately weigh the fluid contents of a small-scale liquid hydrogen test tank has been experimentally verified. It is intended for use as a reference or benchmark system when testing lowgravity liquid quantity gauging concepts in the terrestrial environment. The reference gauging system has shown a repeatable measurement accuracy of better than 0.5 percent of the full tank liquid weight. With further refinement, the system accuracy can be improved to within 0.10 percent of full scale. This report describes the weighing system design, calibration, and operational results. Suggestions are given for further refinement of the system. An example is given to illustrate additional sources of uncertainty when mass measurements are converted to volume equivalents. Specifications of the companion test tank and its multi-layer insulation system are provided.

Small-Grid Dithers for the JWST Coronagraphs

NASA Technical Reports Server (NTRS)

Lajoie, Charles-Philippe; Soummer, Remi; Pueyo, Laurent; Hines, Dean C.; Nelan, Edmund P.; Perrin, Marshall; Clampin, Mark; Isaacs, John C.

2016-01-01

We discuss new results of coronagraphic simulations demonstrating a novel mode for JWST that utilizes sub-pixel dithered reference images, called Small-Grid Dithers, to optimize coronagraphic PSF subtraction. These sub-pixel dithers are executed with the Fine Steering Mirror under fine guidance, are accurate to approx.2-3 milliarcseconds (1-s/axis), and provide ample speckle diversity to reconstruct an optimized synthetic reference PSF using LOCI or KLIP. We also discuss the performance gains of Small-Grid Dithers compared to the standard undithered scenario, and show potential contrast gain factors for the NIRCam and MIRI coronagraphs ranging from 2 to more than 10, respectively.

Indexed variation graphs for efficient and accurate resistome profiling.

PubMed

Rowe, Will P M; Winn, Martyn D

2018-05-14

Antimicrobial resistance remains a major threat to global health. Profiling the collective antimicrobial resistance genes within a metagenome (the "resistome") facilitates greater understanding of antimicrobial resistance gene diversity and dynamics. In turn, this can allow for gene surveillance, individualised treatment of bacterial infections and more sustainable use of antimicrobials. However, resistome profiling can be complicated by high similarity between reference genes, as well as the sheer volume of sequencing data and the complexity of analysis workflows. We have developed an efficient and accurate method for resistome profiling that addresses these complications and improves upon currently available tools. Our method combines a variation graph representation of gene sets with an LSH Forest indexing scheme to allow for fast classification of metagenomic sequence reads using similarity-search queries. Subsequent hierarchical local alignment of classified reads against graph traversals enables accurate reconstruction of full-length gene sequences using a scoring scheme. We provide our implementation, GROOT, and show it to be both faster and more accurate than a current reference-dependent tool for resistome profiling. GROOT runs on a laptop and can process a typical 2 gigabyte metagenome in 2 minutes using a single CPU. Our method is not restricted to resistome profiling and has the potential to improve current metagenomic workflows. GROOT is written in Go and is available at https://github.com/will-rowe/groot (MIT license). will.rowe@stfc.ac.uk. Supplementary data are available at Bioinformatics online.

Recovery of a geocentric reference frame using the present-day GPS system

NASA Technical Reports Server (NTRS)

Malla, Rajendra P.; Wu, Sien-Chong

1990-01-01

A geocentric reference frame adopts the center of mass of the earth as the origin of the coordinate axes. The center of mass of the earth is the natural and unambiguous origin of a geocentric satellite dynamical system. But in practice a kinematically obtained terrestrial reference frame may assume an origin other than the geocenter. The establishment of a geocentric reference frame, to which all relevant observations and results can be referred and in which geodynamic theories or models for the dynamic behavior of earth can be formulated, requires the ability to accurately recover a given coordinate frame origin offset from the geocenter. GPS measurements, because of their abundance and broad distribution, provide a powerful tool to obtain this origin offset in a short period of time. Two effective strategies have been devised. Data from the First Central And South America (Casa Uno) geodynamics experiment has been studied, in order to demonstrate the ability of recovering the geocenter location with present day GPS satellites and receivers.

Co-location of space geodetic techniques carried out at the Geodetic Observatory Wettzell using a closure in time and a multi-technique reference target

NASA Astrophysics Data System (ADS)

Kodet, J.; Schreiber, K. U.; Eckl, J.; Plötz, C.; Mähler, S.; Schüler, T.; Klügel, T.; Riepl, S.

2018-01-01

The quality of the links between the different space geodetic techniques (VLBI, SLR, GNSS and DORIS) is still one of the major limiting factors for the realization of a unique global terrestrial reference frame that is accurate enough to allow the monitoring of the Earth system, i.e., of processes like sea level change, postglacial rebound and silent earthquakes. According to the specifications of the global geodetic observing system of the International Association of Geodesy, such a reference frame should be accurate to 1 mm over decades, with rates of change stable at the level of 0.1 mm/year. The deficiencies arise from inaccurate or incomplete local ties at many fundamental sites as well as from systematic instrumental biases in the individual space geodetic techniques. Frequently repeated surveys, the continuous monitoring of antenna heights and the geometrical mount stability (Lösler et al. in J Geod 90:467-486, 2016. https://doi.org/10.1007/s00190-016-0887-8) have not provided evidence for insufficient antenna stability. Therefore, we have investigated variations in the respective system delays caused by electronic circuits, which is not adequately captured by the calibration process, either because of subtle differences in the circuitry between geodetic measurement and calibration, high temporal variability or because of lacking resolving bandwidth. The measured system delay variations in the electric chain of both VLBI- and SLR systems reach the order of 100 ps, which is equivalent to 3 cm of path length. Most of this variability is usually removed by the calibrations but by far not all. This paper focuses on the development of new technologies and procedures for co-located geodetic instrumentation in order to identify and remove systematic measurement biases within and between the individual measurement techniques. A closed-loop optical time and frequency distribution system and a common inter-technique reference target provide the possibility to remove variable system delays. The main motivation for the newly established central reference target, locked to the station clock, is the combination of all space geodetic instruments at a single reference point at the observatory. On top of that it provides the unique capability to perform a closure measurement based on the observation of time.

Supporting Reform-Oriented Secondary Science Teaching Through the Use of a Framework to Analyze Construction of Scientific Explanations

NASA Astrophysics Data System (ADS)

Richmond, Gail; Parker, Joyce M.; Kaldaras, Leonora

2016-08-01

The Next-Generation Science Standards (NGSS) call for a different approach to learning science. They promote three-dimensional (3D) learning that blends disciplinary core ideas, crosscutting concepts and scientific practices. In this study, we examined explanations constructed by secondary science teacher candidates (TCs) as a scientific practice outlined in the NGSS necessary for supporting students' learning of science in this 3D way. We examined TCs' ability to give explanations that include explicit statements of underlying reasons for natural phenomena, as opposed to simply describing patterns or laws. In their methods courses, TCs were taught to organize explanations into a what/how/why framework, where what refers to what happens in specific cases (data or observations); how refers to how things usually happen and is equivalent to patterns or laws; and why refers to causal explanations or models. We examined TCs' ability to do this spontaneously and in a resource-rich environment as a first step in gauging their preparedness for NGSS-aligned teaching. We found that (1) the ability of TCs to articulate complete and accurate causal scientific explanations for phenomena exists along a continuum; (2) TCs in our sample whose explanations fell on the upper end of this continuum were more likely to provide complete and accurate explanations even in the absence of support from explicit standards; and (3) teacher candidate's ability to construct complete and accurate explanations did not correlate with cross-course performance or academic major. The implications of these findings for the preparation of teachers for NGSS-based science instruction are discussed.

Selection and evaluation of novel reference genes for quantitative reverse transcription PCR (qRT-PCR) based on genome and transcriptome data in Brassica napus L.

PubMed

Yang, Hongli; Liu, Jing; Huang, Shunmou; Guo, Tingting; Deng, Linbin; Hua, Wei

2014-03-15

Selection of reference genes in Brassica napus, a tetraploid (4×) species, is a very difficult task without information on genome and transcriptome. By now, only several traditional reference genes which show significant expression differentiation under different conditions are used in B. napus. In the present study, based on genome and transcriptome data of the rapeseed Zhongshuang-11 cultivar, 14 candidate reference genes were screened for investigation in different tissues, cultivars, and treated conditions of B. napus. These genes were as follows: ELF5, ENTH, F-BOX7, F-BOX2, FYPP1, GDI1, GYF, MCP2d, OTP80, PPR, SPOC, Unknown1, Unknown2 and UBA. Among them, excluding GYF and FYPP1, another 12 genes, were identified to perform better than traditional reference genes ACTIN7 and GAPDH. To further validate the accuracy of the newly developed reference genes in normalization, expression levels of BnCAT1 (B. napus catalase 1) in different rapeseed tissues and seedlings under stress conditions were normalized by the three most stable reference genes PPR, GDI1, and ENTH and little difference existed in normalization results. To the best of our knowledge, this is the first time B. napus reference genes have been provided with the help of complete genome and transcriptome information. The new reference genes provided in this study are more accurate than previously reported reference genes in quantifying expression levels of B. napus genes. Crown Copyright © 2014. Published by Elsevier B.V. All rights reserved.

The limits of boundaries: unpacking localization and cognitive mapping relative to a boundary.

PubMed

Zhou, Ruojing; Mou, Weimin

2018-05-01

Previous research (Zhou, Mou, Journal of Experimental Psychology: Learning, Memory and Cognition 42(8):1316-1323, 2016) showed that learning individual locations relative to a single landmark, compared to learning relative to a boundary, led to more accurate inferences of inter-object spatial relations (cognitive mapping of multiple locations). Following our past findings, the current study investigated whether the larger number of reference points provided by a homogeneous circular boundary, as well as less accessible knowledge of direct spatial relations among the multiple reference points, would lead to less effective cognitive mapping relative to the boundary. Accordingly, we manipulated (a) the number of primary reference points (one segment drawn from a circular boundary, four such segments, vs. the complete boundary) available when participants were localizing four objects sequentially (Experiment 1) and (b) the extendedness of each of the four segments (Experiment 2). The results showed that cognitive mapping was the least accurate in the whole boundary condition. However, expanding each of the four segments did not affect the accuracy of cognitive mapping until the four were connected to form a continuous boundary. These findings indicate that when encoding locations relative to a homogeneous boundary, participants segmented the boundary into differentiated pieces and subsequently chose the most informative local part (i.e., the segment closest in distance to one location) as the primary reference point for a particular location. During this process, direct spatial relations among the reference points were likely not attended to. These findings suggest that people might encode and represent bounded space in a fragmented fashion when localizing within a homogeneous boundary.

On the numerical treatment of selected oscillatory evolutionary problems

NASA Astrophysics Data System (ADS)

Cardone, Angelamaria; Conte, Dajana; D'Ambrosio, Raffaele; Paternoster, Beatrice

2017-07-01

We focus on evolutionary problems whose qualitative behaviour is known a-priori and exploited in order to provide efficient and accurate numerical schemes. For classical numerical methods, depending on constant coefficients, the required computational effort could be quite heavy, due to the necessary employ of very small stepsizes needed to accurately reproduce the qualitative behaviour of the solution. In these situations, it may be convenient to use special purpose formulae, i.e. non-polynomially fitted formulae on basis functions adapted to the problem (see [16, 17] and references therein). We show examples of special purpose strategies to solve two families of evolutionary problems exhibiting periodic solutions, i.e. partial differential equations and Volterra integral equations.

Quantitative aspects of inductively coupled plasma mass spectrometry

NASA Astrophysics Data System (ADS)

Bulska, Ewa; Wagner, Barbara

2016-10-01

Accurate determination of elements in various kinds of samples is essential for many areas, including environmental science, medicine, as well as industry. Inductively coupled plasma mass spectrometry (ICP-MS) is a powerful tool enabling multi-elemental analysis of numerous matrices with high sensitivity and good precision. Various calibration approaches can be used to perform accurate quantitative measurements by ICP-MS. They include the use of pure standards, matrix-matched standards, or relevant certified reference materials, assuring traceability of the reported results. This review critically evaluates the advantages and limitations of different calibration approaches, which are used in quantitative analyses by ICP-MS. Examples of such analyses are provided. This article is part of the themed issue 'Quantitative mass spectrometry'.

Determination of exposure multiples of human metabolites for MIST assessment in preclinical safety species without using reference standards or radiolabeled compounds.

PubMed

Ma, Shuguang; Li, Zhiling; Lee, Keun-Joong; Chowdhury, Swapan K

2010-12-20

A simple, reliable, and accurate method was developed for quantitative assessment of metabolite coverage in preclinical safety species by mixing equal volumes of human plasma with blank plasma of animal species and vice versa followed by an analysis using high-resolution full-scan accurate mass spectrometry. This approach provided comparable results (within (±15%) to those obtained from regulated bioanalysis and did not require synthetic standards or radiolabeled compounds. In addition, both qualitative and quantitative data were obtained from a single LC-MS analysis on all metabolites and, therefore, the coverage of any metabolite of interest can be obtained.

Validation of reference genes for accurate normalization of gene expression for real time-quantitative PCR in strawberry fruits using different cultivars and osmotic stresses.

PubMed

Galli, Vanessa; Borowski, Joyce Moura; Perin, Ellen Cristina; Messias, Rafael da Silva; Labonde, Julia; Pereira, Ivan dos Santos; Silva, Sérgio Delmar Dos Anjos; Rombaldi, Cesar Valmor

2015-01-10

The increasing demand of strawberry (Fragaria×ananassa Duch) fruits is associated mainly with their sensorial characteristics and the content of antioxidant compounds. Nevertheless, the strawberry production has been hampered due to its sensitivity to abiotic stresses. Therefore, to understand the molecular mechanisms highlighting stress response is of great importance to enable genetic engineering approaches aiming to improve strawberry tolerance. However, the study of expression of genes in strawberry requires the use of suitable reference genes. In the present study, seven traditional and novel candidate reference genes were evaluated for transcript normalization in fruits of ten strawberry cultivars and two abiotic stresses, using RefFinder, which integrates the four major currently available software programs: geNorm, NormFinder, BestKeeper and the comparative delta-Ct method. The results indicate that the expression stability is dependent on the experimental conditions. The candidate reference gene DBP (DNA binding protein) was considered the most suitable to normalize expression data in samples of strawberry cultivars and under drought stress condition, and the candidate reference gene HISTH4 (histone H4) was the most stable under osmotic stresses and salt stress. The traditional genes GAPDH (glyceraldehyde-3-phosphate dehydrogenase) and 18S (18S ribosomal RNA) were considered the most unstable genes in all conditions. The expression of phenylalanine ammonia lyase (PAL) and 9-cis epoxycarotenoid dioxygenase (NCED1) genes were used to further confirm the validated candidate reference genes, showing that the use of an inappropriate reference gene may induce erroneous results. This study is the first survey on the stability of reference genes in strawberry cultivars and osmotic stresses and provides guidelines to obtain more accurate RT-qPCR results for future breeding efforts. Copyright © 2014 Elsevier B.V. All rights reserved.

Orsphere: Physics Measurments For Bare, HEU(93.2)-Metal Sphere

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

Marshall, Margaret A.; Bess, John D.; Briggs, J. Blair

In the early 1970s Dr. John T. Mihalczo (team leader), J.J. Lynn, and J.R. Taylor performed experiments at the Oak Ridge Critical Experiments Facility (ORCEF) with highly enriched uranium (HEU) metal (called Oak Ridge Alloy or ORALLOY) in an attempt to recreate GODIVA I results with greater accuracy than those performed at Los Alamos National Laboratory in the 1950s (HEU-MET-FAST-001). The purpose of the Oak Ridge ORALLOY Sphere (ORSphere) experiments was to estimate the unreflected and unmoderated critical mass of an idealized sphere of uranium metal corrected to a density, purity, and enrichment such that it could be compared withmore » the GODIVA I experiments. “The very accurate description of this sphere, as assembled, establishes it as an ideal benchmark for calculational methods and cross-section data files” (Reference 1). While performing the ORSphere experiments care was taken to accurately document component dimensions (±0.0001 inches), masses (±0.01 g), and material data. The experiment was also set up to minimize the amount of structural material in the sphere proximity. Two, correlated spheres were evaluated and judged to be acceptable as criticality benchmark experiments. This evaluation is given in HEU-MET-FAST-100. The second, smaller sphere was used for additional reactor physics measurements. Worth measurements (Reference 1, 2, 3 and 4), the delayed neutron fraction (Reference 3, 4 and 5) and surface material worth coefficient (Reference 1 and 2) are all measured and judged to be acceptable as benchmark data. The prompt neutron decay (Reference 6), relative fission density (Reference 7) and relative neutron importance (Reference 7) were measured, but are not evaluated. Information for the evaluation was compiled from References 1 through 7, the experimental logbooks 8 and 9 ; additional drawings and notes provided by the experimenter; and communication with the lead experimenter, John T. Mihalczo.« less

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

Marshall, Margaret A.

In the early 1970s Dr. John T. Mihalczo (team leader), J.J. Lynn, and J.R. Taylor performed experiments at the Oak Ridge Critical Experiments Facility (ORCEF) with highly enriched uranium (HEU) metal (called Oak Ridge Alloy or ORALLOY) in an attempt to recreate GODIVA I results with greater accuracy than those performed at Los Alamos National Laboratory in the 1950s (HEU-MET-FAST-001). The purpose of the Oak Ridge ORALLOY Sphere (ORSphere) experiments was to estimate the unreflected and unmoderated critical mass of an idealized sphere of uranium metal corrected to a density, purity, and enrichment such that it could be compared withmore » the GODIVA I experiments. “The very accurate description of this sphere, as assembled, establishes it as an ideal benchmark for calculational methods and cross-section data files” (Reference 1). While performing the ORSphere experiments care was taken to accurately document component dimensions (±0.0001 inches), masses (±0.01 g), and material data. The experiment was also set up to minimize the amount of structural material in the sphere proximity. Two, correlated spheres were evaluated and judged to be acceptable as criticality benchmark experiments. This evaluation is given in HEU-MET-FAST-100. The second, smaller sphere was used for additional reactor physics measurements. Worth measurements (Reference 1, 2, 3 and 4), the delayed neutron fraction (Reference 3, 4 and 5) and surface material worth coefficient (Reference 1 and 2) are all measured and judged to be acceptable as benchmark data. The prompt neutron decay (Reference 6), relative fission density (Reference 7) and relative neutron importance (Reference 7) were measured, but are not evaluated. Information for the evaluation was compiled from References 1 through 7, the experimental logbooks 8 and 9 ; additional drawings and notes provided by the experimenter; and communication with the lead experimenter, John T. Mihalczo.« less

A Review on Medical Image Registration as an Optimization Problem

PubMed Central

Song, Guoli; Han, Jianda; Zhao, Yiwen; Wang, Zheng; Du, Huibin

2017-01-01

Objective: In the course of clinical treatment, several medical media are required by a phy-sician in order to provide accurate and complete information about a patient. Medical image registra-tion techniques can provide a richer diagnosis and treatment information to doctors and to provide a comprehensive reference source for the researchers involved in image registration as an optimization problem. Methods: The essence of image registration is associating two or more different images spatial asso-ciation, and getting the translation of their spatial relationship. For medical image registration, its pro-cess is not absolute. Its core purpose is finding the conversion relationship between different images. Result: The major step of image registration includes the change of geometrical dimensions, and change of the image of the combination, image similarity measure, iterative optimization and interpo-lation process. Conclusion: The contribution of this review is sort of related image registration research methods, can provide a brief reference for researchers about image registration. PMID:28845149

Contribution of the International Reference Ionosphere to the progress of the ionospheric representation

NASA Astrophysics Data System (ADS)

Bilitza, Dieter

2017-04-01

The International Reference Ionosphere (IRI), a joint project of the Committee on Space Research (COSPAR) and the International Union of Radio Science (URSI), is a data-based reference model for the ionosphere and since 2014 it is also recognized as the ISO (International Standardization Organization) standard for the ionosphere. The model is a synthesis of most of the available and reliable observations of ionospheric parameters combining ground and space measurements. This presentation reviews the steady progress in achieving a more and more accurate representation of the ionospheric plasma parameters accomplished during the last decade of IRI model improvements. Understandably, a data-based model is only as good as the data foundation on which it is built. We will discuss areas where we are in need of more data to obtain a more solid and continuous data foundation in space and time. We will also take a look at still existing discrepancies between simultaneous measurements of the same parameter with different measurement techniques and discuss the approach taken in the IRI model to deal with these conflicts. In conclusion we will provide an outlook at development activities that may result in significant future improvements of the accurate representation of the ionosphere in the IRI model.

The Uhlenbeck-Ford model: Exact virial coefficients and application as a reference system in fluid-phase free-energy calculations

NASA Astrophysics Data System (ADS)

Paula Leite, Rodolfo; Freitas, Rodrigo; Azevedo, Rodolfo; de Koning, Maurice

2016-11-01

The Uhlenbeck-Ford (UF) model was originally proposed for the theoretical study of imperfect gases, given that all its virial coefficients can be evaluated exactly, in principle. Here, in addition to computing the previously unknown coefficients B11 through B13, we assess its applicability as a reference system in fluid-phase free-energy calculations using molecular simulation techniques. Our results demonstrate that, although the UF model itself is too soft, appropriately scaled Uhlenbeck-Ford (sUF) models provide robust reference systems that allow accurate fluid-phase free-energy calculations without the need for an intermediate reference model. Indeed, in addition to the accuracy with which their free energies are known and their convenient scaling properties, the fluid is the only thermodynamically stable phase for a wide range of sUF models. This set of favorable properties may potentially put the sUF fluid-phase reference systems on par with the standard role that harmonic and Einstein solids play as reference systems for solid-phase free-energy calculations.

Model of critical diagnostic reasoning: achieving expert clinician performance.

PubMed

Harjai, Prashant Kumar; Tiwari, Ruby

2009-01-01

Diagnostic reasoning refers to the analytical processes used to determine patient health problems. While the education curriculum and health care system focus on training nurse clinicians to accurately recognize and rescue clinical situations, assessments of non-expert nurses have yielded less than satisfactory data on diagnostic competency. The contrast between the expert and non-expert nurse clinician raises the important question of how differences in thinking may contribute to a large divergence in accurate diagnostic reasoning. This article recognizes superior organization of one's knowledge base, using prototypes, and quick retrieval of pertinent information, using similarity recognition as two reasons for the expert's superior diagnostic performance. A model of critical diagnostic reasoning, using prototypes and similarity recognition, is proposed and elucidated using case studies. This model serves as a starting point toward bridging the gap between clinical data and accurate problem identification, verification, and management while providing a structure for a knowledge exchange between expert and non-expert clinicians.

A statistical method for assessing peptide identification confidence in accurate mass and time tag proteomics

PubMed Central

Stanley, Jeffrey R.; Adkins, Joshua N.; Slysz, Gordon W.; Monroe, Matthew E.; Purvine, Samuel O.; Karpievitch, Yuliya V.; Anderson, Gordon A.; Smith, Richard D.; Dabney, Alan R.

2011-01-01

Current algorithms for quantifying peptide identification confidence in the accurate mass and time (AMT) tag approach assume that the AMT tags themselves have been correctly identified. However, there is uncertainty in the identification of AMT tags, as this is based on matching LC-MS/MS fragmentation spectra to peptide sequences. In this paper, we incorporate confidence measures for the AMT tag identifications into the calculation of probabilities for correct matches to an AMT tag database, resulting in a more accurate overall measure of identification confidence for the AMT tag approach. The method is referred to as Statistical Tools for AMT tag Confidence (STAC). STAC additionally provides a Uniqueness Probability (UP) to help distinguish between multiple matches to an AMT tag and a method to calculate an overall false discovery rate (FDR). STAC is freely available for download as both a command line and a Windows graphical application. PMID:21692516

Initial Performance of the Attitude Control and Aspect Determination Subsystems on the Chandra Observatory

NASA Technical Reports Server (NTRS)

Cameron, R.; Aldcroft, T.; Podgorski, W. A.; Freeman, M. D.

2000-01-01

The aspect determination system of the Chandra X-ray Observatory plays a key role in realizing the full potential of Chandra's X-ray optics and detectors. We review the performance of the spacecraft hardware components and sub-systems, which provide information for both real time control of the attitude and attitude stability of the Chandra Observatory and also for more accurate post-facto attitude reconstruction. These flight components are comprised of the aspect camera (star tracker) and inertial reference units (gyros), plus the fiducial lights and fiducial transfer optics which provide an alignment null reference system for the science instruments and X-ray optics, together with associated thermal and structural components. Key performance measures will be presented for aspect camera focal plane data, gyro performance both during stable pointing and during maneuvers, alignment stability and mechanism repeatability.

Linear LIDAR versus Geiger-mode LIDAR: impact on data properties and data quality

NASA Astrophysics Data System (ADS)

Ullrich, A.; Pfennigbauer, M.

2016-05-01

LIDAR has become the inevitable technology to provide accurate 3D data fast and reliably even in adverse measurement situations and harsh environments. It provides highly accurate point clouds with a significant number of additional valuable attributes per point. LIDAR systems based on Geiger-mode avalanche photo diode arrays, also called single photon avalanche photo diode arrays, earlier employed for military applications, now seek to enter the commercial market of 3D data acquisition, advertising higher point acquisition speeds from longer ranges compared to conventional techniques. Publications pointing out the advantages of these new systems refer to the other category of LIDAR as "linear LIDAR", as the prime receiver element for detecting the laser echo pulses - avalanche photo diodes - are used in a linear mode of operation. We analyze the differences between the two LIDAR technologies and the fundamental differences in the data they provide. The limitations imposed by physics on both approaches to LIDAR are also addressed and advantages of linear LIDAR over the photon counting approach are discussed.

A simple method for HPLC retention time prediction: linear calibration using two reference substances.

PubMed

Sun, Lei; Jin, Hong-Yu; Tian, Run-Tao; Wang, Ming-Juan; Liu, Li-Na; Ye, Liu-Ping; Zuo, Tian-Tian; Ma, Shuang-Cheng

2017-01-01

Analysis of related substances in pharmaceutical chemicals and multi-components in traditional Chinese medicines needs bulk of reference substances to identify the chromatographic peaks accurately. But the reference substances are costly. Thus, the relative retention (RR) method has been widely adopted in pharmacopoeias and literatures for characterizing HPLC behaviors of those reference substances unavailable. The problem is it is difficult to reproduce the RR on different columns due to the error between measured retention time (t R ) and predicted t R in some cases. Therefore, it is useful to develop an alternative and simple method for prediction of t R accurately. In the present study, based on the thermodynamic theory of HPLC, a method named linear calibration using two reference substances (LCTRS) was proposed. The method includes three steps, procedure of two points prediction, procedure of validation by multiple points regression and sequential matching. The t R of compounds on a HPLC column can be calculated by standard retention time and linear relationship. The method was validated in two medicines on 30 columns. It was demonstrated that, LCTRS method is simple, but more accurate and more robust on different HPLC columns than RR method. Hence quality standards using LCTRS method are easy to reproduce in different laboratories with lower cost of reference substances.

Deriving a geocentric reference frame for satellite positioning and navigation

NASA Technical Reports Server (NTRS)

Malla, R. P.; Wu, S.-C.

1988-01-01

With the advent of Earth-orbiting geodetic satellites, nongeocentric datums or reference frames have become things of the past. Accurate geocentric three-dimensional positioning is now possible and is of great importance for various geodetic and oceanographic applications. While relative positioning accuracy of a few centimeters has become a reality using very long baseline interferometry (VLBI), the uncertainty in the offset of the adopted coordinate system origin from the geocenter is still believed to be on the order of 1 meter. Satellite laser ranging (SLR), however, is capable of determining this offset to better than 10 cm, but this is possible only after years of measurements. Global Positioning System (GPS) measurements provide a powerful tool for an accurate determination of this origin offset. Two strategies are discussed. The first strategy utilizes the precise relative positions that were predetermined by VLBI to fix the frame orientation and the absolute scaling, while the offset from the geocenter is determined from GPS measurements. Three different cases are presented under this strategy. The reference frame thus adopted will be consistent with the VLBI coordinate system. The second strategy establishes a reference frame by holding only the longitude of one of the tracking sites fixed. The absolute scaling is determined by the adopted gravitational constant (GM) of the Earth; and the latitude is inferred from the time signature of the Earth rotation in the GPS measurements. The coordinate system thus defined will be a geocentric Earth-fixed coordinate system.

Quasi-reference electrodes in confined electrochemical cells can result in in situ production of metallic nanoparticles.

PubMed

Perera, Rukshan T; Rosenstein, Jacob K

2018-01-31

Nanoscale working electrodes and miniaturized electroanalytical devices are valuable platforms to probe molecular phenomena and perform chemical analyses. However, the inherent close distance of metallic electrodes integrated into a small volume of electrolyte can complicate classical electroanalytical techniques. In this study, we use a scanning nanopipette contact probe as a model miniaturized electrochemical cell to demonstrate measurable side effects of the reaction occurring at a quasi-reference electrode. We provide evidence for in situ generation of nanoparticles in the absence of any electroactive species and we critically analyze the origin, nucleation, dissolution and dynamic behavior of these nanoparticles as they appear at the working electrode. It is crucial to recognize the implications of using quasi-reference electrodes in confined electrochemical cells, in order to accurately interpret the results of nanoscale electrochemical experiments.

Long Live Old Reference Services and New Technologies.

ERIC Educational Resources Information Center

Katz, Bill

2001-01-01

Reference service technology has passed its first stage of insuring more accurate, rapid delivery of information. The second revolution underway will improve on both acquisition and retrieval of data. New technologies must fit into traditional reference service goals. The human should be given first priority. (Contains 46 references.) (Author/AEF)

Effects of visual information regarding allocentric processing in haptic parallelity matching.

PubMed

Van Mier, Hanneke I

2013-10-01

Research has revealed that haptic perception of parallelity deviates from physical reality. Large and systematic deviations have been found in haptic parallelity matching most likely due to the influence of the hand-centered egocentric reference frame. Providing information that increases the influence of allocentric processing has been shown to improve performance on haptic matching. In this study allocentric processing was stimulated by providing informative vision in haptic matching tasks that were performed using hand- and arm-centered reference frames. Twenty blindfolded participants (ten men, ten women) explored the orientation of a reference bar with the non-dominant hand and subsequently matched (task HP) or mirrored (task HM) its orientation on a test bar with the dominant hand. Visual information was provided by means of informative vision with participants having full view of the test bar, while the reference bar was blocked from their view (task VHP). To decrease the egocentric bias of the hands, participants also performed a visual haptic parallelity drawing task (task VHPD) using an arm-centered reference frame, by drawing the orientation of the reference bar. In all tasks, the distance between and orientation of the bars were manipulated. A significant effect of task was found; performance improved from task HP, to VHP to VHPD, and HM. Significant effects of distance were found in the first three tasks, whereas orientation and gender effects were only significant in tasks HP and VHP. The results showed that stimulating allocentric processing by means of informative vision and reducing the egocentric bias by using an arm-centered reference frame led to most accurate performance on parallelity matching. © 2013 Elsevier B.V. All rights reserved.

Reference Intervals of Alpha-Fetoprotein and Carcinoembryonic Antigen in the Apparently Healthy Population

PubMed Central

Zhang, Gao-Ming; Guo, Xu-Xiao; Ma, Xiao-Bo; Zhang, Guo-Ming

2016-01-01

Background The aim of this study was to calculate 95% reference intervals and double-sided limits of serum alpha-fetoprotein (AFP) and carcinoembryonic antigen (CEA) according to the CLSI EP28-A3 guideline. Material/Methods Serum AFP and CEA values were measured in samples from 26 000 healthy subjects in the Shuyang area receiving general health checkups. The 95% reference intervals and upper limits were calculated by using MedCalc. Results We provided continuous reference intervals from 20 years old to 90 years old for AFP and CEA. The reference intervals were: AFP, 1.31–7.89 ng/ml (males) and 1.01–7.10 ng/ml (females); CEA, 0.51–4.86 ng/ml (males) and 0.35–3.45ng/ml (females). AFP and CEA were significantly positively correlated with age in both males (r=0.196 and r=0.198) and females (r=0.121 and r=0.197). Conclusions Different races or populations and different detection systems may result in different reference intervals for AFP and CEA. Continuous reference intervals of age changes are more accurate than age groups. PMID:27941709

Spinning angle optical calibration apparatus

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

Beer, S.K.; Pratt, H.R.

1991-02-26

This patent describes an optical calibration apparatus provided for calibrating and reproducing spinning angles in cross-polarization, nuclear magnetic resonance spectroscopy. An illuminated magnifying apparatus enables optical setting an accurate reproducing of spinning magic angles in cross-polarization, nuclear magnetic resonance spectroscopy experiments. A reference mark scribed on an edge of a spinning angle test sample holder is illuminated by a light source and viewed through a magnifying scope. When the magic angle of a sample material used as a standard is attained by varying the angular position of the sample holder, the coordinate position of the reference mark relative to amore » graduation or graduations on a reticle in the magnifying scope is noted.« less

Implementation of alanine/EPR as transfer dosimetry system in a radiotherapy audit programme in Belgium.

PubMed

Schaeken, B; Cuypers, R; Lelie, S; Schroeyers, W; Schreurs, S; Janssens, H; Verellen, D

2011-04-01

A measurement procedure based on alanine/electron paramagnetic resonance (EPR) dosimetry was implemented successfully providing simple, stable, and accurate dose-to-water (D(w)) measurements. The correspondence between alanine and ionization chamber measurements in reference conditions was excellent. Alanine/EMR dosimetry might be a valuable alternative to thermoluminescent (TLD) and ionization chamber based measuring procedures in radiotherapy audits. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

The CAFE Experiment: A Joint Seismic and MT Investigation of the Cascadia Subduction System

DTIC Science & Technology

2013-02-01

In this thesis we present results from inversion of data using dense arrays of collocated seismic and magnetotelluric stations located in the Cascadia...implicit in the standard MT inversion provides tools that enable us to generate a more accurate MT model. This final MT model clearly demonstrates...references within, Hacker, 2008) have given us the tools to better interpret geophysical evidence. Improvements in the thermal modeling of subduction zones

Evaluating the performance of Sentinel-3 SRAL SAR Altimetry in the Coastal and Open Ocean, and developing improved retrieval methods - The ESA SCOOP Project.

NASA Astrophysics Data System (ADS)

Benveniste, J.; Cotton, D.; Moreau, T.; Varona, E.; Roca, M.; Cipollini, P.; Cancet, M.; Martin, F.; Fenoglio-Marc, L.; Naeije, M.; Fernandes, J.; Restano, M.; Ambrozio, A.

2016-12-01

The ESA Sentinel-3 satellite, launched in February 2016 as a part of the Copernicus programme, is the second satellite to operate a SAR mode altimeter. The Sentinel 3 Synthetic Aperture Radar Altimeter (SRAL) is based on the heritage from Cryosat-2, but this time complemented by a Microwave Radiometer (MWR) to provide a wet troposphere correction, and operating at Ku and C-Bands to provide an accurate along-track ionospheric correction. Together this instrument package, including both GPS and DORIS instruments for accurate positioning, allows accurate measurements of sea surface height over the ocean, as well as measurements of significant wave height and surface wind speed. SCOOP (SAR Altimetry Coastal & Open Ocean Performance) is a project funded under the ESA SEOM (Scientific Exploitation of Operational Missions) Programme Element, started in September 2015, to characterise the expected performance of Sentinel-3 SRAL SAR mode altimeter products, in the coastal zone and open-ocean, and then to develop and evaluate enhancements to the baseline processing scheme in terms of improvements to ocean measurements. There is also a work package to develop and evaluate an improved Wet Troposphere correction for Sentinel-3, based on the measurements from the on-board MWR, further enhanced mostly in the coastal and polar regions using third party data, and provide recommendations for use. At the end of the project recommendations for further developments and implementations will be provided through a scientific roadmap. In this presentation we provide an overview of the SCOOP project, highlighting the key deliverables and discussing the potential impact of the results in terms of the application of delay-Doppler (SAR) altimeter measurements over the open-ocean and coastal zone. We also present the initial results from the project, including: Key findings from a review of the current "state-of-the-art" for SAR altimetry, Specification of the initial "reference" delay-Doppler and echo modelling /retracking processing schemes, Evaluation of the initial Test Data Set in the Open Ocean and Coastal Zone Overview of modifications planned to the reference delay-Doppler and echo modelling/ re-tracking processing schemes.

Quantitative phylogenetic assessment of microbial communities in diverse environments.

PubMed

von Mering, C; Hugenholtz, P; Raes, J; Tringe, S G; Doerks, T; Jensen, L J; Ward, N; Bork, P

2007-02-23

The taxonomic composition of environmental communities is an important indicator of their ecology and function. We used a set of protein-coding marker genes, extracted from large-scale environmental shotgun sequencing data, to provide a more direct, quantitative, and accurate picture of community composition than that provided by traditional ribosomal RNA-based approaches depending on the polymerase chain reaction. Mapping marker genes from four diverse environmental data sets onto a reference species phylogeny shows that certain communities evolve faster than others. The method also enables determination of preferred habitats for entire microbial clades and provides evidence that such habitat preferences are often remarkably stable over time.

Accuracy of Heart Rate Watches: Implications for Weight Management

PubMed Central

2016-01-01

Background Wrist-worn monitors claim to provide accurate measures of heart rate and energy expenditure. People wishing to lose weight use these devices to monitor energy balance, however the accuracy of these devices to measure such parameters has not been established. Aim To determine the accuracy of four wrist-worn devices (Apple Watch, Fitbit Charge HR, Samsung Gear S and Mio Alpha) to measure heart rate and energy expenditure at rest and during exercise. Methods Twenty-two healthy volunteers (50% female; aged 24 ± 5.6 years) completed ~1-hr protocols involving supine and seated rest, walking and running on a treadmill and cycling on an ergometer. Data from the devices collected during the protocol were compared with reference methods: electrocardiography (heart rate) and indirect calorimetry (energy expenditure). Results None of the devices performed significantly better overall, however heart rate was consistently more accurate than energy expenditure across all four devices. Correlations between the devices and reference methods were moderate to strong for heart rate (0.67–0.95 [0.35 to 0.98]) and weak to strong for energy expenditure (0.16–0.86 [-0.25 to 0.95]). All devices underestimated both outcomes compared to reference methods. The percentage error for heart rate was small across the devices (range: 1–9%) but greater for energy expenditure (9–43%). Similarly, limits of agreement were considerably narrower for heart rate (ranging from -27.3 to 13.1 bpm) than energy expenditure (ranging from -266.7 to 65.7 kcals) across devices. Conclusion These devices accurately measure heart rate. However, estimates of energy expenditure are poor and would have implications for people using these devices for weight loss. PMID:27232714

Accuracy of Heart Rate Watches: Implications for Weight Management.

PubMed

Wallen, Matthew P; Gomersall, Sjaan R; Keating, Shelley E; Wisløff, Ulrik; Coombes, Jeff S

2016-01-01

Wrist-worn monitors claim to provide accurate measures of heart rate and energy expenditure. People wishing to lose weight use these devices to monitor energy balance, however the accuracy of these devices to measure such parameters has not been established. To determine the accuracy of four wrist-worn devices (Apple Watch, Fitbit Charge HR, Samsung Gear S and Mio Alpha) to measure heart rate and energy expenditure at rest and during exercise. Twenty-two healthy volunteers (50% female; aged 24 ± 5.6 years) completed ~1-hr protocols involving supine and seated rest, walking and running on a treadmill and cycling on an ergometer. Data from the devices collected during the protocol were compared with reference methods: electrocardiography (heart rate) and indirect calorimetry (energy expenditure). None of the devices performed significantly better overall, however heart rate was consistently more accurate than energy expenditure across all four devices. Correlations between the devices and reference methods were moderate to strong for heart rate (0.67-0.95 [0.35 to 0.98]) and weak to strong for energy expenditure (0.16-0.86 [-0.25 to 0.95]). All devices underestimated both outcomes compared to reference methods. The percentage error for heart rate was small across the devices (range: 1-9%) but greater for energy expenditure (9-43%). Similarly, limits of agreement were considerably narrower for heart rate (ranging from -27.3 to 13.1 bpm) than energy expenditure (ranging from -266.7 to 65.7 kcals) across devices. These devices accurately measure heart rate. However, estimates of energy expenditure are poor and would have implications for people using these devices for weight loss.

Genotype Imputation with Thousands of Genomes

PubMed Central

Howie, Bryan; Marchini, Jonathan; Stephens, Matthew

2011-01-01

Genotype imputation is a statistical technique that is often used to increase the power and resolution of genetic association studies. Imputation methods work by using haplotype patterns in a reference panel to predict unobserved genotypes in a study dataset, and a number of approaches have been proposed for choosing subsets of reference haplotypes that will maximize accuracy in a given study population. These panel selection strategies become harder to apply and interpret as sequencing efforts like the 1000 Genomes Project produce larger and more diverse reference sets, which led us to develop an alternative framework. Our approach is built around a new approximation that uses local sequence similarity to choose a custom reference panel for each study haplotype in each region of the genome. This approximation makes it computationally efficient to use all available reference haplotypes, which allows us to bypass the panel selection step and to improve accuracy at low-frequency variants by capturing unexpected allele sharing among populations. Using data from HapMap 3, we show that our framework produces accurate results in a wide range of human populations. We also use data from the Malaria Genetic Epidemiology Network (MalariaGEN) to provide recommendations for imputation-based studies in Africa. We demonstrate that our approximation improves efficiency in large, sequence-based reference panels, and we discuss general computational strategies for modern reference datasets. Genome-wide association studies will soon be able to harness the power of thousands of reference genomes, and our work provides a practical way for investigators to use this rich information. New methodology from this study is implemented in the IMPUTE2 software package. PMID:22384356

Assessing bioequivalence of generic antiepilepsy drugs.

PubMed

Krauss, Gregory L; Caffo, Brian; Chang, Yi-Ting; Hendrix, Craig W; Chuang, Kelly

2011-08-01

Patients with epilepsy are often concerned that switching between brand-name and generic formulations of antiepilepsy drugs (AEDs) may cause clinically significant changes in plasma drug concentrations. We assessed bioequivalence (BE) studies for approved generic AEDs to evaluate US Food and Drug Administration claims that: (1) generic AEDs are accurate copies of reference formulations; (2) delivery of reference formulations may be as variable as generic AEDs and so provide no increased benefit; and (3) switches between generic AED formulations are safe and effective. We determined differences in 90% confidence interval limits for total drug exposure (AUC(0-t) ) and peak concentration (Cmax) ratios of generic and reference formulations during fasting and fed BE studies. We simulated BE between generic formulations after adjusting for reference values. AUC(0-t) values of approved reference and generic formulations differed by <15% in 99% of BE studies; Cmax differed by <15% in 89% of studies. Food affected variability of Cmax but not AUC(0-t) . Intersubject variability in Cmax and AUC(0-t) was small and similar for reference and generic products. In simulated switches between 595 pairs of generic AED formulations, estimated AUC(0-t) differed by >15% for 17% of pairs; estimated Cmax differed by >15% for 39%. AEDs with low bioavailability and solubility (eg, oxcarbazepine) had the greatest variability in BE. Most generic AED products provide total drug delivery (AUC) similar to reference products; differences in peak concentrations between formulations are more common. Switches between generic AED products may cause greater changes in plasma drug concentrations than generic substitutions of reference products. Copyright © 2011 American Neurological Association.

Quantitative aspects of inductively coupled plasma mass spectrometry

PubMed Central

Wagner, Barbara

2016-01-01

Accurate determination of elements in various kinds of samples is essential for many areas, including environmental science, medicine, as well as industry. Inductively coupled plasma mass spectrometry (ICP-MS) is a powerful tool enabling multi-elemental analysis of numerous matrices with high sensitivity and good precision. Various calibration approaches can be used to perform accurate quantitative measurements by ICP-MS. They include the use of pure standards, matrix-matched standards, or relevant certified reference materials, assuring traceability of the reported results. This review critically evaluates the advantages and limitations of different calibration approaches, which are used in quantitative analyses by ICP-MS. Examples of such analyses are provided. This article is part of the themed issue ‘Quantitative mass spectrometry’. PMID:27644971

Documentation for assessment of modal pushover-based scaling procedure for nonlinear response history analysis of "ordinary standard" bridges

USGS Publications Warehouse

Kalkan, Erol; Kwong, Neal S.

2010-01-01

The earthquake engineering profession is increasingly utilizing nonlinear response history analyses (RHA) to evaluate seismic performance of existing structures and proposed designs of new structures. One of the main ingredients of nonlinear RHA is a set of ground-motion records representing the expected hazard environment for the structure. When recorded motions do not exist (as is the case for the central United States), or when high-intensity records are needed (as is the case for San Francisco and Los Angeles), ground motions from other tectonically similar regions need to be selected and scaled. The modal-pushover-based scaling (MPS) procedure recently was developed to determine scale factors for a small number of records, such that the scaled records provide accurate and efficient estimates of 'true' median structural responses. The adjective 'accurate' refers to the discrepancy between the benchmark responses and those computed from the MPS procedure. The adjective 'efficient' refers to the record-to-record variability of responses. Herein, the accuracy and efficiency of the MPS procedure are evaluated by applying it to four types of existing 'ordinary standard' bridges typical of reinforced-concrete bridge construction in California. These bridges are the single-bent overpass, multi span bridge, curved-bridge, and skew-bridge. As compared to benchmark analyses of unscaled records using a larger catalog of ground motions, it is demonstrated that the MPS procedure provided an accurate estimate of the engineering demand parameters (EDPs) accompanied by significantly reduced record-to-record variability of the responses. Thus, the MPS procedure is a useful tool for scaling ground motions as input to nonlinear RHAs of 'ordinary standard' bridges.

DRIFT CONTROL IN AN ANALYTICAL GAMMA RAY SPECTROMETER

DOEpatents

Fite, L.E.

1963-08-20

A device for automatically and continuously controlling the over-all drift of a multi-channel analyzer so as to permit the accurate processing of spectrometric analytical data by a digital computer is described. Two sources of reference pulses, one of which is stored in the lower channels and the other being stored in the higher channels of a 256 channel analyzer, are provided. The reference pulses are processed in the same manner as the data pulses. The channels that should contain the reference pulses and the adjacent channels above and below those channels are monitored by comparison circuits such that any drift, upward or downward, of the reference pulses is detected to effect a change in high voltage supply in response to a drift in the upper channel, and to effect a change in the lower discriminator level of the analog to digital converter of the analyzer in response to a drift in the lower channel, thereby maintaining the pulses in the proper channels. (AEC)

FreeSolv: A database of experimental and calculated hydration free energies, with input files

PubMed Central

Mobley, David L.; Guthrie, J. Peter

2014-01-01

This work provides a curated database of experimental and calculated hydration free energies for small neutral molecules in water, along with molecular structures, input files, references, and annotations. We call this the Free Solvation Database, or FreeSolv. Experimental values were taken from prior literature and will continue to be curated, with updated experimental references and data added as they become available. Calculated values are based on alchemical free energy calculations using molecular dynamics simulations. These used the GAFF small molecule force field in TIP3P water with AM1-BCC charges. Values were calculated with the GROMACS simulation package, with full details given in references cited within the database itself. This database builds in part on a previous, 504-molecule database containing similar information. However, additional curation of both experimental data and calculated values has been done here, and the total number of molecules is now up to 643. Additional information is now included in the database, such as SMILES strings, PubChem compound IDs, accurate reference DOIs, and others. One version of the database is provided in the Supporting Information of this article, but as ongoing updates are envisioned, the database is now versioned and hosted online. In addition to providing the database, this work describes its construction process. The database is available free-of-charge via http://www.escholarship.org/uc/item/6sd403pz. PMID:24928188

Validation assessment of shoreline extraction on medium resolution satellite image

NASA Astrophysics Data System (ADS)

Manaf, Syaifulnizam Abd; Mustapha, Norwati; Sulaiman, Md Nasir; Husin, Nor Azura; Shafri, Helmi Zulhaidi Mohd

2017-10-01

Monitoring coastal zones helps provide information about the conditions of the coastal zones, such as erosion or accretion. Moreover, monitoring the shorelines can help measure the severity of such conditions. Such measurement can be performed accurately by using Earth observation satellite images rather than by using traditional ground survey. To date, shorelines can be extracted from satellite images with a high degree of accuracy by using satellite image classification techniques based on machine learning to identify the land and water classes of the shorelines. In this study, the researchers validated the results of extracted shorelines of 11 classifiers using a reference shoreline provided by the local authority. Specifically, the validation assessment was performed to examine the difference between the extracted shorelines and the reference shorelines. The research findings showed that the SVM Linear was the most effective image classification technique, as evidenced from the lowest mean distance between the extracted shoreline and the reference shoreline. Furthermore, the findings showed that the accuracy of the extracted shoreline was not directly proportional to the accuracy of the image classification.

Data mining and visualization of average images in a digital hand atlas

NASA Astrophysics Data System (ADS)

Zhang, Aifeng; Gertych, Arkadiusz; Liu, Brent J.; Huang, H. K.

2005-04-01

We have collected a digital hand atlas containing digitized left hand radiographs of normally developed children grouped accordingly by age, sex, and race. A set of features stored in a database reflecting patient's stage of skeletal development has been calculated by automatic image processing procedures. This paper addresses a new concept, "average" image in the digital hand atlas. The "average" reference image in the digital atlas is selected for each of the groups of normal developed children with the best representative skeletal maturity based on bony features. A data mining procedure was designed and applied to find the average image through average feature vector matching. It also provides a temporary solution for the missing feature problem through polynomial regression. As more cases are added to the digital hand atlas, it can grow to provide clinicians accurate reference images to aid the bone age assessment process.

A high-quality human reference panel reveals the complexity and distribution of genomic structural variants.

PubMed

Hehir-Kwa, Jayne Y; Marschall, Tobias; Kloosterman, Wigard P; Francioli, Laurent C; Baaijens, Jasmijn A; Dijkstra, Louis J; Abdellaoui, Abdel; Koval, Vyacheslav; Thung, Djie Tjwan; Wardenaar, René; Renkens, Ivo; Coe, Bradley P; Deelen, Patrick; de Ligt, Joep; Lameijer, Eric-Wubbo; van Dijk, Freerk; Hormozdiari, Fereydoun; Uitterlinden, André G; van Duijn, Cornelia M; Eichler, Evan E; de Bakker, Paul I W; Swertz, Morris A; Wijmenga, Cisca; van Ommen, Gert-Jan B; Slagboom, P Eline; Boomsma, Dorret I; Schönhuth, Alexander; Ye, Kai; Guryev, Victor

2016-10-06

Structural variation (SV) represents a major source of differences between individual human genomes and has been linked to disease phenotypes. However, the majority of studies provide neither a global view of the full spectrum of these variants nor integrate them into reference panels of genetic variation. Here, we analyse whole genome sequencing data of 769 individuals from 250 Dutch families, and provide a haplotype-resolved map of 1.9 million genome variants across 9 different variant classes, including novel forms of complex indels, and retrotransposition-mediated insertions of mobile elements and processed RNAs. A large proportion are previously under reported variants sized between 21 and 100 bp. We detect 4 megabases of novel sequence, encoding 11 new transcripts. Finally, we show 191 known, trait-associated SNPs to be in strong linkage disequilibrium with SVs and demonstrate that our panel facilitates accurate imputation of SVs in unrelated individuals.

Improved maize reference genome with single-molecule technologies.

PubMed

Jiao, Yinping; Peluso, Paul; Shi, Jinghua; Liang, Tiffany; Stitzer, Michelle C; Wang, Bo; Campbell, Michael S; Stein, Joshua C; Wei, Xuehong; Chin, Chen-Shan; Guill, Katherine; Regulski, Michael; Kumari, Sunita; Olson, Andrew; Gent, Jonathan; Schneider, Kevin L; Wolfgruber, Thomas K; May, Michael R; Springer, Nathan M; Antoniou, Eric; McCombie, W Richard; Presting, Gernot G; McMullen, Michael; Ross-Ibarra, Jeffrey; Dawe, R Kelly; Hastie, Alex; Rank, David R; Ware, Doreen

2017-06-22

Complete and accurate reference genomes and annotations provide fundamental tools for characterization of genetic and functional variation. These resources facilitate the determination of biological processes and support translation of research findings into improved and sustainable agricultural technologies. Many reference genomes for crop plants have been generated over the past decade, but these genomes are often fragmented and missing complex repeat regions. Here we report the assembly and annotation of a reference genome of maize, a genetic and agricultural model species, using single-molecule real-time sequencing and high-resolution optical mapping. Relative to the previous reference genome, our assembly features a 52-fold increase in contig length and notable improvements in the assembly of intergenic spaces and centromeres. Characterization of the repetitive portion of the genome revealed more than 130,000 intact transposable elements, allowing us to identify transposable element lineage expansions that are unique to maize. Gene annotations were updated using 111,000 full-length transcripts obtained by single-molecule real-time sequencing. In addition, comparative optical mapping of two other inbred maize lines revealed a prevalence of deletions in regions of low gene density and maize lineage-specific genes.

MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping.

PubMed

Lee, Wan-Ping; Stromberg, Michael P; Ward, Alistair; Stewart, Chip; Garrison, Erik P; Marth, Gabor T

2014-01-01

MOSAIK is a stable, sensitive and open-source program for mapping second and third-generation sequencing reads to a reference genome. Uniquely among current mapping tools, MOSAIK can align reads generated by all the major sequencing technologies, including Illumina, Applied Biosystems SOLiD, Roche 454, Ion Torrent and Pacific BioSciences SMRT. Indeed, MOSAIK was the only aligner to provide consistent mappings for all the generated data (sequencing technologies, low-coverage and exome) in the 1000 Genomes Project. To provide highly accurate alignments, MOSAIK employs a hash clustering strategy coupled with the Smith-Waterman algorithm. This method is well-suited to capture mismatches as well as short insertions and deletions. To support the growing interest in larger structural variant (SV) discovery, MOSAIK provides explicit support for handling known-sequence SVs, e.g. mobile element insertions (MEIs) as well as generating outputs tailored to aid in SV discovery. All variant discovery benefits from an accurate description of the read placement confidence. To this end, MOSAIK uses a neural-network based training scheme to provide well-calibrated mapping quality scores, demonstrated by a correlation coefficient between MOSAIK assigned and actual mapping qualities greater than 0.98. In order to ensure that studies of any genome are supported, a training pipeline is provided to ensure optimal mapping quality scores for the genome under investigation. MOSAIK is multi-threaded, open source, and incorporated into our command and pipeline launcher system GKNO (http://gkno.me).

MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping

PubMed Central

Lee, Wan-Ping; Stromberg, Michael P.; Ward, Alistair; Stewart, Chip; Garrison, Erik P.; Marth, Gabor T.

2014-01-01

MOSAIK is a stable, sensitive and open-source program for mapping second and third-generation sequencing reads to a reference genome. Uniquely among current mapping tools, MOSAIK can align reads generated by all the major sequencing technologies, including Illumina, Applied Biosystems SOLiD, Roche 454, Ion Torrent and Pacific BioSciences SMRT. Indeed, MOSAIK was the only aligner to provide consistent mappings for all the generated data (sequencing technologies, low-coverage and exome) in the 1000 Genomes Project. To provide highly accurate alignments, MOSAIK employs a hash clustering strategy coupled with the Smith-Waterman algorithm. This method is well-suited to capture mismatches as well as short insertions and deletions. To support the growing interest in larger structural variant (SV) discovery, MOSAIK provides explicit support for handling known-sequence SVs, e.g. mobile element insertions (MEIs) as well as generating outputs tailored to aid in SV discovery. All variant discovery benefits from an accurate description of the read placement confidence. To this end, MOSAIK uses a neural-network based training scheme to provide well-calibrated mapping quality scores, demonstrated by a correlation coefficient between MOSAIK assigned and actual mapping qualities greater than 0.98. In order to ensure that studies of any genome are supported, a training pipeline is provided to ensure optimal mapping quality scores for the genome under investigation. MOSAIK is multi-threaded, open source, and incorporated into our command and pipeline launcher system GKNO (http://gkno.me). PMID:24599324

Identification and validation of reference genes for quantitative real-time PCR normalization and its applications in lycium.

PubMed

Zeng, Shaohua; Liu, Yongliang; Wu, Min; Liu, Xiaomin; Shen, Xiaofei; Liu, Chunzhao; Wang, Ying

2014-01-01

Lycium barbarum and L. ruthenicum are extensively used as traditional Chinese medicinal plants. Next generation sequencing technology provides a powerful tool for analyzing transcriptomic profiles of gene expression in non-model species. Such gene expression can then be confirmed with quantitative real-time polymerase chain reaction (qRT-PCR). Therefore, use of systematically identified suitable reference genes is a prerequisite for obtaining reliable gene expression data. Here, we calculated the expression stability of 18 candidate reference genes across samples from different tissues and grown under salt stress using geNorm and NormFinder procedures. The geNorm-determined rank of reference genes was similar to those defined by NormFinder with some differences. Both procedures confirmed that the single most stable reference gene was ACNTIN1 for L. barbarum fruits, H2B1 for L. barbarum roots, and EF1α for L. ruthenicum fruits. PGK3, H2B2, and PGK3 were identified as the best stable reference genes for salt-treated L. ruthenicum leaves, roots, and stems, respectively. H2B1 and GAPDH1+PGK1 for L. ruthenicum and SAMDC2+H2B1 for L. barbarum were the best single and/or combined reference genes across all samples. Finally, expression of salt-responsive gene NAC, fruit ripening candidate gene LrPG, and anthocyanin genes were investigated to confirm the validity of the selected reference genes. Suitable reference genes identified in this study provide a foundation for accurately assessing gene expression and further better understanding of novel gene function to elucidate molecular mechanisms behind particular biological/physiological processes in Lycium.

Evaluation of droplet digital PCR for characterizing plasmid reference material used for quantifying ammonia oxidizers and denitrifiers.

PubMed

Dong, Lianhua; Meng, Ying; Wang, Jing; Liu, Yingying

2014-02-01

DNA reference materials of certified value have a critical function in many analytical processes of DNA measurement. Quantification of amoA genes in ammonia oxidizing bacteria (AOB) and archaea (AOA), and of nirS and nosZ genes in the denitrifiers is very important for determining their distribution and abundance in the natural environment. A plasmid reference material containing nirS, nosZ, amoA-AOB, and amoA-AOA is developed to provide a DNA standard with copy number concentration for ensuring comparability and reliability of quantification of these genes. Droplet digital PCR (ddPCR) was evaluated for characterization of the plasmid reference material. The result revealed that restriction endonuclease digestion of plasmids can improve amplification efficiency and minimize the measurement bias of ddPCR. Compared with the conformation of the plasmid, the size of the DNA fragment containing the target sequence and the location of the restriction site relative to the target sequence are not significant factors affecting plasmid quantification by ddPCR. Liquid chromatography-isotope dilution mass spectrometry (LC-IDMS) was used to provide independent data for quantifying the plasmid reference material. The copy number concentration of the digested plasmid determined by ddPCR agreed well with that determined by LC-IDMS, improving both the accuracy and reliability of the plasmid reference material. The reference value, with its expanded uncertainty (k = 2), of the plasmid reference material was determined to be (5.19 ± 0.41) × 10(9) copies μL(-1) by averaging the results of two independent measurements. Consideration of the factors revealed in this study can improve the reliability and accuracy of ddPCR; thus, this method has the potential to accurately quantify DNA reference materials.

Accurate Measurement of the Optical Constants for Organic and Organophosphorous Liquid Layers and Drops

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

Myers, Tanya L.; Tonkyn, Russell G.; Danby, Tyler O.

We present accurate measurements for the determination of the optical constants for a series of organic liquids, including organophosphorous compounds. Bulk liquids are rarely encountered in the environment, but more commonly are present as droplets of liquids or thin layers on various substrates. Providing reference spectra to account for the plethora of morphological conditions that may be encountered under different scenarios is a challenge. An alternative approach is to provide the complex optical constants, n and k, which can be used to model the optical phenomena in media and at interfaces, minimizing the need for a vast number of laboratorymore » measurements. In this work, we present improved protocols for measuring the optical constants for a series of liquids that span the range from 7800 to 400 cm-1. The broad spectral range means that one needs to account for both the strong and weak spectral features that are encountered, all of which can be useful for detection, depending on the scenario. To span this dynamic range, both long and short cells are required for accurate measurements. The protocols are presented along with experimental and modeling results for thin layers of silicone oil on aluminum.« less

The first geocenter estimation results using GPS measurements

NASA Technical Reports Server (NTRS)

Malla, R. P.; Wu, S. C.

1990-01-01

The center of mass of the Earth is the natural and unambiguous origin of a geocentric satellite dynamical system. A geocentric reference frame assumes that the origin of its coordinate axes is at the geocenter, in which all relevant observations and results can be referred and in which geodynamic theories or models for the dynamic behavior of Earth can be formulated. In practice, however, a kinematically obtained terrestrial reference frame may assume an origin other than the geocenter. A fast and accurate method of determining origin offset from the geocenter is highly desirable. Global Positioning System (GPS) measurements, because of their abundance and broad distribution, provide a powerful tool to obtain this origin offset in a short period of time. Two effective strategies have been devised. Data from the first Central and South America (Casa Uno) global GPS experiment were studied to demonstrate the ability of recovering the geocenter location with present-day GPS satellites and receivers.

Minimally Invasive Calcaneal Displacement Osteotomy Site Using a Reference Kirschner Wire: A Technique Tip.

PubMed

Lee, Moses; Guyton, Gregory P; Zahoor, Talal; Schon, Lew C

2016-01-01

As a standard open approach, the lateral oblique incision has been widely used for calcaneal displacement osteotomy. However, just as with other orthopedic procedures that use an open approach, complications, including wound healing problems and neurovascular injury in the heel, have been reported. To help avoid these limitations, a percutaneous technique using a Shannon burr for calcaneal displacement osteotomy was introduced. However, relying on a free-hand technique without direct visualization at the osteotomy site has been a major obstacle for this technique. To address this problem, we developed a technical tip using a reference Kirschner wire. A reference Kirschner wire technique provides a reliable and accurate guide for minimally invasive calcaneal displacement osteotomy. Also, the technique should be easy to learn for surgeons new to the procedure. Copyright © 2016 American College of Foot and Ankle Surgeons. Published by Elsevier Inc. All rights reserved.

How accurately can the peak skin dose in fluoroscopy be determined using indirect dose metrics?

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

Jones, A. Kyle, E-mail: kyle.jones@mdanderson.org; Ensor, Joe E.; Pasciak, Alexander S.

Purpose: Skin dosimetry is important for fluoroscopically-guided interventions, as peak skin doses (PSD) that result in skin reactions can be reached during these procedures. There is no consensus as to whether or not indirect skin dosimetry is sufficiently accurate for fluoroscopically-guided interventions. However, measuring PSD with film is difficult and the decision to do so must be madea priori. The purpose of this study was to assess the accuracy of different types of indirect dose estimates and to determine if PSD can be calculated within ±50% using indirect dose metrics for embolization procedures. Methods: PSD were measured directly using radiochromicmore » film for 41 consecutive embolization procedures at two sites. Indirect dose metrics from the procedures were collected, including reference air kerma. Four different estimates of PSD were calculated from the indirect dose metrics and compared along with reference air kerma to the measured PSD for each case. The four indirect estimates included a standard calculation method, the use of detailed information from the radiation dose structured report, and two simplified calculation methods based on the standard method. Indirect dosimetry results were compared with direct measurements, including an analysis of uncertainty associated with film dosimetry. Factors affecting the accuracy of the different indirect estimates were examined. Results: When using the standard calculation method, calculated PSD were within ±35% for all 41 procedures studied. Calculated PSD were within ±50% for a simplified method using a single source-to-patient distance for all calculations. Reference air kerma was within ±50% for all but one procedure. Cases for which reference air kerma or calculated PSD exhibited large (±35%) differences from the measured PSD were analyzed, and two main causative factors were identified: unusually small or large source-to-patient distances and large contributions to reference air kerma from cone beam computed tomography or acquisition runs acquired at large primary gantry angles. When calculated uncertainty limits [−12.8%, 10%] were applied to directly measured PSD, most indirect PSD estimates remained within ±50% of the measured PSD. Conclusions: Using indirect dose metrics, PSD can be determined within ±35% for embolization procedures. Reference air kerma can be used without modification to set notification limits and substantial radiation dose levels, provided the displayed reference air kerma is accurate. These results can reasonably be extended to similar procedures, including vascular and interventional oncology. Considering these results, film dosimetry is likely an unnecessary effort for these types of procedures when indirect dose metrics are available.« less

An Evaluation of Portable Wet Bulb Globe Temperature Monitor Accuracy.

PubMed

Cooper, Earl; Grundstein, Andrew; Rosen, Adam; Miles, Jessica; Ko, Jupil; Curry, Patrick

2017-12-01

  Wet bulb globe temperature (WBGT) is the gold standard for assessing environmental heat stress during physical activity. Many manufacturers of commercially available instruments fail to report WBGT accuracy.   To determine the accuracy of several commercially available WBGT monitors compared with a standardized reference device.   Observational study.   Field test.   Six commercially available WBGT devices.   Data were recorded for 3 sessions (1 in the morning and 2 in the afternoon) at 2-minute intervals for at least 2 hours. Mean absolute error (MAE), root mean square error (RMSE), mean bias error (MBE), and the Pearson correlation coefficient ( r) were calculated to determine instrument performance compared with the reference unit.   The QUESTemp° 34 (MAE = 0.24°C, RMSE = 0.44°C, MBE = -0.64%) and Extech HT30 Heat Stress Wet Bulb Globe Temperature Meter (Extech; MAE = 0.61°C, RMSE = 0.79°C, MBE = 0.44%) demonstrated the least error in relation to the reference standard, whereas the General WBGT8778 Heat Index Checker (General; MAE = 1.18°C, RMSE = 1.34°C, MBE = 4.25%) performed the poorest. The QUESTemp° 34 and Kestrel 4400 Heat Stress Tracker units provided conservative measurements that slightly overestimated the WBGT provided by the reference unit. Finally, instruments using the psychrometric wet bulb temperature (General, REED Heat Index WBGT Meter, and WBGT-103 Heat Stroke Checker) tended to underestimate the WBGT, and the resulting values more frequently fell into WBGT-based activity categories with fewer restrictions as defined by the American College of Sports Medicine.   The QUESTemp° 34, followed by the Extech, had the smallest error compared with the reference unit. Moreover, the QUESTemp° 34, Extech, and Kestrel units appeared to offer conservative yet accurate assessments of the WBGT, potentially minimizing the risk of allowing physical activity to continue in stressful heat environments. Instruments using the psychrometric wet bulb temperature tended to underestimate WBGT under low wind-speed conditions. Accurate WBGT interpretations are important to enable clinicians to guide activities in hot and humid weather conditions.

Determination of reference values for optical properties of liquid phantoms based on Intralipid and India ink

PubMed Central

Spinelli, L.; Botwicz, M.; Zolek, N.; Kacprzak, M.; Milej, D.; Sawosz, P.; Liebert, A.; Weigel, U.; Durduran, T.; Foschum, F.; Kienle, A.; Baribeau, F.; Leclair, S.; Bouchard, J.-P.; Noiseux, I.; Gallant, P.; Mermut, O.; Farina, A.; Pifferi, A.; Torricelli, A.; Cubeddu, R.; Ho, H.-C.; Mazurenka, M.; Wabnitz, H.; Klauenberg, K.; Bodnar, O.; Elster, C.; Bénazech-Lavoué, M.; Bérubé-Lauzière, Y.; Lesage, F.; Khoptyar, D.; Subash, A. A.; Andersson-Engels, S.; Di Ninni, P.; Martelli, F.; Zaccanti, G.

2014-01-01

A multi-center study has been set up to accurately characterize the optical properties of diffusive liquid phantoms based on Intralipid and India ink at near-infrared (NIR) wavelengths. Nine research laboratories from six countries adopting different measurement techniques, instrumental set-ups, and data analysis methods determined at their best the optical properties and relative uncertainties of diffusive dilutions prepared with common samples of the two compounds. By exploiting a suitable statistical model, comprehensive reference values at three NIR wavelengths for the intrinsic absorption coefficient of India ink and the intrinsic reduced scattering coefficient of Intralipid-20% were determined with an uncertainty of about 2% or better, depending on the wavelength considered, and 1%, respectively. Even if in this study we focused on particular batches of India ink and Intralipid, the reference values determined here represent a solid and useful starting point for preparing diffusive liquid phantoms with accurately defined optical properties. Furthermore, due to the ready availability, low cost, long-term stability and batch-to-batch reproducibility of these compounds, they provide a unique fundamental tool for the calibration and performance assessment of diffuse optical spectroscopy instrumentation intended to be used in laboratory or clinical environment. Finally, the collaborative work presented here demonstrates that the accuracy level attained in this work for optical properties of diffusive phantoms is reliable. PMID:25071947

Characterizing tissue microstructure using an ultrasound system-independent spatial autocorrelation function

NASA Astrophysics Data System (ADS)

Dong, Fang

1999-09-01

The research described in this dissertation is related to characterization of tissue microstructure using a system- independent spatial autocorrelation function (SAF). The function was determined using a reference phantom method, which employed a well-defined ``point- scatterer'' reference phantom to account for instrumental factors. The SAF's were estimated for several tissue-mimicking (TM) phantoms and fresh dog livers. Both phantom tests and in vitro dog liver measurements showed that the reference phantom method is relatively simple and fairly accurate, providing the bandwidth of the measurement system is sufficient for the size of the scatterer being involved in the scattering process. Implementation of this method in clinical scanner requires that distortions from patient's body wall be properly accounted for. The SAF's were estimated for two phantoms with body-wall-like distortions. The experimental results demonstrated that body wall distortions have little effect if echo data are acquired from a large scattering volume. One interesting application of the SAF is to form a ``scatterer size image''. The scatterer size image may help providing diagnostic tools for those diseases in which the tissue microstructure is different from the normal. Another method, the BSC method, utilizes information contained in the frequency dependence of the backscatter coefficient to estimate the scatterer size. The SAF technique produced accurate scatterer size images of homogeneous TM phantoms and the BSC method was capable of generating accurate size images for heterogeneous phantoms. In the scatterer size image of dog kidneys, the contrast-to-noise-ratio (CNR) between renal cortex and medulla was improved dramatically compared to the gray- scale image. The effect of nonlinear propagation was investigated by using a custom-designed phantom with overlaying TM fat layer. The results showed that the correlation length decreased when the transmitting power increased. The measurement results support the assumption that nonlinear propagation generates harmonic energies and causes underestimation of scatterer diameters. Nonlinear propagation can be further enhanced by those materials with high B/A value-a parameter which characterizes the degree of nonlinearity. Nine versions of TM fat and non-fat materials were measured for their B/A values using a new measurement technique, the ``simplified finite amplitude insertion substitution'' (SFAIS) method.

Canine and feline hematology reference values for the ADVIA 120 hematology system.

PubMed

Moritz, Andreas; Fickenscher, Yvonne; Meyer, Karin; Failing, Klaus; Weiss, Douglas J

2004-01-01

The ADVIA 120 is a laser-based hematology analyzer with software applications for animal species. Accurate reference values would be useful for the assessment of new hematologic parameters and for interlaboratory comparisons. The goal of this study was to establish reference intervals for CBC results and new parameters for RBC morphology, reticulocytes, and platelets in healthy dogs and cats using the ADVIA 120 hematology system. The ADVIA 120, with multispecies software (version 1.107-MS), was used to analyze whole blood samples from clinically healthy dogs (n=46) and cats (n=61). Data distribution was determined and reference intervals were calculated as 2.5 to 97.5 percentiles and 25 to 75 percentiles. Most data showed Gaussian or log-normal distribution. The numbers of RBCs falling outside the normocytic-normochromic range were slightly higher in cats than in dogs. Both dogs and cats had reticulocytes with low, medium, and high absorbance. Mean numbers of large platelets and platelet clumps were higher in cats compared with dogs. Reference intervals obtained on the ADVIA 120 provide valuable baseline information for assessing new hematologic parameters and for interlaboratory comparisons. Differences compared with previously published reference values can be attributed largely to differences in methodology.

High-speed spectral calibration by complex FIR filter in phase-sensitive optical coherence tomography.

PubMed

Kim, Sangmin; Raphael, Patrick D; Oghalai, John S; Applegate, Brian E

2016-04-01

Swept-laser sources offer a number of advantages for Phase-sensitive Optical Coherence Tomography (PhOCT). However, inter- and intra-sweep variability leads to calibration errors that adversely affect phase sensitivity. While there are several approaches to overcoming this problem, our preferred method is to simply calibrate every sweep of the laser. This approach offers high accuracy and phase stability at the expense of a substantial processing burden. In this approach, the Hilbert phase of the interferogram from a reference interferometer provides the instantaneous wavenumber of the laser, but is computationally expensive. Fortunately, the Hilbert transform may be approximated by a Finite Impulse-Response (FIR) filter. Here we explore the use of several FIR filter based Hilbert transforms for calibration, explicitly considering the impact of filter choice on phase sensitivity and OCT image quality. Our results indicate that the complex FIR filter approach is the most robust and accurate among those considered. It provides similar image quality and slightly better phase sensitivity than the traditional FFT-IFFT based Hilbert transform while consuming fewer resources in an FPGA implementation. We also explored utilizing the Hilbert magnitude of the reference interferogram to calculate an ideal window function for spectral amplitude calibration. The ideal window function is designed to carefully control sidelobes on the axial point spread function. We found that after a simple chromatic correction, calculating the window function using the complex FIR filter and the reference interferometer gave similar results to window functions calculated using a mirror sample and the FFT-IFFT Hilbert transform. Hence, the complex FIR filter can enable accurate and high-speed calibration of the magnitude and phase of spectral interferograms.

High-speed spectral calibration by complex FIR filter in phase-sensitive optical coherence tomography

PubMed Central

Kim, Sangmin; Raphael, Patrick D.; Oghalai, John S.; Applegate, Brian E.

2016-01-01

Swept-laser sources offer a number of advantages for Phase-sensitive Optical Coherence Tomography (PhOCT). However, inter- and intra-sweep variability leads to calibration errors that adversely affect phase sensitivity. While there are several approaches to overcoming this problem, our preferred method is to simply calibrate every sweep of the laser. This approach offers high accuracy and phase stability at the expense of a substantial processing burden. In this approach, the Hilbert phase of the interferogram from a reference interferometer provides the instantaneous wavenumber of the laser, but is computationally expensive. Fortunately, the Hilbert transform may be approximated by a Finite Impulse-Response (FIR) filter. Here we explore the use of several FIR filter based Hilbert transforms for calibration, explicitly considering the impact of filter choice on phase sensitivity and OCT image quality. Our results indicate that the complex FIR filter approach is the most robust and accurate among those considered. It provides similar image quality and slightly better phase sensitivity than the traditional FFT-IFFT based Hilbert transform while consuming fewer resources in an FPGA implementation. We also explored utilizing the Hilbert magnitude of the reference interferogram to calculate an ideal window function for spectral amplitude calibration. The ideal window function is designed to carefully control sidelobes on the axial point spread function. We found that after a simple chromatic correction, calculating the window function using the complex FIR filter and the reference interferometer gave similar results to window functions calculated using a mirror sample and the FFT-IFFT Hilbert transform. Hence, the complex FIR filter can enable accurate and high-speed calibration of the magnitude and phase of spectral interferograms. PMID:27446666

Variation in Responses of Fishes across Multiple Reserves within a Network of Marine Protected Areas in Temperate Waters

PubMed Central

Starr, Richard M.; Wendt, Dean E.; Barnes, Cheryl L.; Marks, Corina I.; Malone, Dan; Waltz, Grant; Schmidt, Katherine T.; Chiu, Jennifer; Launer, Andrea L.; Hall, Nathan C.; Yochum, Noëlle

2015-01-01

Meta-analyses of field studies have shown that biomass, density, species richness, and size of organisms protected by no-take marine reserves generally increase over time. The magnitude and timing of changes in these response variables, however, vary greatly and depend upon the taxonomic groups protected, size and type of reserve, oceanographic regime, and time since the reserve was implemented. We conducted collaborative, fishery-independent surveys of fishes for seven years in and near newly created marine protected areas (MPAs) in central California, USA. Results showed that initially most MPAs contained more and larger fishes than associated reference sites, likely due to differences in habitat quality. The differences between MPAs and reference sites did not greatly change over the seven years of our study, indicating that reserve benefits will be slow to accumulate in California’s temperate eastern boundary current. Fishes in an older reserve that has been closed to fishing since 1973, however, were significantly more abundant and larger than those in associated reference sites. This indicates that reserve benefits are likely to accrue in the California Current ecosystem, but that 20 years or more may be needed to detect significant changes in response variables that are due to MPA implementation. Because of the high spatial and temporal variability of fish recruitment patterns, long-term monitoring is needed to identify positive responses of fishes to protection in the diverse set of habitats in a dynamic eastern boundary current. Qualitative estimates of response variables, such as would be obtained from an expert opinion process, are unlikely to provide an accurate description of MPA performance. Similarly, using one species or one MPA as an indicator is unlikely to provide sufficient resolution to accurately describe the performance of multiple MPAs. PMID:25760856

Astrometric surveys in the Gaia era

NASA Astrophysics Data System (ADS)

Zacharias, Norbert

2018-04-01

The Gaia first data release (DR1) already provides an almost error free optical reference frame on the milli-arcsecond (mas) level allowing significantly better calibration of ground-based astrometric data than ever before. Gaia DR1 provides positions, proper motions and trigonometric parallaxes for just over 2 million stars in the Tycho-2 catalog. For over 1.1 billion additional stars DR1 gives positions. Proper motions for these, mainly fainter stars (G >= 11.5) are currently provided by several new projects which combine earlier epoch ground-based observations with Gaia DR1 positions. These data are very helpful in the interim period but will become obsolete with the second Gaia data release (DR2) expected in April 2018. The era of traditional, ground-based, wide-field astrometry with the goal to provide accurate reference stars has come to an end. Future ground-based astrometry will fill in some gaps (very bright stars, observations needed at many or specific epochs) and mainly will go fainter than the Gaia limit, like the PanSTARRS and the upcoming LSST surveys.

In-vitro evaluation of the accuracy of conventional and digital methods of obtaining full-arch dental impressions.

PubMed

Ender, Andreas; Mehl, Albert

2015-01-01

To investigate the accuracy of conventional and digital impression methods used to obtain full-arch impressions by using an in-vitro reference model. Eight different conventional (polyether, POE; vinylsiloxanether, VSE; direct scannable vinylsiloxanether, VSES; and irreversible hydrocolloid, ALG) and digital (CEREC Bluecam, CER; CEREC Omnicam, OC; Cadent iTero, ITE; and Lava COS, LAV) full-arch impressions were obtained from a reference model with a known morphology, using a highly accurate reference scanner. The impressions obtained were then compared with the original geometry of the reference model and within each test group. A point-to-point measurement of the surface of the model using the signed nearest neighbour method resulted in a mean (10%-90%)/2 percentile value for the difference between the impression and original model (trueness) as well as the difference between impressions within a test group (precision). Trueness values ranged from 11.5 μm (VSE) to 60.2 μm (POE), and precision ranged from 12.3 μm (VSE) to 66.7 μm (POE). Among the test groups, VSE, VSES, and CER showed the highest trueness and precision. The deviation pattern varied with the impression method. Conventional impressions showed high accuracy across the full dental arch in all groups, except POE and ALG. Conventional and digital impression methods show differences regarding full-arch accuracy. Digital impression systems reveal higher local deviations of the full-arch model. Digital intraoral impression systems do not show superior accuracy compared to highly accurate conventional impression techniques. However, they provide excellent clinical results within their indications applying the correct scanning technique.

Accurate mass measurement by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry. II. Measurement of negative radical ions using porphyrin and fullerene standard reference materials.

PubMed

Shao, Zhecheng; Wyatt, Mark F; Stein, Bridget K; Brenton, A Gareth

2010-10-30

A method for the accurate mass measurement of negative radical ions by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOFMS) is described. This is an extension to our previously described method for the accurate mass measurement of positive radical ions (Griffiths NW, Wyatt MF, Kean SD, Graham AE, Stein BK, Brenton AG. Rapid Commun. Mass Spectrom. 2010; 24: 1629). The porphyrin standard reference materials (SRMs) developed for positive mode measurements cannot be observed in negative ion mode, so fullerene and fluorinated porphyrin compounds were identified as effective SRMs. The method is of immediate practical use for the accurate mass measurement of functionalised fullerenes, for which negative ion MALDI-TOFMS is the principal mass spectrometry characterisation technique. This was demonstrated by the accurate mass measurement of six functionalised C(60) compounds. Copyright © 2010 John Wiley & Sons, Ltd.

Multicomponent blood lipid analysis by means of near infrared spectroscopy, in geese.

PubMed

Bazar, George; Eles, Viktoria; Kovacs, Zoltan; Romvari, Robert; Szabo, Andras

2016-08-01

This study provides accurate near infrared (NIR) spectroscopic models on some laboratory determined clinicochemical parameters (i.e. total lipid (5.57±1.95 g/l), triglyceride (2.59±1.36 mmol/l), total cholesterol (3.81±0.68 mmol/l), high density lipoprotein (HDL) cholesterol (2.45±0.58 mmol/l)) of blood serum samples of fattened geese. To increase the performance of multivariate chemometrics, samples significantly deviating from the regression models implying laboratory error were excluded from the final calibration datasets. Reference data of excluded samples having outlier spectra in principal component analysis were not marked as false. Samples deviating from the regression models but having non outlier spectra in PCA were identified as having false reference constituent values. Based on the NIR selection methods, 5% of the reference measurement data were rated as doubtful. The achieved models reached R(2) of 0.864, 0.966, 0.850, 0.793, and RMSE of 0.639 g/l, 0.232 mmol/l, 0.210 mmol/l, 0.241 mmol/l for total lipid, triglyceride, total cholesterol and HDL cholesterol, respectively, during independent validation. Classical analytical techniques focus on single constituents and often require chemicals, time-consuming measurements, and experienced technicians. NIR technique provides a quick, cost effective, non-hazardous alternative method for analysis of several constituents based on one single spectrum of each sample, and it also offers the possibility for looking at the laboratory reference data critically. Evaluation of reference data to identify and exclude falsely analyzed samples can provide warning feedback to the reference laboratory, especially in the case of analyses where laboratory methods are not perfectly suited to the subjected material and there is an increased chance of laboratory error. Copyright © 2016 Elsevier B.V. All rights reserved.

A comparison of three infant skinfold reference standards: Tanner-Whitehouse, Cambridge Infant Growth Study, and WHO Child Growth Standards.

PubMed

Miller, Elizabeth M

2015-10-01

As researchers increasingly focus on early infancy as a critical period of development, there is a greater need for methodological tools that can address all aspects of infant growth. Infant skinfold measures, in particular, are measurements in need of reliable reference standards that encompass all ages of infants and provide an accurate assessment of the relative fatness of a population. This report evaluates three published reference standards for infant skinfold measurements: Tanner-Whitehouse, Cambridge Infant Growth Study, and the World Health Organization (WHO) Child Growth Standards. To assess these standards, triceps skinfolds from a population of rural Kenyan infants (n = 250) and triceps skinfolds and subscapular skinfolds from infants in the National Health and Nutrition Examination Survey 1999-2002 (NHANES; n = 1197) were calculated as z-scores from the lambda-mu-sigma curves provided by each reference population. The Tanner-Whitehouse standards represented both the Kenyan and US populations as lean, while the Cambridge standards represented both populations as overfat. The distribution of z-scores based on the WHO standards fell in the middle, but excluded infants from both populations who were below the age of 3 months. Based on these results, the WHO reference standard is the best skinfold reference standard for infants over the age of 3 months. For populations with infants of all ages, the Tanner-Whitehouse standards are recommended, despite representing both study populations as underfat. Ideally, the WHO will extend their reference standard to include infants between the ages of 0 and 3 months. © 2014 John Wiley & Sons Ltd.

Bushland Reference ET Calculator with QA/QC capabilities and iPhone/iPad application

USDA-ARS?s Scientific Manuscript database

Accurate daily reference evapotranspiration (ET) values are needed to estimate crop water demand for irrigation management and hydrologic modeling purposes. The USDA-ARS Conservation and Production Research Laboratory at Bushland, Texas developed the Bushland Reference ET (BET) Calculator for calcul...

RNA-seq reveals more consistent reference genes for gene expression studies in human non-melanoma skin cancers

PubMed Central

Tan, Jean-Marie; Payne, Elizabeth J.; Lin, Lynlee L.; Sinnya, Sudipta; Raphael, Anthony P.; Lambie, Duncan; Frazer, Ian H.; Dinger, Marcel E.; Soyer, H. Peter

2017-01-01

Identification of appropriate reference genes (RGs) is critical to accurate data interpretation in quantitative real-time PCR (qPCR) experiments. In this study, we have utilised next generation RNA sequencing (RNA-seq) to analyse the transcriptome of a panel of non-melanoma skin cancer lesions, identifying genes that are consistently expressed across all samples. Genes encoding ribosomal proteins were amongst the most stable in this dataset. Validation of this RNA-seq data was examined using qPCR to confirm the suitability of a set of highly stable genes for use as qPCR RGs. These genes will provide a valuable resource for the normalisation of qPCR data for the analysis of non-melanoma skin cancer. PMID:28852586

Orbital-free bond breaking via machine learning

NASA Astrophysics Data System (ADS)

Snyder, John C.; Rupp, Matthias; Hansen, Katja; Blooston, Leo; Müller, Klaus-Robert; Burke, Kieron

2013-12-01

Using a one-dimensional model, we explore the ability of machine learning to approximate the non-interacting kinetic energy density functional of diatomics. This nonlinear interpolation between Kohn-Sham reference calculations can (i) accurately dissociate a diatomic, (ii) be systematically improved with increased reference data and (iii) generate accurate self-consistent densities via a projection method that avoids directions with no data. With relatively few densities, the error due to the interpolation is smaller than typical errors in standard exchange-correlation functionals.

Absolute and relative height-pixel accuracy of SRTM-GL1 over the South American Andean Plateau

NASA Astrophysics Data System (ADS)

Satge, Frédéric; Denezine, Matheus; Pillco, Ramiro; Timouk, Franck; Pinel, Sébastien; Molina, Jorge; Garnier, Jérémie; Seyler, Frédérique; Bonnet, Marie-Paule

2016-11-01

Previously available only over the Continental United States (CONUS), the 1 arc-second mesh size (spatial resolution) SRTM-GL1 (Shuttle Radar Topographic Mission - Global 1) product has been freely available worldwide since November 2014. With a relatively small mesh size, this digital elevation model (DEM) provides valuable topographic information over remote regions. SRTM-GL1 is assessed for the first time over the South American Andean Plateau in terms of both the absolute and relative vertical point-to-point accuracies at the regional scale and for different slope classes. For comparison, SRTM-v4 and GDEM-v2 Global DEM version 2 (GDEM-v2) generated by ASTER (Advanced Spaceborne Thermal Emission and Reflection Radiometer) are also considered. A total of approximately 160,000 ICESat/GLAS (Ice, Cloud and Land Elevation Satellite/Geoscience Laser Altimeter System) data are used as ground reference measurements. Relative error is often neglected in DEM assessments due to the lack of reference data. A new methodology is proposed to assess the relative accuracies of SRTM-GL1, SRTM-v4 and GDEM-v2 based on a comparison with ICESat/GLAS measurements. Slope values derived from DEMs and ICESat/GLAS measurements from approximately 265,000 ICESat/GLAS point pairs are compared using quantitative and categorical statistical analysis introducing a new index: the False Slope Ratio (FSR). Additionally, a reference hydrological network is derived from Google Earth and compared with river networks derived from the DEMs to assess each DEM's potential for hydrological applications over the region. In terms of the absolute vertical accuracy on a global scale, GDEM-v2 is the most accurate DEM, while SRTM-GL1 is more accurate than SRTM-v4. However, a simple bias correction makes SRTM-GL1 the most accurate DEM over the region in terms of vertical accuracy. The relative accuracy results generally did not corroborate the absolute vertical accuracy. GDEM-v2 presents the lowest statistical results based on the relative accuracy, while SRTM-GL1 is the most accurate. Vertical accuracy and relative accuracy are two independent components that must be jointly considered when assessing a DEM's potential. DEM accuracies increased with slope. In terms of hydrological potential, SRTM products are more accurate than GDEM-v2. However, the DEMs exhibit river extraction limitations over the region due to the low regional slope gradient.

Identification of Importin 8 (IPO8) as the most accurate reference gene for the clinicopathological analysis of lung specimens

PubMed Central

Nguewa, Paul A; Agorreta, Jackeline; Blanco, David; Lozano, Maria Dolores; Gomez-Roman, Javier; Sanchez, Blas A; Valles, Iñaki; Pajares, Maria J; Pio, Ruben; Rodriguez, Maria Jose; Montuenga, Luis M; Calvo, Alfonso

2008-01-01

Background The accurate normalization of differentially expressed genes in lung cancer is essential for the identification of novel therapeutic targets and biomarkers by real time RT-PCR and microarrays. Although classical "housekeeping" genes, such as GAPDH, HPRT1, and beta-actin have been widely used in the past, their accuracy as reference genes for lung tissues has not been proven. Results We have conducted a thorough analysis of a panel of 16 candidate reference genes for lung specimens and lung cell lines. Gene expression was measured by quantitative real time RT-PCR and expression stability was analyzed with the softwares GeNorm and NormFinder, mean of |ΔCt| (= |Ct Normal-Ct tumor|) ± SEM, and correlation coefficients among genes. Systematic comparison between candidates led us to the identification of a subset of suitable reference genes for clinical samples: IPO8, ACTB, POLR2A, 18S, and PPIA. Further analysis showed that IPO8 had a very low mean of |ΔCt| (0.70 ± 0.09), with no statistically significant differences between normal and malignant samples and with excellent expression stability. Conclusion Our data show that IPO8 is the most accurate reference gene for clinical lung specimens. In addition, we demonstrate that the commonly used genes GAPDH and HPRT1 are inappropriate to normalize data derived from lung biopsies, although they are suitable as reference genes for lung cell lines. We thus propose IPO8 as a novel reference gene for lung cancer samples. PMID:19014639

Selecting and validating reference genes for quantitative real-time PCR in Plutella xylostella (L.).

PubMed

You, Yanchun; Xie, Miao; Vasseur, Liette; You, Minsheng

2018-05-01

Gene expression analysis provides important clues regarding gene functions, and quantitative real-time PCR (qRT-PCR) is a widely used method in gene expression studies. Reference genes are essential for normalizing and accurately assessing gene expression. In the present study, 16 candidate reference genes (ACTB, CyPA, EF1-α, GAPDH, HSP90, NDPk, RPL13a, RPL18, RPL19, RPL32, RPL4, RPL8, RPS13, RPS4, α-TUB, and β-TUB) from Plutella xylostella were selected to evaluate gene expression stability across different experimental conditions using five statistical algorithms (geNorm, NormFinder, Delta Ct, BestKeeper, and RefFinder). The results suggest that different reference genes or combinations of reference genes are suitable for normalization in gene expression studies of P. xylostella according to the different developmental stages, strains, tissues, and insecticide treatments. Based on the given experimental sets, the most stable reference genes were RPS4 across different developmental stages, RPL8 across different strains and tissues, and EF1-α across different insecticide treatments. A comprehensive and systematic assessment of potential reference genes for gene expression normalization is essential for post-genomic functional research in P. xylostella, a notorious pest with worldwide distribution and a high capacity to adapt and develop resistance to insecticides.

Extraction and Analysis of Traditional Chinese Medicine Crops Based on Multitemporal High Resolution Data-Taking Qiaocheng District of Bozhou as AN Example

NASA Astrophysics Data System (ADS)

Yu, H.; He, J.; Zhou, H.; Guan, F.; Li, L.; Ren, B.; Wang, Z.

2018-04-01

Remote sensing technology has become an important method to rapidly acquireing of planting layout and composition of regional crops.It is very important to accurately master the planting area of Chinese medicine crops in the Characteristic planting area because it relations to accurately master the cultivation of Chinese medicine crops, formulate related policies and adjustment of crop planting structure.The author puts forward a method of using remote sencing technology for momitoring Chinese medicine which has good applicability and generalization. This paper took Qiaocheng District of Bozhou as an example to Verify the feasibility of the method, providing a reference for solving the problem of interpretation and extraction of Chinese medicinal materials in the region.

CAR: contig assembly of prokaryotic draft genomes using rearrangements.

PubMed

Lu, Chin Lung; Chen, Kun-Tze; Huang, Shih-Yuan; Chiu, Hsien-Tai

2014-11-28

Next generation sequencing technology has allowed efficient production of draft genomes for many organisms of interest. However, most draft genomes are just collections of independent contigs, whose relative positions and orientations along the genome being sequenced are unknown. Although several tools have been developed to order and orient the contigs of draft genomes, more accurate tools are still needed. In this study, we present a novel reference-based contig assembly (or scaffolding) tool, named as CAR, that can efficiently and more accurately order and orient the contigs of a prokaryotic draft genome based on a reference genome of a related organism. Given a set of contigs in multi-FASTA format and a reference genome in FASTA format, CAR can output a list of scaffolds, each of which is a set of ordered and oriented contigs. For validation, we have tested CAR on a real dataset composed of several prokaryotic genomes and also compared its performance with several other reference-based contig assembly tools. Consequently, our experimental results have shown that CAR indeed performs better than all these other reference-based contig assembly tools in terms of sensitivity, precision and genome coverage. CAR serves as an efficient tool that can more accurately order and orient the contigs of a prokaryotic draft genome based on a reference genome. The web server of CAR is freely available at http://genome.cs.nthu.edu.tw/CAR/ and its stand-alone program can also be downloaded from the same website.

snoU6 and 5S RNAs are not reliable miRNA reference genes in neuronal differentiation.

PubMed

Lim, Q E; Zhou, L; Ho, Y K; Wan, G; Too, H P

2011-12-29

Accurate profiling of microRNAs (miRNAs) is an essential step for understanding the functional significance of these small RNAs in both physiological and pathological processes. Quantitative real-time PCR (qPCR) has gained acceptance as a robust and reliable transcriptomic method to profile subtle changes in miRNA levels and requires reference genes for accurate normalization of gene expression. 5S and snoU6 RNAs are commonly used as reference genes in microRNA quantification. It is currently unknown if these small RNAs are stably expressed during neuronal differentiation. Panels of miRNAs have been suggested as alternative reference genes to 5S and snoU6 in various physiological contexts. To test the hypothesis that miRNAs may serve as stable references during neuronal differentiation, the expressions of eight miRNAs, 5S and snoU6 RNAs in five differentiating neuronal cell types were analyzed using qPCR. The stabilities of the expressions were evaluated using two complementary statistical approaches (geNorm and Normfinder). Expressions of 5S and snoU6 RNAs were stable under some but not all conditions of neuronal differentiation and thus are not suitable reference genes. In contrast, a combination of three miRNAs (miR-103, miR-106b and miR-26b) allowed accurate expression normalization across different models of neuronal differentiation. Copyright © 2011 IBRO. Published by Elsevier Ltd. All rights reserved.

Accuracy and variability of tumor burden measurement on multi-parametric MRI

NASA Astrophysics Data System (ADS)

Salarian, Mehrnoush; Gibson, Eli; Shahedi, Maysam; Gaed, Mena; Gómez, José A.; Moussa, Madeleine; Romagnoli, Cesare; Cool, Derek W.; Bastian-Jordan, Matthew; Chin, Joseph L.; Pautler, Stephen; Bauman, Glenn S.; Ward, Aaron D.

2014-03-01

Measurement of prostate tumour volume can inform prognosis and treatment selection, including an assessment of the suitability and feasibility of focal therapy, which can potentially spare patients the deleterious side effects of radical treatment. Prostate biopsy is the clinical standard for diagnosis but provides limited information regarding tumour volume due to sparse tissue sampling. A non-invasive means for accurate determination of tumour burden could be of clinical value and an important step toward reduction of overtreatment. Multi-parametric magnetic resonance imaging (MPMRI) is showing promise for prostate cancer diagnosis. However, the accuracy and inter-observer variability of prostate tumour volume estimation based on separate expert contouring of T2-weighted (T2W), dynamic contrastenhanced (DCE), and diffusion-weighted (DW) MRI sequences acquired using an endorectal coil at 3T is currently unknown. We investigated this question using a histologic reference standard based on a highly accurate MPMRIhistology image registration and a smooth interpolation of planimetric tumour measurements on histology. Our results showed that prostate tumour volumes estimated based on MPMRI consistently overestimated histological reference tumour volumes. The variability of tumour volume estimates across the different pulse sequences exceeded interobserver variability within any sequence. Tumour volume estimates on DCE MRI provided the lowest inter-observer variability and the highest correlation with histology tumour volumes, whereas the apparent diffusion coefficient (ADC) maps provided the lowest volume estimation error. If validated on a larger data set, the observed correlations could support the development of automated prostate tumour volume segmentation algorithms as well as correction schemes for tumour burden estimation on MPMRI.

An Optical Fibre Depth (Pressure) Sensor for Remote Operated Vehicles in Underwater Applications

PubMed Central

Duraibabu, Dinesh Babu; Poeggel, Sven; Omerdic, Edin; Capocci, Romano; Lewis, Elfed; Newe, Thomas; Leen, Gabriel; Toal, Daniel; Dooly, Gerard

2017-01-01

A miniature sensor for accurate measurement of pressure (depth) with temperature compensation in the ocean environment is described. The sensor is based on an optical fibre Extrinsic Fabry-Perot interferometer (EFPI) combined with a Fibre Bragg Grating (FBG). The EFPI provides pressure measurements while the Fibre Bragg Grating (FBG) provides temperature measurements. The sensor is mechanically robust, corrosion-resistant and suitable for use in underwater applications. The combined pressure and temperature sensor system was mounted on-board a mini remotely operated underwater vehicle (ROV) in order to monitor the pressure changes at various depths. The reflected optical spectrum from the sensor was monitored online and a pressure or temperature change caused a corresponding observable shift in the received optical spectrum. The sensor exhibited excellent stability when measured over a 2 h period underwater and its performance is compared with a commercially available reference sensor also mounted on the ROV. The measurements illustrates that the EFPI/FBG sensor is more accurate for depth measurements (depth of ~0.020 m). PMID:28218727

Image Geometric Corrections for a New EMCCD-based Dual Modular X-ray Imager

PubMed Central

Qu, Bin; Huang, Ying; Wang, Weiyuan; Cartwright, Alexander N.; Titus, Albert H.; Bednarek, Daniel R.; Rudin, Stephen

2012-01-01

An EMCCD-based dual modular x-ray imager was recently designed and developed from the component level, providing a high dynamic range of 53 dB and an effective pixel size of 26 μm for angiography and fluoroscopy. The unique 2×1 array design efficiently increased the clinical field of view, and also can be readily expanded to an M×N array implementation. Due to the alignment mismatches between the EMCCD sensors and the fiber optic tapers in each module, the output images or video sequences result in a misaligned 2048×1024 digital display if uncorrected. In this paper, we present a method for correcting display registration using a custom-designed two layer printed circuit board. This board was designed with grid lines to serve as the calibration pattern, and provides an accurate reference and sufficient contrast to enable proper display registration. Results show an accurate and fine stitching of the two outputs from the two modules. PMID:22254882

Chaos synchronization and Nelder-Mead search for parameter estimation in nonlinear pharmacological systems: Estimating tumor antigenicity in a model of immunotherapy.

PubMed

Pillai, Nikhil; Craig, Morgan; Dokoumetzidis, Aristeidis; Schwartz, Sorell L; Bies, Robert; Freedman, Immanuel

2018-06-19

In mathematical pharmacology, models are constructed to confer a robust method for optimizing treatment. The predictive capability of pharmacological models depends heavily on the ability to track the system and to accurately determine parameters with reference to the sensitivity in projected outcomes. To closely track chaotic systems, one may choose to apply chaos synchronization. An advantageous byproduct of this methodology is the ability to quantify model parameters. In this paper, we illustrate the use of chaos synchronization combined with Nelder-Mead search to estimate parameters of the well-known Kirschner-Panetta model of IL-2 immunotherapy from noisy data. Chaos synchronization with Nelder-Mead search is shown to provide more accurate and reliable estimates than Nelder-Mead search based on an extended least squares (ELS) objective function. Our results underline the strength of this approach to parameter estimation and provide a broader framework of parameter identification for nonlinear models in pharmacology. Copyright © 2018 Elsevier Ltd. All rights reserved.

How many records should be used in ASCE/SEI-7 ground motion scaling procedure?

USGS Publications Warehouse

Reyes, Juan C.; Kalkan, Erol

2012-01-01

U.S. national building codes refer to the ASCE/SEI-7 provisions for selecting and scaling ground motions for use in nonlinear response history analysis of structures. Because the limiting values for the number of records in the ASCE/SEI-7 are based on engineering experience, this study examines the required number of records statistically, such that the scaled records provide accurate, efficient, and consistent estimates of “true” structural responses. Based on elastic–perfectly plastic and bilinear single-degree-of-freedom systems, the ASCE/SEI-7 scaling procedure is applied to 480 sets of ground motions; the number of records in these sets varies from three to ten. As compared to benchmark responses, it is demonstrated that the ASCE/SEI-7 scaling procedure is conservative if fewer than seven ground motions are employed. Utilizing seven or more randomly selected records provides more accurate estimate of the responses. Selecting records based on their spectral shape and design spectral acceleration increases the accuracy and efficiency of the procedure.

Multisystem altruistic metadynamics—Well-tempered variant

NASA Astrophysics Data System (ADS)

Hošek, Petr; Kříž, Pavel; Toulcová, Daniela; Spiwok, Vojtěch

2017-03-01

Metadynamics method has been widely used to enhance sampling in molecular simulations. Its original form suffers two major drawbacks, poor convergence in complex (especially biomolecular) systems and its serial nature. The first drawback has been addressed by introduction of a convergent variant known as well-tempered metadynamics. The second was addressed by introduction of a parallel multisystem metadynamics referred to as altruistic metadynamics. Here, we combine both approaches into well-tempered altruistic metadynamics. We provide mathematical arguments and trial simulations to show that it accurately predicts free energy surfaces.

Multisystem altruistic metadynamics-Well-tempered variant.

PubMed

Hošek, Petr; Kříž, Pavel; Toulcová, Daniela; Spiwok, Vojtěch

2017-03-28

Metadynamics method has been widely used to enhance sampling in molecular simulations. Its original form suffers two major drawbacks, poor convergence in complex (especially biomolecular) systems and its serial nature. The first drawback has been addressed by introduction of a convergent variant known as well-tempered metadynamics. The second was addressed by introduction of a parallel multisystem metadynamics referred to as altruistic metadynamics. Here, we combine both approaches into well-tempered altruistic metadynamics. We provide mathematical arguments and trial simulations to show that it accurately predicts free energy surfaces.

Leveling

USGS Publications Warehouse

1966-01-01

Geodetic leveling by the U.S. Geological Survey provides a framework of accurate elevations for topographic mapping. Elevations are referred to the Sea Level Datum of 1929. Lines of leveling may be run either with automatic or with precise spirit levels, by either the center-wire or the three-wire method. For future use, the surveys are monumented with bench marks, using standard metal tablets or other marking devices. The elevations are adjusted by least squares or other suitable method and are published in lists of control.

Absolute Salinity, ''Density Salinity'' and the Reference-Composition Salinity Scale: present and future use in the seawater standard TEOS-10

NASA Astrophysics Data System (ADS)

Wright, D. G.; Pawlowicz, R.; McDougall, T. J.; Feistel, R.; Marion, G. M.

2011-01-01

Salinity plays a key role in the determination of the thermodynamic properties of seawater and the new TEOS-101 standard provides a consistent and effective approach to dealing with relationships between salinity and these thermodynamic properties. However, there are a number of practical issues that arise in the application of TEOS-10, both in terms of accuracy and scope, including its use in the reduction of field data and in numerical models. First, in the TEOS-10 formulation for IAPSO Standard Seawater, the Gibbs function takes the Reference Salinity as its salinity argument, denoted SR, which provides a measure of the mass fraction of dissolved material in solution based on the Reference Composition approximation for Standard Seawater. We discuss uncertainties in both the Reference Composition and the Reference-Composition Salinity Scale on which Reference Salinity is reported. The Reference Composition provides a much-needed fixed benchmark but modified reference states will inevitably be required to improve the representation of Standard Seawater for some studies. However, the Reference-Composition Salinity Scale should remain unaltered to provide a stable representation of salinity for use with the TEOS-10 Gibbs function and in climate change detection studies. Second, when composition anomalies are present in seawater, no single salinity variable can fully represent the influence of dissolved material on the thermodynamic properties of seawater. We consider three distinct representations of salinity that have been used in previous studies and discuss the connections and distinctions between them. One of these variables provides the most accurate representation of density possible as well as improvements over Reference Salinity for the determination of other thermodynamic properties. It is referred to as "Density Salinity" and is represented by the symbol SAdens; it stands out as the most appropriate representation of salinity for use in dynamical physical oceanography. The other two salinity variables provide alternative measures of the mass fraction of dissolved material in seawater. "Solution Salinity", denoted SAsoln, is the most obvious extension of Reference Salinity to allow for composition anomalies; it provides a direct estimate of the mass fraction of dissolved material in solution. "Added-Mass Salinity", denoted SAadd, is motivated by a method used to report laboratory experiments; it represents the component of dissolved material added to Standard Seawater in terms of the mass of material before it enters solution. We also discuss a constructed conservative variable referred to as "Preformed Salinity", denoted S∗, which will be useful in process-oriented numerical modelling studies. Finally, a conceptual framework for the incorporation of composition anomalies in numerical models is presented that builds from studies in which composition anomalies are simply ignored up to studies in which the influences of composition anomalies are accounted for using the results of biogeochemical models. 1TEOS-10: international Thermodynamic Equation of Seawater 2010, http://www.teos-10.org/.

Absolute Salinity, "Density Salinity" and the Reference-Composition Salinity Scale: present and future use in the seawater standard TEOS-10

NASA Astrophysics Data System (ADS)

Wright, D. G.; Pawlowicz, R.; McDougall, T. J.; Feistel, R.; Marion, G. M.

2010-08-01

Salinity plays a key role in the determination of the thermodynamic properties of seawater and the new TEOS-101 standard provides a consistent and effective approach to dealing with relationships between salinity and these thermodynamic properties. However, there are a number of practical issues that arise in the application of TEOS-10, both in terms of accuracy and scope, including its use in the reduction of field data and in numerical models. First, in the TEOS-10 formulation for IAPSO Standard Seawater, the Gibbs function takes the Reference Salinity as its salinity argument, denoted SR, which provides a measure of the mass fraction of dissolved material in solution based on the Reference Composition approximation for Standard Seawater. We discuss uncertainties in both the Reference Composition and the Reference-Composition Salinity Scale on which Reference Salinity is reported. The Reference Composition provides a much-needed fixed benchmark but modified reference states will inevitably be required to improve the representation of Standard Seawater for some studies. The Reference-Composition Salinity Scale should remain unaltered to provide a stable representation of salinity for use with the TEOS-10 Gibbs function and in climate change detection studies. Second, when composition anomalies are present in seawater, no single salinity variable can fully represent the influence of dissolved material on the thermodynamic properties of seawater. We consider three distinct representations of salinity that have been used in previous studies and discuss the connections and distinctions between them. One of these variables provides the most accurate representation of density possible as well as improvements over Reference Salinity for the determination of other thermodynamic properties. It is referred to as "Density Salinity" and is represented by the symbol SAdens; it stands out as the most appropriate representation of salinity for use in dynamical physical oceanography. The other two salinity variables provide alternative measures of the mass fraction of dissolved material in seawater. "Solution Salinity", denoted SAsoln, is the most obvious extension of Reference Salinity to allow for composition anomalies; it provides a direct estimate of the mass fraction of dissolved material in solution. "Added-Mass Salinity", denoted SAadd, is motivated by a method used to report laboratory experiments; it represents the component of dissolved material added to Standard Seawater in terms of the mass of material before it enters solution. We also discuss a constructed conservative variable referred to as "Preformed Salinity", denoted S*, which will be useful in process-oriented numerical modelling studies. Finally, a conceptual framework for the incorporation of composition anomalies in numerical models is presented that builds from studies in which composition anomalies are simply ignored up to studies in which the influences of composition anomalies are accounted for using the results of biogeochemical models. 1TEOS-10: international thermodynamic equation of seawater 2010, http://www.teos-10.org.

Development of a machine learning potential for graphene

NASA Astrophysics Data System (ADS)

Rowe, Patrick; Csányi, Gábor; Alfè, Dario; Michaelides, Angelos

2018-02-01

We present an accurate interatomic potential for graphene, constructed using the Gaussian approximation potential (GAP) machine learning methodology. This GAP model obtains a faithful representation of a density functional theory (DFT) potential energy surface, facilitating highly accurate (approaching the accuracy of ab initio methods) molecular dynamics simulations. This is achieved at a computational cost which is orders of magnitude lower than that of comparable calculations which directly invoke electronic structure methods. We evaluate the accuracy of our machine learning model alongside that of a number of popular empirical and bond-order potentials, using both experimental and ab initio data as references. We find that whilst significant discrepancies exist between the empirical interatomic potentials and the reference data—and amongst the empirical potentials themselves—the machine learning model introduced here provides exemplary performance in all of the tested areas. The calculated properties include: graphene phonon dispersion curves at 0 K (which we predict with sub-meV accuracy), phonon spectra at finite temperature, in-plane thermal expansion up to 2500 K as compared to NPT ab initio molecular dynamics simulations and a comparison of the thermally induced dispersion of graphene Raman bands to experimental observations. We have made our potential freely available online at [http://www.libatoms.org].

A new, high-precision measurement of the X-ray Cu K α spectrum

NASA Astrophysics Data System (ADS)

Mendenhall, Marcus H.; Cline, James P.; Henins, Albert; Hudson, Lawrence T.; Szabo, Csilla I.; Windover, Donald

2016-03-01

One of the primary measurement issues addressed with NIST Standard Reference Materials (SRMs) for powder diffraction is that of line position. SRMs for this purpose are certified with respect to lattice parameter, traceable to the SI through precise measurement of the emission spectrum of the X-ray source. Therefore, accurate characterization of the emission spectrum is critical to a minimization of the error bounds on the certified parameters. The presently accepted sources for the SI traceable characterization of the Cu K α emission spectrum are those of Härtwig, Hölzer et al., published in the 1990s. The structure of the X-ray emission lines of the Cu K α complex has been remeasured on a newly commissioned double-crystal instrument, with six-bounce Si (440) optics, in a manner directly traceable to the SI definition of the meter. In this measurement, the entire region from 8020 eV to 8100 eV has been covered with a highly precise angular scale and well-defined system efficiency, providing accurate wavelengths and relative intensities. This measurement is in modest disagreement with reference values for the wavelength of the Kα1 line, and strong disagreement for the wavelength of the Kα2 line.

Lateral attenuation of aircraft sound levels over an acoustically hard water surface : Logan airport study

DOT National Transportation Integrated Search

2002-01-31

Accurate modeling of the lateral attenuation of sound is : essential for accurate prediction of aircraft noise. Lateral : attenuation contains many aspects of sound generation and : propagation, including ground effects (sometimes referred to :...

Accurate bond energies of hydrocarbons from complete basis set extrapolated multi-reference singles and doubles configuration interaction.

PubMed

Oyeyemi, Victor B; Pavone, Michele; Carter, Emily A

2011-12-09

Quantum chemistry has become one of the most reliable tools for characterizing the thermochemical underpinnings of reactions, such as bond dissociation energies (BDEs). The accurate prediction of these particular properties (BDEs) are challenging for ab initio methods based on perturbative corrections or coupled cluster expansions of the single-determinant Hartree-Fock wave function: the processes of bond breaking and forming are inherently multi-configurational and require an accurate description of non-dynamical electron correlation. To this end, we present a systematic ab initio approach for computing BDEs that is based on three components: 1) multi-reference single and double excitation configuration interaction (MRSDCI) for the electronic energies; 2) a two-parameter scheme for extrapolating MRSDCI energies to the complete basis set limit; and 3) DFT-B3LYP calculations of minimum-energy structures and vibrational frequencies to account for zero point energy and thermal corrections. We validated our methodology against a set of reliable experimental BDE values of CC and CH bonds of hydrocarbons. The goal of chemical accuracy is achieved, on average, without applying any empirical corrections to the MRSDCI electronic energies. We then use this composite scheme to make predictions of BDEs in a large number of hydrocarbon molecules for which there are no experimental data, so as to provide needed thermochemical estimates for fuel molecules. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The importance of information on relatives for the prediction of genomic breeding values and the implications for the makeup of reference data sets in livestock breeding schemes.

PubMed

Clark, Samuel A; Hickey, John M; Daetwyler, Hans D; van der Werf, Julius H J

2012-02-09

The theory of genomic selection is based on the prediction of the effects of genetic markers in linkage disequilibrium with quantitative trait loci. However, genomic selection also relies on relationships between individuals to accurately predict genetic value. This study aimed to examine the importance of information on relatives versus that of unrelated or more distantly related individuals on the estimation of genomic breeding values. Simulated and real data were used to examine the effects of various degrees of relationship on the accuracy of genomic selection. Genomic Best Linear Unbiased Prediction (gBLUP) was compared to two pedigree based BLUP methods, one with a shallow one generation pedigree and the other with a deep ten generation pedigree. The accuracy of estimated breeding values for different groups of selection candidates that had varying degrees of relationships to a reference data set of 1750 animals was investigated. The gBLUP method predicted breeding values more accurately than BLUP. The most accurate breeding values were estimated using gBLUP for closely related animals. Similarly, the pedigree based BLUP methods were also accurate for closely related animals, however when the pedigree based BLUP methods were used to predict unrelated animals, the accuracy was close to zero. In contrast, gBLUP breeding values, for animals that had no pedigree relationship with animals in the reference data set, allowed substantial accuracy. An animal's relationship to the reference data set is an important factor for the accuracy of genomic predictions. Animals that share a close relationship to the reference data set had the highest accuracy from genomic predictions. However a baseline accuracy that is driven by the reference data set size and the overall population effective population size enables gBLUP to estimate a breeding value for unrelated animals within a population (breed), using information previously ignored by pedigree based BLUP methods.

Next Day Building Load Predictions based on Limited Input Features Using an On-Line Laterally Primed Adaptive Resonance Theory Artificial Neural Network.

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

Jones, Christian Birk; Robinson, Matt; Yasaei, Yasser

Optimal integration of thermal energy storage within commercial building applications requires accurate load predictions. Several methods exist that provide an estimate of a buildings future needs. Methods include component-based models and data-driven algorithms. This work implemented a previously untested algorithm for this application that is called a Laterally Primed Adaptive Resonance Theory (LAPART) artificial neural network (ANN). The LAPART algorithm provided accurate results over a two month period where minimal historical data and a small amount of input types were available. These results are significant, because common practice has often overlooked the implementation of an ANN. ANN have often beenmore » perceived to be too complex and require large amounts of data to provide accurate results. The LAPART neural network was implemented in an on-line learning manner. On-line learning refers to the continuous updating of training data as time occurs. For this experiment, training began with a singe day and grew to two months of data. This approach provides a platform for immediate implementation that requires minimal time and effort. The results from the LAPART algorithm were compared with statistical regression and a component-based model. The comparison was based on the predictions linear relationship with the measured data, mean squared error, mean bias error, and cost savings achieved by the respective prediction techniques. The results show that the LAPART algorithm provided a reliable and cost effective means to predict the building load for the next day.« less

Evaluating the Reference Interview: A Theoretical Discussion of the Desirability and Achievability of Evaluation.

ERIC Educational Resources Information Center

Smith, Lisa L.

1991-01-01

Review and examination of the current literature on reference interview evaluation explores the degree to which such evaluative practices are both desirable and achievable. It is concluded that, if both quantitative and qualitative techniques are appropriately used, accurate mechanisms of evaluation are possible and desirable. (17 references) (LRW)

Serial fusion of Eulerian and Lagrangian approaches for accurate heart-rate estimation using face videos.

PubMed

Gupta, Puneet; Bhowmick, Brojeshwar; Pal, Arpan

2017-07-01

Camera-equipped devices are ubiquitous and proliferating in the day-to-day life. Accurate heart rate (HR) estimation from the face videos acquired from the low cost cameras in a non-contact manner, can be used in many real-world scenarios and hence, require rigorous exploration. This paper has presented an accurate and near real-time HR estimation system using these face videos. It is based on the phenomenon that the color and motion variations in the face video are closely related to the heart beat. The variations also contain the noise due to facial expressions, respiration, eye blinking and environmental factors which are handled by the proposed system. Neither Eulerian nor Lagrangian temporal signals can provide accurate HR in all the cases. The cases where Eulerian temporal signals perform spuriously are determined using a novel poorness measure and then both the Eulerian and Lagrangian temporal signals are employed for better HR estimation. Such a fusion is referred as serial fusion. Experimental results reveal that the error introduced in the proposed algorithm is 1.8±3.6 which is significantly lower than the existing well known systems.

Performance of ground attitude determination procedures for HEAO-1

NASA Technical Reports Server (NTRS)

Fallon, L., III; Sturch, C. R.

1978-01-01

Ground attitude support for HEAO 1 provided at GSFC by the HEAO 1 Attitude Ground Support System (AGSS) is described. Information telemetered from Sun sensors, gyroscopes, star trackers, and an onboard computer are used by the AGSS to compute updates to the onboard attitude reference and gyro calibration parameters. The onboard computer utilizes these updates in providing continuous attitudes (accurate to 0.25degree) for use in the observatory's attitude control procedures. The relationship between HEAO 1 onboard and ground processing, the procedures used by the AGSS in computing attitude and gyro calibration updates, and the performance of these procedures in the HEAO 1 postlaunch environment is discussed.

Assessment of reference genes for reliable analysis of gene transcription by RT-qPCR in ovine leukocytes.

PubMed

Mahakapuge, T A N; Scheerlinck, J-P Y; Rojas, C A Alvarez; Every, A L; Hagen, J

2016-03-01

With the availability of genetic sequencing data, quantitative reverse transcription PCR (RT-qPCR) is increasingly being used for the quantification of gene transcription across species. Too often there is little regard to the selection of reference genes and the impact that a poor choice has on data interpretation. Indeed, RT-qPCR provides a snapshot of relative gene transcription at a given time-point, and hence is highly dependent on the stability of the transcription of the reference gene(s). Using ovine efferent lymph cells and peripheral blood mono-nuclear cells (PBMCs), the two most frequently used leukocytes in immunological studies, we have compared the stability of transcription of the most commonly used ovine reference genes: YWHAZ, RPL-13A, PGK1, B2M, GAPDH, HPRT, SDHA and ACTB. Using established algorithms for reference gene normalization "geNorm" and "Norm Finder", PGK1, GAPDH and YWHAZ were deemed the most stably transcribed genes for efferent leukocytes and PGK1, YWHAZ and SDHA were optimal in PBMCs. These genes should therefore be considered for accurate and reproducible RT-qPCR data analysis of gene transcription in sheep. Copyright © 2016. Published by Elsevier B.V.

Identification of suitable qPCR reference genes in leaves of Brassica oleracea under abiotic stresses.

PubMed

Brulle, Franck; Bernard, Fabien; Vandenbulcke, Franck; Cuny, Damien; Dumez, Sylvain

2014-04-01

Real-time quantitative PCR is nowadays a standard method to study gene expression variations in various samples and experimental conditions. However, to interpret results accurately, data normalization with appropriate reference genes appears to be crucial. The present study describes the identification and the validation of suitable reference genes in Brassica oleracea leaves. Expression stability of eight candidates was tested following drought and cold abiotic stresses by using three different softwares (BestKeeper, NormFinder and geNorm). Four genes (BolC.TUB6, BolC.SAND1, BolC.UBQ2 and BolC.TBP1) emerged as the most stable across the tested conditions. Further gene expression analysis of a drought- and a cold-responsive gene (BolC.DREB2A and BolC.ELIP, respectively), confirmed the stability and the reliability of the identified reference genes when used for normalization in the leaves of B. oleracea. These four genes were finally tested upon a benzene exposure and all appeared to be useful reference genes along this toxicological condition. These results provide a good starting point for future studies involving gene expression measurement on leaves of B. oleracea exposed to environmental modifications.

Analyses on hydrophobicity and attractiveness of all-atom distance-dependent potentials

PubMed Central

Shirota, Matsuyuki; Ishida, Takashi; Kinoshita, Kengo

2009-01-01

Accurate model evaluation is a crucial step in protein structure prediction. For this purpose, statistical potentials, which evaluate a model structure based on the observed atomic distance frequencies in comparison with those in reference states, have been widely used. The reference state is a virtual state where all of the atomic interactions are turned off, and it provides a standard to measure the observed frequencies. In this study, we examined seven all-atom distance-dependent potentials with different reference states. As results, we observed that the variations of atom pair composition and those of distance distributions in the reference states produced systematic changes in the hydrophobic and attractive characteristics of the potentials. The performance evaluations with the CASP7 structures indicated that the preference of hydrophobic interactions improved the correlation between the energy and the GDT-TS score, but decreased the Z-score of the native structure. The attractiveness of potential improved both the correlation and Z-score for template-based modeling targets, but the benefit was smaller in free modeling targets. These results indicated that the performances of the potentials were more strongly influenced by their characteristics than by the accuracy of the definitions of the reference states. PMID:19588493

Block correlated second order perturbation theory with a generalized valence bond reference function.

PubMed

Xu, Enhua; Li, Shuhua

2013-11-07

The block correlated second-order perturbation theory with a generalized valence bond (GVB) reference (GVB-BCPT2) is proposed. In this approach, each geminal in the GVB reference is considered as a "multi-orbital" block (a subset of spin orbitals), and each occupied or virtual spin orbital is also taken as a single block. The zeroth-order Hamiltonian is set to be the summation of the individual Hamiltonians of all blocks (with explicit two-electron operators within each geminal) so that the GVB reference function and all excited configuration functions are its eigenfunctions. The GVB-BCPT2 energy can be directly obtained without iteration, just like the second order Mo̸ller-Plesset perturbation method (MP2), both of which are size consistent. We have applied this GVB-BCPT2 method to investigate the equilibrium distances and spectroscopic constants of 7 diatomic molecules, conformational energy differences of 8 small molecules, and bond-breaking potential energy profiles in 3 systems. GVB-BCPT2 is demonstrated to have noticeably better performance than MP2 for systems with significant multi-reference character, and provide reasonably accurate results for some systems with large active spaces, which are beyond the capability of all CASSCF-based methods.

A content analysis of the quantity and accuracy of dietary supplement information found in magazines with high adolescent readership.

PubMed

Shaw, Patricia; Zhang, Vivien; Metallinos-Katsaras, Elizabeth

2009-02-01

The objective of this study was to examine the quantity and accuracy of dietary supplement (DS) information through magazines with high adolescent readership. Eight (8) magazines (3 teen and 5 adult with high teen readership) were selected. A content analysis for DS was conducted on advertisements and editorials (i.e., articles, advice columns, and bulletins). Noted claims/cautions regarding DS were evaluated for accuracy using Medlineplus.gov and Naturaldatabase.com. Claims for dietary supplements with three or more types of ingredients and those in advertisements were not evaluated. Advertisements were evaluated with respect to size, referenced research, testimonials, and Dietary Supplement Health and Education Act of 1994 (DSHEA) warning visibility. Eighty-eight (88) issues from eight magazines yielded 238 DS references. Fifty (50) issues from five magazines contained no DS reference. Among teen magazines, seven DS references were found: five in the editorials and two in advertisements. In adult magazines, 231 DS references were found: 139 in editorials and 92 in advertisements. Of the 88 claims evaluated, 15% were accurate, 23% were inconclusive, 3% were inaccurate, 5% were partially accurate, and 55% were unsubstantiated (i.e., not listed in reference databases). Of the 94 DS evaluated in advertisements, 43% were full page or more, 79% did not have a DSHEA warning visible, 46% referred to research, and 32% used testimonials. Teen magazines contain few references to DS, none accurate. Adult magazines that have a high teen readership contain a substantial amount of DS information with questionable accuracy, raising concerns that this information may increase the chances of inappropriate DS use by adolescents, thereby increasing the potential for unexpected effects or possible harm.

Comparative assessment of a real-time particle monitor against the reference gravimetric method for PM10 and PM2.5 in indoor air

NASA Astrophysics Data System (ADS)

Tasić, Viša; Jovašević-Stojanović, Milena; Vardoulakis, Sotiris; Milošević, Novica; Kovačević, Renata; Petrović, Jelena

2012-07-01

Accurate monitoring of indoor mass concentrations of particulate matter is very important for health risk assessment as people in developed countries spend approximately 90% of their time indoors. The direct reading, aerosol monitoring device, Turnkey, OSIRIS Particle Monitor (Model 2315) and the European reference low volume sampler, LVS3 (Sven/Leckel LVS3) with size-selective inlets for PM10 and PM2.5 fractions were used to assess the comparability of available optical and gravimetric methods for particulate matter characterization in indoor air. Simultaneous 24-hour samples were collected in an indoor environment for 60 sampling periods in the town of Bor, Serbia. The 24-hour mean PM10 levels from the OSIRIS monitor were well correlated with the LVS3 levels (R2 = 0.87) and did not show statistically significant bias. The 24-hour mean PM2.5 levels from the OSIRIS monitor were moderately correlated with the LVS3 levels (R2 = 0.71), but show statistically significant bias. The results suggest that the OSIRIS monitor provides sufficiently accurate measurements for PM10. The OSIRIS monitor underestimated the indoor PM10 concentrations by approximately 12%, relative to the reference LVS3 sampler. The accuracy of PM10 measurements could be further improved through empirical adjustment. For the fine fraction of particulate matter, PM2.5, it was found that the OSIRIS monitor underestimated indoor concentrations by approximately 63%, relative to the reference LVS3 sampler. This could lead to exposure misclassification in health effects studies relying on PM2.5 measurements collected with this instrument in indoor environments.

A minimum drives automatic target definition procedure for multi-axis random control testing

NASA Astrophysics Data System (ADS)

Musella, Umberto; D'Elia, Giacomo; Carrella, Alex; Peeters, Bart; Mucchi, Emiliano; Marulo, Francesco; Guillaume, Patrick

2018-07-01

Multiple-Input Multiple-Output (MIMO) vibration control tests are able to closely replicate, via shakers excitation, the vibration environment that a structure needs to withstand during its operational life. This feature is fundamental to accurately verify the experienced stress state, and ultimately the fatigue life, of the tested structure. In case of MIMO random tests, the control target is a full reference Spectral Density Matrix in the frequency band of interest. The diagonal terms are the Power Spectral Densities (PSDs), representative for the acceleration operational levels, and the off-diagonal terms are the Cross Spectral Densities (CSDs). The specifications of random vibration tests are however often given in terms of PSDs only, coming from a legacy of single axis testing. Information about the CSDs is often missing. An accurate definition of the CSD profiles can further enhance the MIMO random testing practice, as these terms influence both the responses and the shaker's voltages (the so-called drives). The challenges are linked to the algebraic constraint that the full reference matrix must be positive semi-definite in the entire bandwidth, with no flexibility in modifying the given PSDs. This paper proposes a newly developed method that automatically provides the full reference matrix without modifying the PSDs, considered as test specifications. The innovative feature is the capability of minimizing the drives required to match the reference PSDs and, at the same time, to directly guarantee that the obtained full matrix is positive semi-definite. The drives minimization aims on one hand to reach the fixed test specifications without stressing the delicate excitation system; on the other hand it potentially allows to further increase the test levels. The detailed analytic derivation and implementation steps of the proposed method are followed by real-life testing considering different scenarios.

The need for accurate total cholesterol measurement. Recommended analytical goals, current state of reliability, and guidelines for better determinations.

PubMed

Naito, H K

1989-03-01

We have approached a dawn of a new era in detection, evaluation, treatment, and monitoring of individuals with elevated blood cholesterol levels who are at increased risk for CHD. The NHLBI's National Cholesterol Education Program will be the major force underlying this national awareness program, which is dependent on the clinical laboratories providing reliable data. Precision or reproducibility of results is not a problem for most of the laboratories, but accuracy is a major concern. Both the manufacturers and laboratorians need to standardize the measurement for cholesterol so that the accuracy base is traceable to the NCCLS NRS/CHOL. The manufacturers need to adopt a uniform policy that will ensure that the values assigned to calibration, quality control, and quality assurance or survey materials are accurate and traceable to the NCCLS/CHOL. Since, at present, there are some limitations of these materials caused by matrix effects, laboratories are encouraged to use the CDC-NHLBI National Reference Laboratory Network to evaluate and monitor their ability to measure patient blood cholesterol levels accurately. Major areas of analytical problems are identified and general, as well as specific, recommendations are provided to help ensure reliable measurement of cholesterol in patient specimens.

Genome-Wide Identification and Testing of Superior Reference Genes for Transcript Normalization in Arabidopsis1[w

PubMed Central

Czechowski, Tomasz; Stitt, Mark; Altmann, Thomas; Udvardi, Michael K.; Scheible, Wolf-Rüdiger

2005-01-01

Gene transcripts with invariant abundance during development and in the face of environmental stimuli are essential reference points for accurate gene expression analyses, such as RNA gel-blot analysis or quantitative reverse transcription-polymerase chain reaction (PCR). An exceptionally large set of data from Affymetrix ATH1 whole-genome GeneChip studies provided the means to identify a new generation of reference genes with very stable expression levels in the model plant species Arabidopsis (Arabidopsis thaliana). Hundreds of Arabidopsis genes were found that outperform traditional reference genes in terms of expression stability throughout development and under a range of environmental conditions. Most of these were expressed at much lower levels than traditional reference genes, making them very suitable for normalization of gene expression over a wide range of transcript levels. Specific and efficient primers were developed for 22 genes and tested on a diverse set of 20 cDNA samples. Quantitative reverse transcription-PCR confirmed superior expression stability and lower absolute expression levels for many of these genes, including genes encoding a protein phosphatase 2A subunit, a coatomer subunit, and an ubiquitin-conjugating enzyme. The developed PCR primers or hybridization probes for the novel reference genes will enable better normalization and quantification of transcript levels in Arabidopsis in the future. PMID:16166256

Multiconfiguration Pair-Density Functional Theory: A New Way To Treat Strongly Correlated Systems.

PubMed

Gagliardi, Laura; Truhlar, Donald G; Li Manni, Giovanni; Carlson, Rebecca K; Hoyer, Chad E; Bao, Junwei Lucas

2017-01-17

The electronic energy of a system provides the Born-Oppenheimer potential energy for internuclear motion and thus determines molecular structure and spectra, bond energies, conformational energies, reaction barrier heights, and vibrational frequencies. The development of more efficient and more accurate ways to calculate the electronic energy of systems with inherently multiconfigurational electronic structure is essential for many applications, including transition metal and actinide chemistry, systems with partially broken bonds, many transition states, and most electronically excited states. Inherently multiconfigurational systems are called strongly correlated systems or multireference systems, where the latter name refers to the need for using more than one ("multiple") configuration state function to provide a good zero-order reference wave function. This Account describes multiconfiguration pair-density functional theory (MC-PDFT), which was developed as a way to combine the advantages of wave function theory (WFT) and density functional theory (DFT) to provide a better treatment of strongly correlated systems. First we review background material: the widely used Kohn-Sham DFT (which uses only a single Slater determinant as reference wave function), multiconfiguration WFT methods that treat inherently multiconfigurational systems based on an active space, and previous attempts to combine multiconfiguration WFT with DFT. Then we review the formulation of MC-PDFT. It is a generalization of Kohn-Sham DFT in that the electron kinetic energy and classical electrostatic energy are calculated from a reference wave function, while the rest of the energy is obtained from a density functional. However, there are two main differences with respent to Kohn-Sham DFT: (i) The reference wave function is multiconfigurational rather than being a single Slater determinant. (ii) The density functional is a function of the total density and the on-top pair density rather than being a function of the spin-up and spin-down densities. In work carried out so far, the multiconfigurational wave function is a multiconfiguration self-consistent-field wave function. The new formulation has the advantage that the reference wave function has the correct spatial and spin symmetry and can describe bond dissociation (of both single and multiple bonds) and electronic excitations in a formally and physically correct way. We then review the formulation of density functionals in terms of the on-top pair density. Finally we review successful applications of the theory to bond energies and bond dissociation potential energy curves of main-group and transition metal bonds, to barrier heights (including pericyclic reactions), to proton affinities, to the hydrogen bond energy of water dimer, to ground- and excited-state charge transfer, to valence and Rydberg excitations of molecules, and to singlet-triplet splittings of radicals. We find that that MC-PDFT can give accurate results not only with complete-active-space multiconfiguration wave functions but also with generalized-active-space multiconfiguration wave functions, which are practical for larger numbers of active electrons and active orbitals than are complete-active-space wave functions. The separated-pair approximation, which is a special case of generalized active space self-consistent-field theory, is especially promising. MC-PDFT, because it requires much less computer time and storage than pure WFT methods, has the potential to open larger and more complex strongly correlated systems to accurate simulation.

Properties of coupled-cluster equations originating in excitation sub-algebras

NASA Astrophysics Data System (ADS)

Kowalski, Karol

2018-03-01

In this paper, we discuss properties of single-reference coupled cluster (CC) equations associated with the existence of sub-algebras of excitations that allow one to represent CC equations in a hybrid fashion where the cluster amplitudes associated with these sub-algebras can be obtained by solving the corresponding eigenvalue problem. For closed-shell formulations analyzed in this paper, the hybrid representation of CC equations provides a natural way for extending active-space and seniority number concepts to provide an accurate description of electron correlation effects. Moreover, a new representation can be utilized to re-define iterative algorithms used to solve CC equations, especially for tough cases defined by the presence of strong static and dynamical correlation effects. We will also explore invariance properties associated with excitation sub-algebras to define a new class of CC approximations referred to in this paper as the sub-algebra-flow-based CC methods. We illustrate the performance of these methods on the example of ground- and excited-state calculations for commonly used small benchmark systems.

Research on Robust Control Strategies for VSC-HVDC

NASA Astrophysics Data System (ADS)

Zhu, Kaicheng; Bao, Hai

2018-01-01

In the control system of VSC-HVDC, the phase locked loop provides phase signals to voltage vector control and trigger pulses to generate the required reference phase. The PLL is a typical second-order system. When the system is in unstable state, it will oscillate, make the trigger angle shift, produce harmonic, and make active power and reactive power coupled. Thus, considering the external disturbances introduced by the PLL in VSC-HVDC control system, the parameter perturbations of the controller and the model uncertainties, a H∞ robust controller of mixed sensitivity optimization problem is designed by using the Hinf function provided by the robust control toolbox. Then, compare it with the proportional integral controller through the MATLAB simulation experiment. By contrast, when the H∞ robust controller is added, active and reactive power of the converter station can track the change of reference values more accurately and quickly, and reduce overshoot. When the step change of active and reactive power occurs, mutual influence is reduced and better independent regulation is achieved.

Verification of ARES transport code system with TAKEDA benchmarks

NASA Astrophysics Data System (ADS)

Zhang, Liang; Zhang, Bin; Zhang, Penghe; Chen, Mengteng; Zhao, Jingchang; Zhang, Shun; Chen, Yixue

2015-10-01

Neutron transport modeling and simulation are central to many areas of nuclear technology, including reactor core analysis, radiation shielding and radiation detection. In this paper the series of TAKEDA benchmarks are modeled to verify the critical calculation capability of ARES, a discrete ordinates neutral particle transport code system. SALOME platform is coupled with ARES to provide geometry modeling and mesh generation function. The Koch-Baker-Alcouffe parallel sweep algorithm is applied to accelerate the traditional transport calculation process. The results show that the eigenvalues calculated by ARES are in excellent agreement with the reference values presented in NEACRP-L-330, with a difference less than 30 pcm except for the first case of model 3. Additionally, ARES provides accurate fluxes distribution compared to reference values, with a deviation less than 2% for region-averaged fluxes in all cases. All of these confirms the feasibility of ARES-SALOME coupling and demonstrate that ARES has a good performance in critical calculation.

Sigma: Strain-level inference of genomes from metagenomic analysis for biosurveillance

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

Ahn, Tae-Hyuk; Chai, Juanjuan; Pan, Chongle

Motivation: Metagenomic sequencing of clinical samples provides a promising technique for direct pathogen detection and characterization in biosurveillance. Taxonomic analysis at the strain level can be used to resolve serotypes of a pathogen in biosurveillance. Sigma was developed for strain-level identification and quantification of pathogens using their reference genomes based on metagenomic analysis. Results: Sigma provides not only accurate strain-level inferences, but also three unique capabilities: (i) Sigma quantifies the statistical uncertainty of its inferences, which includes hypothesis testing of identified genomes and confidence interval estimation of their relative abundances; (ii) Sigma enables strain variant calling by assigning metagenomic readsmore » to their most likely reference genomes; and (iii) Sigma supports parallel computing for fast analysis of large datasets. In conclusion, the algorithm performance was evaluated using simulated mock communities and fecal samples with spike-in pathogen strains. Availability and Implementation: Sigma was implemented in C++ with source codes and binaries freely available at http://sigma.omicsbio.org.« less

Sigma: Strain-level inference of genomes from metagenomic analysis for biosurveillance

DOE PAGES

Ahn, Tae-Hyuk; Chai, Juanjuan; Pan, Chongle

2014-09-29

Motivation: Metagenomic sequencing of clinical samples provides a promising technique for direct pathogen detection and characterization in biosurveillance. Taxonomic analysis at the strain level can be used to resolve serotypes of a pathogen in biosurveillance. Sigma was developed for strain-level identification and quantification of pathogens using their reference genomes based on metagenomic analysis. Results: Sigma provides not only accurate strain-level inferences, but also three unique capabilities: (i) Sigma quantifies the statistical uncertainty of its inferences, which includes hypothesis testing of identified genomes and confidence interval estimation of their relative abundances; (ii) Sigma enables strain variant calling by assigning metagenomic readsmore » to their most likely reference genomes; and (iii) Sigma supports parallel computing for fast analysis of large datasets. In conclusion, the algorithm performance was evaluated using simulated mock communities and fecal samples with spike-in pathogen strains. Availability and Implementation: Sigma was implemented in C++ with source codes and binaries freely available at http://sigma.omicsbio.org.« less

Label-free viscosity measurement of complex fluids using reversal flow switching manipulation in a microfluidic channel

PubMed Central

Jun Kang, Yang; Ryu, Jeongeun; Lee, Sang-Joon

2013-01-01

The accurate viscosity measurement of complex fluids is essential for characterizing fluidic behaviors in blood vessels and in microfluidic channels of lab-on-a-chip devices. A microfluidic platform that accurately identifies biophysical properties of blood can be used as a promising tool for the early detections of cardiovascular and microcirculation diseases. In this study, a flow-switching phenomenon depending on hydrodynamic balancing in a microfluidic channel was adopted to conduct viscosity measurement of complex fluids with label-free operation. A microfluidic device for demonstrating this proposed method was designed to have two inlets for supplying the test and reference fluids, two side channels in parallel, and a junction channel connected to the midpoint of the two side channels. According to this proposed method, viscosities of various fluids with different phases (aqueous, oil, and blood) in relation to that of reference fluid were accurately determined by measuring the switching flow-rate ratio between the test and reference fluids, when a reverse flow of the test or reference fluid occurs in the junction channel. An analytical viscosity formula was derived to measure the viscosity of a test fluid in relation to that of the corresponding reference fluid using a discrete circuit model for the microfluidic device. The experimental analysis for evaluating the effects of various parameters on the performance of the proposed method revealed that the fluidic resistance ratio (RJL/RL, fluidic resistance in the junction channel (RJL) to fluidic resistance in the side channel (RL)) strongly affects the measurement accuracy. The microfluidic device with smaller RJL/RL values is helpful to measure accurately the viscosity of the test fluid. The proposed method accurately measured the viscosities of various fluids, including single-phase (Glycerin and plasma) and oil-water phase (oil vs. deionized water) fluids, compared with conventional methods. The proposed method was also successfully applied to measure viscosities of blood with varying hematocrits, chemically fixed RBCS, and channel sizes. Based on these experimental results, the proposed method can be effectively used to measure the viscosities of various fluids easily, without any fluorescent labeling and tedious calibration procedures. PMID:24404040

The CC/DFT Route towards Accurate Structures and Spectroscopic Features for Observed and Elusive Conformers of Flexible Molecules: Pyruvic Acid as Case Study

PubMed Central

Barone, Vincenzo; Biczysko, Malgorzata; Bloino, Julien; Cimino, Paola; Penocchio, Emanuele; Puzzarini, Cristina

2018-01-01

The structures, relative stabilities as well as the rotational and vibrational spectra of the three low-energy conformers of Pyruvic acid (PA) have been characterized using a state-of-the-art quantum-mechanical approach designed for flexible molecules. By making use of the available experimental rotational constants for several isotopologues of the most stable PA conformer, Tc-PA, the semi-experimental equilibrium structure has been derived. The latter provides a reference for the pure theoretical determination of the equilibrium geometries for all conformers, thus confirming for these structures an accuracy of 0.001 Å and 0.1 deg. for bond lengths and angles, respectively. Highly accurate relative energies of all conformers (Tc-, Tt- and Ct-PA) and of the transition states connecting them are provided along with the thermodynamic properties at low and high temperatures, thus leading to conformational enthalpies accurate to 1 kJ mol−1. Concerning microwave spectroscopy, rotational constants accurate to about 20 MHz are provided for the Tt- and Ct-PA conformers, together with the computed centrifugal-distortion constants and dipole moments required to simulate their rotational spectra. For Ct-PA, vibrational frequencies in the mid-infrared region accurate to 10 cm−1 are reported along with theoretical estimates for the transitions in the near-infrared range, and the corresponding infrared spectrum including fundamental transitions, overtones and combination bands has been simulated. In addition to the new data described above, theoretical results for the Tc- and Tt-PA conformers are compared with all available experimental data to further confirm the accuracy of the hybrid coupled-cluster/density functional theory (CC/DFT) protocol applied in the present study. Finally, we discuss in detail the accuracy of computational models fully based on double-hybrid DFT functionals (mainly at the B2PLYP/aug-cc-pVTZ level) that avoid the use of very expensive CC calculations. PMID:26575928

Availability and provision of misoprostol and other medicines for menstrual regulation among pharmacies in Bangladesh via mystery client survey.

PubMed

Huda, Fauzia A; Ngo, Thoai D; Ahmed, Anisuddin; Alam, Anadil; Reichenbach, Laura

2014-02-01

To explore the availability and provision of misoprostol and other medicines for menstrual regulation (MR) among pharmacies in Bangladesh. Between March and November 2011, a cross-sectional study using mystery client visits was conducted among pharmacy workers in Dhaka and Gazipur Districts, Bangladesh. Mystery clients were trained to present 1 of 4 pre-developed situations to pharmacy workers to elicit information on the regimen, adverse effects, and complications of misoprostol use. Mystery clients visited 331 pharmacies. Among the 331 pharmacy workers, 45.8% offered the mystery clients misoprostol and/or other medicines for MR; 25.7% referred them to private clinics or hospitals. Only 7% recommended an effective regimen of misoprostol for MR; 65% suggested administering vaginal and oral misoprostol together. Overall, 72.4% did not provide any advice on complications; the remainder suggested visiting trained providers for complications. Counseling on excessive bleeding as a danger sign was provided by 46% of pharmacy workers. Most (94%) did not provide or refer for post-MR family planning. Pharmacy workers in urban Bangladesh are providing ineffective drugs and regimens for MR. A training package is needed to strengthen service delivery by providing accurate information, high-quality products, and referral mechanisms for women seeking MR through pharmacies. © 2013.

Populating a Control Point Database: A cooperative effort between the USGS, Grand Canyon Monitoring and Research Center and the Grand Canyon Youth Organization

NASA Astrophysics Data System (ADS)

Brown, K. M.; Fritzinger, C.; Wharton, E.

2004-12-01

The Grand Canyon Monitoring and Research Center measures the effects of Glen Canyon Dam operations on the resources along the Colorado River from Glen Canyon Dam to Lake Mead in support of the Grand Canyon Adaptive Management Program. Control points are integral for geo-referencing the myriad of data collected in the Grand Canyon including aerial photography, topographic and bathymetric data used for classification and change-detection analysis of physical, biologic and cultural resources. The survey department has compiled a list of 870 control points installed by various organizations needing to establish a consistent reference for data collected at field sites along the 240 mile stretch of Colorado River in the Grand Canyon. This list is the foundation for the Control Point Database established primarily for researchers, to locate control points and independently geo-reference collected field data. The database has the potential to be a valuable mapping tool for assisting researchers to easily locate a control point and reduce the occurrance of unknowingly installing new control points within close proximity of an existing control point. The database is missing photographs and accurate site description information. Current site descriptions do not accurately define the location of the point but refer to the project that used the point, or some other interesting fact associated with the point. The Grand Canyon Monitoring and Research Center (GCMRC) resolved this problem by turning the data collection effort into an educational exercise for the participants of the Grand Canyon Youth organization. Grand Canyon Youth is a non-profit organization providing experiential education for middle and high school aged youth. GCMRC and the Grand Canyon Youth formed a partnership where GCMRC provided the logistical support, equipment, and training to conduct the field work, and the Grand Canyon Youth provided the time and personnel to complete the field work. Two data collection efforts were conducted during the 2004 summer allowing 40 youth the opportunity to contribute valuable information to the Control Point Database. This information included: verification of point existence, photographs, accurate site descriptions concisely describing the location of the point, how to reach the point, the specific point location and detailed bearings to visible and obvious land marks. The youth learned to locate themselves and find the points using 1:1000 airphotos, write detailed site descriptions, take bearings with a compass, measure vertical and horizontal distances, and use a digital camera. The youth found information for 252 control points (29% of the total points).

A novel technique for reference point generation to aid in intraoral scan alignment.

PubMed

Renne, Walter G; Evans, Zachary P; Mennito, Anthony; Ludlow, Mark

2017-11-12

When using a completely digital workflow on larger prosthetic cases it is often difficult to communicate to the laboratory or chairside Computer Aided Design and Computer Aided Manufacturing system the provisional prosthetic information. The problem arises when common hard tissue data points are limited or non-existent such as in complete arch cases in which the 3D model of the complete arch provisional restorations must be aligned perfectly with the 3D model of the complete arch preparations. In these instances, soft tissue is not enough to ensure an accurate automatic or manual alignment due to a lack of well-defined reference points. A new technique is proposed for the proper digital alignment of the 3D virtual model of the provisional prosthetic to the 3D virtual model of the prepared teeth in cases where common and coincident hard tissue data points are limited. Clinical considerations: A technique is described in which fiducial composite resin dots are temporarily placed on the intraoral keratinized tissue in strategic locations prior to final impressions. These fiducial dots provide coincident and clear 3D data points that when scanned into a digital impression allow superimposition of the 3D models. Composite resin dots on keratinized tissue were successful at allowing accurate merging of provisional restoration and post-preparation 3D models for the purpose of using the provisional restorations as a guide for final CLINICAL SIGNIFICANCE: Composite resin dots placed temporarily on attached tissue were successful at allowing accurate merging of the provisional restoration 3D models to the preparation 3D models for the purposes of using the provisional restorations as a guide for final restoration design and manufacturing. In this case, they allowed precise superimposition of the 3D models made in the absence of any other hard tissue reference points, resulting in the fabrication of ideal final restorations. © 2017 Wiley Periodicals, Inc.

Fast and accurate: high-speed metrological large-range AFM for surface and nanometrology

NASA Astrophysics Data System (ADS)

Dai, Gaoliang; Koenders, Ludger; Fluegge, Jens; Hemmleb, Matthias

2018-05-01

Low measurement speed remains a major shortcoming of the scanning probe microscopic technique. It not only leads to a low measurement throughput, but a significant measurement drift over the long measurement time needed (up to hours or even days). To overcome this challenge, PTB, the national metrology institute of Germany, has developed a high-speed metrological large-range atomic force microscope (HS Met. LR-AFM) capable of measuring speeds up to 1 mm s‑1. This paper has introduced the design concept in detail. After modelling scanning probe microscopic measurements, our results suggest that the signal spectrum of the surface to be measured is the spatial spectrum of the surface scaled by the scanning speed. The higher the scanning speed , the broader the spectrum to be measured. To realise an accurate HS Met. LR-AFM, our solution is to combine different stages/sensors synchronously in measurements, which provide a much larger spectrum area for high-speed measurement capability. Two application examples have been demonstrated. The first is a new concept called reference areal surface metrology. Using the developed HS Met. LR-AFM, surfaces are measured accurately and traceably at a speed of 500 µm s‑1 and the results are applied as a reference 3D data map of the surfaces. By correlating the reference 3D data sets and 3D data sets of tools under calibration, which are measured at the same surface, it has the potential to comprehensively characterise the tools, for instance, the spectrum properties of the tools. The investigation results of two commercial confocal microscopes are demonstrated, indicating very promising results. The second example is the calibration of a kind of 3D nano standard, which has spatially distributed landmarks, i.e. special unique features defined by 3D-coordinates. Experimental investigations confirmed that the calibration accuracy is maintained at a measurement speed of 100 µm s‑1, which improves the calibration efficiency by a factor of 10.

Validation of reference genes for RT-qPCR studies of gene expression in banana fruit under different experimental conditions.

PubMed

Chen, Lei; Zhong, Hai-ying; Kuang, Jian-fei; Li, Jian-guo; Lu, Wang-jin; Chen, Jian-ye

2011-08-01

Reverse transcription quantitative real-time PCR (RT-qPCR) is a sensitive technique for quantifying gene expression, but its success depends on the stability of the reference gene(s) used for data normalization. Only a few studies on validation of reference genes have been conducted in fruit trees and none in banana yet. In the present work, 20 candidate reference genes were selected, and their expression stability in 144 banana samples were evaluated and analyzed using two algorithms, geNorm and NormFinder. The samples consisted of eight sample sets collected under different experimental conditions, including various tissues, developmental stages, postharvest ripening, stresses (chilling, high temperature, and pathogen), and hormone treatments. Our results showed that different suitable reference gene(s) or combination of reference genes for normalization should be selected depending on the experimental conditions. The RPS2 and UBQ2 genes were validated as the most suitable reference genes across all tested samples. More importantly, our data further showed that the widely used reference genes, ACT and GAPDH, were not the most suitable reference genes in many banana sample sets. In addition, the expression of MaEBF1, a gene of interest that plays an important role in regulating fruit ripening, under different experimental conditions was used to further confirm the validated reference genes. Taken together, our results provide guidelines for reference gene(s) selection under different experimental conditions and a foundation for more accurate and widespread use of RT-qPCR in banana.

Rapid Polymer Sequencer

NASA Technical Reports Server (NTRS)

Stolc, Viktor (Inventor); Brock, Matthew W (Inventor)

2013-01-01

Method and system for rapid and accurate determination of each of a sequence of unknown polymer components, such as nucleic acid components. A self-assembling monolayer of a selected substance is optionally provided on an interior surface of a pipette tip, and the interior surface is immersed in a selected liquid. A selected electrical field is impressed in a longitudinal direction, or in a transverse direction, in the tip region, a polymer sequence is passed through the tip region, and a change in an electrical current signal is measured as each polymer component passes through the tip region. Each of the measured changes in electrical current signals is compared with a database of reference electrical change signals, with each reference signal corresponding to an identified polymer component, to identify the unknown polymer component with a reference polymer component. The nanopore preferably has a pore inner diameter of no more than about 40 nm and is prepared by heating and pulling a very small section of a glass tubing.

Techniques of Photometry and Astrometry with APASS, Gaia, and Pan-STARRs Results (Abstract)

NASA Astrophysics Data System (ADS)

Green, W.

2017-12-01

(Abstract only) The databases with the APASS DR9, Gaia DR1, and the Pan-STARRs 3pi DR1 data releases are publicly available for use. There is a bit of data-mining involved to download and manage these reference stars. This paper discusses the use of these databases to acquire accurate photometric references as well as techniques for improving results. Images are prepared in the usual way: zero, dark, flat-fields, and WCS solutions with Astrometry.net. Images are then processed with Sextractor to produce an ASCII table of identifying photometric features. The database manages photometics catalogs and images converted to ASCII tables. Scripts convert the files into SQL and assimilate them into database tables. Using SQL techniques, each image star is merged with reference data to produce publishable results. The VYSOS has over 13,000 images of the ONC5 field to process with roughly 100 total fields in the campaign. This paper provides the overview for this daunting task.

Remote sensing and the Mississippi high accuracy reference network

NASA Technical Reports Server (NTRS)

Mick, Mark; Alexander, Timothy M.; Woolley, Stan

1994-01-01

Since 1986, NASA's Commercial Remote Sensing Program (CRSP) at Stennis Space Center has supported commercial remote sensing partnerships with industry. CRSP's mission is to maximize U.S. market exploitation of remote sensing and related space-based technologies and to develop advanced technical solutions for spatial information requirements. Observation, geolocation, and communications technologies are converging and their integration is critical to realize the economic potential for spatial informational needs. Global positioning system (GPS) technology enables a virtual revolution in geopositionally accurate remote sensing of the earth. A majority of states are creating GPS-based reference networks, or high accuracy reference networks (HARN). A HARN can be defined for a variety of local applications and tied to aerial or satellite observations to provide an important contribution to geographic information systems (GIS). This paper details CRSP's experience in the design and implementation of a HARN in Mississippi and the design and support of future applications of integrated earth observations, geolocation, and communications technology.

Robust iterative closest point algorithm based on global reference point for rotation invariant registration.

PubMed

Du, Shaoyi; Xu, Yiting; Wan, Teng; Hu, Huaizhong; Zhang, Sirui; Xu, Guanglin; Zhang, Xuetao

2017-01-01

The iterative closest point (ICP) algorithm is efficient and accurate for rigid registration but it needs the good initial parameters. It is easily failed when the rotation angle between two point sets is large. To deal with this problem, a new objective function is proposed by introducing a rotation invariant feature based on the Euclidean distance between each point and a global reference point, where the global reference point is a rotation invariant. After that, this optimization problem is solved by a variant of ICP algorithm, which is an iterative method. Firstly, the accurate correspondence is established by using the weighted rotation invariant feature distance and position distance together. Secondly, the rigid transformation is solved by the singular value decomposition method. Thirdly, the weight is adjusted to control the relative contribution of the positions and features. Finally this new algorithm accomplishes the registration by a coarse-to-fine way whatever the initial rotation angle is, which is demonstrated to converge monotonically. The experimental results validate that the proposed algorithm is more accurate and robust compared with the original ICP algorithm.

Robust iterative closest point algorithm based on global reference point for rotation invariant registration

PubMed Central

Du, Shaoyi; Xu, Yiting; Wan, Teng; Zhang, Sirui; Xu, Guanglin; Zhang, Xuetao

2017-01-01

The iterative closest point (ICP) algorithm is efficient and accurate for rigid registration but it needs the good initial parameters. It is easily failed when the rotation angle between two point sets is large. To deal with this problem, a new objective function is proposed by introducing a rotation invariant feature based on the Euclidean distance between each point and a global reference point, where the global reference point is a rotation invariant. After that, this optimization problem is solved by a variant of ICP algorithm, which is an iterative method. Firstly, the accurate correspondence is established by using the weighted rotation invariant feature distance and position distance together. Secondly, the rigid transformation is solved by the singular value decomposition method. Thirdly, the weight is adjusted to control the relative contribution of the positions and features. Finally this new algorithm accomplishes the registration by a coarse-to-fine way whatever the initial rotation angle is, which is demonstrated to converge monotonically. The experimental results validate that the proposed algorithm is more accurate and robust compared with the original ICP algorithm. PMID:29176780

An evaluation of children's metered-dose inhaler technique for asthma medications.

PubMed

Burkhart, Patricia V; Rayens, Mary Kay; Bowman, Roxanne K

2005-03-01

Regardless of the medication delivery system, health care providers need to teach accurate medication administration techniques to their patients, educate them about the particular nuances of the prescribed delivery system (eg, proper storage), and reinforce these issues at each health encounter. A single instruction session is not sufficient to maintain appropriate inhaler techniques for patients who require continued use. Providing written steps for the administration technique is helpful so that the patient can refer to them later when using the medication. The National Heart, Lung, and Blood Institute's "Practical Guide for the Diagnosis and Management of Asthma" recommends that practitioners follow these steps for effective inhaler technique training when first prescribing an inhaler: 1. Teach patients the steps and give written instruction handouts. 2. Demonstrate how to use the inhaler step-by-step. 3. Ask patients to demonstrate how to use the inhaler. Let the patient refer to the handout on the first training. Then use the handout asa checklist to assess the patient's future technique. 4. Provide feedback to patients about what they did right and what they need to improve. Have patients demonstrate their technique again, if necessary. The last two steps should be performed (ie, demonstration and providing feedback on what patients did right and what they need to improve) at every subsequent visit. If the patient makes multiple errors, it is advisable to focus on improving one or two key steps at a time. With improvements in drug delivery come challenges, necessitating that practitioners stay current with new medication administration techniques. Teaching and reinforcing accurate technique at each health care encounter are critical to help ensure medication efficacy for patients with asthma. Since one fifth of children in the study performed incorrect medication technique even after education, checklists of steps for the correct use of inhalation devices, such as those provided in this article, should be given to patients for home use and for use by clinicians to evaluate patient technique at each health encounter.

Response to “Accurate Risk-Based Chemical Screening Relies on Robust Exposure Estimates”

EPA Science Inventory

This is a correspondence (letter to the editor) with reference to comments by Rudel and Perovich on the article "Integration of Dosimetry, Exposure, and High-Throughput Screening Data in Chemical Toxicity Assessment". Article Reference: SI # 238882

Multicenter Evaluation of the Vitek MS Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry System for Identification of Gram-Positive Aerobic Bacteria

PubMed Central

Burnham, Carey-Ann D.; Bythrow, Maureen; Garner, Omai B.; Ginocchio, Christine C.; Jennemann, Rebecca; Lewinski, Michael A.; Manji, Ryhana; Mochon, A. Brian; Procop, Gary W.; Richter, Sandra S.; Sercia, Linda; Westblade, Lars F.; Ferraro, Mary Jane; Branda, John A.

2013-01-01

Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF) is gaining momentum as a tool for bacterial identification in the clinical microbiology laboratory. Compared with conventional methods, this technology can more readily and conveniently identify a wide range of organisms. Here, we report the findings from a multicenter study to evaluate the Vitek MS v2.0 system (bioMérieux, Inc.) for the identification of aerobic Gram-positive bacteria. A total of 1,146 unique isolates, representing 13 genera and 42 species, were analyzed, and results were compared to those obtained by nucleic acid sequence-based identification as the reference method. For 1,063 of 1,146 isolates (92.8%), the Vitek MS provided a single identification that was accurate to the species level. For an additional 31 isolates (2.7%), multiple possible identifications were provided, all correct at the genus level. Mixed-genus or single-choice incorrect identifications were provided for 18 isolates (1.6%). Although no identification was obtained for 33 isolates (2.9%), there was no specific bacterial species for which the Vitek MS consistently failed to provide identification. In a subset of 463 isolates representing commonly encountered important pathogens, 95% were accurately identified to the species level and there were no misidentifications. Also, in all but one instance, the Vitek MS correctly differentiated Streptococcus pneumoniae from other viridans group streptococci. The findings demonstrate that the Vitek MS system is highly accurate for the identification of Gram-positive aerobic bacteria in the clinical laboratory setting. PMID:23658261

Loss of life expectancy derived from a standardized mortality ratio in Denmark, Finland, Norway and Sweden.

PubMed

Skriver, Mette Vinther; Væth, Michael; Støvring, Henrik

2018-01-01

The standardized mortality ratio (SMR) is a widely used measure. A recent methodological study provided an accurate approximate relationship between an SMR and difference in lifetime expectancies. This study examines the usefulness of the theoretical relationship, when comparing historic mortality data in four Scandinavian populations. For Denmark, Finland, Norway and Sweden, data on mortality every fifth year in the period 1950 to 2010 were obtained. Using 1980 as the reference year, SMRs and difference in life expectancy were calculated. The assumptions behind the theoretical relationship were examined graphically. The theoretical relationship predicts a linear association with a slope, [Formula: see text], between log(SMR) and difference in life expectancies, and the theoretical prediction and calculated differences in lifetime expectancies were compared. We examined the linear association both for life expectancy at birth and at age 30. All analyses were done for females, males and the total population. The approximate relationship provided accurate predictions of actual differences in lifetime expectancies. The accuracy of the predictions was better when age was restricted to above 30, and improved if the changes in mortality rate were close to a proportional change. Slopes of the linear relationship were generally around 9 for females and 10 for males. The theoretically derived relationship between SMR and difference in life expectancies provides an accurate prediction for comparing populations with approximately proportional differences in mortality, and was relatively robust. The relationship may provide a useful prediction of differences in lifetime expectancies, which can be more readily communicated and understood.

Multicenter evaluation of the Vitek MS matrix-assisted laser desorption ionization-time of flight mass spectrometry system for identification of Gram-positive aerobic bacteria.

PubMed

Rychert, Jenna; Burnham, Carey-Ann D; Bythrow, Maureen; Garner, Omai B; Ginocchio, Christine C; Jennemann, Rebecca; Lewinski, Michael A; Manji, Ryhana; Mochon, A Brian; Procop, Gary W; Richter, Sandra S; Sercia, Linda; Westblade, Lars F; Ferraro, Mary Jane; Branda, John A

2013-07-01

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF) is gaining momentum as a tool for bacterial identification in the clinical microbiology laboratory. Compared with conventional methods, this technology can more readily and conveniently identify a wide range of organisms. Here, we report the findings from a multicenter study to evaluate the Vitek MS v2.0 system (bioMérieux, Inc.) for the identification of aerobic Gram-positive bacteria. A total of 1,146 unique isolates, representing 13 genera and 42 species, were analyzed, and results were compared to those obtained by nucleic acid sequence-based identification as the reference method. For 1,063 of 1,146 isolates (92.8%), the Vitek MS provided a single identification that was accurate to the species level. For an additional 31 isolates (2.7%), multiple possible identifications were provided, all correct at the genus level. Mixed-genus or single-choice incorrect identifications were provided for 18 isolates (1.6%). Although no identification was obtained for 33 isolates (2.9%), there was no specific bacterial species for which the Vitek MS consistently failed to provide identification. In a subset of 463 isolates representing commonly encountered important pathogens, 95% were accurately identified to the species level and there were no misidentifications. Also, in all but one instance, the Vitek MS correctly differentiated Streptococcus pneumoniae from other viridans group streptococci. The findings demonstrate that the Vitek MS system is highly accurate for the identification of Gram-positive aerobic bacteria in the clinical laboratory setting.

Indoor Modelling Benchmark for 3D Geometry Extraction

NASA Astrophysics Data System (ADS)

Thomson, C.; Boehm, J.

2014-06-01

A combination of faster, cheaper and more accurate hardware, more sophisticated software, and greater industry acceptance have all laid the foundations for an increased desire for accurate 3D parametric models of buildings. Pointclouds are the data source of choice currently with static terrestrial laser scanning the predominant tool for large, dense volume measurement. The current importance of pointclouds as the primary source of real world representation is endorsed by CAD software vendor acquisitions of pointcloud engines in 2011. Both the capture and modelling of indoor environments require great effort in time by the operator (and therefore cost). Automation is seen as a way to aid this by reducing the workload of the user and some commercial packages have appeared that provide automation to some degree. In the data capture phase, advances in indoor mobile mapping systems are speeding up the process, albeit currently with a reduction in accuracy. As a result this paper presents freely accessible pointcloud datasets of two typical areas of a building each captured with two different capture methods and each with an accurate wholly manually created model. These datasets are provided as a benchmark for the research community to gauge the performance and improvements of various techniques for indoor geometry extraction. With this in mind, non-proprietary, interoperable formats are provided such as E57 for the scans and IFC for the reference model. The datasets can be found at: http://indoor-bench.github.io/indoor-bench.

Endogenous glucocorticoid analysis by liquid chromatography-tandem mass spectrometry in routine clinical laboratories.

PubMed

Hawley, James M; Keevil, Brian G

2016-09-01

Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is a powerful analytical technique that offers exceptional selectivity and sensitivity. Used optimally, LC-MS/MS provides accurate and precise results for a wide range of analytes at concentrations that are difficult to quantitate with other methodologies. Its implementation into routine clinical biochemistry laboratories has revolutionised our ability to analyse small molecules such as glucocorticoids. Whereas immunoassays can suffer from matrix effects and cross-reactivity due to interactions with structural analogues, the selectivity offered by LC-MS/MS has largely overcome these limitations. As many clinical guidelines are now beginning to acknowledge the importance of the methodology used to provide results, the advantages associated with LC-MS/MS are gaining wider recognition. With their integral role in both the diagnosis and management of hypo- and hyperadrenal disorders, coupled with their widespread pharmacological use, the accurate measurement of glucocorticoids is fundamental to effective patient care. Here, we provide an up-to-date review of the LC-MS/MS techniques used to successfully measure endogenous glucocorticoids, particular reference is made to serum, urine and salivary cortisol. Copyright © 2016 Elsevier Ltd. All rights reserved.

Mechanism For Adjustment Of Commutation Of Brushless Motor

NASA Technical Reports Server (NTRS)

Schaefer, Richard E.

1995-01-01

Mechanism enables adjustment of angular position of set of Hall-effect devices that sense instantaneous shaft angle of brushless dc motor. Outputs of sensors fed to commutation circuitry. Measurement of shaft angle essential for commutation; that is, application of voltage to stator windings must be synchronized with shaft angle. To obtain correct angle measurement for commutation, Hall-effect angle sensors positioned at proper reference angle. The present mechanism accelerates adjustment procedure and makes it possible to obtain more accurate indication of minimum-current position because it provides for adjustment while motor running.

New train of thought in troubleshooting of modern automobiles

NASA Astrophysics Data System (ADS)

Chen, Zhaojun

2018-03-01

With the rapid development of social economy in our country, the car has also been popularized more and more widely. In order to ensure the normal running of the car, it is very important to make proper maintenance and safeguard measures. To achieve the effective enhancement of the quality of vehicle maintenance, we must be able to accurately determine the vehicle fault with the shortest possible time. This article focuses on the new ideas of modern vehicle troubleshooting carried out related research, analysis, hoping to provide some valuable reference to the staff.

Ab initio interatomic potentials and the thermodynamic properties of fluids

NASA Astrophysics Data System (ADS)

Vlasiuk, Maryna; Sadus, Richard J.

2017-07-01

Monte Carlo simulations with accurate ab initio interatomic potentials are used to investigate the key thermodynamic properties of argon and krypton in both vapor and liquid phases. Data are reported for the isochoric and isobaric heat capacities, the Joule-Thomson coefficient, and the speed of sound calculated using various two-body interatomic potentials and different combinations of two-body plus three-body terms. The results are compared to either experimental or reference data at state points between the triple and critical points. Using accurate two-body ab initio potentials, combined with three-body interaction terms such as the Axilrod-Teller-Muto and Marcelli-Wang-Sadus potentials, yields systematic improvements to the accuracy of thermodynamic predictions. The effect of three-body interactions is to lower the isochoric and isobaric heat capacities and increase both the Joule-Thomson coefficient and speed of sound. The Marcelli-Wang-Sadus potential is a computationally inexpensive way to utilize accurate two-body ab initio potentials for the prediction of thermodynamic properties. In particular, it provides a very effective way of extending two-body ab initio potentials to liquid phase properties.

Improving distance estimates to nearby bright stars: Combining astrometric data from Hipparcos, Nano-JASMINE and Gaia

NASA Astrophysics Data System (ADS)

Michalik, Daniel; Lindegren, Lennart; Hobbs, David; Lammers, Uwe; Yamada, Yoshiyuki

2013-02-01

Starting in 2013, Gaia will deliver highly accurate astrometric data, which eventually will supersede most other stellar catalogues in accuracy and completeness. It is, however, limited to observations from magnitude 6 to 20 and will therefore not include the brightest stars. Nano-JASMINE, an ultrasmall Japanese astrometry satellite, will observe these bright stars, but with much lower accuracy. Hence, the Hipparcos catalogue from 1997 will likely remain the main source of accurate distances to bright nearby stars. We are investigating how this might be improved by optimally combining data from all three missions through a joint astrometric solution. This would take advantage of the unique features of each mission: the historic bright-star measurements of Hipparcos, the updated bright-star observations of Nano-JASMINE, and the very accurate reference frame of Gaia. The long temporal baseline between the missions provides additional benefits for the determination of proper motions and binary detection, which indirectly improve the parallax determination further. We present a quantitative analysis of the expected gains based on simulated data for all three missions.

Ab initio interatomic potentials and the thermodynamic properties of fluids.

PubMed

Vlasiuk, Maryna; Sadus, Richard J

2017-07-14

Monte Carlo simulations with accurate ab initio interatomic potentials are used to investigate the key thermodynamic properties of argon and krypton in both vapor and liquid phases. Data are reported for the isochoric and isobaric heat capacities, the Joule-Thomson coefficient, and the speed of sound calculated using various two-body interatomic potentials and different combinations of two-body plus three-body terms. The results are compared to either experimental or reference data at state points between the triple and critical points. Using accurate two-body ab initio potentials, combined with three-body interaction terms such as the Axilrod-Teller-Muto and Marcelli-Wang-Sadus potentials, yields systematic improvements to the accuracy of thermodynamic predictions. The effect of three-body interactions is to lower the isochoric and isobaric heat capacities and increase both the Joule-Thomson coefficient and speed of sound. The Marcelli-Wang-Sadus potential is a computationally inexpensive way to utilize accurate two-body ab initio potentials for the prediction of thermodynamic properties. In particular, it provides a very effective way of extending two-body ab initio potentials to liquid phase properties.

Effect of endogenous reference genes on digital PCR assessment of genetically engineered canola events.

PubMed

Demeke, Tigst; Eng, Monika

2018-05-01

Droplet digital PCR (ddPCR) has been used for absolute quantification of genetically engineered (GE) events. Absolute quantification of GE events by duplex ddPCR requires the use of appropriate primers and probes for target and reference gene sequences in order to accurately determine the amount of GE materials. Single copy reference genes are generally preferred for absolute quantification of GE events by ddPCR. Study has not been conducted on a comparison of reference genes for absolute quantification of GE canola events by ddPCR. The suitability of four endogenous reference sequences ( HMG-I/Y , FatA(A), CruA and Ccf) for absolute quantification of GE canola events by ddPCR was investigated. The effect of DNA extraction methods and DNA quality on the assessment of reference gene copy numbers was also investigated. ddPCR results were affected by the use of single vs. two copy reference genes. The single copy, FatA(A), reference gene was found to be stable and suitable for absolute quantification of GE canola events by ddPCR. For the copy numbers measured, the HMG-I/Y reference gene was less consistent than FatA(A) reference gene. The expected ddPCR values were underestimated when CruA and Ccf (two copy endogenous Cruciferin sequences) were used because of high number of copies. It is important to make an adjustment if two copy reference genes are used for ddPCR in order to obtain accurate results. On the other hand, real-time quantitative PCR results were not affected by the use of single vs. two copy reference genes.

Normal Variants and Pitfalls Encountered in PET Assessment of Gynecologic Malignancies.

PubMed

Yu, Jian Q; Doss, Mohan; Alpaugh, R Katherine

2018-04-01

Combined PET/computed tomography is used for oncological indications. PET/computed tomography benefits from the metabolic information of PET and the anatomic localization of computed tomography. The integrated scanner provides data with accurate registration of anatomy and molecular information. Many physiologic conditions, normal variants, and benign lesions within the pelvis and the body can cause confusion and uncertainty. False-negative results owing to low 18 F-fluorodeoxyglucose uptake from the tumor can produce diagnostic challenges and inaccurate conclusions. This article reviews normal variants and potential pitfalls encountered in PET assessment of gynecologic malignancies to provide useful information for the referring and reporting physicians. Copyright © 2017 Elsevier Inc. All rights reserved.

Validation of reference genes aiming accurate normalization of qRT-PCR data in Dendrocalamus latiflorus Munro.

PubMed

Liu, Mingying; Jiang, Jing; Han, Xiaojiao; Qiao, Guirong; Zhuo, Renying

2014-01-01

Dendrocalamus latiflorus Munro distributes widely in subtropical areas and plays vital roles as valuable natural resources. The transcriptome sequencing for D. latiflorus Munro has been performed and numerous genes especially those predicted to be unique to D. latiflorus Munro were revealed. qRT-PCR has become a feasible approach to uncover gene expression profiling, and the accuracy and reliability of the results obtained depends upon the proper selection of stable reference genes for accurate normalization. Therefore, a set of suitable internal controls should be validated for D. latiflorus Munro. In this report, twelve candidate reference genes were selected and the assessment of gene expression stability was performed in ten tissue samples and four leaf samples from seedlings and anther-regenerated plants of different ploidy. The PCR amplification efficiency was estimated, and the candidate genes were ranked according to their expression stability using three software packages: geNorm, NormFinder and Bestkeeper. GAPDH and EF1α were characterized to be the most stable genes among different tissues or in all the sample pools, while CYP showed low expression stability. RPL3 had the optimal performance among four leaf samples. The application of verified reference genes was illustrated by analyzing ferritin and laccase expression profiles among different experimental sets. The analysis revealed the biological variation in ferritin and laccase transcript expression among the tissues studied and the individual plants. geNorm, NormFinder, and BestKeeper analyses recommended different suitable reference gene(s) for normalization according to the experimental sets. GAPDH and EF1α had the highest expression stability across different tissues and RPL3 for the other sample set. This study emphasizes the importance of validating superior reference genes for qRT-PCR analysis to accurately normalize gene expression of D. latiflorus Munro.

Wave-Ice Interaction and the Marginal Ice Zone

DTIC Science & Technology

2013-09-30

concept, using a high-quality attitude and heading reference system ( AHRS ) together with an accurate twin-antennae GPS compass. The instruments logged...the AHRS parameters at 50Hz, together with GPS-derived fixes, heading (accurate to better than 1o) and velocities at 10Hz. The 30MB hourly files

Treating knee pain: history taking and accurate diagnoses.

PubMed

Barratt, Julian

2010-07-01

Prompt and effective diagnosis and treatment for common knee problems depend on practitioners' ability to distinguish between traumatic and inflammatory knee conditions. This article aims to enable practitioners to make accurate assessments, carry out knee examinations and undertake selected special tests as necessary before discharging or referring patients.

Field precision machining technology of target chamber in ICF lasers

NASA Astrophysics Data System (ADS)

Xu, Yuanli; Wu, Wenkai; Shi, Sucun; Duan, Lin; Chen, Gang; Wang, Baoxu; Song, Yugang; Liu, Huilin; Zhu, Mingzhi

2016-10-01

In ICF lasers, many independent laser beams are required to be positioned on target with a very high degree of accuracy during a shot. The target chamber provides a precision platform and datum reference for final optics assembly and target collimation and location system. The target chamber consists of shell with welded flanges, reinforced concrete pedestal, and lateral support structure. The field precision machining technology of target chamber in ICF lasers have been developed based on ShenGuangIII (SGIII). The same center of the target chamber is adopted in the process of design, fabrication, and alignment. The technologies of beam collimation and datum reference transformation are developed for the fabrication, positioning and adjustment of target chamber. A supporting and rotating mechanism and a special drilling machine are developed to bore the holes of ports. An adjustment mechanism is designed to accurately position the target chamber. In order to ensure the collimation requirements of the beam leading and focusing and the target positioning, custom-machined spacers are used to accurately correct the alignment error of the ports. Finally, this paper describes the chamber center, orientation, and centering alignment error measurements of SGIII. The measurements show the field precision machining of SGIII target chamber meet its design requirement. These information can be used on similar systems.

Study on Calculation of Liquid Level And Storage of Tanks for LNG-fueled Vessels

NASA Astrophysics Data System (ADS)

Li, Kun; Wang, Guoqing; Liu, Chang

2018-01-01

As the ongoing development of the application of LNG as a clean energy in waterborne transport industry, the fleet scale of LNG-fueled vessels enlarged and the safety operation has attracted more attention in the industry. Especially the accurate detection of liquid level of LNG tanks is regarded as an important issue to ensure a safe and stable operation of LNG-fueled ships and a key parameter to keep the proper functioning of marine fuel storage system, supply system and safety control system. At present, detection of LNG tank liquid level mainly adopts differential pressure detection method. Liquid level condition could be found from the liquid level reference tables. However in practice, since LNG-fueled vessels are generally not in a stationary state, liquid state within the LNG tanks will constantly change, the detection of storage of tanks only by reference to the tables will cause deviation to some extent. By analyzing the temperature under different pressure, the effects of temperature change on density and volume integration calculation, a method of calculating the liquid level and storage of LNG tanks is put forward making the calculation of liquid level and actual storage of LNG tanks more accurately and providing a more reliable basis for the calculation of energy consumption level and operation economy for LNG-fueled vessels.

A Robust Protocol for Using Multiplexed Droplet Digital PCR to Quantify Somatic Copy Number Alterations in Clinical Tissue Specimens.

PubMed

Hughesman, Curtis B; Lu, X J David; Liu, Kelly Y P; Zhu, Yuqi; Poh, Catherine F; Haynes, Charles

2016-01-01

The ability of droplet digital PCR (ddPCR) to accurately determine the concentrations of amplifiable targets makes it a promising platform for measuring copy number alterations (CNAs) in genomic biomarkers. However, its application to clinical samples, particularly formalin-fixed paraffin-embedded specimens, will require strategies to reliably determine CNAs in DNA of limited quantity and quality. When applied to cancerous tissue, those methods must also account for global genetic instability and the associated probability that the abundance(s) of one or more chosen reference loci do not represent the average ploidy of cells comprising the specimen. Here we present an experimental design strategy and associated data analysis tool that enables accurate determination of CNAs in a panel of biomarkers using multiplexed ddPCR. The method includes strategies to optimize primer and probes design to cleanly segregate droplets in the data output from reaction wells amplifying multiple independent templates, and to correct for bias from artifacts such as DNA fragmentation. We demonstrate how a panel of reference loci can be used to determine a stable CNA-neutral benchmark. These innovations, when taken together, provide a comprehensive strategy that can be used to reliably detect biomarker CNAs in DNA extracted from either frozen or FFPE tissue biopsies.

Radiometer calibration methods and resulting irradiance differences: Radiometer calibration methods and resulting irradiance differences

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

Habte, Aron; Sengupta, Manajit; Andreas, Afshin

Accurate solar radiation measured by radiometers depends on instrument performance specifications, installation method, calibration procedure, measurement conditions, maintenance practices, location, and environmental conditions. This study addresses the effect of different calibration methodologies and resulting differences provided by radiometric calibration service providers such as the National Renewable Energy Laboratory (NREL) and manufacturers of radiometers. Some of these methods calibrate radiometers indoors and some outdoors. To establish or understand the differences in calibration methodologies, we processed and analyzed field-measured data from radiometers deployed for 10 months at NREL's Solar Radiation Research Laboratory. These different methods of calibration resulted in a difference ofmore » +/-1% to +/-2% in solar irradiance measurements. Analyzing these differences will ultimately assist in determining the uncertainties of the field radiometer data and will help develop a consensus on a standard for calibration. Further advancing procedures for precisely calibrating radiometers to world reference standards that reduce measurement uncertainties will help the accurate prediction of the output of planned solar conversion projects and improve the bankability of financing solar projects.« less

Direct Measurements of Quantum Kinetic Energy Tensor in Stable and Metastable Water near the Triple Point: An Experimental Benchmark.

PubMed

Andreani, Carla; Romanelli, Giovanni; Senesi, Roberto

2016-06-16

This study presents the first direct and quantitative measurement of the nuclear momentum distribution anisotropy and the quantum kinetic energy tensor in stable and metastable (supercooled) water near its triple point, using deep inelastic neutron scattering (DINS). From the experimental spectra, accurate line shapes of the hydrogen momentum distributions are derived using an anisotropic Gaussian and a model-independent framework. The experimental results, benchmarked with those obtained for the solid phase, provide the state of the art directional values of the hydrogen mean kinetic energy in metastable water. The determinations of the direction kinetic energies in the supercooled phase, provide accurate and quantitative measurements of these dynamical observables in metastable and stable phases, that is, key insight in the physical mechanisms of the hydrogen quantum state in both disordered and polycrystalline systems. The remarkable findings of this study establish novel insight into further expand the capacity and accuracy of DINS investigations of the nuclear quantum effects in water and represent reference experimental values for theoretical investigations.

NREL Pyrheliometer Comparisons: September 26-October 7, 2016 (NPC-2016)

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

Reda, Ibrahim; Dooraghi, Mike; Andreas, Afshin

Accurate measurements of direct normal (beam) solar irradiance from pyrheliometers are important for developing and deploying solar energy conversion systems, improving our understanding of the Earth's energy budget for climate change studies, and for other science and technology applications involving solar flux. Providing these measurements places many demands on the quality system used by the operator of commercially available radiometers. Maintaining accurate radiometer calibrations that are traceable to an international standard is the first step in producing research-quality solar irradiance measurements. National Renewable Energy Laboratory (NREL) pyrheliometer comparisons (NPCs) are held annually at the Solar Radiation Research Laboratory (SRRL) inmore » Golden, Colorado. Open to all pyrheliometer owners and operators, each NPC provides an opportunity to determine the unique World Radiometric Reference transfer factor (WRR-TF) for each participating pyrheliometer. By adjusting all subsequent pyrheliometer measurements by the appropriate WRR-TF, the solar irradiance data are traceable to the WRR. NPC-2016 was September 26 through October 7, 2016. Participants operated 45 absolute cavity radiometers and 27 conventional thermopile-based pyrheliometers to simultaneously measure clear-sky, direct normal solar irradiance during this period.« less

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

PubMed Central

2014-01-01

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

Measuring body composition in dogs using multifrequency bioelectrical impedance analysis and dual energy X-ray absorptiometry.

PubMed

Rae, L S; Vankan, D M; Rand, J S; Flickinger, E A; Ward, L C

2016-06-01

Thirty-five healthy, neutered, mixed breed dogs were used to determine the ability of multifrequency bioelectrical impedance analysis (MFBIA) to predict accurately fat-free mass (FFM) in dogs using dual energy X-ray absorptiometry (DXA)-measured FFM as reference. A second aim was to compare MFBIA predictions with morphometric predictions. MFBIA-based predictors provided an accurate measure of FFM, within 1.5% when compared to DXA-derived FFM, in normal weight dogs. FFM estimates were most highly correlated with DXA-measured FFM when the prediction equation included resistance quotient, bodyweight, and body condition score. At the population level, the inclusion of impedance as a predictor variable did not add substantially to the predictive power achieved with morphometric variables alone; in individual dogs, impedance predictors were more valuable than morphometric predictors. These results indicate that, following further validation, MFBIA could provide a useful tool in clinical practice to objectively measure FFM in canine patients and help improve compliance with prevention and treatment programs for obesity in dogs. Copyright © 2016. Published by Elsevier Ltd.

Validation of a Biofeedback System for Wheelchair Propulsion Training

PubMed Central

Guo, Liyun; Kwarciak, Andrew M.; Rodriguez, Russell; Sarkar, Nilanjan; Richter, W. Mark

2011-01-01

This paper describes the design and validation of the OptiPush Biofeedback System, a commercially available, instrumented wheel system that records handrim biomechanics and provides stroke-by-stroke biofeedback and targeting for 11 propulsion variables. Testing of the system revealed accurate measurement of wheel angle (0.02% error), wheel speed (0.06% error), and handrim loads. The maximum errors in static force and torque measurements were 3.80% and 2.05%, respectively. Measured forces were also found to be highly linear (0.985 < slope < 1.011) and highly correlated to the reference forces (r 2 > .998). Dynamic measurements of planar forces (F x and F y) and axle torque also had low error (−0.96 N to 0.83 N for force and 0.10 Nm to 0.14 Nm for torque) and were highly correlated (r > .986) with expected force and torque values. Overall, the OptiPush Biofeedback System provides accurate measurement of wheel dynamics and handrim biomechanics and may be a useful tool for improving manual wheelchair propulsion. PMID:22110977

A brief overview of computational structures technology related activities at NASA Lewis Research Center

NASA Technical Reports Server (NTRS)

Hopkins, Dale A.

1992-01-01

The presentation gives a partial overview of research and development underway in the Structures Division of LeRC, which collectively is referred to as the Computational Structures Technology Program. The activities in the program are diverse and encompass four major categories: (1) composite materials and structures; (2) probabilistic analysis and reliability; (3) design optimization and expert systems; and (4) computational methods and simulation. The approach of the program is comprehensive and entails exploration of fundamental theories of structural mechanics to accurately represent the complex physics governing engine structural performance, formulation, and implementation of computational techniques and integrated simulation strategies to provide accurate and efficient solutions of the governing theoretical models by exploiting the emerging advances in computer technology, and validation and verification through numerical and experimental tests to establish confidence and define the qualities and limitations of the resulting theoretical models and computational solutions. The program comprises both in-house and sponsored research activities. The remainder of the presentation provides a sample of activities to illustrate the breadth and depth of the program and to demonstrate the accomplishments and benefits that have resulted.

CLARREO Approach for Reference Intercalibration of Reflected Solar Sensors: On-Orbit Data Matching and Sampling

NASA Technical Reports Server (NTRS)

Roithmayr, Carlos; Lukashin, Constantine; Speth, Paul W.; Kopp, Gregg; Thome, Kurt; Wielicki, Bruce A.; Young, David F.

2014-01-01

The implementation of the Climate Absolute Radiance and Refractivity Observatory (CLARREO) mission was recommended by the National Research Council in 2007 to provide an on-orbit intercalibration standard with accuracy of 0.3% (k = 2) for relevant Earth observing sensors. The goal of reference intercalibration, as established in the Decadal Survey, is to enable rigorous high-accuracy observations of critical climate change parameters, including reflected broadband radiation [Clouds and Earth's Radiant Energy System (CERES)], cloud properties [Visible Infrared Imaging Radiometer Suite (VIIRS)], and changes in surface albedo, including snow and ice albedo feedback. In this paper, we describe the CLARREO approach for performing intercalibration on orbit in the reflected solar (RS) wavelength domain. It is based on providing highly accurate spectral reflectance and reflected radiance measurements from the CLARREO Reflected Solar Spectrometer (RSS) to establish an on-orbit reference for existing sensors, namely, CERES and VIIRS on Joint Polar Satellite System satellites, Advanced Very High Resolution Radiometer and follow-on imagers on MetOp, Landsat imagers, and imagers on geostationary platforms. One of two fundamental CLARREO mission goals is to provide sufficient sampling of high-accuracy observations that are matched in time, space, and viewing angles with measurements made by existing instruments, to a degree that overcomes the random error sources from imperfect data matching and instrument noise. The data matching is achieved through CLARREO RSS pointing operations on orbit that align its line of sight with the intercalibrated sensor. These operations must be planned in advance; therefore, intercalibration events must be predicted by orbital modeling. If two competing opportunities are identified, one target sensor must be given priority over the other. The intercalibration method is to monitor changes in targeted sensor response function parameters: effective offset, gain, nonlinearity, optics spectral response, and sensitivity to polarization. In this paper, we use existing satellite data and orbital simulationmethods to determinemission requirements for CLARREO, its instrument pointing ability, methodology, and needed intercalibration sampling and data matching for accurate intercalibration of RS radiation sensors on orbit.

A localization algorithm of adaptively determining the ROI of the reference circle in image

NASA Astrophysics Data System (ADS)

Xu, Zeen; Zhang, Jun; Zhang, Daimeng; Liu, Xiaomao; Tian, Jinwen

2018-03-01

Aiming at solving the problem of accurately positioning the detection probes underwater, this paper proposed a method based on computer vision which can effectively solve this problem. The theory of this method is that: First, because the shape information of the heat tube is similar to a circle in the image, we can find a circle which physical location is well known in the image, we set this circle as the reference circle. Second, we calculate the pixel offset between the reference circle and the probes in the picture, and adjust the steering gear through the offset. As a result, we can accurately measure the physical distance between the probes and the under test heat tubes, then we can know the precise location of the probes underwater. However, how to choose reference circle in image is a difficult problem. In this paper, we propose an algorithm that can adaptively confirm the area of reference circle. In this area, there will be only one circle, and the circle is the reference circle. The test results show that the accuracy of the algorithm of extracting the reference circle in the whole picture without using ROI (region of interest) of the reference circle is only 58.76% and the proposed algorithm is 95.88%. The experimental results indicate that the proposed algorithm can effectively improve the efficiency of the tubes detection.

RATT: Rapid Annotation Transfer Tool

PubMed Central

Otto, Thomas D.; Dillon, Gary P.; Degrave, Wim S.; Berriman, Matthew

2011-01-01

Second-generation sequencing technologies have made large-scale sequencing projects commonplace. However, making use of these datasets often requires gene function to be ascribed genome wide. Although tool development has kept pace with the changes in sequence production, for tasks such as mapping, de novo assembly or visualization, genome annotation remains a challenge. We have developed a method to rapidly provide accurate annotation for new genomes using previously annotated genomes as a reference. The method, implemented in a tool called RATT (Rapid Annotation Transfer Tool), transfers annotations from a high-quality reference to a new genome on the basis of conserved synteny. We demonstrate that a Mycobacterium tuberculosis genome or a single 2.5 Mb chromosome from a malaria parasite can be annotated in less than five minutes with only modest computational resources. RATT is available at http://ratt.sourceforge.net. PMID:21306991

Spinning angle optical calibration apparatus

DOEpatents

Beer, Stephen K.; Pratt, II, Harold R.

1991-01-01

An optical calibration apparatus is provided for calibrating and reproducing spinning angles in cross-polarization, nuclear magnetic resonance spectroscopy. An illuminated magnifying apparatus enables optical setting an accurate reproducing of spinning "magic angles" in cross-polarization, nuclear magnetic resonance spectroscopy experiments. A reference mark scribed on an edge of a spinning angle test sample holder is illuminated by a light source and viewed through a magnifying scope. When the "magic angle" of a sample material used as a standard is attained by varying the angular position of the sample holder, the coordinate position of the reference mark relative to a graduation or graduations on a reticle in the magnifying scope is noted. Thereafter, the spinning "magic angle" of a test material having similar nuclear properties to the standard is attained by returning the sample holder back to the originally noted coordinate position.

De novo transciptome assembly in polyploid species

USDA-ARS?s Scientific Manuscript database

In the absence of a reference genome, the ultimate goal of a de novo transcriptome assembly is to accurately and comprehensively reconstruct the set of messenger RNA transcripts represented in the sample. Non-reference assembly of the transcriptome of polyploid species poses a particular challenge b...

The Influence of the Terrestrial Reference Frame on Studies of Sea Level Change

NASA Astrophysics Data System (ADS)

Nerem, R. S.; Bar-Sever, Y. E.; Haines, B. J.; Desai, S.; Heflin, M. B.

2015-12-01

The terrestrial reference frame (TRF) provides the foundation for the accurate monitoring of sea level using both ground-based (tide gauges) and space-based (satellite altimetry) techniques. For the latter, tide gauges are also used to monitor drifts in the satellite instruments over time. The accuracy of the terrestrial reference frame (TRF) is thus a critical component for both types of sea level measurements. The TRF is central to the formation of geocentric sea-surface height (SSH) measurements from satellite altimeter data. The computed satellite orbits are linked to a particular TRF via the assumed locations of the ground-based tracking systems. The manner in which TRF errors are expressed in the orbit solution (and thus SSH) is not straightforward, and depends on the models of the forces underlying the satellite's motion. We discuss this relationship, and provide examples of the systematic TRF-induced errors in the altimeter derived sea-level record. The TRF is also crucial to the interpretation of tide-gauge measurements, as it enables the separation of vertical land motion from volumetric changes in the water level. TRF errors affect tide gauge measurements through GNSS estimates of the vertical land motion at each tide gauge. This talk will discuss the current accuracy of the TRF and how errors in the TRF impact both satellite altimeter and tide gauge sea level measurements. We will also discuss simulations of how the proposed Geodetic Reference Antenna in SPace (GRASP) satellite mission could reduce these errors and revolutionize how reference frames are computed in general.

Using Multiple Barometers to Detect the Floor Location of Smart Phones with Built-in Barometric Sensors for Indoor Positioning

PubMed Central

Xia, Hao; Wang, Xiaogang; Qiao, Yanyou; Jian, Jun; Chang, Yuanfei

2015-01-01

Following the popularity of smart phones and the development of mobile Internet, the demands for accurate indoor positioning have grown rapidly in recent years. Previous indoor positioning methods focused on plane locations on a floor and did not provide accurate floor positioning. In this paper, we propose a method that uses multiple barometers as references for the floor positioning of smart phones with built-in barometric sensors. Some related studies used barometric formula to investigate the altitude of mobile devices and compared the altitude with the height of the floors in a building to obtain the floor number. These studies assume that the accurate height of each floor is known, which is not always the case. They also did not consider the difference in the barometric-pressure pattern at different floors, which may lead to errors in the altitude computation. Our method does not require knowledge of the accurate heights of buildings and stories. It is robust and less sensitive to factors such as temperature and humidity and considers the difference in the barometric-pressure change trends at different floors. We performed a series of experiments to validate the effectiveness of this method. The results are encouraging. PMID:25835189

Seasonal cultivated and fallow cropland mapping using MODIS-based automated cropland classification algorithm

USGS Publications Warehouse

Wu, Zhuoting; Thenkabail, Prasad S.; Mueller, Rick; Zakzeski, Audra; Melton, Forrest; Johnson, Lee; Rosevelt, Carolyn; Dwyer, John; Jones, Jeanine; Verdin, James P.

2014-01-01

Increasing drought occurrences and growing populations demand accurate, routine, and consistent cultivated and fallow cropland products to enable water and food security analysis. The overarching goal of this research was to develop and test automated cropland classification algorithm (ACCA) that provide accurate, consistent, and repeatable information on seasonal cultivated as well as seasonal fallow cropland extents and areas based on the Moderate Resolution Imaging Spectroradiometer remote sensing data. Seasonal ACCA development process involves writing series of iterative decision tree codes to separate cultivated and fallow croplands from noncroplands, aiming to accurately mirror reliable reference data sources. A pixel-by-pixel accuracy assessment when compared with the U.S. Department of Agriculture (USDA) cropland data showed, on average, a producer’s accuracy of 93% and a user’s accuracy of 85% across all months. Further, ACCA-derived cropland maps agreed well with the USDA Farm Service Agency crop acreage-reported data for both cultivated and fallow croplands with R-square values over 0.7 and field surveys with an accuracy of ≥95% for cultivated croplands and ≥76% for fallow croplands. Our results demonstrated the ability of ACCA to generate cropland products, such as cultivated and fallow cropland extents and areas, accurately, automatically, and repeatedly throughout the growing season.

A method for the rapid detection of urinary tract infections.

PubMed

Olsson, Carl; Kapoor, Deepak; Howard, Glenn

2012-04-01

To determine the reliability of a rapid detection method compared with the reference standard streaked agar plate in diagnosing the presence of urinary tract infection (UTI). De-identified clean catch urine specimens from 980 office visit patients were processed during a 30-day period. Classic 1-μL and 10-μL streaked agar plates were used in parallel with the new CultureStat Rapid UTI Detection System (CSRUDS). Urine results were evaluated using the CSRUDS at 30 and 90 minutes after collection. A comparative analysis of the subsequent plate results versus the CSRUDS results was achieved for 973 of these samples. Positive UTI conditions were accurately identified by both CSRUDS and agar streak plate methods. CSRUDS accurately identified UTI negative conditions with 99.3% reliability at 90 minutes. The negative predictive value of CSRUDS was 99.2% at 30 minutes. Current agar plating for first-round UTI screening has substantial documented problems that can negatively affect an accurate and timely UTI diagnosis. A novel rapid detection system, the CSRUDS provides UTI negative/positive same-day results in ≤ 90 minutes from the start of test. Such rapidly available results will enable more accurate and timely clinical decisions to be made in the urology office, particularly regarding infection status before urologic instrumentation. Copyright © 2012 Elsevier Inc. All rights reserved.

Seasonal cultivated and fallow cropland mapping using MODIS-based automated cropland classification algorithm

NASA Astrophysics Data System (ADS)

Wu, Zhuoting; Thenkabail, Prasad S.; Mueller, Rick; Zakzeski, Audra; Melton, Forrest; Johnson, Lee; Rosevelt, Carolyn; Dwyer, John; Jones, Jeanine; Verdin, James P.

2014-01-01

Increasing drought occurrences and growing populations demand accurate, routine, and consistent cultivated and fallow cropland products to enable water and food security analysis. The overarching goal of this research was to develop and test automated cropland classification algorithm (ACCA) that provide accurate, consistent, and repeatable information on seasonal cultivated as well as seasonal fallow cropland extents and areas based on the Moderate Resolution Imaging Spectroradiometer remote sensing data. Seasonal ACCA development process involves writing series of iterative decision tree codes to separate cultivated and fallow croplands from noncroplands, aiming to accurately mirror reliable reference data sources. A pixel-by-pixel accuracy assessment when compared with the U.S. Department of Agriculture (USDA) cropland data showed, on average, a producer's accuracy of 93% and a user's accuracy of 85% across all months. Further, ACCA-derived cropland maps agreed well with the USDA Farm Service Agency crop acreage-reported data for both cultivated and fallow croplands with R-square values over 0.7 and field surveys with an accuracy of ≥95% for cultivated croplands and ≥76% for fallow croplands. Our results demonstrated the ability of ACCA to generate cropland products, such as cultivated and fallow cropland extents and areas, accurately, automatically, and repeatedly throughout the growing season.

A new method for wind speed forecasting based on copula theory.

PubMed

Wang, Yuankun; Ma, Huiqun; Wang, Dong; Wang, Guizuo; Wu, Jichun; Bian, Jinyu; Liu, Jiufu

2018-01-01

How to determine representative wind speed is crucial in wind resource assessment. Accurate wind resource assessments are important to wind farms development. Linear regressions are usually used to obtain the representative wind speed. However, terrain flexibility of wind farm and long distance between wind speed sites often lead to low correlation. In this study, copula method is used to determine the representative year's wind speed in wind farm by interpreting the interaction of the local wind farm and the meteorological station. The result shows that the method proposed here can not only determine the relationship between the local anemometric tower and nearby meteorological station through Kendall's tau, but also determine the joint distribution without assuming the variables to be independent. Moreover, the representative wind data can be obtained by the conditional distribution much more reasonably. We hope this study could provide scientific reference for accurate wind resource assessments. Copyright © 2017 Elsevier Inc. All rights reserved.

Quo vadis, analytical chemistry?

PubMed

Valcárcel, Miguel

2016-01-01

This paper presents an open, personal, fresh approach to the future of Analytical Chemistry in the context of the deep changes Science and Technology are anticipated to experience. Its main aim is to challenge young analytical chemists because the future of our scientific discipline is in their hands. A description of not completely accurate overall conceptions of our discipline, both past and present, to be avoided is followed by a flexible, integral definition of Analytical Chemistry and its cornerstones (viz., aims and objectives, quality trade-offs, the third basic analytical reference, the information hierarchy, social responsibility, independent research, transfer of knowledge and technology, interfaces to other scientific-technical disciplines, and well-oriented education). Obsolete paradigms, and more accurate general and specific that can be expected to provide the framework for our discipline in the coming years are described. Finally, the three possible responses of analytical chemists to the proposed changes in our discipline are discussed.

Novel prescribed performance neural control of a flexible air-breathing hypersonic vehicle with unknown initial errors.

PubMed

Bu, Xiangwei; Wu, Xiaoyan; Zhu, Fujing; Huang, Jiaqi; Ma, Zhen; Zhang, Rui

2015-11-01

A novel prescribed performance neural controller with unknown initial errors is addressed for the longitudinal dynamic model of a flexible air-breathing hypersonic vehicle (FAHV) subject to parametric uncertainties. Different from traditional prescribed performance control (PPC) requiring that the initial errors have to be known accurately, this paper investigates the tracking control without accurate initial errors via exploiting a new performance function. A combined neural back-stepping and minimal learning parameter (MLP) technology is employed for exploring a prescribed performance controller that provides robust tracking of velocity and altitude reference trajectories. The highlight is that the transient performance of velocity and altitude tracking errors is satisfactory and the computational load of neural approximation is low. Finally, numerical simulation results from a nonlinear FAHV model demonstrate the efficacy of the proposed strategy. Copyright © 2015 ISA. Published by Elsevier Ltd. All rights reserved.

[Comparison of color reappearance between metal-ceram restoration and foundry-ceram restoration using crystaleye spectrophotometer].

PubMed

Shi, Tao; Zhang, Ning; Kong, Fan-wen; Zhan, De-song

2010-10-01

To study the color reappearance effect of metal-ceram restoration and foundry-ceram restoration using Crystaleye spectrophotometer. 58 metal-ceram restorations and 58 foundry-ceram restorations according to the result of the Crystaleye spectrophotometer were made respectively. The deltaE between restorations and natural teeth as referenced were analyzed. And satisfaction of dentists and patients were evaluated. The deltaE between metal-ceram restorations and natural teeth was 7.13 +/- 0.74. The deltaE between foundry-ceram restorations and teeth was 1.47 +/- 0.84. There were statistical differences between the deltaE (P < 0.01). The satisnatural faction of dentists and patients to the foundry-ceram restorations were higher than to the metal-ceram restorations (P < 0.05). Crystaleye spectrophotometer can provide accurate reference for foundry-ceram restoration, but for metal-ceram restoration it is not accurate.

Thinking inside the box: Spatial frames of reference for drawing in Williams syndrome and typical development.

PubMed

Hudson, Kerry D; Farran, Emily K

2017-09-01

Successfully completing a drawing relies on the ability to accurately impose and manipulate spatial frames of reference for the object that is being drawn and for the drawing space. Typically developing (TD) children use cues such as the page boundary as a frame of reference to guide the orientation of drawn lines. Individuals with Williams syndrome (WS) typically produce incohesive drawings; this is proposed to reflect a local processing bias. Across two studies, we provide the first investigation of the effect of using a frame of reference when drawing simple lines and shapes in WS and TD groups (matched for non-verbal ability). Individuals with WS (N=17 Experiment 1; N=18 Experiment 2) and TD children matched by non-verbal ability drew single lines (Experiment One) and whole shapes (Experiment Two) within a neutral, incongruent or congruent frame. The angular deviation of the drawn line/shape, relative to the model line/shape, was measured. Both groups were sensitive to spatial frames of reference when drawing single lines and whole shapes, imposed by a frame around the drawing space. A local processing bias in WS cannot explain poor drawing performance in WS. Crown Copyright © 2017. Published by Elsevier Ltd. All rights reserved.

Methods to estimate irrigated reference crop evapotranspiration - a review.

PubMed

Kumar, R; Jat, M K; Shankar, V

2012-01-01

Efficient water management of crops requires accurate irrigation scheduling which, in turn, requires the accurate measurement of crop water requirement. Irrigation is applied to replenish depleted moisture for optimum plant growth. Reference evapotranspiration plays an important role for the determination of water requirements for crops and irrigation scheduling. Various models/approaches varying from empirical to physically base distributed are available for the estimation of reference evapotranspiration. Mathematical models are useful tools to estimate the evapotranspiration and water requirement of crops, which is essential information required to design or choose best water management practices. In this paper the most commonly used models/approaches, which are suitable for the estimation of daily water requirement for agricultural crops grown in different agro-climatic regions, are reviewed. Further, an effort has been made to compare the accuracy of various widely used methods under different climatic conditions.

CD-SEM real time bias correction using reference metrology based modeling

NASA Astrophysics Data System (ADS)

Ukraintsev, V.; Banke, W.; Zagorodnev, G.; Archie, C.; Rana, N.; Pavlovsky, V.; Smirnov, V.; Briginas, I.; Katnani, A.; Vaid, A.

2018-03-01

Accuracy of patterning impacts yield, IC performance and technology time to market. Accuracy of patterning relies on optical proximity correction (OPC) models built using CD-SEM inputs and intra die critical dimension (CD) control based on CD-SEM. Sub-nanometer measurement uncertainty (MU) of CD-SEM is required for current technologies. Reported design and process related bias variation of CD-SEM is in the range of several nanometers. Reference metrology and numerical modeling are used to correct SEM. Both methods are slow to be used for real time bias correction. We report on real time CD-SEM bias correction using empirical models based on reference metrology (RM) data. Significant amount of currently untapped information (sidewall angle, corner rounding, etc.) is obtainable from SEM waveforms. Using additional RM information provided for specific technology (design rules, materials, processes) CD extraction algorithms can be pre-built and then used in real time for accurate CD extraction from regular CD-SEM images. The art and challenge of SEM modeling is in finding robust correlation between SEM waveform features and bias of CD-SEM as well as in minimizing RM inputs needed to create accurate (within the design and process space) model. The new approach was applied to improve CD-SEM accuracy of 45 nm GATE and 32 nm MET1 OPC 1D models. In both cases MU of the state of the art CD-SEM has been improved by 3x and reduced to a nanometer level. Similar approach can be applied to 2D (end of line, contours, etc.) and 3D (sidewall angle, corner rounding, etc.) cases.

Modernizing the National Spatial Reference System

NASA Astrophysics Data System (ADS)

Smith, D. A.

2016-12-01

The National Spatial Reference System (NSRS) is that system of datums, reference frames, shorelines, software and standards which serve the entire federal civilian geospatial community. It is the mission of the National Geodetic Survey (NGS) to define, maintain and provide access to the NSRS. Currently the NSRS contains three geometric reference frames (NAD 83(2011), NAD 83(PA11) and NAD 83(MA11)), one dynamic height datum (IGLD 85) and 6 vertical datums (NAVD 88, PRVD02, ASVD02, NMVD03, GUVD04, VIVD09). All of these datums are built on aging technology and contain systematic errors that grow more noticeable as access to accurate positioning becomes more widespread. It was determined by NGS in 2007 that this was not sustainable and as such, all datums and reference frames are scheduled to be replaced in 2022. [At the time of this abstract, the exact names of the replacements are being finalized and are expected to be announced by the AGU fall meeting.] Replacing the official datums and reference frames requires a carefully coordinated effort of dozens of interrelated technical projects spanning years (over a decade in some cases) and involving a majority of NGS employees. This talk will cover the plans thus far, projects completed, projects underway and will summarize the NSRS as it is expected to look and be accessed in 2022 and beyond.

Validation of Reference Genes for Gene Expression by Quantitative Real-Time RT-PCR in Stem Segments Spanning Primary to Secondary Growth in Populus tomentosa.

PubMed

Wang, Ying; Chen, Yajuan; Ding, Liping; Zhang, Jiewei; Wei, Jianhua; Wang, Hongzhi

2016-01-01

The vertical segments of Populus stems are an ideal experimental system for analyzing the gene expression patterns involved in primary and secondary growth during wood formation. Suitable internal control genes are indispensable to quantitative real time PCR (qRT-PCR) assays of gene expression. In this study, the expression stability of eight candidate reference genes was evaluated in a series of vertical stem segments of Populus tomentosa. Analysis through software packages geNorm, NormFinder and BestKeeper showed that genes ribosomal protein (RP) and tubulin beta (TUBB) were the most unstable across the developmental stages of P. tomentosa stems, and the combination of the three reference genes, eukaryotic translation initiation factor 5A (eIF5A), Actin (ACT6) and elongation factor 1-beta (EF1-beta) can provide accurate and reliable normalization of qRT-PCR analysis for target gene expression in stem segments undergoing primary and secondary growth in P. tomentosa. These results provide crucial information for transcriptional analysis in the P. tomentosa stem, which may help to improve the quality of gene expression data in these vertical stem segments, which constitute an excellent plant system for the study of wood formation.

An Evaluation of the Pea Pod System for Assessing Body Composition of Moderately Premature Infants.

PubMed

Forsum, Elisabet; Olhager, Elisabeth; Törnqvist, Caroline

2016-04-22

(1) BACKGROUND: Assessing the quality of growth in premature infants is important in order to be able to provide them with optimal nutrition. The Pea Pod device, based on air displacement plethysmography, is able to assess body composition of infants. However, this method has not been sufficiently evaluated in premature infants; (2) METHODS: In 14 infants in an age range of 3-7 days, born after 32-35 completed weeks of gestation, body weight, body volume, fat-free mass density (predicted by the Pea Pod software), and total body water (isotope dilution) were assessed. Reference estimates of fat-free mass density and body composition were obtained using a three-component model; (3) RESULTS: Fat-free mass density values, predicted using Pea Pod, were biased but not significantly (p > 0.05) different from reference estimates. Body fat (%), assessed using Pea Pod, was not significantly different from reference estimates. The biological variability of fat-free mass density was 0.55% of the average value (1.0627 g/mL); (4) CONCLUSION: The results indicate that the Pea Pod system is accurate for groups of newborn, moderately premature infants. However, more studies where this system is used for premature infants are needed, and we provide suggestions regarding how to develop this area.

Measurement of Longitudinal β-Amyloid Change with 18F-Florbetapir PET and Standardized Uptake Value Ratios

PubMed Central

Landau, Susan M.; Fero, Allison; Baker, Suzanne L.; Koeppe, Robert; Mintun, Mark; Chen, Kewei; Reiman, Eric M.; Jagust, William J.

2017-01-01

The accurate measurement of β-amyloid (Aβ) change using amyloid PET imaging is important for Alzheimer disease research and clinical trials but poses several unique challenges. In particular, reference region measurement instability may lead to spurious changes in cortical regions of interest. To optimize our ability to measure 18F-florbetapir longitudinal change, we evaluated several candidate regions of interest and their influence on cortical florbetapir change over a 2-y period in participants from the Alzheimer Disease Neuroimaging Initiative (ADNI). Methods We examined the agreement in cortical florbetapir change detected using 6 candidate reference regions (cerebellar gray matter, whole cerebellum, brain stem/pons, eroded subcortical white matter [WM], and 2 additional combinations of these regions) in 520 ADNI subjects. We used concurrent cerebrospinal fluid Aβ1–42 measurements to identify subgroups of ADNI subjects expected to remain stable over follow-up (stable Aβ group; n = 14) and subjects expected to increase (increasing Aβ group; n = 91). We then evaluated reference regions according to whether cortical change was minimal in the stable Aβ group and cortical retention increased in the increasing Aβ group. Results There was poor agreement across reference regions in the amount of cortical change observed across all 520 ADNI subjects. Within the stable Aβ group, however, cortical florbetapir change was 1%–2% across all reference regions, indicating high consistency. In the increasing Aβ group, cortical increases were significant with all reference regions. Reference regions containing WM (as opposed to cerebellum or pons) enabled detection of cortical change that was more physiologically plausible and more likely to increase over time. Conclusion Reference region selection has an important influence on the detection of florbetapir change. Compared with cerebellum or pons alone, reference regions that included subcortical WM resulted in change measurements that are more accurate. In addition, because use of WM-containing reference regions involves dividing out cortical signal contained in the reference region (via partial-volume effects), use of these WM-containing regions may result in more conservative estimates of actual change. Future analyses using different tracers, tracer–kinetic models, pipelines, and comparisons with other biomarkers will further optimize our ability to accurately measure Aβ changes over time. PMID:25745095

Microfluidic nitrogen-assisted nanoelectrospray emitter: A monolithic interface for accurate mass measurements based on a single nozzle.

PubMed

Wang, Lingling; Wang, Yujiao; Jiang, Shichang; Ye, Mingyue; Su, Ping; Xiong, Bo

2016-10-28

Nitrogen-assisted nanoelectrospray emitter (NANE) was developed to achieve accurate mass-to-charge ratio (m/z) measurements with a single monolithic nozzle. Deposition patterns of generated electrosprays from NANE confirmed their wrapped configurations. Additionally, the intensity of the sample ion and its ratio relative to a reference ion was inclined to focus on the central region of the spray; this trend further supported the existence of wrapped configurations. Further, the proposed NANE was fabricated from poly-(dimethylsiloxane) (PDMS) with octadecyltrichlorosilane modification to restrain the dissolution of PDMS monomers. Assist nitrogen flows were introduced to improve the ionization of reference ions. Moreover, the NANE could regulate the distribution of reference ions by microfluidic three dimensional hydrodynamic focusing. By regulating the distribution of reference ions, the ionization depression was reduced to some degree, and an improved sensitivity was accomplished compared with the mixing of sample and reference solutions. Achieved relative errors of m/z were between 0.2-4.5ppm and 5.2-9.2ppm for ten organic molecules and four biological macromolecules, respectively. Acceptable linear ranges were obtained in quantifications for rhodamine B and emamectin benzoate. Finally, the NANE was compatible with broad infusion rates (from 50nLmin -1 to 15μLmin -1 ) and solutions of different compositions (from 100% methanol to 100% water). Considering the comprehensive application of PDMS in microfluidics, the proposed NANE could be used as a compact and monolithic interface to achieve accurate m/z measurements. Copyright © 2016 Elsevier B.V. All rights reserved.

MOISTURE IN COTTON BY THE KARL FISCHER TITRATION REFERENCE METHOD

USDA-ARS?s Scientific Manuscript database

Moisture is a critical parameter that influences many aspects of cotton fiber from harvesting and ginning to various fiber properties. Because of their importance, reference moisture methods that are more accurate than the existing oven-drying techniques and relatively easy to generate results are ...

Progress toward a low budget reference grade genome assembly

USDA-ARS?s Scientific Manuscript database

Reference quality de novo genome assemblies were once solely the domain of large, well-funded genome projects. While next-generation short read technology removed some of the cost barriers, accurate chromosome-scale assembly remains a real challenge. Here we present efforts to de novo assemble the...

Evolutionary interrogation of human biology in well-annotated genomic framework of rhesus macaque.

PubMed

Zhang, Shi-Jian; Liu, Chu-Jun; Yu, Peng; Zhong, Xiaoming; Chen, Jia-Yu; Yang, Xinzhuang; Peng, Jiguang; Yan, Shouyu; Wang, Chenqu; Zhu, Xiaotong; Xiong, Jingwei; Zhang, Yong E; Tan, Bertrand Chin-Ming; Li, Chuan-Yun

2014-05-01

With genome sequence and composition highly analogous to human, rhesus macaque represents a unique reference for evolutionary studies of human biology. Here, we developed a comprehensive genomic framework of rhesus macaque, the RhesusBase2, for evolutionary interrogation of human genes and the associated regulations. A total of 1,667 next-generation sequencing (NGS) data sets were processed, integrated, and evaluated, generating 51.2 million new functional annotation records. With extensive NGS annotations, RhesusBase2 refined the fine-scale structures in 30% of the macaque Ensembl transcripts, reporting an accurate, up-to-date set of macaque gene models. On the basis of these annotations and accurate macaque gene models, we further developed an NGS-oriented Molecular Evolution Gateway to access and visualize macaque annotations in reference to human orthologous genes and associated regulations (www.rhesusbase.org/molEvo). We highlighted the application of this well-annotated genomic framework in generating hypothetical link of human-biased regulations to human-specific traits, by using mechanistic characterization of the DIEXF gene as an example that provides novel clues to the understanding of digestive system reduction in human evolution. On a global scale, we also identified a catalog of 9,295 human-biased regulatory events, which may represent novel elements that have a substantial impact on shaping human transcriptome and possibly underpin recent human phenotypic evolution. Taken together, we provide an NGS data-driven, information-rich framework that will broadly benefit genomics research in general and serves as an important resource for in-depth evolutionary studies of human biology.

Child protective services utilization of child abuse pediatricians: A mixed methods study.

PubMed

Girardet, Rebecca; Bolton, Kelly; Hashmi, Syed; Sedlock, Emily; Khatri, Rachna; Lahoti, Nina; Lukefahr, James

2018-02-01

Several children's hospitals and medical schools across Texas have child abuse pediatricians (CAPs) who work closely with child protection workers to help ensure accurate assessments of the likelihood of maltreatment in cases of suspected abuse and neglect. Since the state does not mandate which cases should be referred to a CAP center, we were interested in studying factors that may influence workers' decisions to consult a CAP. We used a mixed methods study design consisting of a focus group followed by a survey. The focus group identified multiple factors that impact workers' decision-making, including several that involve medical providers. Responses from 436 completed surveys were compared to employees' number of years of employment and to the state region in which they worked. Focus group findings and survey responses revealed frustration among many workers when dealing with medical providers, and moderate levels of confidence in workers' abilities to make accurate determinations in cases involving medical information. Workers were more likely to refer cases involving serious physical injury than other types of cases. Among workers who reported prior interactions with a CAP, experiences and attitudes regarding CAPs were typically positive. The survey also revealed significant variability in referral practices by state region. Our results suggest that standard guidelines regarding CAP referrals may help workers who deal with cases involving medical information. Future research and quality improvement efforts to improve transfers of information and to better understand the qualities that CPS workers appreciate in CAP teams should improve CAP-CPS coordination. Copyright © 2017 Elsevier Ltd. All rights reserved.

Direct quantification of molar masses of copolymers by online liquid chromatography under critical conditions-nuclear magnetic resonance and size exclusion chromatography-nuclear magnetic resonance.

PubMed

Hehn, Mathias; Wagner, Thomas; Hiller, Wolf

2014-01-07

Online LCCC-NMR and SEC-NMR are compared regarding the determination of molar masses of block copolymers. Two different direct referencing methods are particularly demonstrated in LCCC-NMR for a detailed characterization of diblock copolymers and their co-monomers. First, an intramolecular reference group was used for the direct determination of block lengths and molar masses. For the first time, it was shown that LCCC-NMR can be used for an accurate determination of Mw and Mn of copolymers. These data were in perfect agreement with SEC-NMR measurements using the same intramolecular referencing method. In contrast, the determination of molar masses with common relative methods based on calibrations with homopolymers delivered inaccurate results for all investigated diblock copolymers due to different hydrodynamic volumes of the diblock copolymer compared to their homopolymers. The intramolecular referencing method provided detailed insights in the co-monomer behavior during the chromatographic separation of LCCC. Especially, accurate chain lengths and chemical compositions of the "invisible" and "visible" blocks were quantified during the elution under critical conditions and provided new aspects to the concept of critical conditions. Second, an external reference NMR signal was used to directly determine concentrations and molar masses of the block copolymers from the chromatographic elution profile. Consequently, the intensity axes of the resulting chromatograms were converted to molar amounts and masses, allowing for determination of the amount of polymer chains with respect to elution volume, the evaluation of the limiting magnitude of concentration for LCCC-NMR, and determination of the molar masses of copolymers.

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

PubMed Central

Parks, Donovan H.; Imelfort, Michael; Skennerton, Connor T.; Hugenholtz, Philip; Tyson, Gene W.

2015-01-01

Large-scale recovery of genomes from isolates, single cells, and metagenomic data has been made possible by advances in computational methods and substantial reductions in sequencing costs. Although this increasing breadth of draft genomes is providing key information regarding the evolutionary and functional diversity of microbial life, it has become impractical to finish all available reference genomes. Making robust biological inferences from draft genomes requires accurate estimates of their completeness and contamination. Current methods for assessing genome quality are ad hoc and generally make use of a limited number of “marker” genes conserved across all bacterial or archaeal genomes. Here we introduce CheckM, an automated method for assessing the quality of a genome using a broader set of marker genes specific to the position of a genome within a reference genome tree and information about the collocation of these genes. We demonstrate the effectiveness of CheckM using synthetic data and a wide range of isolate-, single-cell-, and metagenome-derived genomes. CheckM is shown to provide accurate estimates of genome completeness and contamination and to outperform existing approaches. Using CheckM, we identify a diverse range of errors currently impacting publicly available isolate genomes and demonstrate that genomes obtained from single cells and metagenomic data vary substantially in quality. In order to facilitate the use of draft genomes, we propose an objective measure of genome quality that can be used to select genomes suitable for specific gene- and genome-centric analyses of microbial communities. PMID:25977477

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes.

PubMed

Parks, Donovan H; Imelfort, Michael; Skennerton, Connor T; Hugenholtz, Philip; Tyson, Gene W

2015-07-01

Large-scale recovery of genomes from isolates, single cells, and metagenomic data has been made possible by advances in computational methods and substantial reductions in sequencing costs. Although this increasing breadth of draft genomes is providing key information regarding the evolutionary and functional diversity of microbial life, it has become impractical to finish all available reference genomes. Making robust biological inferences from draft genomes requires accurate estimates of their completeness and contamination. Current methods for assessing genome quality are ad hoc and generally make use of a limited number of "marker" genes conserved across all bacterial or archaeal genomes. Here we introduce CheckM, an automated method for assessing the quality of a genome using a broader set of marker genes specific to the position of a genome within a reference genome tree and information about the collocation of these genes. We demonstrate the effectiveness of CheckM using synthetic data and a wide range of isolate-, single-cell-, and metagenome-derived genomes. CheckM is shown to provide accurate estimates of genome completeness and contamination and to outperform existing approaches. Using CheckM, we identify a diverse range of errors currently impacting publicly available isolate genomes and demonstrate that genomes obtained from single cells and metagenomic data vary substantially in quality. In order to facilitate the use of draft genomes, we propose an objective measure of genome quality that can be used to select genomes suitable for specific gene- and genome-centric analyses of microbial communities. © 2015 Parks et al.; Published by Cold Spring Harbor Laboratory Press.

Enhanced Sampling in Free Energy Calculations: Combining SGLD with the Bennett's Acceptance Ratio and Enveloping Distribution Sampling Methods.

PubMed

König, Gerhard; Miller, Benjamin T; Boresch, Stefan; Wu, Xiongwu; Brooks, Bernard R

2012-10-09

One of the key requirements for the accurate calculation of free energy differences is proper sampling of conformational space. Especially in biological applications, molecular dynamics simulations are often confronted with rugged energy surfaces and high energy barriers, leading to insufficient sampling and, in turn, poor convergence of the free energy results. In this work, we address this problem by employing enhanced sampling methods. We explore the possibility of using self-guided Langevin dynamics (SGLD) to speed up the exploration process in free energy simulations. To obtain improved free energy differences from such simulations, it is necessary to account for the effects of the bias due to the guiding forces. We demonstrate how this can be accomplished for the Bennett's acceptance ratio (BAR) and the enveloping distribution sampling (EDS) methods. While BAR is considered among the most efficient methods available for free energy calculations, the EDS method developed by Christ and van Gunsteren is a promising development that reduces the computational costs of free energy calculations by simulating a single reference state. To evaluate the accuracy of both approaches in connection with enhanced sampling, EDS was implemented in CHARMM. For testing, we employ benchmark systems with analytical reference results and the mutation of alanine to serine. We find that SGLD with reweighting can provide accurate results for BAR and EDS where conventional molecular dynamics simulations fail. In addition, we compare the performance of EDS with other free energy methods. We briefly discuss the implications of our results and provide practical guidelines for conducting free energy simulations with SGLD.

The Impact of Indoor and Outdoor Radiometer Calibration on Solar Measurements: Preprint

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

Habte, Aron; Sengupta, Manajit; Andreas, Afshin

2016-07-01

Accurate solar radiation data sets are critical to reducing the expenses associated with mitigating performance risk for solar energy conversion systems, and they help utility planners and grid system operators understand the impacts of solar resource variability. The accuracy of solar radiation measured by radiometers depends on the instrument performance specification, installation method, calibration procedure, measurement conditions, maintenance practices, location, and environmental conditions. This study addresses the effect of calibration methodologies and the resulting calibration responsivities provided by radiometric calibration service providers such as the National Renewable Energy Laboratory (NREL) and manufacturers of radiometers. Some of these radiometers are calibratedmore » indoors, and some are calibrated outdoors. To establish or understand the differences in calibration methodology, we processed and analyzed field-measured data from these radiometers. This study investigates calibration responsivities provided by NREL's broadband outdoor radiometer calibration (BORCAL) and a few prominent manufacturers. The reference radiometer calibrations are traceable to the World Radiometric Reference. These different methods of calibration demonstrated 1% to 2% differences in solar irradiance measurement. Analyzing these values will ultimately assist in determining the uncertainties of the radiometer data and will assist in developing consensus on a standard for calibration.« less

Using CRANID to test the population affinity of known crania.

PubMed

Kallenberger, Lauren; Pilbrow, Varsha

2012-11-01

CRANID is a statistical program used to infer the source population of a cranium of unknown origin by comparing its cranial dimensions with a worldwide craniometric database. It has great potential for estimating ancestry in archaeological, forensic and repatriation cases. In this paper we test the validity of CRANID in classifying crania of known geographic origin. Twenty-three crania of known geographic origin but unknown sex were selected from the osteological collections of the University of Melbourne. Only 18 crania showed good statistical match with the CRANID database. Without considering accuracy of sex allocation, 11 crania were accurately classified into major geographic regions and nine were correctly classified to geographically closest available reference populations. Four of the five crania with poor statistical match were nonetheless correctly allocated to major geographical regions, although none was accurately assigned to geographically closest reference samples. We conclude that if sex allocations are overlooked, CRANID can accurately assign 39% of specimens to geographically closest matching reference samples and 48% to major geographic regions. Better source population representation may improve goodness of fit, but known sex-differentiated samples are needed to further test the utility of CRANID. © 2012 The Authors Journal of Anatomy © 2012 Anatomical Society.

Robust Vision-Based Pose Estimation Algorithm for AN Uav with Known Gravity Vector

NASA Astrophysics Data System (ADS)

Kniaz, V. V.

2016-06-01

Accurate estimation of camera external orientation with respect to a known object is one of the central problems in photogrammetry and computer vision. In recent years this problem is gaining an increasing attention in the field of UAV autonomous flight. Such application requires a real-time performance and robustness of the external orientation estimation algorithm. The accuracy of the solution is strongly dependent on the number of reference points visible on the given image. The problem only has an analytical solution if 3 or more reference points are visible. However, in limited visibility conditions it is often needed to perform external orientation with only 2 visible reference points. In such case the solution could be found if the gravity vector direction in the camera coordinate system is known. A number of algorithms for external orientation estimation for the case of 2 known reference points and a gravity vector were developed to date. Most of these algorithms provide analytical solution in the form of polynomial equation that is subject to large errors in the case of complex reference points configurations. This paper is focused on the development of a new computationally effective and robust algorithm for external orientation based on positions of 2 known reference points and a gravity vector. The algorithm implementation for guidance of a Parrot AR.Drone 2.0 micro-UAV is discussed. The experimental evaluation of the algorithm proved its computational efficiency and robustness against errors in reference points positions and complex configurations.

Small-Grid Dithering Strategy for Improved Coronagraphic Performance with JWST

NASA Astrophysics Data System (ADS)

Lajoie, Charles-Philippe; Soummer, Remi; Pueyo, Laurent; Hines, Dean C.; Nelan, Edmund P.; JWST Coronagraphs Working Group

2015-01-01

Contrast performances for most coronagraph designs typically depend rather strongly on the accuracy of target acquisition. For JWST, target acquisition away from the center of the coronagraphs will allow for centroid measurement, which will in turn be used to command a small-angle maneuver (SAM) to accurately place the star behind the coronagraphic mask. With this approach, the SAM accuracy inherently limits the contrast performance of the coronagraphs, especially given that a reference star (or self-reference after telescope roll) might also be required. For such differential measurements, the reproducibility of the TA is therefore a very important factor. Here, we propose a novel coronagraphic observation concept whereby the reference PSF is first acquired using a standard TA, followed by coronagraphic observations on a small grid of dithered positions. Sub-pixel dithers (5-10mas each) provide a small reference PSF library that sample the possible variations in the PSF shape due to imperfect TAs. This small library can then be used for example with principal component analysis for PSF subtraction (e.g; LOCI or KLIP algorithms). Such very small dithers can be achieved with the JWST attitude control system without overhead and with higher accuracy than a SAM since they take advantage of the fine steering mirror under closed-loop fine guidance. We discuss and evaluate the performance gains from this observation scenario compared to the standard TA for MIRI Four-Quadrant Phase Mask coronagraphs and provide numerical simulations for a some astrophysical targets of interest.

Stewardship of the Maize B73 feference genome assembly

USDA-ARS?s Scientific Manuscript database

The release of version 4 of the B73 reference genome assembly is imminent. However, continued improvement of the assembly is likely to fall to the maize research community. Toward this end, and recognizing the importance of an accurate and well-curated reference genome, MaizeGDB, Gramene, and the Ge...

Gaussian process models for reference ET estimation from alternative meteorological data sources

USDA-ARS?s Scientific Manuscript database

Accurate estimates of daily crop evapotranspiration (ET) are needed for efficient irrigation management, especially in arid and semi-arid regions where crop water demand exceeds rainfall. Daily grass or alfalfa reference ET values and crop coefficients are widely used to estimate crop water demand. ...

Identification and Validation of Reference Genes for RT-qPCR Analysis in Non-Heading Chinese Cabbage Flowers

PubMed Central

Wang, Cheng; Cui, Hong-Mi; Huang, Tian-Hong; Liu, Tong-Kun; Hou, Xi-Lin; Li, Ying

2016-01-01

Non-heading Chinese cabbage (Brassica rapa ssp. chinensis Makino) is an important vegetable member of Brassica rapa crops. It exhibits a typical sporophytic self-incompatibility (SI) system and is an ideal model plant to explore the mechanism of SI. Gene expression research are frequently used to unravel the complex genetic mechanism and in such studies appropriate reference selection is vital. Validation of reference genes have neither been conducted in Brassica rapa flowers nor in SI trait. In this study, 13 candidate reference genes were selected and examined systematically in 96 non-heading Chinese cabbage flower samples that represent four strategic groups in compatible and self-incompatible lines of non-heading Chinese cabbage. Two RT-qPCR analysis software, geNorm and NormFinder, were used to evaluate the expression stability of these genes systematically. Results revealed that best-ranked references genes should be selected according to specific sample subsets. DNAJ, UKN1, and PP2A were identified as the most stable reference genes among all samples. Moreover, our research further revealed that the widely used reference genes, CYP and ACP, were the least suitable reference genes in most non-heading Chinese cabbage flower sample sets. To further validate the suitability of the reference genes identified in this study, the expression level of SRK and Exo70A1 genes which play important roles in regulating interaction between pollen and stigma were studied. Our study presented the first systematic study of reference gene(s) selection for SI study and provided guidelines to obtain more accurate RT-qPCR results in non-heading Chinese cabbage. PMID:27375663

Selection of suitable endogenous reference genes for qPCR in kidney and hypothalamus of rats under testosterone influence

PubMed Central

2017-01-01

Real-time quantitative PCR (qPCR) is the most reliable and accurate technique for analyses of gene expression. Endogenous reference genes are being used to normalize qPCR data even though their expression may vary under different conditions and in different tissues. Nonetheless, verification of expression of reference genes in selected studied tissue is essential in order to accurately assess the level of expression of target genes of interest. Therefore, in this study, we attempted to examine six commonly used reference genes in order to identify the gene being expressed most constantly under the influence of testosterone in the kidneys and hypothalamus. The reference genes include glyceraldehyde-3-phosphate dehydrogenase (GAPDH), actin beta (ACTB), beta-2 microglobulin (B2m), hypoxanthine phosphoribosyltransferase 1 (HPRT), peptidylprolylisomerase A (Ppia) and hydroxymethylbilane synthase (Hmbs). The cycle threshold (Ct) value for each gene was determined and data obtained were analyzed using the software programs NormFinder, geNorm, BestKeeper, and rank aggregation. Results showed that Hmbs and Ppia genes were the most stably expressed in the hypothalamus. Meanwhile, in kidneys, Hmbs and GAPDH appeared to be the most constant genes. In conclusion, variations in expression levels of reference genes occur in kidneys and hypothalamus under similar conditions; thus, it is important to verify reference gene levels in these tissues prior to commencing any studies. PMID:28591185

Selection and testing of reference genes for accurate RT-qPCR in rice seedlings under iron toxicity.

PubMed

Santos, Fabiane Igansi de Castro Dos; Marini, Naciele; Santos, Railson Schreinert Dos; Hoffman, Bianca Silva Fernandes; Alves-Ferreira, Marcio; de Oliveira, Antonio Costa

2018-01-01

Reverse Transcription quantitative PCR (RT-qPCR) is a technique for gene expression profiling with high sensibility and reproducibility. However, to obtain accurate results, it depends on data normalization by using endogenous reference genes whose expression is constitutive or invariable. Although the technique is widely used in plant stress analyzes, the stability of reference genes for iron toxicity in rice (Oryza sativa L.) has not been thoroughly investigated. Here, we tested a set of candidate reference genes for use in rice under this stressful condition. The test was performed using four distinct methods: NormFinder, BestKeeper, geNorm and the comparative ΔCt. To achieve reproducible and reliable results, Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines were followed. Valid reference genes were found for shoot (P2, OsGAPDH and OsNABP), root (OsEF-1a, P8 and OsGAPDH) and root+shoot (OsNABP, OsGAPDH and P8) enabling us to perform further reliable studies for iron toxicity in both indica and japonica subspecies. The importance of the study of other than the traditional endogenous genes for use as normalizers is also shown here.

Selection and testing of reference genes for accurate RT-qPCR in rice seedlings under iron toxicity

PubMed Central

dos Santos, Fabiane Igansi de Castro; Marini, Naciele; dos Santos, Railson Schreinert; Hoffman, Bianca Silva Fernandes; Alves-Ferreira, Marcio

2018-01-01

Reverse Transcription quantitative PCR (RT-qPCR) is a technique for gene expression profiling with high sensibility and reproducibility. However, to obtain accurate results, it depends on data normalization by using endogenous reference genes whose expression is constitutive or invariable. Although the technique is widely used in plant stress analyzes, the stability of reference genes for iron toxicity in rice (Oryza sativa L.) has not been thoroughly investigated. Here, we tested a set of candidate reference genes for use in rice under this stressful condition. The test was performed using four distinct methods: NormFinder, BestKeeper, geNorm and the comparative ΔCt. To achieve reproducible and reliable results, Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines were followed. Valid reference genes were found for shoot (P2, OsGAPDH and OsNABP), root (OsEF-1a, P8 and OsGAPDH) and root+shoot (OsNABP, OsGAPDH and P8) enabling us to perform further reliable studies for iron toxicity in both indica and japonica subspecies. The importance of the study of other than the traditional endogenous genes for use as normalizers is also shown here. PMID:29494624

Evaluation of new geological reference materials for uranium-series measurements: Chinese Geological Standard Glasses (CGSG) and macusanite obsidian.

PubMed

Denton, J S; Murrell, M T; Goldstein, S J; Nunn, A J; Amato, R S; Hinrichs, K A

2013-10-15

Recent advances in high-resolution, rapid, in situ microanalytical techniques present numerous opportunities for the analytical community, provided accurately characterized reference materials are available. Here, we present multicollector thermal ionization mass spectrometry (MC-TIMS) and multicollector inductively coupled plasma mass spectrometry (MC-ICP-MS) uranium and thorium concentration and isotopic data obtained by isotope dilution for a suite of newly available Chinese Geological Standard Glasses (CGSG) designed for microanalysis. These glasses exhibit a range of compositions including basalt, syenite, andesite, and a soil. Uranium concentrations for these glasses range from ∼2 to 14 μg g(-1), Th/U weight ratios range from ∼4 to 6, (234)U/(238)U activity ratios range from 0.93 to 1.02, and (230)Th/(238)U activity ratios range from 0.98 to 1.12. Uranium and thorium concentration and isotopic data are also presented for a rhyolitic obsidian from Macusani, SE Peru (macusanite). This glass can also be used as a rhyolitic reference material, has a very low Th/U weight ratio (around 0.077), and is approximately in (238)U-(234)U-(230)Th secular equilibrium. The U-Th concentration data agree with but are significantly more precise than those previously measured. U-Th concentration and isotopic data agree within estimated errors for the two measurement techniques, providing validation of the two methods. The large (238)U-(234)U-(230)Th disequilibria for some of the glasses, along with the wide range in their chemical compositions and Th/U ratios should provide useful reference points for the U-series analytical community.

Thermal Measurement during Electrolysis of Pd-Ni Thin-film -Cathodes in Li2SO4/H2O Solution

NASA Astrophysics Data System (ADS)

Castano, C. H.; Lipson, A. G.; S-O, Kim; Miley, G. H.

2002-03-01

Using LENR - open type calorimeters, measurements of excess heat production were carried out during electrolysis in Li_2SO_4/H_2O solution with a Pt-anode and Pd-Ni thin film cathodes (2000-8000 Åthick) sputtered on the different dielectric substrates. In order to accurately evaluate actual performance during electrolysis runs in the open-type calorimeter used, considering effects of heat convection, bubbling and possible H_2+O2 recombination, smooth Pt sheets were used as cathodes. Pt provides a reference since it does not produce excess heat in the light water electrolyte. To increase the accuracy of measurements the water dissociation potential was determined for each cathode taking into account its individual over-voltage value. It is found that this design for the Pd-Ni cathodes resulted in the excess heat production of ~ 20-25 % of input power, equivalent to ~300 mW. In cases of the Pd/Ni- film fracture (or detachment from substrate) no excess heat was detected, providing an added reference point. These experiments plus use of optimized films will be presented.

Cheap but accurate calculation of chemical reaction rate constants from ab initio data, via system-specific, black-box force fields

NASA Astrophysics Data System (ADS)

Steffen, Julien; Hartke, Bernd

2017-10-01

Building on the recently published quantum-mechanically derived force field (QMDFF) and its empirical valence bond extension, EVB-QMDFF, it is now possible to generate a reliable potential energy surface for any given elementary reaction step in an essentially black box manner. This requires a limited and pre-defined set of reference data near the reaction path and generates an accurate approximation of the reference potential energy surface, on and off the reaction path. This intermediate representation can be used to generate reaction rate data, with far better accuracy and reliability than with traditional approaches based on transition state theory (TST) or variational extensions thereof (VTST), even if those include sophisticated tunneling corrections. However, the additional expense at the reference level remains very modest. We demonstrate all this for three arbitrarily chosen example reactions.

Reference gene identification for reliable normalisation of quantitative RT-PCR data in Setaria viridis.

PubMed

Nguyen, Duc Quan; Eamens, Andrew L; Grof, Christopher P L

2018-01-01

Quantitative real-time polymerase chain reaction (RT-qPCR) is the key platform for the quantitative analysis of gene expression in a wide range of experimental systems and conditions. However, the accuracy and reproducibility of gene expression quantification via RT-qPCR is entirely dependent on the identification of reliable reference genes for data normalisation. Green foxtail ( Setaria viridis ) has recently been proposed as a potential experimental model for the study of C 4 photosynthesis and is closely related to many economically important crop species of the Panicoideae subfamily of grasses, including Zea mays (maize), Sorghum bicolor (sorghum) and Sacchurum officinarum (sugarcane). Setaria viridis (Accession 10) possesses a number of key traits as an experimental model, namely; (i) a small sized, sequenced and well annotated genome; (ii) short stature and generation time; (iii) prolific seed production, and; (iv) is amendable to Agrobacterium tumefaciens -mediated transformation. There is currently however, a lack of reference gene expression information for Setaria viridis ( S. viridis ). We therefore aimed to identify a cohort of suitable S. viridis reference genes for accurate and reliable normalisation of S. viridis RT-qPCR expression data. Eleven putative candidate reference genes were identified and examined across thirteen different S. viridis tissues. Of these, the geNorm and NormFinder analysis software identified SERINE / THERONINE - PROTEIN PHOSPHATASE 2A ( PP2A ), 5 '- ADENYLYLSULFATE REDUCTASE 6 ( ASPR6 ) and DUAL SPECIFICITY PHOSPHATASE ( DUSP ) as the most suitable combination of reference genes for the accurate and reliable normalisation of S. viridis RT-qPCR expression data. To demonstrate the suitability of the three selected reference genes, PP2A , ASPR6 and DUSP , were used to normalise the expression of CINNAMYL ALCOHOL DEHYDROGENASE ( CAD ) genes across the same tissues. This approach readily demonstrated the suitably of the three selected reference genes for the accurate and reliable normalisation of S. viridis RT-qPCR expression data. Further, the work reported here forms a highly useful platform for future gene expression quantification in S. viridis and can also be potentially directly translatable to other closely related and agronomically important C 4 crop species.

Pediatric reference intervals for alkaline phosphatase.

PubMed

Zierk, Jakob; Arzideh, Farhad; Haeckel, Rainer; Cario, Holger; Frühwald, Michael C; Groß, Hans-Jürgen; Gscheidmeier, Thomas; Hoffmann, Reinhard; Krebs, Alexander; Lichtinghagen, Ralf; Neumann, Michael; Ruf, Hans-Georg; Steigerwald, Udo; Streichert, Thomas; Rascher, Wolfgang; Metzler, Markus; Rauh, Manfred

2017-01-01

Interpretation of alkaline phosphatase activity in children is challenging due to extensive changes with growth and puberty leading to distinct sex- and age-specific dynamics. Continuous percentile charts from birth to adulthood allow accurate consideration of these dynamics and seem reasonable for an analyte as closely linked to growth as alkaline phosphatase. However, the ethical and practical challenges unique to pediatric reference intervals have restricted the creation of such percentile charts, resulting in limitations when clinical decisions are based on alkaline phosphatase activity. We applied an indirect method to generate percentile charts for alkaline phosphatase activity using clinical laboratory data collected during the clinical care of patients. A total of 361,405 samples from 124,440 patients from six German tertiary care centers and one German laboratory service provider measured between January 2004 and June 2015 were analyzed. Measurement of alkaline phosphatase activity was performed on Roche Cobas analyzers using the IFCC's photometric method. We created percentile charts for alkaline phosphatase activity in girls and boys from birth to 18 years which can be used as reference intervals. Additionally, data tables of age- and sex-specific percentile values allow the incorporation of these results into laboratory information systems. The percentile charts provided enable the appropriate differential diagnosis of changes in alkaline phosphatase activity due to disease and changes due to physiological development. After local validation, integration of the provided percentile charts into result reporting facilitates precise assessment of alkaline phosphatase dynamics in pediatrics.

S66: A Well-balanced Database of Benchmark Interaction Energies Relevant to Biomolecular Structures

PubMed Central

2011-01-01

With numerous new quantum chemistry methods being developed in recent years and the promise of even more new methods to be developed in the near future, it is clearly critical that highly accurate, well-balanced, reference data for many different atomic and molecular properties be available for the parametrization and validation of these methods. One area of research that is of particular importance in many areas of chemistry, biology, and material science is the study of noncovalent interactions. Because these interactions are often strongly influenced by correlation effects, it is necessary to use computationally expensive high-order wave function methods to describe them accurately. Here, we present a large new database of interaction energies calculated using an accurate CCSD(T)/CBS scheme. Data are presented for 66 molecular complexes, at their reference equilibrium geometries and at 8 points systematically exploring their dissociation curves; in total, the database contains 594 points: 66 at equilibrium geometries, and 528 in dissociation curves. The data set is designed to cover the most common types of noncovalent interactions in biomolecules, while keeping a balanced representation of dispersion and electrostatic contributions. The data set is therefore well suited for testing and development of methods applicable to bioorganic systems. In addition to the benchmark CCSD(T) results, we also provide decompositions of the interaction energies by means of DFT-SAPT calculations. The data set was used to test several correlated QM methods, including those parametrized specifically for noncovalent interactions. Among these, the SCS-MI-CCSD method outperforms all other tested methods, with a root-mean-square error of 0.08 kcal/mol for the S66 data set. PMID:21836824

An optimized method for the accurate determination of patulin in apple products by isotope dilution-liquid chromatography/mass spectrometry.

PubMed

Seo, Miyeong; Kim, Byungjoo; Baek, Song-Yee

2015-07-01

Patulin, a mycotoxin produced by several molds in fruits, has been frequently detected in apple products. Therefore, regulatory bodies have established recommended maximum permitted patulin concentrations for each type of apple product. Although several analytical methods have been adopted to determine patulin in food, quality control of patulin analysis is not easy, as reliable certified reference materials (CRMs) are not available. In this study, as a part of a project for developing CRMs for patulin analysis, we developed isotope dilution liquid chromatography-tandem mass spectrometry (ID-LC/MS/MS) as a higher-order reference method for the accurate value-assignment of CRMs. (13)C7-patulin was used as internal standard. Samples were extracted with ethyl acetate to improve recovery. For further sample cleanup with solid-phase extraction (SPE), the HLB SPE cartridge was chosen after comparing with several other types of SPE cartridges. High-performance liquid chromatography was performed on a multimode column for proper retention and separation of highly polar and water-soluble patulin from sample interferences. Sample extracts were analyzed by LC/MS/MS with electrospray ionization in negative ion mode with selected reaction monitoring of patulin and (13)C7-patulin at m/z 153→m/z 109 and m/z 160→m/z 115, respectively. The validity of the method was tested by measuring gravimetrically fortified samples of various apple products. In addition, the repeatability and the reproducibility of the method were tested to evaluate the performance of the method. The method was shown to provide accurate measurements in the 3-40 μg/kg range with a relative expanded uncertainty of around 1%.

The Magsat three axis arc second precision attitude transfer system

NASA Technical Reports Server (NTRS)

Schenkel, F. W.; Heins, R. J.

1981-01-01

The Magsat Attitude Transfer System (ATS), which provides attitude alteration in pitch, yaw, and roll is described. A remote vector magnetometer extends from Magsat on a 20 ft boom, requiring vector orientation by reference to coordinate axes determined by a set of star mapping cameras. The ATS was designed to perform in a solar illuminated environment by using an optically narrow bandwidth with synchronous demodulation at 9300 A. The pitch/yaw optical design, the electrooptics, and signal and switching diagrams are provided. Simple mirrors with no moving parts are placed on the magnetometer to reflect a collimated beam from the ATS for attitude indication, which is accurate to one part in 96. Alignment was completed within 24 hr after launch.

Practicality of electronic beam steering for MST/ST radars, part 6.2A

NASA Technical Reports Server (NTRS)

Clark, W. L.; Green, J. L.

1984-01-01

Electronic beam steering is described as complex and expensive. The Sunset implementation of electronic steering is described, and it is demonstrated that such systems are cost effective, versatile, and no more complex than fixed beam alternatives, provided three or more beams are needed. The problem of determining accurate meteorological wind components in the presence of spatial variation is considered. A cost comparison of steerable and fixed systems allowing solution of this problem is given. The concepts and relations involved in phase steering are given, followed by the description of the Sunset ST radar steering system. The implications are discussed, references to the competing SAD method are provided, and a recommendation concerning the design of the future Doppler ST/MST systems is made.

Rapid Polymer Sequencer

NASA Technical Reports Server (NTRS)

Stolc, Viktor (Inventor); Brock, Mathew W. (Inventor)

2011-01-01

Method and system for rapid and accurate determination of each of a sequence of unknown polymer components, such as nucleic acid components. A self-assembling monolayer of a selected substance is optionally provided on an interior surface of a pipette tip, and the interior surface is immersed in a selected liquid. A selected electrical field is impressed in a longitudinal or transverse direction at the tip, a polymer sequence is passed through the tip, and a change in an electrical current signal is measured as each polymer component passes through the tip. Each measured change in electrical current signals is compared with a database of reference signals, with each reference signal identified with a polymer component, to identify the unknown polymer component. The tip preferably has a pore inner diameter of no more than about 40 nm and is prepared by heating and pulling a very small section of a glass tubing.

Venus radar mapper attitude reference quaternion

NASA Technical Reports Server (NTRS)

Lyons, D. T.

1986-01-01

Polynomial functions of time are used to specify the components of the quaternion which represents the nominal attitude of the Venus Radar mapper spacecraft during mapping. The following constraints must be satisfied in order to obtain acceptable synthetic array radar data: the nominal attitude function must have a large dynamic range, the sensor orientation must be known very accurately, the attitude reference function must use as little memory as possible, and the spacecraft must operate autonomously. Fitting polynomials to the components of the desired quaternion function is a straightforward method for providing a very dynamic nominal attitude using a minimum amount of on-board computer resources. Although the attitude from the polynomials may not be exactly the one requested by the radar designers, the polynomial coefficients are known, so they do not contribute to the attitude uncertainty. Frequent coefficient updates are not required, so the spacecraft can operate autonomously.

Spinning angle optical calibration apparatus

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

Beer, S.K.; Pratt, H.R. II.

1989-09-12

An optical calibration apparatus is provided for calibrating and reproducing spinning angles in cross-polarization, nuclear magnetic resonance spectroscopy. An illuminated magnifying apparatus enables optical setting and accurate reproducing of spinning magic angles in cross-polarization, nuclear magnetic resonance spectroscopy experiments. A reference mark scribed on an edge of a spinning angle test sample holder is illuminated by a light source and viewed through a magnifying scope. When the magic angle of a sample material used as a standard is attained by varying the angular position of the sample holder, the coordinate position of the reference mark relative to a graduation ormore » graduations on a reticle in the magnifying scope is noted. Thereafter, the spinning magic angle of a test material having similar nuclear properties to the standard is attained by returning the sample holder back to the originally noted coordinate position. 2 figs.« less

Critical Evaluation of Kinetic Method Measurements: Possible Origins of Nonlinear Effects

NASA Astrophysics Data System (ADS)

Bourgoin-Voillard, Sandrine; Afonso, Carlos; Lesage, Denis; Zins, Emilie-Laure; Tabet, Jean-Claude; Armentrout, P. B.

2013-03-01

The kinetic method is a widely used approach for the determination of thermochemical data such as proton affinities (PA) and gas-phase acidities ( ΔH° acid ). These data are easily obtained from decompositions of noncovalent heterodimers if care is taken in the choice of the method, references used, and experimental conditions. Previously, several papers have focused on theoretical considerations concerning the nature of the references. Few investigations have been devoted to conditions required to validate the quality of the experimental results. In the present work, we are interested in rationalizing the origin of nonlinear effects that can be obtained with the kinetic method. It is shown that such deviations result from intrinsic properties of the systems investigated but can also be enhanced by artifacts resulting from experimental issues. Overall, it is shown that orthogonal distance regression (ODR) analysis of kinetic method data provides the optimum way of acquiring accurate thermodynamic information.

Response of personal noise dosimeters to continuous and impulse-like signals

NASA Astrophysics Data System (ADS)

Evans, D. J.; Flynn, D. R.; Nedzelnitsky, V.; Burnett, E. D.

1991-06-01

A study of the capabilities of noise dosimeters to measure personal exposure to time varying and impulse-like noises was carried out. Ten commercial noise dosimeters were obtained. A laboratory reference noise dosimeter was constructed to provide a demonstrably accurate basis with which to compare the commercial noise dosimeters. Each commercial dosimeter, when ordered from the manufacturer, was specified to have a threshold A-weighted sound level of 80 dB, a criterion sound level of 90 dB, and an exchange rate of 5 dB and/or 3 dB. The performance of the commercial dosimeters was compared with theory and with results obtained from the reference dosimeter. Except in a few isolated cases, the commercial dosimeters were in general agreement with the performance specification of the appropriate American National Standard and with the Occupational Safety and Health Administration (OSHA) regulations.

Earned Value Management (EVM) Implementation Handbook

NASA Technical Reports Server (NTRS)

2013-01-01

The purpose of this handbook is to provide Earned Value Management (EVM) guidance for the effective application, implementation, and utilization of EVM on NASA programs, projects, major contracts and subcontracts in a consolidated reference document. EVM is a project management process that effectively integrates a project s scope of work with schedule and cost elements for optimum project planning and control. The goal is to achieve timely and accurate quantification of progress that will facilitate management by exception and enable early visibility into the nature and the magnitude of technical problems as well as the intended course and success of corrective actions.

High accuracy OMEGA timekeeping

NASA Technical Reports Server (NTRS)

Imbier, E. A.

1982-01-01

The Smithsonian Astrophysical Observatory (SAO) operates a worldwide satellite tracking network which uses a combination of OMEGA as a frequency reference, dual timing channels, and portable clock comparisons to maintain accurate epoch time. Propagational charts from the U.S. Coast Guard OMEGA monitor program minimize diurnal and seasonal effects. Daily phase value publications of the U.S. Naval Observatory provide corrections to the field collected timing data to produce an averaged time line comprised of straight line segments called a time history file (station clock minus UTC). Depending upon clock location, reduced time data accuracies of between two and eight microseconds are typical.

Earned Value Management (EVM) Implementation Handbook

NASA Technical Reports Server (NTRS)

Terrell, Stefanie M.; Richards, Brad W.

2018-01-01

The purpose of this handbook is to provide Earned Value Management (EVM) guidance for the effective application, implementation, and utilization of EVM on NASA programs, projects, major contracts and subcontracts in a consolidated reference document. EVM is a project management process that effectively integrates a project?s scope of work with schedule and cost elements for optimum project planning and control. The goal is to achieve timely and accurate quantification of progress that will facilitate management by exception and enable early visibility into the nature and the magnitude of technical problems as well as the intended course and success of corrective actions.

A dynamic gravimetric standard for trace water.

PubMed

Brewer, P J; Goody, B A; Woods, P T; Milton, M J T

2011-10-01

A system for generating traceable reference standards of water vapor at trace levels between 5 and 2000 nmol/mol has been developed. It can provide different amount fractions of trace water vapor by using continuous accurate measurements of mass loss from a permeation device coupled with a dilution system based on an array of critical flow orifices. An estimated relative expanded uncertainty of ±2% has been achieved for most amount fractions generated. The system has been used in an international comparison and demonstrates excellent comparability with National Metrology Institutes maintaining standards of water vapor in this range using other methods.

Free-energy analyses of a proton transfer reaction by simulated-tempering umbrella sampling and first-principles molecular dynamics simulations.

PubMed

Mori, Yoshiharu; Okamoto, Yuko

2013-02-01

A simulated tempering method, which is referred to as simulated-tempering umbrella sampling, for calculating the free energy of chemical reactions is proposed. First principles molecular dynamics simulations with this simulated tempering were performed to study the intramolecular proton transfer reaction of malonaldehyde in an aqueous solution. Conformational sampling in reaction coordinate space can be easily enhanced with this method, and the free energy along a reaction coordinate can be calculated accurately. Moreover, the simulated-tempering umbrella sampling provides trajectory data more efficiently than the conventional umbrella sampling method.

New Brunswick Laboratory: Progress report, October 1987--September 1988

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

Not Available

NBL has been tasked by the DOE Office of Safeguards and Security, Defense Programs (OSS/DP) to assure the application of accurate and reliable measurement technology for the safeguarding of special nuclear materials. NBL is fulfilling its mission responsibilities by identifying and addressing the measurement and measurement-related needs of the nuclear material safeguards community. These responsibilities are being addressed by activities in the following program areas: (1) reference and calibration materials, (2) measurement development, (3) measurement services, (4) measurement evaluation, (5) safeguards assessment, and (6) site-specific assistance. Highlights of each of these programs areas are provided in this summary.

Spatial resolution limitation of liquid crystal spatial light modulator

NASA Astrophysics Data System (ADS)

Wang, Xinghua; Wang, Bin; McManamon, Paul F., III; Pouch, John J.; Miranda, Felix A.; Anderson, James E.; Bos, Philip J.

2004-10-01

The effect of fringing electric fields in a liquid crystal (LC) Optical Phased Array (OPA), also referred to as a spatial light modulator (SLM), is a governing factor that determines the diffraction efficiency (DE) of the LC OPA for high resolution spatial phase modulation. In this article, the fringing field effect in a high resolution LC OPA is studied by accurate modeling the DE of the LC blazed gratings by LC director simulation and Finite Difference Time Domain (FDTD) simulation. Influence factors that contribute significantly to the DE are discussed. Such results provide fundamental understanding for high resolution LC devices.

Subgenome-anchored physical frameworks of the allotetraploid Upland cotton (Gossypium hirsutum L.) genome, and an approach toward reference-grade assemblies of polyploids

USDA-ARS?s Scientific Manuscript database

Like many agricultural crops, the cultivated cotton genome is large and polyploid (~2.5Gb), consisting of two very similar repeat-rich subgenomes, whose size and complexity pose significant challenges for accurate genome reconstruction using whole-genome shotgun approaches. A strategy for accurately...

Improving Photometric Calibration of Meteor Video Camera Systems.

PubMed

Ehlert, Steven; Kingery, Aaron; Suggs, Robert

2017-09-01

We present the results of new calibration tests performed by the NASA Meteoroid Environment Office (MEO) designed to help quantify and minimize systematic uncertainties in meteor photometry from video camera observations. These systematic uncertainties can be categorized by two main sources: an imperfect understanding of the linearity correction for the MEO's Watec 902H2 Ultimate video cameras and uncertainties in meteor magnitudes arising from transformations between the Watec camera's Sony EX-View HAD bandpass and the bandpasses used to determine reference star magnitudes. To address the first point, we have measured the linearity response of the MEO's standard meteor video cameras using two independent laboratory tests on eight cameras. Our empirically determined linearity correction is critical for performing accurate photometry at low camera intensity levels. With regards to the second point, we have calculated synthetic magnitudes in the EX bandpass for reference stars. These synthetic magnitudes enable direct calculations of the meteor's photometric flux within the camera band pass without requiring any assumptions of its spectral energy distribution. Systematic uncertainties in the synthetic magnitudes of individual reference stars are estimated at ∼ 0.20 mag, and are limited by the available spectral information in the reference catalogs. These two improvements allow for zero-points accurate to ∼ 0.05 - 0.10 mag in both filtered and unfiltered camera observations with no evidence for lingering systematics. These improvements are essential to accurately measuring photometric masses of individual meteors and source mass indexes.

Improving Photometric Calibration of Meteor Video Camera Systems

NASA Technical Reports Server (NTRS)

Ehlert, Steven; Kingery, Aaron; Suggs, Robert

2017-01-01

We present the results of new calibration tests performed by the NASA Meteoroid Environment Office (MEO) designed to help quantify and minimize systematic uncertainties in meteor photometry from video camera observations. These systematic uncertainties can be categorized by two main sources: an imperfect understanding of the linearity correction for the MEO's Watec 902H2 Ultimate video cameras and uncertainties in meteor magnitudes arising from transformations between the Watec camera's Sony EX-View HAD bandpass and the bandpasses used to determine reference star magnitudes. To address the first point, we have measured the linearity response of the MEO's standard meteor video cameras using two independent laboratory tests on eight cameras. Our empirically determined linearity correction is critical for performing accurate photometry at low camera intensity levels. With regards to the second point, we have calculated synthetic magnitudes in the EX bandpass for reference stars. These synthetic magnitudes enable direct calculations of the meteor's photometric flux within the camera bandpass without requiring any assumptions of its spectral energy distribution. Systematic uncertainties in the synthetic magnitudes of individual reference stars are estimated at approx. 0.20 mag, and are limited by the available spectral information in the reference catalogs. These two improvements allow for zero-points accurate to 0.05 - 0.10 mag in both filtered and unfiltered camera observations with no evidence for lingering systematics. These improvements are essential to accurately measuring photometric masses of individual meteors and source mass indexes.

Comparison of Three Enzyme-Linked Immunosorbent Assays for Detection of Immunoglobulin G Antibodies to Tetanus Toxoid with Reference Standards and the Impact on Clinical Practice▿

PubMed Central

van Hoeven, Karen H.; Dale, Connie; Foster, Phil; Body, Barbara

2008-01-01

Accurate determination of the concentrations of immunoglobulin G (IgG) antibody to tetanus toxoid is important in order to evaluate the immunogenicity of tetanus toxoid vaccines, determine immune competence in individual patients, and measure the prevalence of immunity in populations. The performance of three commercially available enzyme-linked immunosorbent assays (ELISAs) for IgG antibodies to tetanus toxoid were evaluated. Serially diluted NIBSC 76/589 and TE-3 human tetanus IgG immunoglobulin international reference standards were analyzed in quadruplicate using ELISAs manufactured by The Binding Site, Inc. (VaccZyme); Scimedx; and Euroimmun. In addition, IgG antibodies to tetanus toxoid were measured in 83 deidentified serum specimens using each manufacturer's ELISA. Each ELISA provided linear results when evaluated with the reference preparations. The Binding Site ELISA provided results that closely corresponded to the reference preparations (y = 1.09x − 0.08), whereas the Scimedx ELISA gave results that were consistently lower (y = 0.21x − 0.07) and the Euroimmun ELISA gave results that were consistently higher (y = 1.5x + 0.30) than the reference preparation concentrations. Using the recommended cutoff for each ELISA (<0.10 IU/ml), the overall agreement of all of the ELISA methods was 78%. Three of eighty-three (3.6%) human serum samples demonstrated inadequate immunity with all three assays. The Binding Site ELISA yielded nonprotective antibody concentrations in only these 3 samples, whereas 19 samples (22.9%) according to the Scimedx ELISA and 6 samples (7.2%) according to the Euroimmun ELISA demonstrated nonprotective concentrations. The performance characteristics of ELISAs for tetanus immunoglobulin titers were manufacturer dependent, and the differences translated into important disparities in reported results. PMID:18845832

Identification and evaluation of reliable reference genes for quantitative real-time PCR analysis in tea plant (Camellia sinensis (L.) O. Kuntze)

USDA-ARS?s Scientific Manuscript database

Quantitative real-time polymerase chain reaction (qRT-PCR) is a commonly used technique for measuring gene expression levels due to its simplicity, specificity, and sensitivity. Reliable reference selection for the accurate quantification of gene expression under various experimental conditions is a...

Experimental Validation of Lightning-Induced Electromagnetic (Indirect) Coupling to Short Monopole Antennas

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

Crull, E W; Brown Jr., C G; Perkins, M P

2008-07-30

For short monopoles in this low-power case, it has been shown that a simple circuit model is capable of accurate predictions for the shape and magnitude of the antenna response to lightning-generated electric field coupling effects, provided that the elements of the circuit model have accurate values. Numerical EM simulation can be used to provide more accurate values for the circuit elements than the simple analytical formulas, since the analytical formulas are used outside of their region of validity. However, even with the approximate analytical formulas the simple circuit model produces reasonable results, which would improve if more accurate analyticalmore » models were used. This report discusses the coupling analysis approaches taken to understand the interaction between a time-varying EM field and a short monopole antenna, within the context of lightning safety for nuclear weapons at DOE facilities. It describes the validation of a simple circuit model using laboratory study in order to understand the indirect coupling of energy into a part, and the resulting voltage. Results show that in this low-power case, the circuit model predicts peak voltages within approximately 32% using circuit component values obtained from analytical formulas and about 13% using circuit component values obtained from numerical EM simulation. We note that the analytical formulas are used outside of their region of validity. First, the antenna is insulated and not a bare wire and there are perhaps fringing field effects near the termination of the outer conductor that the formula does not take into account. Also, the effective height formula is for a monopole directly over a ground plane, while in the time-domain measurement setup the monopole is elevated above the ground plane by about 1.5-inch (refer to Figure 5).« less

Validation of Reference Genes for Gene Expression Studies in Virus-Infected Nicotiana benthamiana Using Quantitative Real-Time PCR

PubMed Central

Han, Chenggui; Yu, Jialin; Li, Dawei; Zhang, Yongliang

2012-01-01

Nicotiana benthamiana is the most widely-used experimental host in plant virology. The recent release of the draft genome sequence for N. benthamiana consolidates its role as a model for plant–pathogen interactions. Quantitative real-time PCR (qPCR) is commonly employed for quantitative gene expression analysis. For valid qPCR analysis, accurate normalisation of gene expression against an appropriate internal control is required. Yet there has been little systematic investigation of reference gene stability in N. benthamiana under conditions of viral infections. In this study, the expression profiles of 16 commonly used housekeeping genes (GAPDH, 18S, EF1α, SAMD, L23, UK, PP2A, APR, UBI3, SAND, ACT, TUB, GBP, F-BOX, PPR and TIP41) were determined in N. benthamiana and those with acceptable expression levels were further selected for transcript stability analysis by qPCR of complementary DNA prepared from N. benthamiana leaf tissue infected with one of five RNA plant viruses (Tobacco necrosis virus A, Beet black scorch virus, Beet necrotic yellow vein virus, Barley stripe mosaic virus and Potato virus X). Gene stability was analysed in parallel by three commonly-used dedicated algorithms: geNorm, NormFinder and BestKeeper. Statistical analysis revealed that the PP2A, F-BOX and L23 genes were the most stable overall, and that the combination of these three genes was sufficient for accurate normalisation. In addition, the suitability of PP2A, F-BOX and L23 as reference genes was illustrated by expression-level analysis of AGO2 and RdR6 in virus-infected N. benthamiana leaves. This is the first study to systematically examine and evaluate the stability of different reference genes in N. benthamiana. Our results not only provide researchers studying these viruses a shortlist of potential housekeeping genes to use as normalisers for qPCR experiments, but should also guide the selection of appropriate reference genes for gene expression studies of N. benthamiana under other biotic and abiotic stress conditions. PMID:23029521

Noninvasive assessment of extracellular and intracellular dehydration in healthy humans using the resistance-reactance-score graph method.

PubMed

Heavens, Kristen R; Charkoudian, Nisha; O'Brien, Catherine; Kenefick, Robert W; Cheuvront, Samuel N

2016-03-01

Few dehydration assessment measures provide accurate information; most are based on reference change values and very few are diagnostically accurate from a single observation or measure. Bioelectrical impedance may lack the precision to detect common forms of dehydration in healthy individuals. Limitations in bioimpedance may be addressed by a unique resistance-reactance (RXc)-score graph method, which transforms vector components into z scores for use with any impedance analyzer in any population. We tested whether the RXc-score graph method provides accurate single or serial assessments of dehydration when compared with gold-standard measures of total body water by using stable isotope dilution (deuterium oxide) combined with body-weight changes. We retrospectively analyzed data from a previous study in which 9 healthy young men participated in 3 trials: euhydration (EUH), extracellular dehydration (ED; via a diuretic), and intracellular dehydration (ID; via exercise in the heat). Participants lost 4-5% of their body weight during the dehydration trials; volume loss was similar between trials (ID compared with ED group: 3.5 ± 0.8 compared with 3.0 ± 0.6 L; P > 0.05). Despite significant losses of body water, most RXc vector scores for ED and ID groups were classified as "normal" (within the 75% population tolerance ellipse). However, directional displacement of vectors was consistent with loss of volume in both ED and ID conditions compared with the EUH condition and tended to be longer in ED than in ID conditions (P = 0.054). We conclude that, whereas individual RXc-score graph values do not provide accurate detection of dehydration from single measurements, directional changes in vector values from serial measurements are consistent with fluid loss for both ED and ID conditions. The RXc-score graph method may therefore alert clinicians to changes in hydration state, which may bolster the interpretation of other recognized change measures of hydration. © 2016 American Society for Nutrition.

Global forest cover mapping for the United Nations Food and Agriculture Organization forest resources assessment 2000 program

USGS Publications Warehouse

Zhu, Z.; Waller, E.

2003-01-01

Many countries periodically produce national reports on the status and changes of forest resources, using statistical surveys and spatial mapping of remotely sensed data. At the global level, the Food and Agriculture Organization (FAO) of the United Nations has conducted a Forest Resources Assessment (FRA) program every 10 yr since 1980, producing statistics and analysis that give a global synopsis of forest resources in the world. For the year 2000 of the FRA program (FRA2000), a global forest cover map was produced to provide spatial context to the extensive survey. The forest cover map, produced at the U.S. Geological Survey (USGS) EROS Data Center (EDC), has five classes: closed forest, open or fragmented forest, other wooded land, other land cover, and water. The first two forested classes at the global scale were delineated using combinations of temporal compositing, modified mixture analysis, geographic stratification, and other classification techniques. The remaining three FAO classes were derived primarily from the USGS global land cover characteristics database (Loveland et al. 1999). Validated on the basis of existing reference data sets, the map is estimated to be 77% accurate for the first four classes (no reference data were available for water), and 86% accurate for the forest and nonforest classification. The final map will be published as an insert to the FAO FRA2000 report.

Astrometric satellites

NASA Astrophysics Data System (ADS)

Lindegren, Lennart

2012-01-01

The launch of the Hipparcos satellite in 1989 and the Hubble Space Telescope in 1990 revolutionized astrometry. By no means does this imply that not much progress was made in the ground-based techniques used exclusively until then. On the contrary, the 1960s to 1980s saw an intense development of new or highly improved instruments, including photoelectric meridian circles, automated plate measuring machines, and the use of chargecoupled device (CCD) detectors for small-field differential astrometry (for a review of optical astrometry at the time, see Monet 1988). In the radio domain, very long baseline interferometry (VLBI) astrometry already provided an extragalactic reference frame accurate to about 1 milliarcsecond (mas) (Ma et al. 1990). Spectacular improvements were made in terms of accuracy, the faintness of the observed objects, and their numbers. However, there was a widening gulf between small-angle astrometry, where differential techniques could overcome atmospheric effects down to below 1 mas, and large-angle astrometry, where conventional instruments such as meridian circles seemed to have hit a barrier in the underlying systematic errors at about 100 mas. Though very precise, the small-angle measurements were of limited use for the determination of positions and proper motions, due to the lack of suitable reference objects in the small fields, and even for parallaxes the necessary correction for the mean parallax of background stars was highly non-trivial. Linking the optical observations to the accurate VLBI frame also proved extremely difficult.

Analysis of Natural Toxins by Liquid Chromatography-Chemiluminescence Nitrogen Detection and Application to the Preparation of Certified Reference Materials.

PubMed

Thomas, Krista; Wechsler, Dominik; Chen, Yi-Min; Crain, Sheila; Quilliam, Michael A

2016-09-01

The implementation of instrumental analytical methods such as LC-MS for routine monitoring of toxins requires the availability of accurate calibration standards. This is a challenge because many toxins are rare, expensive, dangerous to handle, and/or unstable, and simple gravimetric procedures are not reliable for establishing accurate concentrations in solution. NMR has served as one method of qualitative and quantitative characterization of toxin calibration solution Certified Reference Materials (CRMs). LC with chemiluminescence N detection (LC-CLND) was selected as a complementary method for comprehensive characterization of CRMs because it provides a molar response to N. Here we report on our investigation of LC-CLND as a method suitable for quantitative analysis of nitrogenous toxins. It was demonstrated that a wide range of toxins could be analyzed quantitatively by LC-CLND. Furthermore, equimolar responses among diverse structures were established and it was shown that a single high-purity standard such as caffeine could be used for instrument calibration. The limit of detection was approximately 0.6 ng N. Measurement of several of Canada's National Research Council toxin CRMs with caffeine as the calibrant showed precision averaging 2% RSD and accuracy ranging from 97 to 102%. Application of LC-CLND to the production of calibration solution CRMs and the establishment of traceability of measurement results are presented.

Comparison of permutationally invariant polynomials, neural networks, and Gaussian approximation potentials in representing water interactions through many-body expansions

NASA Astrophysics Data System (ADS)

Nguyen, Thuong T.; Székely, Eszter; Imbalzano, Giulio; Behler, Jörg; Csányi, Gábor; Ceriotti, Michele; Götz, Andreas W.; Paesani, Francesco

2018-06-01

The accurate representation of multidimensional potential energy surfaces is a necessary requirement for realistic computer simulations of molecular systems. The continued increase in computer power accompanied by advances in correlated electronic structure methods nowadays enables routine calculations of accurate interaction energies for small systems, which can then be used as references for the development of analytical potential energy functions (PEFs) rigorously derived from many-body (MB) expansions. Building on the accuracy of the MB-pol many-body PEF, we investigate here the performance of permutationally invariant polynomials (PIPs), neural networks, and Gaussian approximation potentials (GAPs) in representing water two-body and three-body interaction energies, denoting the resulting potentials PIP-MB-pol, Behler-Parrinello neural network-MB-pol, and GAP-MB-pol, respectively. Our analysis shows that all three analytical representations exhibit similar levels of accuracy in reproducing both two-body and three-body reference data as well as interaction energies of small water clusters obtained from calculations carried out at the coupled cluster level of theory, the current gold standard for chemical accuracy. These results demonstrate the synergy between interatomic potentials formulated in terms of a many-body expansion, such as MB-pol, that are physically sound and transferable, and machine-learning techniques that provide a flexible framework to approximate the short-range interaction energy terms.

A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies

PubMed Central

Howie, Bryan N.; Donnelly, Peter; Marchini, Jonathan

2009-01-01

Genotype imputation methods are now being widely used in the analysis of genome-wide association studies. Most imputation analyses to date have used the HapMap as a reference dataset, but new reference panels (such as controls genotyped on multiple SNP chips and densely typed samples from the 1,000 Genomes Project) will soon allow a broader range of SNPs to be imputed with higher accuracy, thereby increasing power. We describe a genotype imputation method (IMPUTE version 2) that is designed to address the challenges presented by these new datasets. The main innovation of our approach is a flexible modelling framework that increases accuracy and combines information across multiple reference panels while remaining computationally feasible. We find that IMPUTE v2 attains higher accuracy than other methods when the HapMap provides the sole reference panel, but that the size of the panel constrains the improvements that can be made. We also find that imputation accuracy can be greatly enhanced by expanding the reference panel to contain thousands of chromosomes and that IMPUTE v2 outperforms other methods in this setting at both rare and common SNPs, with overall error rates that are 15%–20% lower than those of the closest competing method. One particularly challenging aspect of next-generation association studies is to integrate information across multiple reference panels genotyped on different sets of SNPs; we show that our approach to this problem has practical advantages over other suggested solutions. PMID:19543373

Update on VLBA Astrometry of Cassini

NASA Astrophysics Data System (ADS)

Jones, Dayton L.; Folkner, William M.; Jacobson, Robert A.; Jacobs, Christopher S.; Romney, Jon; Dhawan, Vivek; Fomalont, Edward B.

2015-01-01

The NRAO Very Long Baseline Array (VLBA) has been used to measure positions of the Cassini spacecraft 2-3 times per year during the decade since it arrived at Saturn. Combining these measurements with fits for Cassini's orbit about Saturn from Doppler tracking by the NASA Deep Space Network provides accurate positions for the Saturn system barycenter in the inertial International Celestial Reference Frame (ICRF) at each observing epoch. These positions in turn help to improve our knowledge of Saturn's orbit and thus the planetary ephemeris on which future interplanetary spacecraft navigation, pulsar timing, and studies of solar system dynamics depend. This observational program will continue to the end of Cassini's mission in 2017, thereby covering as large a fraction of Saturn's orbital period as possible. A multi-year period of accurate astrometry also increases the range of times over which ephemeris improvements can be extrapolated. Our current residuals with respect to JPL's DE430 ephemeris are approximately 0.2 mas in right ascension and 0.3 mas in declination. The primary error sources are residual troposphere delay calibration errors and uncertainties in the ICRF positions of some of our phase reference sources. The reference source position uncertainties are being reduced by continuing VLBI observations. Similar VLBI techniques will be applied to the Juno spacecraft when it begins orbiting Jupiter in 2016, thereby improving the orbit for this planet as well. This work has been carried out at the Jet Propulsion Laboratory, California Institute of Technology, under contract with the National Aeronautics and Space Administration. Support from the NASA Planetary Astronomy Program is gratefully acknowledged. The VLBA is a facility of the National Radio Astronomy Observatory, which is operated by Associated Universities, Inc, under a cooperative agreement with the National Science Foundation.

Effects of Visual Feedback and Memory on Unintentional Drifts in Performance During Finger Pressing Tasks

PubMed Central

Solnik, Stanislaw; Qiao, Mu; Latash, Mark L.

2017-01-01

This study tested two hypotheses on the nature of unintentional force drifts elicited by removing visual feedback during accurate force production tasks. The role of working memory (memory hypothesis) was explored in tasks with continuous force production, intermittent force production, and rest intervals over the same time interval. The assumption of unintentional drifts in referent coordinate for the fingertips was tested using manipulations of visual feedback: Young healthy subjects performed accurate steady-state force production tasks by pressing with the two index fingers on individual force sensors with visual feedback on the total force, sharing ratio, both, or none. Predictions based on the memory hypothesis have been falsified. In particular, we observed consistent force drifts to lower force values during continuous force production trials only. No force drift or drifts to higher forces were observed during intermittent force production trials and following rest intervals. The hypotheses based on the idea of drifts in referent finger coordinates have been confirmed. In particular, we observed superposition of two drift processes: A drift of total force to lower magnitudes and a drift of the sharing ratio to 50:50. When visual feedback on total force only was provided, the two finger forces showed drifts in opposite directions. We interpret the findings as evidence for the control of motor actions with changes in referent coordinates for participating effectors. Unintentional drifts in performance are viewed as natural relaxation processes in the involved systems; their typical time reflects stability in the direction of the drift. The magnitude of the drift was higher in the right (dominant) hand, which is consistent with the dynamic dominance hypothesis. PMID:28168396

Accurate and robust brain image alignment using boundary-based registration.

PubMed

Greve, Douglas N; Fischl, Bruce

2009-10-15

The fine spatial scales of the structures in the human brain represent an enormous challenge to the successful integration of information from different images for both within- and between-subject analysis. While many algorithms to register image pairs from the same subject exist, visual inspection shows that their accuracy and robustness to be suspect, particularly when there are strong intensity gradients and/or only part of the brain is imaged. This paper introduces a new algorithm called Boundary-Based Registration, or BBR. The novelty of BBR is that it treats the two images very differently. The reference image must be of sufficient resolution and quality to extract surfaces that separate tissue types. The input image is then aligned to the reference by maximizing the intensity gradient across tissue boundaries. Several lower quality images can be aligned through their alignment with the reference. Visual inspection and fMRI results show that BBR is more accurate than correlation ratio or normalized mutual information and is considerably more robust to even strong intensity inhomogeneities. BBR also excels at aligning partial-brain images to whole-brain images, a domain in which existing registration algorithms frequently fail. Even in the limit of registering a single slice, we show the BBR results to be robust and accurate.

Doppler ultrasound-based measurement of tendon velocity and displacement for application toward detecting user-intended motion.

PubMed

Stegman, Kelly J; Park, Edward J; Dechev, Nikolai

2012-07-01

The motivation of this research is to non-invasively monitor the wrist tendon's displacement and velocity, for purposes of controlling a prosthetic device. This feasibility study aims to determine if the proposed technique using Doppler ultrasound is able to accurately estimate the tendon's instantaneous velocity and displacement. This study is conducted with a tendon mimicking experiment consisting of two different materials: a commercial ultrasound scanner, and a reference linear motion stage set-up. Audio-based output signals are acquired from the ultrasound scanner, and are processed with our proposed Fourier technique to obtain the tendon's velocity and displacement estimates. We then compare our estimates to an external reference system, and also to the ultrasound scanner's own estimates based on its proprietary software. The proposed tendon motion estimation method has been shown to be repeatable, effective and accurate in comparison to the external reference system, and is generally more accurate than the scanner's own estimates. After establishing this feasibility study, future testing will include cadaver-based studies to test the technique on the human arm tendon anatomy, and later on live human test subjects in order to further refine the proposed method for the novel purpose of detecting user-intended tendon motion for controlling wearable prosthetic devices.

An online open-source tool for automated quantification of liver and myocardial iron concentrations by T2* magnetic resonance imaging.

PubMed

Git, K-A; Fioravante, L A B; Fernandes, J L

2015-09-01

To assess whether an online open-source tool would provide accurate calculations of T2(*) values for iron concentrations in the liver and heart compared with a standard reference software. An online open-source tool, written in pure HTML5/Javascript, was tested in 50 patients (age 26.0 ± 18.9 years, 46% males) who underwent T2(*) MRI of the liver and heart for iron overload assessment as part of their routine workup. Automated truncation correction was the default with optional manual adjustment provided if needed. The results were compared against a standard reference measurement using commercial software with manual truncation (CVI(42)(®) v. 5.1; Circle Cardiovascular Imaging; Calgary, AB). The mean liver T2(*) values calculated with the automated tool was 4.3 ms [95% confidence interval (CI) 3.1 to 5.5 ms] vs 4.26 ms using the reference software (95% CI 3.1 to 5.4 ms) without any significant differences (p = 0.71). In the liver, the mean difference was 0.036 ms (95% CI -0.1609 to 0.2329 ms) with a regression correlation coefficient of 0.97. For the heart, the automated T2(*) value was 26.0 ms (95% CI 22.9 to 29.0 ms) vs 25.3 ms (95% CI 22.3 to 28.3 ms), p = 0.28. The mean difference was 0.72 ms (95% CI 0.08191 to 1.3621 ms) with a correlation coefficient of 0.96. The automated online tool provides similar T2(*) values for the liver and myocardial iron concentrations as compared with a standard reference software. The online program provides an open-source tool for the calculation of T2(*) values, incorporating an automated correction algorithm in a simple and easy-to-use interface.

Validation of Reference Genes for RT-qPCR Studies of Gene Expression in Preharvest and Postharvest Longan Fruits under Different Experimental Conditions

PubMed Central

Wu, Jianyang; Zhang, Hongna; Liu, Liqin; Li, Weicai; Wei, Yongzan; Shi, Shengyou

2016-01-01

Reverse transcription quantitative PCR (RT-qPCR) as the accurate and sensitive method is use for gene expression analysis, but the veracity and reliability result depends on whether select appropriate reference gene or not. To date, several reliable reference gene validations have been reported in fruits trees, but none have been done on preharvest and postharvest longan fruits. In this study, 12 candidate reference genes, namely, CYP, RPL, GAPDH, TUA, TUB, Fe-SOD, Mn-SOD, Cu/Zn-SOD, 18SrRNA, Actin, Histone H3, and EF-1a, were selected. Expression stability of these genes in 150 longan samples was evaluated and analyzed using geNorm and NormFinder algorithms. Preharvest samples consisted of seven experimental sets, including different developmental stages, organs, hormone stimuli (NAA, 2,4-D, and ethephon) and abiotic stresses (bagging and girdling with defoliation). Postharvest samples consisted of different temperature treatments (4 and 22°C) and varieties. Our findings indicate that appropriate reference gene(s) should be picked for each experimental condition. Our data further showed that the commonly used reference gene Actin does not exhibit stable expression across experimental conditions in longan. Expression levels of the DlACO gene, which is a key gene involved in regulating fruit abscission under girdling with defoliation treatment, was evaluated to validate our findings. In conclusion, our data provide a useful framework for choice of suitable reference genes across different experimental conditions for RT-qPCR analysis of preharvest and postharvest longan fruits. PMID:27375640

Innovations in energy expenditure assessment.

PubMed

Achamrah, Najate; Oshima, Taku; Genton, Laurence

2018-06-15

Optimal nutritional therapy has been associated with better clinical outcomes and requires providing energy as closed as possible to measured energy expenditure. We reviewed the current innovations in energy expenditure assessment in humans, focusing on indirect calorimetry and other new alternative methods. Although considered the reference method to measure energy expenditure, the use of indirect calorimetry is currently limited by the lack of an adequate device. However, recent technical developments may allow a broader use of indirect calorimetry for in-patients and out-patients. An ongoing international academic initiative to develop a new indirect calorimeter aimed to provide innovative and affordable technical solutions for many of the current limitations of indirect calorimetry. New alternative methods to indirect calorimetry, including CO2 measurements in mechanically ventilated patients, isotopic approaches and accelerometry-based fitness equipments, show promises but have been either poorly studied and/or are not accurate compared to indirect calorimetry. Therefore, to date, energy expenditure measured by indirect calorimetry remains the gold standard to guide nutritional therapy. Some new innovative methods are demonstrating promises in energy expenditure assessment, but still need to be validated. There is an ongoing need for easy-to-use, accurate and affordable indirect calorimeter for daily use in in-patients and out-patients.

Semisupervised learning using denoising autoencoders for brain lesion detection and segmentation.

PubMed

Alex, Varghese; Vaidhya, Kiran; Thirunavukkarasu, Subramaniam; Kesavadas, Chandrasekharan; Krishnamurthi, Ganapathy

2017-10-01

The work explores the use of denoising autoencoders (DAEs) for brain lesion detection, segmentation, and false-positive reduction. Stacked denoising autoencoders (SDAEs) were pretrained using a large number of unlabeled patient volumes and fine-tuned with patches drawn from a limited number of patients ([Formula: see text], 40, 65). The results show negligible loss in performance even when SDAE was fine-tuned using 20 labeled patients. Low grade glioma (LGG) segmentation was achieved using a transfer learning approach in which a network pretrained with high grade glioma data was fine-tuned using LGG image patches. The networks were also shown to generalize well and provide good segmentation on unseen BraTS 2013 and BraTS 2015 test data. The manuscript also includes the use of a single layer DAE, referred to as novelty detector (ND). ND was trained to accurately reconstruct nonlesion patches. The reconstruction error maps of test data were used to localize lesions. The error maps were shown to assign unique error distributions to various constituents of the glioma, enabling localization. The ND learns the nonlesion brain accurately as it was also shown to provide good segmentation performance on ischemic brain lesions in images from a different database.

On magnetic field strength effect on velocity and turbulence characterization using Phase-Contrast Magnetic Resonance Imaging (PC-MRI)

NASA Astrophysics Data System (ADS)

van de Moortele, Pierre-Francois; Amili, Omid; Coletti, Filippo; Toloui, Mostafa

2017-11-01

Cardiovascular flows are predominantly laminar. Nevertheless, transient and even turbulent flows have been observed in the vicinity of the heart (e.g. valves, ascending aorta, valvular/vascular stenosis). Effective in-vivo hemodynamic-based diagnostics in these sites require both high-resolution velocity measurements (especially in the near-vessel wall regions) and accurate evaluation of blood flow turbulence level (e.g. in terms of TKE). In addition to phase contrast (PC), appropriately designed PC-MRI sequences provide intravoxel incoherent motion encoding, a unique tool for simultaneous, non-invasive evaluation of velocity 3D vector fields and Reynolds stresses in cardiovascular flows in vivo. However, limited spatial and temporal resolution of PC-MRI result in inaccuracies in the estimation of hemodynamics (e.g. WSS) and of flow turbulence characteristics. This study aims to assess whether SNR gains at higher magnetic field could overcome these limits, providing more accurate velocity and turbulence characterization at higher spatial resolution. Experiments are conducted on MR Scanners at 3 and 7 Tesla with a U-bent pipe flow shaped phantom. 3D velocity fields, Reynolds stresses and TKE are analyzed and compared to a reference PIV experiments.

LC-QTOF MS screening of more than 1,000 licit and illicit drugs and their metabolites in wastewater and surface waters from the area of Bogotá, Colombia.

PubMed

Hernández, Félix; Ibáñez, María; Botero-Coy, Ana-María; Bade, Richard; Bustos-López, Martha Cristina; Rincón, Javier; Moncayo, Alejandro; Bijlsma, Lubertus

2015-08-01

A large screening of around 1,000 emerging contaminants, focused on licit and illicit drugs and their metabolites, has been made in urban wastewaters (both influent and effluent) and surface waters from the area of Bogotá, Colombia. After a simple generic solid-phase extraction (SPE) step with Oasis hydrophilic-lipophilic balanced (HLB) cartridges, analyses were made by ultra high-performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry (UHPLC-QTOF MS) under MS(E) mode (sequential acquisition of mass spectra at low energy (LE) and high collision energy (HE)). Accurate mass measurements and the information provided by MS(E) on the presence of the (de)protonated molecule and fragment ions allowed the reliable identification of the compounds detected, even without reference standards being available in some cases (tentative identification). The compounds most frequently found were acetaminophen/paracetamol, carbamazepine and its dihydro-dihydroxylated metabolite, clarithromycin, diclofenac, ibuprofen, gemfibrozil, lincomycin, losartan, valsartan, the two metabolites of metamizole (4-acetamido-antipyrine and 4-formylamino-antipyrine), sucralose, and cocaine and its main metabolite benzoylecgonine. Caffeine, the sweetener saccharin, and two hydroxylated metabolites of losartan were tentatively identified in almost all samples analyzed. Pharmaceutical lidocaine was tentatively identified and subsequently confirmed with reference standard. For the first time, a general overview of the occurrence of drugs and their metabolites in the aquatic environment of Colombia has been reported. In the near future, target methodologies, typically based on liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS), will need to be set up for accurate and sensitive quantification of the contaminants selected on the basis on the information provided in the present paper.

Assessing performance of closed-loop insulin delivery systems by continuous glucose monitoring: drawbacks and way forward.

PubMed

Hovorka, Roman; Nodale, Marianna; Haidar, Ahmad; Wilinska, Malgorzata E

2013-01-01

We investigated whether continuous glucose monitoring (CGM) levels can accurately assess glycemic control while directing closed-loop insulin delivery. Data were analyzed retrospectively from 33 subjects with type 1 diabetes who underwent closed-loop and conventional pump therapy on two separate nights. Glycemic control was evaluated by reference plasma glucose and contrasted against three methods based on Navigator (Abbott Diabetes Care, Alameda, CA) CGM levels. Glucose mean and variability were estimated by unmodified CGM levels with acceptable clinical accuracy. Time when glucose was in target range was overestimated by CGM during closed-loop nights (CGM vs. plasma glucose median [interquartile range], 86% [65-97%] vs. 75% [59-91%]; P=0.04) but not during conventional pump therapy (57% [32-72%] vs. 51% [29-68%]; P=0.82) providing comparable treatment effect (mean [SD], 28% [29%] vs. 23% [21%]; P=0.11). Using the CGM measurement error of 15% derived from plasma glucose-CGM pairs (n=4,254), stochastic interpretation of CGM gave unbiased estimate of time in target during both closed-loop (79% [62-86%] vs. 75% [59-91%]; P=0.24) and conventional pump therapy (54% [33-66%] vs. 51% [29-68%]; P=0.44). Treatment effect (23% [24%] vs. 23% [21%]; P=0.96) and time below target were accurately estimated by stochastic CGM. Recalibrating CGM using reference plasma glucose values taken at the start and end of overnight closed-loop was not superior to stochastic CGM. CGM is acceptable to estimate glucose mean and variability, but without adjustment it may overestimate benefit of closed-loop. Stochastic CGM provided unbiased estimate of time when glucose is in target and below target and may be acceptable for assessment of closed-loop in the outpatient setting.

Assessment of modal-pushover-based scaling procedure for nonlinear response history analysis of ordinary standard bridges

USGS Publications Warehouse

Kalkan, E.; Kwong, N.

2012-01-01

The earthquake engineering profession is increasingly utilizing nonlinear response history analyses (RHA) to evaluate seismic performance of existing structures and proposed designs of new structures. One of the main ingredients of nonlinear RHA is a set of ground motion records representing the expected hazard environment for the structure. When recorded motions do not exist (as is the case in the central United States) or when high-intensity records are needed (as is the case in San Francisco and Los Angeles), ground motions from other tectonically similar regions need to be selected and scaled. The modal-pushover-based scaling (MPS) procedure was recently developed to determine scale factors for a small number of records such that the scaled records provide accurate and efficient estimates of “true” median structural responses. The adjective “accurate” refers to the discrepancy between the benchmark responses and those computed from the MPS procedure. The adjective “efficient” refers to the record-to-record variability of responses. In this paper, the accuracy and efficiency of the MPS procedure are evaluated by applying it to four types of existing Ordinary Standard bridges typical of reinforced concrete bridge construction in California. These bridges are the single-bent overpass, multi-span bridge, curved bridge, and skew bridge. As compared with benchmark analyses of unscaled records using a larger catalog of ground motions, it is demonstrated that the MPS procedure provided an accurate estimate of the engineering demand parameters (EDPs) accompanied by significantly reduced record-to-record variability of the EDPs. Thus, it is a useful tool for scaling ground motions as input to nonlinear RHAs of Ordinary Standard bridges.

Benefits of a Pharmacology Antimalarial Reference Standard and Proficiency Testing Program Provided by the Worldwide Antimalarial Resistance Network (WWARN)

PubMed Central

Lourens, Chris; Lindegardh, Niklas; Barnes, Karen I.; Guerin, Philippe J.; Sibley, Carol H.; White, Nicholas J.

2014-01-01

Comprehensive assessment of antimalarial drug resistance should include measurements of antimalarial blood or plasma concentrations in clinical trials and in individual assessments of treatment failure so that true resistance can be differentiated from inadequate drug exposure. Pharmacometric modeling is necessary to assess pharmacokinetic-pharmacodynamic relationships in different populations to optimize dosing. To accomplish both effectively and to allow comparison of data from different laboratories, it is essential that drug concentration measurement is accurate. Proficiency testing (PT) of laboratory procedures is necessary for verification of assay results. Within the Worldwide Antimalarial Resistance Network (WWARN), the goal of the quality assurance/quality control (QA/QC) program is to facilitate and sustain high-quality antimalarial assays. The QA/QC program consists of an international PT program for pharmacology laboratories and a reference material (RM) program for the provision of antimalarial drug standards, metabolites, and internal standards for laboratory use. The RM program currently distributes accurately weighed quantities of antimalarial drug standards, metabolites, and internal standards to 44 pharmacology, in vitro, and drug quality testing laboratories. The pharmacology PT program has sent samples to eight laboratories in four rounds of testing. WWARN technical experts have provided advice for correcting identified problems to improve performance of subsequent analysis and ultimately improved the quality of data. Many participants have demonstrated substantial improvements over subsequent rounds of PT. The WWARN QA/QC program has improved the quality and value of antimalarial drug measurement in laboratories globally. It is a model that has potential to be applied to strengthening laboratories more widely and improving the therapeutics of other infectious diseases. PMID:24777099

Daily reference crop evapotranspiration in the humid environments of Azores islands using reduced data sets: accuracy of FAO-PM temperature and Hargreaves-Samani methods

NASA Astrophysics Data System (ADS)

Paredes, P.; Fontes, J. C.; Azevedo, E. B.; Pereira, L. S.

2017-11-01

Reference crop evapotranspiration (ETo) estimations using the FAO Penman-Monteith equation (PM-ETo) require several weather variables that are often not available. Then, ETo may be computed with procedures proposed in FAO56, either using the PM-ETo equation with temperature estimates of actual vapor pressure (e a) and solar radiation (R s), and default wind speed values (u 2), the PMT method, or using the Hargreaves-Samani equation (HS). The accuracy of estimates of daily e a, R s, and u 2 is provided in a companion paper (Paredes et al. 2017) applied to data of 20 locations distributed through eight islands of Azores, thus focusing on humid environments. Both estimation procedures using the PMT method (ETo PMT) and the HS equation (ETo HS) were assessed by statistically comparing their results with those obtained for the PM-ETo with data of the same 20 locations. Results show that both approaches provide for accurate ETo estimations, with RMSE for PMT ranging 0.48-0.73 mm day-1 and for HS varying 0.47-0.86 mm day-1. It was observed that ETo PMT is linearly related with PM-ETo, while non-linearity was observed for ETo HS in weather stations located at high elevation. Impacts of wind were not important for HS but required proper adjustments in the case of PMT. Results show that the PMT approach is more accurate than HS. Moreover, PMT allows the use of observed variables together with estimators of the missing ones, which improves the accuracy of the PMT approach. The preference for the PMT method, fully based upon the PM-ETo equation, is therefore obvious.

DNA Barcoding Coupled with High Resolution Melting Analysis Enables Rapid and Accurate Distinction of Aspergillus species.

PubMed

Fidler, Gabor; Kocsube, Sandor; Leiter, Eva; Biro, Sandor; Paholcsek, Melinda

2017-08-01

We describe a high-resolution melting (HRM) analysis method that is rapid, reproducible, and able to identify reference strains and further 40 clinical isolates of Aspergillus fumigatus (14), A. lentulus (3), A. terreus (7), A. flavus (8), A. niger (2), A. welwitschiae (4), and A. tubingensis (2). Asp1 and Asp2 primer sets were designed to amplify partial sequences of the Aspergillus benA (beta-tubulin) genes in a closed-, single-tube system. Human placenta DNA, further Aspergillus (3), Candida (9), Fusarium (6), and Scedosporium (2) nucleic acids from type strains and clinical isolates were also included in this study to evaluate cross reactivity with other relevant pathogens causing invasive fungal infections. The barcoding capacity of this method proved to be 100% providing distinctive binomial scores; 14, 34, 36, 35, 25, 15, 26 when tested among species, while the within-species distinction capacity of the assay proved to be 0% based on the aligned thermodynamic profiles of the Asp1, Asp2 melting clusters allowing accurate species delimitation of all tested clinical isolates. The identification limit of this HRM assay was also estimated on Aspergillus reference gDNA panels where it proved to be 10-102 genomic equivalents (GE) except the A. fumigatus panel where it was 103 only. Furthermore, misidentification was not detected with human genomic DNA or with Candida, Fusarium, and Scedosporium strains. Our DNA barcoding assay introduced here provides results within a few hours, and it may possess further diagnostic utility when analyzing standard cultures supporting adequate therapeutic decisions. © The Author 2016. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

The use of digital PCR to improve the application of quantitative molecular diagnostic methods for tuberculosis.

PubMed

Devonshire, Alison S; O'Sullivan, Denise M; Honeyborne, Isobella; Jones, Gerwyn; Karczmarczyk, Maria; Pavšič, Jernej; Gutteridge, Alice; Milavec, Mojca; Mendoza, Pablo; Schimmel, Heinz; Van Heuverswyn, Fran; Gorton, Rebecca; Cirillo, Daniela Maria; Borroni, Emanuele; Harris, Kathryn; Barnard, Marinus; Heydenrych, Anthenette; Ndusilo, Norah; Wallis, Carole L; Pillay, Keshree; Barry, Thomas; Reddington, Kate; Richter, Elvira; Mozioğlu, Erkan; Akyürek, Sema; Yalçınkaya, Burhanettin; Akgoz, Muslum; Žel, Jana; Foy, Carole A; McHugh, Timothy D; Huggett, Jim F

2016-08-03

Real-time PCR (qPCR) based methods, such as the Xpert MTB/RIF, are increasingly being used to diagnose tuberculosis (TB). While qualitative methods are adequate for diagnosis, the therapeutic monitoring of TB patients requires quantitative methods currently performed using smear microscopy. The potential use of quantitative molecular measurements for therapeutic monitoring has been investigated but findings have been variable and inconclusive. The lack of an adequate reference method and reference materials is a barrier to understanding the source of such disagreement. Digital PCR (dPCR) offers the potential for an accurate method for quantification of specific DNA sequences in reference materials which can be used to evaluate quantitative molecular methods for TB treatment monitoring. To assess a novel approach for the development of quality assurance materials we used dPCR to quantify specific DNA sequences in a range of prototype reference materials and evaluated accuracy between different laboratories and instruments. The materials were then also used to evaluate the quantitative performance of qPCR and Xpert MTB/RIF in eight clinical testing laboratories. dPCR was found to provide results in good agreement with the other methods tested and to be highly reproducible between laboratories without calibration even when using different instruments. When the reference materials were analysed with qPCR and Xpert MTB/RIF by clinical laboratories, all laboratories were able to correctly rank the reference materials according to concentration, however there was a marked difference in the measured magnitude. TB is a disease where the quantification of the pathogen could lead to better patient management and qPCR methods offer the potential to rapidly perform such analysis. However, our findings suggest that when precisely characterised materials are used to evaluate qPCR methods, the measurement result variation is too high to determine whether molecular quantification of Mycobacterium tuberculosis would provide a clinically useful readout. The methods described in this study provide a means by which the technical performance of quantitative molecular methods can be evaluated independently of clinical variability to improve accuracy of measurement results. These will assist in ultimately increasing the likelihood that such approaches could be used to improve patient management of TB.

De novo assembly of highly polymorphic metagenomic data using in situ generated reference sequences and a novel BLAST-based assembly pipeline.

PubMed

Lin, You-Yu; Hsieh, Chia-Hung; Chen, Jiun-Hong; Lu, Xuemei; Kao, Jia-Horng; Chen, Pei-Jer; Chen, Ding-Shinn; Wang, Hurng-Yi

2017-04-26

The accuracy of metagenomic assembly is usually compromised by high levels of polymorphism due to divergent reads from the same genomic region recognized as different loci when sequenced and assembled together. A viral quasispecies is a group of abundant and diversified genetically related viruses found in a single carrier. Current mainstream assembly methods, such as Velvet and SOAPdenovo, were not originally intended for the assembly of such metagenomics data, and therefore demands for new methods to provide accurate and informative assembly results for metagenomic data. In this study, we present a hybrid method for assembling highly polymorphic data combining the partial de novo-reference assembly (PDR) strategy and the BLAST-based assembly pipeline (BBAP). The PDR strategy generates in situ reference sequences through de novo assembly of a randomly extracted partial data set which is subsequently used for the reference assembly for the full data set. BBAP employs a greedy algorithm to assemble polymorphic reads. We used 12 hepatitis B virus quasispecies NGS data sets from a previous study to assess and compare the performance of both PDR and BBAP. Analyses suggest the high polymorphism of a full metagenomic data set leads to fragmentized de novo assembly results, whereas the biased or limited representation of external reference sequences included fewer reads into the assembly with lower assembly accuracy and variation sensitivity. In comparison, the PDR generated in situ reference sequence incorporated more reads into the final PDR assembly of the full metagenomics data set along with greater accuracy and higher variation sensitivity. BBAP assembly results also suggest higher assembly efficiency and accuracy compared to other assembly methods. Additionally, BBAP assembly recovered HBV structural variants that were not observed amongst assembly results of other methods. Together, PDR/BBAP assembly results were significantly better than other compared methods. Both PDR and BBAP independently increased the assembly efficiency and accuracy of highly polymorphic data, and assembly performances were further improved when used together. BBAP also provides nucleotide frequency information. Together, PDR and BBAP provide powerful tools for metagenomic data studies.

How do reference montage and electrodes setup affect the measured scalp EEG potentials?

NASA Astrophysics Data System (ADS)

Hu, Shiang; Lai, Yongxiu; Valdes-Sosa, Pedro A.; Bringas-Vega, Maria L.; Yao, Dezhong

2018-04-01

Objective. Human scalp electroencephalogram (EEG) is widely applied in cognitive neuroscience and clinical studies due to its non-invasiveness and ultra-high time resolution. However, the representativeness of the measured EEG potentials for the underneath neural activities is still a problem under debate. This study aims to investigate systematically how both reference montage and electrodes setup affect the accuracy of EEG potentials. Approach. First, the standard EEG potentials are generated by the forward calculation with a single dipole in the neural source space, for eleven channel numbers (10, 16, 21, 32, 64, 85, 96, 128, 129, 257, 335). Here, the reference is the ideal infinity implicitly determined by forward theory. Then, the standard EEG potentials are transformed to recordings with different references including five mono-polar references (Left earlobe, Fz, Pz, Oz, Cz), and three re-references (linked mastoids (LM), average reference (AR) and reference electrode standardization technique (REST)). Finally, the relative errors between the standard EEG potentials and the transformed ones are evaluated in terms of channel number, scalp regions, electrodes layout, dipole source position and orientation, as well as sensor noise and head model. Main results. Mono-polar reference recordings are usually of large distortions; thus, a re-reference after online mono-polar recording should be adopted in general to mitigate this effect. Among the three re-references, REST is generally superior to AR for all factors compared, and LM performs worst. REST is insensitive to head model perturbation. AR is subject to electrodes coverage and dipole orientation but no close relation with channel number. Significance. These results indicate that REST would be the first choice of re-reference and AR may be an alternative option for high level sensor noise case. Our findings may provide the helpful suggestions on how to obtain the EEG potentials as accurately as possible for cognitive neuroscientists and clinicians.

Neural network feedforward control of a closed-circuit wind tunnel

NASA Astrophysics Data System (ADS)

Sutcliffe, Peter

Accurate control of wind-tunnel test conditions can be dramatically enhanced using feedforward control architectures which allow operating conditions to be maintained at a desired setpoint through the use of mathematical models as the primary source of prediction. However, as the desired accuracy of the feedforward prediction increases, the model complexity also increases, so that an ever increasing computational load is incurred. This drawback can be avoided by employing a neural network that is trained offline using the output of a high fidelity wind-tunnel mathematical model, so that the neural network can rapidly reproduce the predictions of the model with a greatly reduced computational overhead. A novel neural network database generation method, developed through the use of fractional factorial arrays, was employed such that a neural network can accurately predict wind-tunnel parameters across a wide range of operating conditions whilst trained upon a highly efficient database. The subsequent network was incorporated into a Neural Network Model Predictive Control (NNMPC) framework to allow an optimised output schedule capable of providing accurate control of the wind-tunnel operating parameters. Facilitation of an optimised path through the solution space is achieved through the use of a chaos optimisation algorithm such that a more globally optimum solution is likely to be found with less computational expense than the gradient descent method. The parameters associated with the NNMPC such as the control horizon are determined through the use of a Taguchi methodology enabling the minimum number of experiments to be carried out to determine the optimal combination. The resultant NNMPC scheme was employed upon the Hessert Low Speed Wind Tunnel at the University of Notre Dame to control the test-section temperature such that it follows a pre-determined reference trajectory during changes in the test-section velocity. Experimental testing revealed that the derived NNMPC controller provided an excellent level of control over the test-section temperature in adherence to a reference trajectory even when faced with unforeseen disturbances such as rapid changes in the operating environment.

High precision optomechanical assembly using threads as mechanical reference

NASA Astrophysics Data System (ADS)

Lamontagne, Frédéric; Desnoyers, Nichola; Bergeron, Guy; Cantin, Mario

2016-09-01

A convenient method to assemble optomechanical components is to use threaded interface. For example, lenses are often secured inside barrels using threaded rings. In other cases, multiple optical sub-assemblies such as lens barrels can be threaded to each other. Threads have the advantage to provide a simple assembly method, to be easy to manufacture, and to offer a compact mechanical design. On the other hand, threads are not considered to provide accurate centering between parts because of the assembly clearance between the inner and outer threads. For that reason, threads are often used in conjunction with precision cylindrical surfaces to limit the radial clearance between the parts to be centered. Therefore, tight manufacturing tolerances are needed on these pilot diameters, which affect the cost of the optical assembly. This paper presents a new optomechanical approach that uses threads as mechanical reference. This innovative method relies on geometric principles to auto-center parts to each other with a very low centering error that is usually less than 5 μm. The method allows to auto-center an optical group in a main barrel, to perform an axial adjustment of an optical group inside a main barrel, and to perform stacking of multiple barrels. In conjunction with the lens auto-centering method that also used threads as a mechanical reference, this novel solution opens new possibilities to realize a variety of different high precision optomechanical assemblies at lower cost.

Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology.

PubMed

Otto, Thomas D; Sanders, Mandy; Berriman, Matthew; Newbold, Chris

2010-07-15

The accuracy of reference genomes is important for downstream analysis but a low error rate requires expensive manual interrogation of the sequence. Here, we describe a novel algorithm (Iterative Correction of Reference Nucleotides) that iteratively aligns deep coverage of short sequencing reads to correct errors in reference genome sequences and evaluate their accuracy. Using Plasmodium falciparum (81% A + T content) as an extreme example, we show that the algorithm is highly accurate and corrects over 2000 errors in the reference sequence. We give examples of its application to numerous other eukaryotic and prokaryotic genomes and suggest additional applications. The software is available at http://icorn.sourceforge.net

Comparison of Kinetic Models for Dual-Tracer Receptor Concentration Imaging in Tumors

PubMed Central

Hamzei, Nazanin; Samkoe, Kimberley S; Elliott, Jonathan T; Holt, Robert W; Gunn, Jason R; Hasan, Tayyaba; Pogue, Brian W; Tichauer, Kenneth M

2014-01-01

Molecular differences between cancerous and healthy tissue have become key targets for novel therapeutics specific to tumor receptors. However, cancer cell receptor expression can vary within and amongst different tumors, making strategies that can quantify receptor concentration in vivo critical for the progression of targeted therapies. Recently a dual-tracer imaging approach capable of providing quantitative measures of receptor concentration in vivo was developed. It relies on the simultaneous injection and imaging of receptor-targeted tracer and an untargeted tracer (to account for non-specific uptake of the targeted tracer). Early implementations of this approach have been structured on existing “reference tissue” imaging methods that have not been optimized for or validated in dual-tracer imaging. Using simulations and mouse tumor model experimental data, the salient findings in this study were that all widely used reference tissue kinetic models can be used for dual-tracer imaging, with the linearized simplified reference tissue model offering a good balance of accuracy and computational efficiency. Moreover, an alternate version of the full two-compartment reference tissue model can be employed accurately by assuming that the K1s of the targeted and untargeted tracers are similar to avoid assuming an instantaneous equilibrium between bound and free states (made by all other models). PMID:25414912

Time-efficient high-resolution whole-brain three-dimensional macromolecular proton fraction mapping

PubMed Central

Yarnykh, Vasily L.

2015-01-01

Purpose Macromolecular proton fraction (MPF) mapping is a quantitative MRI method that reconstructs parametric maps of a relative amount of macromolecular protons causing the magnetization transfer (MT) effect and provides a biomarker of myelination in neural tissues. This study aimed to develop a high-resolution whole-brain MPF mapping technique utilizing a minimal possible number of source images for scan time reduction. Methods The described technique is based on replacement of an actually acquired reference image without MT saturation by a synthetic one reconstructed from R1 and proton density maps, thus requiring only three source images. This approach enabled whole-brain three-dimensional MPF mapping with isotropic 1.25×1.25×1.25 mm3 voxel size and scan time of 20 minutes. The synthetic reference method was validated against standard MPF mapping with acquired reference images based on data from 8 healthy subjects. Results Mean MPF values in segmented white and gray matter appeared in close agreement with no significant bias and small within-subject coefficients of variation (<2%). High-resolution MPF maps demonstrated sharp white-gray matter contrast and clear visualization of anatomical details including gray matter structures with high iron content. Conclusions Synthetic reference method improves resolution of MPF mapping and combines accurate MPF measurements with unique neuroanatomical contrast features. PMID:26102097

An automated protocol for performance benchmarking a widefield fluorescence microscope.

PubMed

Halter, Michael; Bier, Elianna; DeRose, Paul C; Cooksey, Gregory A; Choquette, Steven J; Plant, Anne L; Elliott, John T

2014-11-01

Widefield fluorescence microscopy is a highly used tool for visually assessing biological samples and for quantifying cell responses. Despite its widespread use in high content analysis and other imaging applications, few published methods exist for evaluating and benchmarking the analytical performance of a microscope. Easy-to-use benchmarking methods would facilitate the use of fluorescence imaging as a quantitative analytical tool in research applications, and would aid the determination of instrumental method validation for commercial product development applications. We describe and evaluate an automated method to characterize a fluorescence imaging system's performance by benchmarking the detection threshold, saturation, and linear dynamic range to a reference material. The benchmarking procedure is demonstrated using two different materials as the reference material, uranyl-ion-doped glass and Schott 475 GG filter glass. Both are suitable candidate reference materials that are homogeneously fluorescent and highly photostable, and the Schott 475 GG filter glass is currently commercially available. In addition to benchmarking the analytical performance, we also demonstrate that the reference materials provide for accurate day to day intensity calibration. Published 2014 Wiley Periodicals Inc. Published 2014 Wiley Periodicals Inc. This article is a US government work and, as such, is in the public domain in the United States of America.

Examination and Treatment of Hamstring Related Injuries

PubMed Central

2012-01-01

Context: There is a wide spectrum of hamstring-related injuries that can occur in the athlete. Accurate diagnosis is imperative to prevent delayed return to sport, injury recurrence, and accurate clinical decision making regarding the most efficacious treatment. Evidence Acquisition: This review highlights current evidence related to the diagnosis and treatment of hamstring-related injuries in athletes. Data sources were limited to peer-reviewed publications indexed in MEDLINE from 1988 through May 2011. Results: An accurate diagnostic process for athletes with posterior thigh–related complaints should include a detailed and discriminative history, followed by a thorough clinical examination. Diagnostic imaging should be utilized when considering hamstring avulsion or ischial apophyseal avulsion. Diagnostic imaging may also be needed to further define the cause of referred posterior thigh pain. Conclusions: Differentiating acute hamstring strains, hamstring tendon avulsions, ischial apophyseal avulsions, proximal hamstring tendinopathies, and referred posterior thigh pain is critical in determining the most appropriate treatment and expediting safe return to play. PMID:23016076

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

PubMed

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

2012-07-06

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

Selection of low-variance expressed Malus x domestica (apple) genes for use as quantitative PCR reference genes (housekeepers)

USDA-ARS?s Scientific Manuscript database

To accurately measure gene expression using PCR-based approaches, there is the need for reference genes that have low variance in expression (housekeeping genes) to normalise the data for RNA quantity and quality. For non-model species such as Malus x domestica (apples), previously, the selection of...

Reference Directions and Reference Objects in Spatial Memory of a Briefly Viewed Layout

ERIC Educational Resources Information Center

Mou, Weimin; Xiao, Chengli; McNamara, Timothy P.

2008-01-01

Two experiments investigated participants' spatial memory of a briefly viewed layout. Participants saw an array of five objects on a table and, after a short delay, indicated whether the target object indicated by the experimenter had been moved. Experiment 1 showed that change detection was more accurate when non-target objects were stationary…

Who's Who? Memory Updating and Character Reference in Children's Narratives

ERIC Educational Resources Information Center

Whitely, Cristy; Colozzo, Paola

2013-01-01

Purpose: The capacity to update and monitor the contents of working memory is an executive function presumed to play a critical role in language processing. The current study used an individual differences approach to consider the relationship between memory updating and accurate reference to story characters in the narratives of typically…

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

PubMed Central

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

2015-01-01

Background: Liver fibrosis staging provides prognostic value, although hampered by observer variability. We used digital analysis to develop diagnostic morphometric scores for significant fibrosis, cirrhosis and fibrosis staging in chronic hepatitis C. Materials and Methods: We automated the measurement of 44 classical and new morphometric descriptors. The reference was histological METAVIR fibrosis (F) staging (F0 to F4) on liver biopsies. The derivation population included 416 patients and liver biopsies ≥20 mm-length. Two validation population included 438 patients. Results: In the derivation population, the area under the receiver operating characteristic (AUROC) for clinically significant fibrosis (F stage ≥2) of a logistic score combining 5 new descriptors (stellar fibrosis area, edge linearity, bridge thickness, bridge number, nodularity) was 0.957. The AUROC for cirrhosis of 6 new descriptors (edge linearity, nodularity, portal stellar fibrosis area, portal distance, granularity, fragmentation) was 0.994. Predicted METAVIR F staging combining 8 morphometric descriptors agreed well with METAVIR F staging by pathologists: κ = 0.868. Morphometric score of clinically significant fibrosis had a higher correlation with porto-septal fibrosis area (rs = 0.835) than METAVIR F staging (rs = 0.756, P < 0.001) and the same correlations with fibrosis biomarkers, e.g., serum hyaluronate: rs = 0.484 versus rs = 0.476 for METAVIR F (P = 0.862). In the validation population, the AUROCs of clinically significant fibrosis and cirrhosis scores were, respectively: 0.893 and 0.993 in 153 patients (biopsy < 20 mm); 0.955 and 0.994 in 285 patients (biopsy ≥ 20 mm). The three morphometric diagnoses agreed with consensus expert reference as well as or better than diagnoses by first-line pathologists in 285 patients, respectively: significant fibrosis: 0.733 versus 0.733 (κ), cirrhosis: 0.900 versus 0.827, METAVIR F: 0.881 versus 0.865. Conclusion: The new automated morphometric scores provide reproducible and accurate diagnoses of fibrosis stages via “virtual expert pathologist.” PMID:26110088

Stability evaluation of reference genes for gene expression analysis by RT-qPCR in soybean under different conditions.

PubMed

Wan, Qiao; Chen, Shuilian; Shan, Zhihui; Yang, Zhonglu; Chen, Limiao; Zhang, Chanjuan; Yuan, Songli; Hao, Qinnan; Zhang, Xiaojuan; Qiu, Dezhen; Chen, Haifeng; Zhou, Xinan

2017-01-01

Real-time quantitative reverse transcription PCR is a sensitive and widely used technique to quantify gene expression. To achieve a reliable result, appropriate reference genes are highly required for normalization of transcripts in different samples. In this study, 9 previously published reference genes (60S, Fbox, ELF1A, ELF1B, ACT11, TUA5, UBC4, G6PD, CYP2) of soybean [Glycine max (L.) Merr.] were selected. The expression stability of the 9 genes was evaluated under conditions of biotic stress caused by infection with soybean mosaic virus, nitrogen stress, across different cultivars and developmental stages. ΔCt and geNorm algorithms were used to evaluate and rank the expression stability of the 9 reference genes. Results obtained from two algorithms showed high consistency. Moreover, results of pairwise variation showed that two reference genes were sufficient to normalize the expression levels of target genes under each experimental setting. For virus infection, ELF1A and ELF1B were the most stable reference genes for accurate normalization. For different developmental stages, Fbox and G6PD had the highest expression stability between two soybean cultivars (Tanlong No. 1 and Tanlong No. 2). ELF1B and ACT11 were identified as the most stably expressed reference genes both under nitrogen stress and among different cultivars. The results showed that none of the candidate reference genes were uniformly expressed at different conditions, and selecting appropriate reference genes was pivotal for gene expression studies with particular condition and tissue. The most stable combination of genes identified in this study will help to achieve more accurate and reliable results in a wide variety of samples in soybean.

Reference Genes for Accurate Transcript Normalization in Citrus Genotypes under Different Experimental Conditions

PubMed Central

Mafra, Valéria; Kubo, Karen S.; Alves-Ferreira, Marcio; Ribeiro-Alves, Marcelo; Stuart, Rodrigo M.; Boava, Leonardo P.; Rodrigues, Carolina M.; Machado, Marcos A.

2012-01-01

Real-time reverse transcription PCR (RT-qPCR) has emerged as an accurate and widely used technique for expression profiling of selected genes. However, obtaining reliable measurements depends on the selection of appropriate reference genes for gene expression normalization. The aim of this work was to assess the expression stability of 15 candidate genes to determine which set of reference genes is best suited for transcript normalization in citrus in different tissues and organs and leaves challenged with five pathogens (Alternaria alternata, Phytophthora parasitica, Xylella fastidiosa and Candidatus Liberibacter asiaticus). We tested traditional genes used for transcript normalization in citrus and orthologs of Arabidopsis thaliana genes described as superior reference genes based on transcriptome data. geNorm and NormFinder algorithms were used to find the best reference genes to normalize all samples and conditions tested. Additionally, each biotic stress was individually analyzed by geNorm. In general, FBOX (encoding a member of the F-box family) and GAPC2 (GAPDH) was the most stable candidate gene set assessed under the different conditions and subsets tested, while CYP (cyclophilin), TUB (tubulin) and CtP (cathepsin) were the least stably expressed genes found. Validation of the best suitable reference genes for normalizing the expression level of the WRKY70 transcription factor in leaves infected with Candidatus Liberibacter asiaticus showed that arbitrary use of reference genes without previous testing could lead to misinterpretation of data. Our results revealed FBOX, SAND (a SAND family protein), GAPC2 and UPL7 (ubiquitin protein ligase 7) to be superior reference genes, and we recommend their use in studies of gene expression in citrus species and relatives. This work constitutes the first systematic analysis for the selection of superior reference genes for transcript normalization in different citrus organs and under biotic stress. PMID:22347455

Bacterial reference genes for gene expression studies by RT-qPCR: survey and analysis.

PubMed

Rocha, Danilo J P; Santos, Carolina S; Pacheco, Luis G C

2015-09-01

The appropriate choice of reference genes is essential for accurate normalization of gene expression data obtained by the method of reverse transcription quantitative real-time PCR (RT-qPCR). In 2009, a guideline called the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) highlighted the importance of the selection and validation of more than one suitable reference gene for obtaining reliable RT-qPCR results. Herein, we searched the recent literature in order to identify the bacterial reference genes that have been most commonly validated in gene expression studies by RT-qPCR (in the first 5 years following publication of the MIQE guidelines). Through a combination of different search parameters with the text mining tool MedlineRanker, we identified 145 unique bacterial genes that were recently tested as candidate reference genes. Of these, 45 genes were experimentally validated and, in most of the cases, their expression stabilities were verified using the software tools geNorm and NormFinder. It is noteworthy that only 10 of these reference genes had been validated in two or more of the studies evaluated. An enrichment analysis using Gene Ontology classifications demonstrated that genes belonging to the functional categories of DNA Replication (GO: 0006260) and Transcription (GO: 0006351) rendered a proportionally higher number of validated reference genes. Three genes in the former functional class were also among the top five most stable genes identified through an analysis of gene expression data obtained from the Pathosystems Resource Integration Center. These results may provide a guideline for the initial selection of candidate reference genes for RT-qPCR studies in several different bacterial species.

Evaluation and Validation of Reference Genes for qRT-PCR Normalization in Frankliniella occidentalis (Thysanoptera:Thripidae)

PubMed Central

Zheng, Yu-Tao; Li, Hong-Bo; Lu, Ming-Xing; Du, Yu-Zhou

2014-01-01

Quantitative real time PCR (qRT-PCR) has emerged as a reliable and reproducible technique for studying gene expression analysis. For accurate results, the normalization of data with reference genes is particularly essential. Once the transcriptome sequencing of Frankliniella occidentalis was completed, numerous unigenes were identified and annotated. Unfortunately, there are no studies on the stability of reference genes used in F. occidentalis. In this work, seven candidate reference genes, including actin, 18S rRNA, H3, tubulin, GAPDH, EF-1 and RPL32, were evaluated for their suitability as normalization genes under different experimental conditions using the statistical software programs BestKeeper, geNorm, Normfinder and the comparative ΔCt method. Because the rankings of the reference genes provided by each of the four programs were different, we chose a user-friendly web-based comprehensive tool RefFinder to get the final ranking. The result demonstrated that EF-1 and RPL32 displayed the most stable expression in different developmental stages; RPL32 and GAPDH showed the most stable expression at high temperatures, while 18S and EF-1 exhibited the most stable expression at low temperatures. In this study, we validated the suitable reference genes in F. occidentalis for gene expression profiling under different experimental conditions. The choice of internal standard is very important in the normalization of the target gene expression levels, thus validating and selecting the best genes will help improve the quality of gene expression data of F. occidentalis. What is more, these validated reference genes could serve as the basis for the selection of candidate reference genes in other insects. PMID:25356721

Evaluation and validation of reference genes for qRT-PCR normalization in Frankliniella occidentalis (Thysanoptera: Thripidae).

PubMed

Zheng, Yu-Tao; Li, Hong-Bo; Lu, Ming-Xing; Du, Yu-Zhou

2014-01-01

Quantitative real time PCR (qRT-PCR) has emerged as a reliable and reproducible technique for studying gene expression analysis. For accurate results, the normalization of data with reference genes is particularly essential. Once the transcriptome sequencing of Frankliniella occidentalis was completed, numerous unigenes were identified and annotated. Unfortunately, there are no studies on the stability of reference genes used in F. occidentalis. In this work, seven candidate reference genes, including actin, 18S rRNA, H3, tubulin, GAPDH, EF-1 and RPL32, were evaluated for their suitability as normalization genes under different experimental conditions using the statistical software programs BestKeeper, geNorm, Normfinder and the comparative ΔCt method. Because the rankings of the reference genes provided by each of the four programs were different, we chose a user-friendly web-based comprehensive tool RefFinder to get the final ranking. The result demonstrated that EF-1 and RPL32 displayed the most stable expression in different developmental stages; RPL32 and GAPDH showed the most stable expression at high temperatures, while 18S and EF-1 exhibited the most stable expression at low temperatures. In this study, we validated the suitable reference genes in F. occidentalis for gene expression profiling under different experimental conditions. The choice of internal standard is very important in the normalization of the target gene expression levels, thus validating and selecting the best genes will help improve the quality of gene expression data of F. occidentalis. What is more, these validated reference genes could serve as the basis for the selection of candidate reference genes in other insects.

Selection of Reliable Reference Genes for Gene Expression Studies on Rhododendron molle G. Don.

PubMed

Xiao, Zheng; Sun, Xiaobo; Liu, Xiaoqing; Li, Chang; He, Lisi; Chen, Shangping; Su, Jiale

2016-01-01

The quantitative real-time polymerase chain reaction (qRT-PCR) approach has become a widely used method to analyze expression patterns of target genes. The selection of an optimal reference gene is a prerequisite for the accurate normalization of gene expression in qRT-PCR. The present study constitutes the first systematic evaluation of potential reference genes in Rhododendron molle G. Don. Eleven candidate reference genes in different tissues and flowers at different developmental stages of R. molle were assessed using the following three software packages: GeNorm, NormFinder, and BestKeeper. The results showed that EF1- α (elongation factor 1-alpha), 18S (18s ribosomal RNA), and RPL3 (ribosomal protein L3) were the most stable reference genes in developing rhododendron flowers and, thus, in all of the tested samples, while tublin ( TUB ) was the least stable. ACT5 (actin), RPL3 , 18S , and EF1- α were found to be the top four choices for different tissues, whereas TUB was not found to favor qRT-PCR normalization in these tissues. Three stable reference genes are recommended for the normalization of qRT-PCR data in R. molle . Furthermore, the expression profiles of RmPSY (phytoene synthase) and RmPDS (phytoene dehydrogenase) were assessed using EF1- α, 18S , ACT5 , RPL3 , and their combination as internals. Similar trends were found, but these trends varied when the least stable reference gene TUB was used. The results further prove that it is necessary to validate the stability of reference genes prior to their use for normalization under different experimental conditions. This study provides useful information for reliable qRT-PCR data normalization in gene studies of R. molle .

A Novel Time-Varying Spectral Filtering Algorithm for Reconstruction of Motion Artifact Corrupted Heart Rate Signals During Intense Physical Activities Using a Wearable Photoplethysmogram Sensor

PubMed Central

Salehizadeh, Seyed M. A.; Dao, Duy; Bolkhovsky, Jeffrey; Cho, Chae; Mendelson, Yitzhak; Chon, Ki H.

2015-01-01

Accurate estimation of heart rates from photoplethysmogram (PPG) signals during intense physical activity is a very challenging problem. This is because strenuous and high intensity exercise can result in severe motion artifacts in PPG signals, making accurate heart rate (HR) estimation difficult. In this study we investigated a novel technique to accurately reconstruct motion-corrupted PPG signals and HR based on time-varying spectral analysis. The algorithm is called Spectral filter algorithm for Motion Artifacts and heart rate reconstruction (SpaMA). The idea is to calculate the power spectral density of both PPG and accelerometer signals for each time shift of a windowed data segment. By comparing time-varying spectra of PPG and accelerometer data, those frequency peaks resulting from motion artifacts can be distinguished from the PPG spectrum. The SpaMA approach was applied to three different datasets and four types of activities: (1) training datasets from the 2015 IEEE Signal Process. Cup Database recorded from 12 subjects while performing treadmill exercise from 1 km/h to 15 km/h; (2) test datasets from the 2015 IEEE Signal Process. Cup Database recorded from 11 subjects while performing forearm and upper arm exercise. (3) Chon Lab dataset including 10 min recordings from 10 subjects during treadmill exercise. The ECG signals from all three datasets provided the reference HRs which were used to determine the accuracy of our SpaMA algorithm. The performance of the SpaMA approach was calculated by computing the mean absolute error between the estimated HR from the PPG and the reference HR from the ECG. The average estimation errors using our method on the first, second and third datasets are 0.89, 1.93 and 1.38 beats/min respectively, while the overall error on all 33 subjects is 1.86 beats/min and the performance on only treadmill experiment datasets (22 subjects) is 1.11 beats/min. Moreover, it was found that dynamics of heart rate variability can be accurately captured using the algorithm where the mean Pearson’s correlation coefficient between the power spectral densities of the reference and the reconstructed heart rate time series was found to be 0.98. These results show that the SpaMA method has a potential for PPG-based HR monitoring in wearable devices for fitness tracking and health monitoring during intense physical activities. PMID:26703618

When species matches are unavailable are DNA barcodes correctly assigned to higher taxa? An assessment using sphingid moths

PubMed Central

2011-01-01

Background When a specimen belongs to a species not yet represented in DNA barcode reference libraries there is disagreement over the effectiveness of using sequence comparisons to assign the query accurately to a higher taxon. Library completeness and the assignment criteria used have been proposed as critical factors affecting the accuracy of such assignments but have not been thoroughly investigated. We explored the accuracy of assignments to genus, tribe and subfamily in the Sphingidae, using the almost complete global DNA barcode reference library (1095 species) available for this family. Costa Rican sphingids (118 species), a well-documented, diverse subset of the family, with each of the tribes and subfamilies represented were used as queries. We simulated libraries with different levels of completeness (10-100% of the available species), and recorded assignments (positive or ambiguous) and their accuracy (true or false) under six criteria. Results A liberal tree-based criterion assigned 83% of queries accurately to genus, 74% to tribe and 90% to subfamily, compared to a strict tree-based criterion, which assigned 75% of queries accurately to genus, 66% to tribe and 84% to subfamily, with a library containing 100% of available species (but excluding the species of the query). The greater number of true positives delivered by more relaxed criteria was negatively balanced by the occurrence of more false positives. This effect was most sharply observed with libraries of the lowest completeness where, for example at the genus level, 32% of assignments were false positives with the liberal criterion versus < 1% when using the strict. We observed little difference (< 8% using the liberal criterion) however, in the overall accuracy of the assignments between the lowest and highest levels of library completeness at the tribe and subfamily level. Conclusions Our results suggest that when using a strict tree-based criterion for higher taxon assignment with DNA barcodes, the likelihood of assigning a query a genus name incorrectly is very low, if a genus name is provided it has a high likelihood of being accurate, and if no genus match is available the query can nevertheless be assigned to a subfamily with high accuracy regardless of library completeness. DNA barcoding often correctly assigned sphingid moths to higher taxa when species matches were unavailable, suggesting that barcode reference libraries can be useful for higher taxon assignments long before they achieve complete species coverage. PMID:21806794

A Novel Time-Varying Spectral Filtering Algorithm for Reconstruction of Motion Artifact Corrupted Heart Rate Signals During Intense Physical Activities Using a Wearable Photoplethysmogram Sensor.

PubMed

Salehizadeh, Seyed M A; Dao, Duy; Bolkhovsky, Jeffrey; Cho, Chae; Mendelson, Yitzhak; Chon, Ki H

2015-12-23

Accurate estimation of heart rates from photoplethysmogram (PPG) signals during intense physical activity is a very challenging problem. This is because strenuous and high intensity exercise can result in severe motion artifacts in PPG signals, making accurate heart rate (HR) estimation difficult. In this study we investigated a novel technique to accurately reconstruct motion-corrupted PPG signals and HR based on time-varying spectral analysis. The algorithm is called Spectral filter algorithm for Motion Artifacts and heart rate reconstruction (SpaMA). The idea is to calculate the power spectral density of both PPG and accelerometer signals for each time shift of a windowed data segment. By comparing time-varying spectra of PPG and accelerometer data, those frequency peaks resulting from motion artifacts can be distinguished from the PPG spectrum. The SpaMA approach was applied to three different datasets and four types of activities: (1) training datasets from the 2015 IEEE Signal Process. Cup Database recorded from 12 subjects while performing treadmill exercise from 1 km/h to 15 km/h; (2) test datasets from the 2015 IEEE Signal Process. Cup Database recorded from 11 subjects while performing forearm and upper arm exercise. (3) Chon Lab dataset including 10 min recordings from 10 subjects during treadmill exercise. The ECG signals from all three datasets provided the reference HRs which were used to determine the accuracy of our SpaMA algorithm. The performance of the SpaMA approach was calculated by computing the mean absolute error between the estimated HR from the PPG and the reference HR from the ECG. The average estimation errors using our method on the first, second and third datasets are 0.89, 1.93 and 1.38 beats/min respectively, while the overall error on all 33 subjects is 1.86 beats/min and the performance on only treadmill experiment datasets (22 subjects) is 1.11 beats/min. Moreover, it was found that dynamics of heart rate variability can be accurately captured using the algorithm where the mean Pearson's correlation coefficient between the power spectral densities of the reference and the reconstructed heart rate time series was found to be 0.98. These results show that the SpaMA method has a potential for PPG-based HR monitoring in wearable devices for fitness tracking and health monitoring during intense physical activities.

Unstable Expression of Commonly Used Reference Genes in Rat Pancreatic Islets Early after Isolation Affects Results of Gene Expression Studies.

PubMed

Kosinová, Lucie; Cahová, Monika; Fábryová, Eva; Týcová, Irena; Koblas, Tomáš; Leontovyč, Ivan; Saudek, František; Kříž, Jan

2016-01-01

The use of RT-qPCR provides a powerful tool for gene expression studies; however, the proper interpretation of the obtained data is crucially dependent on accurate normalization based on stable reference genes. Recently, strong evidence has been shown indicating that the expression of many commonly used reference genes may vary significantly due to diverse experimental conditions. The isolation of pancreatic islets is a complicated procedure which creates severe mechanical and metabolic stress leading possibly to cellular damage and alteration of gene expression. Despite of this, freshly isolated islets frequently serve as a control in various gene expression and intervention studies. The aim of our study was to determine expression of 16 candidate reference genes and one gene of interest (F3) in isolated rat pancreatic islets during short-term cultivation in order to find a suitable endogenous control for gene expression studies. We compared the expression stability of the most commonly used reference genes and evaluated the reliability of relative and absolute quantification using RT-qPCR during 0-120 hrs after isolation. In freshly isolated islets, the expression of all tested genes was markedly depressed and it increased several times throughout the first 48 hrs of cultivation. We observed significant variability among samples at 0 and 24 hrs but substantial stabilization from 48 hrs onwards. During the first 48 hrs, relative quantification failed to reflect the real changes in respective mRNA concentrations while in the interval 48-120 hrs, the relative expression generally paralleled the results determined by absolute quantification. Thus, our data call into question the suitability of relative quantification for gene expression analysis in pancreatic islets during the first 48 hrs of cultivation, as the results may be significantly affected by unstable expression of reference genes. However, this method could provide reliable information from 48 hrs onwards.

Reference Standards for Cardiorespiratory Fitness Measured With Cardiopulmonary Exercise Testing Using Cycle Ergometry: Data From the Fitness Registry and the Importance of Exercise National Database (FRIEND) Registry.

PubMed

Kaminsky, Leonard A; Imboden, Mary T; Arena, Ross; Myers, Jonathan

2017-02-01

The importance of cardiorespiratory fitness (CRF) is well established. This report provides newly developed standards for CRF reference values derived from cardiopulmonary exercise testing (CPX) using cycle ergometry in the United States. Ten laboratories in the United States experienced in CPX administration with established quality control procedures contributed to the "Fitness Registry and the Importance of Exercise: A National Database" (FRIEND) Registry from April 2014 through May 2016. Data from 4494 maximal (respiratory exchange ratio, ≥1.1) cycle ergometer tests from men and women (20-79 years) from 27 states, without cardiovascular disease, were used to develop these references values. Percentiles of maximum oxygen consumption (VO 2max ) for men and women were determined for each decade from age 20 years through age 79 years. Comparisons of VO 2max were made to reference data established with CPX data from treadmill data in the FRIEND Registry and previously published reports. As expected, there were significant differences between sex and age groups for VO 2max (P<.01). For cycle tests within the FRIEND Registry, the 50th percentile VO 2max of men and women aged 20 to 29 years declined from 41.9 and 31.0 mLO 2 /kg/min to 19.5 and 14.8 mLO 2 /kg/min for ages 70 to 79 years, respectively. The rate of decline in this cohort was approximately 10% per decade. The FRIEND Registry reference data will be useful in providing more accurate interpretations for the US population of CPX-measured VO 2max from exercise tests using cycle ergometry compared with previous approaches based on estimations of standard differences from treadmill testing reference values. Copyright © 2016 Mayo Foundation for Medical Education and Research. All rights reserved.

Dental computed tomographic imaging as age estimation: morphological analysis of the third molar of a group of Turkish population.

PubMed

Cantekin, Kenan; Sekerci, Ahmet Ercan; Buyuk, Suleyman Kutalmis

2013-12-01

Computed tomography (CT) is capable of providing accurate and measurable 3-dimensional images of the third molar. The aims of this study were to analyze the development of the mandibular third molar and its relation to chronological age and to create new reference data for a group of Turkish participants aged 9 to 25 years on the basis of cone-beam CT images. All data were obtained from the patients' records including medical, social, and dental anamnesis and cone-beam CT images of 752 patients. Linear regression analysis was performed to obtain regression formulas for dental age calculation with chronological age and to determine the coefficient of determination (r) for each sex. Statistical analysis showed a strong correlation between age and third-molar development for the males (r2 = 0.80) and the females (r2 = 0.78). Computed tomographic images are clinically useful for accurate and reliable estimation of dental ages of children and youth.

Swarm Deployable Boom Assembly (DBA) Development of a Deployable Magnetometer Boom for the Swarm Spacecraft

NASA Astrophysics Data System (ADS)

McMahon, Paul; Jung, Hans-Juergen; Edwards, Jeff

2013-09-01

The Swarm programme consists of 3 magnetically clean satellites flying in close formation designed to measure the Earth's magnetic field using 2 Magnetometers mounted on a 4.3m long deployable boom.Deployment is initiated by releasing 3 HDRMs, once released the boom oscillates back and forth on a pair of pivots, similar to a restaurant kitchen door hinge, for around 120 seconds before coming to rest on 3 kinematic mounts which are used to provide an accurate reference location in the deployed position. Motion of the boom is damped through a combination of friction, spring hysteresis and flexing of the 120+ cables crossing the hinge. Considerable development work and accurate numerical modelling of the hinge motion was required to predict performance across a wide temperature range and ensure that during the 1st overshoot the boom did not damage itself, the harness or the spacecraft.Due to the magnetic cleanliness requirements of the spacecraft no magnetic materials could be used in the design of the hardware.

Prediction of intramuscular fat levels in Texel lamb loins using X-ray computed tomography scanning.

PubMed

Clelland, N; Bunger, L; McLean, K A; Conington, J; Maltin, C; Knott, S; Lambe, N R

2014-10-01

For the consumer, tenderness, juiciness and flavour are often described as the most important factors for meat eating quality, all of which have a close association with intramuscular fat (IMF). X-ray computed tomography (CT) can measure fat, muscle and bone volumes and weights, in vivo in sheep and CT predictions of carcass composition have been used in UK sheep breeding programmes over the last few decades. This study aimed to determine the most accurate combination of CT variables to predict IMF percentage of M. longissimus lumborum in Texel lambs. As expected, predicted carcass fat alone accounted for a moderate amount of the variation (R(2)=0.51) in IMF. Prediction accuracies were significantly improved (Adj R(2)>0.65) using information on fat and muscle densities measured from three CT reference scans, showing that CT can provide an accurate prediction of IMF in the loin of purebred Texel sheep. Copyright © 2014. Published by Elsevier Ltd.

Reference level winds from balloon platforms

NASA Technical Reports Server (NTRS)

Lally, Vincent E.

1985-01-01

The superpressure balloon was developed to provide a method of obtaining global winds at all altitudes from 5 to 30 km. If a balloon could be made to fly for several weeks at a constant altitude, and if it could be tracked accurately on its global circuits, the balloon would provide a tag for the air parcel in which it was embedded. The Lagrangian data on the atmospheric circulation would provide a superior data input to the numerical model. The Global Atmospheric Research Program (GARP) was initiated in large part based on the promise of this technique coupled with free-floating ocean buoys and satellite radiometers. The initial name proposed by Charney for GARP was SABABURA 'SAtellite BAlloon BUoy RAdiometric system' (Charney, 1966). However, although the superpressure balloon exceeded its designers' expectations for flight duration in the stratosphere (longest flight duration of 744 days), flight duration below 10 km was limited by icing in super-cooled clouds to a few days. The balloon was relegated to a secondary role during the GARP Special Observing Periods. The several major superpressure balloon programs for global wind measurement are described as well as those new developments which make the balloon once again an attractive vehicle for measurement of global winds as a reference and bench-mark system for future satellite systems.

Evaluating the provenance of Permian-Triassic and Palaeocene-Eocene ash beds by high precision U-Pb and Lu-Hf isotopic analyses of zircons: linking local sedimentary records to global events

NASA Astrophysics Data System (ADS)

Eivind Augland, Lars; Jones, Morgan; Planke, Sverre; Svensen, Henrik; Tegner, Christian

2016-04-01

Zircons are a powerful tool in geochronology and isotope geochemistry, as their affinity for U and Hf in the crystal structure and the low initial Pb and Lu allow for precise and accurate dating by U-Pb ID-TIMS and precise and accurate determination of initial Hf isotopic composition by solution MC-ICP-MS analysis. The U-Pb analyses provide accurate chronostratigraphic controls on the sedimentary successions and absolute age frames for the biotic evolution across geological boundaries. Moreover, the analyses of Lu-Hf by solution MC-ICP-MS after Hf-purification column chemistry provide a powerful and robust fingerprinting tool to test the provenance of individual ash beds. Here we focus on ash beds from Permian-Triassic and Palaeocene successions in Svalbard and from the Palaeocene-Eocene Thermal Maximum (PETM) in Fur, Denmark. Used in combination with whole rock geochemistry from the ash layers and the available geochemical and isotopic data from potential source volcanoes, these data are used to evaluate the provenance of the Permian-Triassic and Palaeocene ashes preserved in Svalbard and PETM ashes in Denmark. If explosive eruptions from volcanic centres such as the Siberian Traps and the North Atlantic Igneous Province (NAIP) can be traced to distal basins as ash layers, they provide robust tests of hypotheses of global synchronicity of environmental changes and biotic crises. In addition, the potential correlation of ash layers with source volcanoes will aid in constraining the extent of explosive volcanism in the respective volcanic centres. The new integrated data sets will also contribute to establish new reference sections for the study of these boundary events when combined with stable isotope data and biostratigraphy.

Revealing the missing expressed genes beyond the human reference genome by RNA-Seq.

PubMed

Chen, Geng; Li, Ruiyuan; Shi, Leming; Qi, Junyi; Hu, Pengzhan; Luo, Jian; Liu, Mingyao; Shi, Tieliu

2011-12-02

The complete and accurate human reference genome is important for functional genomics researches. Therefore, the incomplete reference genome and individual specific sequences have significant effects on various studies. we used two RNA-Seq datasets from human brain tissues and 10 mixed cell lines to investigate the completeness of human reference genome. First, we demonstrated that in previously identified ~5 Mb Asian and ~5 Mb African novel sequences that are absent from the human reference genome of NCBI build 36, ~211 kb and ~201 kb of them could be transcribed, respectively. Our results suggest that many of those transcribed regions are not specific to Asian and African, but also present in Caucasian. Then, we found that the expressions of 104 RefSeq genes that are unalignable to NCBI build 37 in brain and cell lines are higher than 0.1 RPKM. 55 of them are conserved across human, chimpanzee and macaque, suggesting that there are still a significant number of functional human genes absent from the human reference genome. Moreover, we identified hundreds of novel transcript contigs that cannot be aligned to NCBI build 37, RefSeq genes and EST sequences. Some of those novel transcript contigs are also conserved among human, chimpanzee and macaque. By positioning those contigs onto the human genome, we identified several large deletions in the reference genome. Several conserved novel transcript contigs were further validated by RT-PCR. Our findings demonstrate that a significant number of genes are still absent from the incomplete human reference genome, highlighting the importance of further refining the human reference genome and curating those missing genes. Our study also shows the importance of de novo transcriptome assembly. The comparative approach between reference genome and other related human genomes based on the transcriptome provides an alternative way to refine the human reference genome.

Hearing the Sound in the Brain: Influences of Different EEG References.

PubMed

Wu, Dan

2018-01-01

If the scalp potential signals, the electroencephalogram (EEG), are due to neural "singers" in the brain, how could we listen to them with less distortion? One crucial point is that the data recording on the scalp should be faithful and accurate, thus the choice of reference electrode is a vital factor determining the faithfulness of the data. In this study, music on the scalp derived from data in the brain using three different reference electrodes were compared, including approximate zero reference-reference electrode standardization technique (REST), average reference (AR), and linked mastoids reference (LM). The classic music pieces in waveform format were used as simulated sources inside a head model, and they were forward calculated to scalp as standard potential recordings, i.e., waveform format music from the brain with true zero reference. Then these scalp music was re-referenced into REST, AR, and LM based data, and compared with the original forward data (true zero reference). For real data, the EEG recorded in an orthodontic pain control experiment were utilized for music generation with the three references, and the scale free index (SFI) of these music pieces were compared. The results showed that in the simulation for only one source, different references do not change the music/waveform; for two sources or more, REST provide the most faithful music/waveform to the original ones inside the brain, and the distortions caused by AR and LM were spatial locations of both source and scalp electrode dependent. The brainwave music from the real EEG data showed that REST and AR make the differences of SFI between two states more recognized and found the frontal is the main region that producing the music. In conclusion, REST can reconstruct the true signals approximately, and it can be used to help to listen to the true voice of the neural singers in the brain.

Characterization of iris pattern stretches and application to the measurement of roll axis eye movements.

PubMed

Nishiyama, Junpei; Hashimoto, Tsutomu; Sakashita, Yusuke; Fujiyoshi, Hironobu; Hirata, Yutaka

2008-01-01

Eye movements are utilized in many scientific studies as a probe that reflects the neural representation of 3 dimensional extrapersonal space. This study proposes a method to accurately measure the roll component of eye movements under the conditions in which the pupil diameter changes. Generally, the iris pattern matching between a reference and a test iris image is performed to estimate roll angle of the test image. However, iris patterns are subject to change when the pupil size changes, thus resulting in less accurate roll angle estimation if the pupil sizes in the test and reference images are different. We characterized non-uniform iris pattern contraction/expansion caused by pupil dilation/constriction, and developed an algorithm to convert an iris pattern with an arbitrary pupil size into that with the same pupil size as the reference iris pattern. It was demonstrated that the proposed method improved the accuracy of the measurement of roll eye movement by up to 76.9%.

IDLN-MSP: Idiolocal normalization of real-time methylation-specific PCR for genetic imbalanced DNA specimens.

PubMed

Santourlidis, Simeon; Ghanjati, Foued; Beermann, Agnes; Hermanns, Thomas; Poyet, Cédric

2016-02-01

Sensitive, accurate, and reliable measurements of tumor cell-specific DNA methylation changes are of fundamental importance in cancer diagnosis, prognosis, and monitoring. Real-time methylation-specific PCR (MSP) using intercalating dyes is an established method of choice for this purpose. Here we present a simple but crucial adaptation of this widely applied method that overcomes a major obstacle: genetic abnormalities in the DNA samples, such as aneuploidy or copy number variations, that could result in inaccurate results due to improper normalization if the copy numbers of the target and reference sequences are not the same. In our idiolocal normalization (IDLN) method, the locus for the normalizing, methylation-independent reference amplification is chosen close to the locus of the methylation-dependent target amplification. This ensures that the copy numbers of both the target and reference sequences will be identical in most cases if they are close enough to each other, resulting in accurate normalization and reliable comparative measurements of DNA methylation in clinical samples when using real-time MSP.

A wavelet approach to binary blackholes with asynchronous multitasking

NASA Astrophysics Data System (ADS)

Lim, Hyun; Hirschmann, Eric; Neilsen, David; Anderson, Matthew; Debuhr, Jackson; Zhang, Bo

2016-03-01

Highly accurate simulations of binary black holes and neutron stars are needed to address a variety of interesting problems in relativistic astrophysics. We present a new method for the solving the Einstein equations (BSSN formulation) using iterated interpolating wavelets. Wavelet coefficients provide a direct measure of the local approximation error for the solution and place collocation points that naturally adapt to features of the solution. Further, they exhibit exponential convergence on unevenly spaced collection points. The parallel implementation of the wavelet simulation framework presented here deviates from conventional practice in combining multi-threading with a form of message-driven computation sometimes referred to as asynchronous multitasking.

Calibration of an arbitrarily arranged projection moiré system for 3D shape measurement

NASA Astrophysics Data System (ADS)

Tang, Ying; Yao, Jun; Zhou, Yihao; Sun, Chen; Yang, Peng; Miao, Hong; Chen, Jubing

2018-05-01

An arbitrarily arranged projection moiré system is presented for three-dimensional shape measurement. We develop a model for projection moiré system and derive a universal formula expressing the relation between height and phase variation before and after we put the object on the reference plane. With so many system parameters involved, a system calibration technique is needed. In this work, we provide a robust and accurate calibration method for an arbitrarily arranged projection moiré system. The system no longer puts restrictions on the configuration of the optical setup. Real experiments have been conducted to verify the validity of this method.

High-resolution interferometic microscope for traceable dimensional nanometrology in Brazil

NASA Astrophysics Data System (ADS)

Malinovski, I.; França, R. S.; Lima, M. S.; Bessa, M. S.; Silva, C. R.; Couceiro, I. B.

2016-07-01

The double color interferometric microscope is developed for step height standards nanometrology traceable to meter definition via primary wavelength laser standards. The setup is based on two stabilized lasers to provide traceable measurements of highest possible resolution down to the physical limits of the optical instruments in sub-nanometer to micrometer range of the heights. The wavelength reference is He-Ne 633 nm stabilized laser, the secondary source is Blue-Green 488 nm grating laser diode. Accurate fringe portion is measured by modulated phase-shift technique combined with imaging interferometry and Fourier processing. Self calibrating methods are developed to correct systematic interferometric errors.

Differential identification of Candida species and other yeasts by analysis of (/sup 35/S)methionine-labeled polypeptide profiles

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

Shen, H.D.; Choo, K.B.; Tsai, W.C.

1988-12-01

This paper describes a scheme for differential identification of Candida species and other yeasts based on autoradiographic analysis of protein profiles of (/sup 35/S)methionine-labeled cellular proteins separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Using ATCC strains as references, protein profile analysis showed that different Candida and other yeast species produced distinctively different patterns. Good agreement in results obtained with this approach and with other conventional systems was observed. Being accurate and reproducible, this approach provides a basis for the development of an alternative method for the identification of yeasts isolated from clinical specimens.

Operation Greenhouse. Scientific Director's report of atomic-weapon tests at Eniwetok, 1951. Annex 1. 11. Timing and firing and fiducial markers

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

Grier, H.E.

1985-09-01

An automatic remote-control system armed and fired the bomb and sent out a sequence of time signals to experimental equipment on the atoll. A central station at Parry Island sent signals via submarine cables to a timer station on a shot island. The timer station controlled signals to the zero station and to experiments on the island, and through auxiliary stations, it also controlled signal distribution on adjacent islands. Light-sensitive triggering units for apparatus and for accurate standard zero-time reference were provided in the form of Blue Boxes, or fiducial markers.

Discussion on Comprehensive Utilization Value of Scutellaria Baicalensis Flower

NASA Astrophysics Data System (ADS)

Song, Yagang; Miao, Mingsan

2018-01-01

The chemical constituents of Scutellaria baicalensis flower are flavonoids, volatile oils and melanin, It has anti-tumor, anti-inflammatory, antioxidant, anti angiogenic and antithrombotic pharmacological effects, and it has the effect of clearing away heat and relieving lung fire. Scutellaria baicalensis flower is rich in resources, cheap, easy to obtain, accurate effect, With the prevention and treatment of a variety of diseases. In this paper, the ancient application, chemical constituents, pharmacological actions and comprehensive utilization of Scutellaria baicalensis flower were reviewed, The purpose of this study was to explore the value of its development and utilization, so as to provide reference for the comprehensive utilization of Scutellaria baicalensis flower.

Accurate Determination of the Dynamical Polarizability of Dysprosium

NASA Astrophysics Data System (ADS)

Ravensbergen, C.; Corre, V.; Soave, E.; Kreyer, M.; Tzanova, S.; Kirilov, E.; Grimm, R.

2018-06-01

We report a measurement of the dynamical polarizability of dysprosium atoms in their electronic ground state at the optical wavelength of 1064 nm, which is of particular interest for laser trapping experiments. Our method is based on collective oscillations in an optical dipole trap, and reaches unprecedented accuracy and precision by comparison with an alkali atom (potassium) as a reference species. We obtain values of 184.4(2.4) and 1.7(6) a.u. for the scalar and tensor polarizability, respectively. Our experiments have reached a level that permits meaningful tests of current theoretical descriptions and provides valuable information for future experiments utilizing the intriguing properties of heavy lanthanide atoms.

Biomimetic Cross-Reactive Sensor Arrays: Prospects in Biodiagnostics

PubMed Central

Fitzgerald, J. E.

2016-01-01

Biomimetic cross-reactive sensor arrays have been used to detect and analyze a wide variety of vapour and liquid components in applications such as food science, public health and safety, and diagnostics. As technology has advanced over the past three decades, these systems have become selective, sensitive, and affordable. Currently, the need for non-invasive and accurate devices for early disease diagnosis remains a challenge. This review provides an overview of the various types of Biomimetic cross-reactive sensor arrays (also referred to as electronic noses and tongues in the literature), their current use and future directions, and an outlook for future technological development. PMID:28217300

Microfabricated fuel heating value monitoring device

DOEpatents

Robinson, Alex L [Albuquerque, NM; Manginell, Ronald P [Albuquerque, NM; Moorman, Matthew W [Albuquerque, NM

2010-05-04

A microfabricated fuel heating value monitoring device comprises a microfabricated gas chromatography column in combination with a catalytic microcalorimeter. The microcalorimeter can comprise a reference thermal conductivity sensor to provide diagnostics and surety. Using microfabrication techniques, the device can be manufactured in production quantities at a low per-unit cost. The microfabricated fuel heating value monitoring device enables continuous calorimetric determination of the heating value of natural gas with a 1 minute analysis time and 1.5 minute cycle time using air as a carrier gas. This device has applications in remote natural gas mining stations, pipeline switching and metering stations, turbine generators, and other industrial user sites. For gas pipelines, the device can improve gas quality during transfer and blending, and provide accurate financial accounting. For industrial end users, the device can provide continuous feedback of physical gas properties to improve combustion efficiency during use.

Fast and accurate reference-free alignment of subtomograms.

PubMed

Chen, Yuxiang; Pfeffer, Stefan; Hrabe, Thomas; Schuller, Jan Michael; Förster, Friedrich

2013-06-01

In cryoelectron tomography alignment and averaging of subtomograms, each dnepicting the same macromolecule, improves the resolution compared to the individual subtomogram. Major challenges of subtomogram alignment are noise enhancement due to overfitting, the bias of an initial reference in the iterative alignment process, and the computational cost of processing increasingly large amounts of data. Here, we propose an efficient and accurate alignment algorithm via a generalized convolution theorem, which allows computation of a constrained correlation function using spherical harmonics. This formulation increases computational speed of rotational matching dramatically compared to rotation search in Cartesian space without sacrificing accuracy in contrast to other spherical harmonic based approaches. Using this sampling method, a reference-free alignment procedure is proposed to tackle reference bias and overfitting, which also includes contrast transfer function correction by Wiener filtering. Application of the method to simulated data allowed us to obtain resolutions near the ground truth. For two experimental datasets, ribosomes from yeast lysate and purified 20S proteasomes, we achieved reconstructions of approximately 20Å and 16Å, respectively. The software is ready-to-use and made public to the community. Copyright © 2013 Elsevier Inc. All rights reserved.

Reference interval computation: which method (not) to choose?

PubMed

Pavlov, Igor Y; Wilson, Andrew R; Delgado, Julio C

2012-07-11

When different methods are applied to reference interval (RI) calculation the results can sometimes be substantially different, especially for small reference groups. If there are no reliable RI data available, there is no way to confirm which method generates results closest to the true RI. We randomly drawn samples obtained from a public database for 33 markers. For each sample, RIs were calculated by bootstrapping, parametric, and Box-Cox transformed parametric methods. Results were compared to the values of the population RI. For approximately half of the 33 markers, results of all 3 methods were within 3% of the true reference value. For other markers, parametric results were either unavailable or deviated considerably from the true values. The transformed parametric method was more accurate than bootstrapping for sample size of 60, very close to bootstrapping for sample size 120, but in some cases unavailable. We recommend against using parametric calculations to determine RIs. The transformed parametric method utilizing Box-Cox transformation would be preferable way of RI calculation, if it satisfies normality test. If not, the bootstrapping is always available, and is almost as accurate and precise as the transformed parametric method. Copyright © 2012 Elsevier B.V. All rights reserved.

Generating Artificial Reference Images for Open Loop Correlation Wavefront Sensors

NASA Astrophysics Data System (ADS)

Townson, M. J.; Love, G. D.; Saunter, C. D.

2018-05-01

Shack-Hartmann wavefront sensors for both solar and laser guide star adaptive optics (with elongated spots) need to observe extended objects. Correlation techniques have been successfully employed to measure the wavefront gradient in solar adaptive optics systems and have been proposed for laser guide star systems. In this paper we describe a method for synthesising reference images for correlation Shack-Hartmann wavefront sensors with a larger field of view than individual sub-apertures. We then show how these supersized reference images can increase the performance of correlation wavefront sensors in regimes where large relative shifts are induced between sub-apertures, such as those observed in open-loop wavefront sensors. The technique we describe requires no external knowledge outside of the wavefront-sensor images, making it available as an entirely "software" upgrade to an existing adaptive optics system. For solar adaptive optics we show the supersized reference images extend the magnitude of shifts which can be accurately measured from 12% to 50% of the field of view of a sub-aperture and in laser guide star wavefront sensors the magnitude of centroids that can be accurately measured is increased from 12% to 25% of the total field of view of the sub-aperture.

Identifying optimal reference genes for the normalization of microRNA expression in cucumber under viral stress

PubMed Central

Liang, Chaoqiong; Hao, Jianjun; Meng, Yan; Luo, Laixin; Li, Jianqiang

2018-01-01

Cucumber green mottle mosaic virus (CGMMV) is an economically important pathogen and causes significant reduction of both yield and quality of cucumber (Cucumis sativus). Currently, there were no satisfied strategies for controlling the disease. A better understanding of microRNA (miRNA) expression related to the regulation of plant-virus interactions and virus resistance would be of great assistance when developing control strategies for CGMMV. However, accurate expression analysis is highly dependent on robust and reliable reference gene used as an internal control for normalization of miRNA expression. Most commonly used reference genes involved in CGMMV-infected cucumber are not universally expressed depending on tissue types and stages of plant development. It is therefore crucial to identify suitable reference genes in investigating the role of miRNA expression. In this study, seven reference genes, including Actin, Tubulin, EF-1α, 18S rRNA, Ubiquitin, GAPDH and Cyclophilin, were evaluated for the most accurate results in analyses using reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Gene expression was assayed on cucumber leaves, stems and roots that were collected at different days post inoculation with CGMMV. The expression data were analyzed using algorithms including delta-Ct, geNorm, NormFinder, and BestKeeper as well as the comparative tool RefFinder. The reference genes were subsequently validated using miR159. The results showed that EF-1α and GAPDH were the most reliable reference genes for normalizing miRNA expression in leaf, root and stem samples, while Ubiquitin and EF-1α were the most suitable combination overall. PMID:29543906

Advancing reference emission levels in subnational and national REDD+ initiatives: a CLASlite approach

PubMed Central

Asner, Gregory P; Joseph, Shijo

2015-01-01

Conservation and monitoring of tropical forests requires accurate information on their extent and change dynamics. Cloud cover, sensor errors and technical barriers associated with satellite remote sensing data continue to prevent many national and sub-national REDD+ initiatives from developing their reference deforestation and forest degradation emission levels. Here we present a framework for large-scale historical forest cover change analysis using free multispectral satellite imagery in an extremely cloudy tropical forest region. The CLASlite approach provided highly automated mapping of tropical forest cover, deforestation and degradation from Landsat satellite imagery. Critically, the fractional cover of forest photosynthetic vegetation, non-photosynthetic vegetation, and bare substrates calculated by CLASlite provided scene-invariant quantities for forest cover, allowing for systematic mosaicking of incomplete satellite data coverage. A synthesized satellite-based data set of forest cover was thereby created, reducing image incompleteness caused by clouds, shadows or sensor errors. This approach can readily be implemented by single operators with highly constrained budgets. We test this framework on tropical forests of the Colombian Pacific Coast (Chocó) – one of the cloudiest regions on Earth, with successful comparison to the Colombian government’s deforestation map and a global deforestation map. PMID:25678933

Computer-aided technique for automatic determination of the relationship between transglottal pressure change and voice fundamental frequency.

PubMed

Deguchi, Shinji; Kawashima, Kazutaka; Washio, Seiichi

2008-12-01

The effect of artificially altered transglottal pressures on the voice fundamental frequency (F0) is known to be associated with vocal fold stiffness. Its measurement, though useful as a potential diagnostic tool for noncontact assessment of vocal fold stiffness, often requires manual and painstaking determination of an unstable F0 of voice. Here, we provide a computer-aided technique that enables one to carry out the determination easily and accurately. Human subjects vocalized in accordance with a series of reference sounds from a speaker controlled by a computer. Transglottal pressures were altered by means of a valve embedded in a mouthpiece. Time-varying vocal F0 was extracted, without manual procedures, from a specific range of the voice spectrum determined on the basis of the controlled reference sounds. The validity of the proposed technique was assessed for 11 healthy subjects. Fluctuating voice F0 was tracked automatically during experiments, providing the relationship between transglottal pressure change and F0 on the computer. The proposed technique overcomes the difficulty in automatic determination of the voice F0, which tends to be transient both in normal voice and in some types of pathological voice.

A Direct Georeferencing Method for Terrestrial Laser Scanning Using GNSS Data and the Vertical Deflection from Global Earth Gravity Models

PubMed Central

Borkowski, Andrzej; Owczarek-Wesołowska, Magdalena; Gromczak, Anna

2017-01-01

Terrestrial laser scanning is an efficient technique in providing highly accurate point clouds for various geoscience applications. The point clouds have to be transformed to a well-defined reference frame, such as the global Geodetic Reference System 1980. The transformation to the geocentric coordinate frame is based on estimating seven Helmert parameters using several GNSS (Global Navigation Satellite System) referencing points. This paper proposes a method for direct point cloud georeferencing that provides coordinates in the geocentric frame. The proposed method employs the vertical deflection from an external global Earth gravity model and thus demands a minimum number of GNSS measurements. The proposed method can be helpful when the number of georeferencing GNSS points is limited, for instance in city corridors. It needs only two georeferencing points. The validation of the method in a field test reveals that the differences between the classical georefencing and the proposed method amount at maximum to 7 mm with the standard deviation of 8 mm for all of three coordinate components. The proposed method may serve as an alternative for the laser scanning data georeferencing, especially when the number of GNSS points is insufficient for classical methods. PMID:28672795

A Direct Georeferencing Method for Terrestrial Laser Scanning Using GNSS Data and the Vertical Deflection from Global Earth Gravity Models.

PubMed

Osada, Edward; Sośnica, Krzysztof; Borkowski, Andrzej; Owczarek-Wesołowska, Magdalena; Gromczak, Anna

2017-06-24

Terrestrial laser scanning is an efficient technique in providing highly accurate point clouds for various geoscience applications. The point clouds have to be transformed to a well-defined reference frame, such as the global Geodetic Reference System 1980. The transformation to the geocentric coordinate frame is based on estimating seven Helmert parameters using several GNSS (Global Navigation Satellite System) referencing points. This paper proposes a method for direct point cloud georeferencing that provides coordinates in the geocentric frame. The proposed method employs the vertical deflection from an external global Earth gravity model and thus demands a minimum number of GNSS measurements. The proposed method can be helpful when the number of georeferencing GNSS points is limited, for instance in city corridors. It needs only two georeferencing points. The validation of the method in a field test reveals that the differences between the classical georefencing and the proposed method amount at maximum to 7 mm with the standard deviation of 8 mm for all of three coordinate components. The proposed method may serve as an alternative for the laser scanning data georeferencing, especially when the number of GNSS points is insufficient for classical methods.

Pressure and cold pain threshold reference values in a large, young adult, pain-free population.

PubMed

Waller, Robert; Smith, Anne Julia; O'Sullivan, Peter Bruce; Slater, Helen; Sterling, Michele; McVeigh, Joanne Alexandra; Straker, Leon Melville

2016-10-01

Currently there is a lack of large population studies that have investigated pain sensitivity distributions in healthy pain free people. The aims of this study were: (1) to provide sex-specific reference values of pressure and cold pain thresholds in young pain-free adults; (2) to examine the association of potential correlates of pain sensitivity with pain threshold values. This study investigated sex specific pressure and cold pain threshold estimates for young pain free adults aged 21-24 years. A cross-sectional design was utilised using participants (n=617) from the Western Australian Pregnancy Cohort (Raine) Study at the 22-year follow-up. The association of site, sex, height, weight, smoking, health related quality of life, psychological measures and activity with pain threshold values was examined. Pressure pain threshold (lumbar spine, tibialis anterior, neck and dorsal wrist) and cold pain threshold (dorsal wrist) were assessed using standardised quantitative sensory testing protocols. Reference values for pressure pain threshold (four body sites) stratified by sex and site, and cold pain threshold (dorsal wrist) stratified by sex are provided. Statistically significant, independent correlates of increased pressure pain sensitivity measures were site (neck, dorsal wrist), sex (female), higher waist-hip ratio and poorer mental health. Statistically significant, independent correlates of increased cold pain sensitivity measures were, sex (female), poorer mental health and smoking. These data provide the most comprehensive and robust sex specific reference values for pressure pain threshold specific to four body sites and cold pain threshold at the dorsal wrist for young adults aged 21-24 years. Establishing normative values in this young age group is important given that the transition from adolescence to adulthood is a critical temporal period during which trajectories for persistent pain can be established. These data will provide an important research resource to enable more accurate profiling and interpretation of pain sensitivity in clinical pain disorders in young adults. The robust and comprehensive data can assist interpretation of future clinical pain studies and provide further insight into the complex associations of pain sensitivity that can be used in future research. Crown Copyright © 2016. Published by Elsevier B.V. All rights reserved.

A Railway Track Geometry Measuring Trolley System Based on Aided INS

PubMed Central

Chen, Qijin; Niu, Xiaoji; Zuo, Lili; Zhang, Tisheng; Xiao, Fuqin; Liu, Yi; Liu, Jingnan

2018-01-01

Accurate measurement of the railway track geometry is a task of fundamental importance to ensure the track quality in both the construction phase and the regular maintenance stage. Conventional track geometry measuring trolleys (TGMTs) in combination with classical geodetic surveying apparatus such as total stations alone cannot meet the requirements of measurement accuracy and surveying efficiency at the same time. Accurate and fast track geometry surveying applications call for an innovative surveying method that can measure all or most of the track geometric parameters in short time without interrupting the railway traffic. We provide a novel solution to this problem by integrating an inertial navigation system (INS) with a geodetic surveying apparatus, and design a modular TGMT system based on aided INS, which can be configured according to different surveying tasks including precise adjustment of slab track, providing tamping measurements, measuring track deformation and irregularities, and determination of the track axis. TGMT based on aided INS can operate in mobile surveying mode to significantly improve the surveying efficiency. Key points in the design of the TGMT’s architecture and the data processing concept and workflow are introduced in details, which should benefit subsequent research and provide a reference for the implementation of this kind of TGMT. The surveying performance of proposed TGMT with different configurations is assessed in the track geometry surveying experiments and actual projects. PMID:29439423

Determination of tire cross-sectional geometric characteristics from a digitally scanned image

NASA Astrophysics Data System (ADS)

Danielson, Kent T.

1995-08-01

A semi-automated procedure is described for the accurate determination of geometrical characteristics using a scanned image of the tire cross-section. The procedure can be useful for cases when CAD drawings are not available or when a description of the actual cured tire is desired. Curves representing the perimeter of the tire cross-section are determined by an edge tracing scheme, and the plyline and cord-end positions are determined by locations of color intensities. The procedure provides an accurate description of the perimeter of the tire cross-section and the locations of plylines and cord-ends. The position, normals, and curvatures of the cross-sectional surface are included in this description. The locations of the plylines provide the necessary information for determining the ply thicknesses and relative position to a reference surface. Finally, the locations of the cord-ends provide a means to calculate the cord-ends per inch (epi). Menu driven software has been developed to facilitate the procedure using the commercial code, PV-Wave by Visual Numerics, Inc., to display the images. From a single user interface, separate modules are executed for image enhancement, curve fitting the edge trace of the cross-sectional perimeter, and determining the plyline and cord-end locations. The code can run on SUN or SGI workstations and requires the use of a mouse to specify options or identify items on the scanned image.

Determination of tire cross-sectional geometric characteristics from a digitally scanned image

NASA Technical Reports Server (NTRS)

Danielson, Kent T.

1995-01-01

A semi-automated procedure is described for the accurate determination of geometrical characteristics using a scanned image of the tire cross-section. The procedure can be useful for cases when CAD drawings are not available or when a description of the actual cured tire is desired. Curves representing the perimeter of the tire cross-section are determined by an edge tracing scheme, and the plyline and cord-end positions are determined by locations of color intensities. The procedure provides an accurate description of the perimeter of the tire cross-section and the locations of plylines and cord-ends. The position, normals, and curvatures of the cross-sectional surface are included in this description. The locations of the plylines provide the necessary information for determining the ply thicknesses and relative position to a reference surface. Finally, the locations of the cord-ends provide a means to calculate the cord-ends per inch (epi). Menu driven software has been developed to facilitate the procedure using the commercial code, PV-Wave by Visual Numerics, Inc., to display the images. From a single user interface, separate modules are executed for image enhancement, curve fitting the edge trace of the cross-sectional perimeter, and determining the plyline and cord-end locations. The code can run on SUN or SGI workstations and requires the use of a mouse to specify options or identify items on the scanned image.

Selection of novel reference genes for use in the human central nervous system: a BrainNet Europe Study.

PubMed

Durrenberger, Pascal F; Fernando, Francisca S; Magliozzi, Roberta; Kashefi, Samira N; Bonnert, Timothy P; Ferrer, Isidro; Seilhean, Danielle; Nait-Oumesmar, Brahim; Schmitt, Andrea; Gebicke-Haerter, Peter J; Falkai, Peter; Grünblatt, Edna; Palkovits, Miklos; Parchi, Piero; Capellari, Sabina; Arzberger, Thomas; Kretzschmar, Hans; Roncaroli, Federico; Dexter, David T; Reynolds, Richard

2012-12-01

The use of an appropriate reference gene to ensure accurate normalisation is crucial for the correct quantification of gene expression using qPCR assays and RNA arrays. The main criterion for a gene to qualify as a reference gene is a stable expression across various cell types and experimental settings. Several reference genes are commonly in use but more and more evidence reveals variations in their expression due to the presence of on-going neuropathological disease processes, raising doubts concerning their use. We conducted an analysis of genome-wide changes of gene expression in the human central nervous system (CNS) covering several neurological disorders and regions, including the spinal cord, and were able to identify a number of novel stable reference genes. We tested the stability of expression of eight novel (ATP5E, AARS, GAPVD1, CSNK2B, XPNPEP1, OSBP, NAT5 and DCTN2) and four more commonly used (BECN1, GAPDH, QARS and TUBB) reference genes in a smaller cohort using RT-qPCR. The most stable genes out of the 12 reference genes were tested as normaliser to validate increased levels of a target gene in CNS disease. We found that in human post-mortem tissue the novel reference genes, XPNPEP1 and AARS, were efficient in replicating microarray target gene expression levels and that XPNPEP1 was more efficient as a normaliser than BECN1, which has been shown to change in expression as a consequence of neuronal cell loss. We provide herein one more suitable novel reference gene, XPNPEP1, with no current neuroinflammatory or neurodegenerative associations that can be used for gene quantitative gene expression studies with human CNS post-mortem tissue and also suggest a list of potential other candidates. These data also emphasise the importance of organ/tissue-specific stably expressed genes as reference genes for RNA studies.

Hearing the Sound in the Brain: Influences of Different EEG References

PubMed Central

Wu, Dan

2018-01-01

If the scalp potential signals, the electroencephalogram (EEG), are due to neural “singers” in the brain, how could we listen to them with less distortion? One crucial point is that the data recording on the scalp should be faithful and accurate, thus the choice of reference electrode is a vital factor determining the faithfulness of the data. In this study, music on the scalp derived from data in the brain using three different reference electrodes were compared, including approximate zero reference—reference electrode standardization technique (REST), average reference (AR), and linked mastoids reference (LM). The classic music pieces in waveform format were used as simulated sources inside a head model, and they were forward calculated to scalp as standard potential recordings, i.e., waveform format music from the brain with true zero reference. Then these scalp music was re-referenced into REST, AR, and LM based data, and compared with the original forward data (true zero reference). For real data, the EEG recorded in an orthodontic pain control experiment were utilized for music generation with the three references, and the scale free index (SFI) of these music pieces were compared. The results showed that in the simulation for only one source, different references do not change the music/waveform; for two sources or more, REST provide the most faithful music/waveform to the original ones inside the brain, and the distortions caused by AR and LM were spatial locations of both source and scalp electrode dependent. The brainwave music from the real EEG data showed that REST and AR make the differences of SFI between two states more recognized and found the frontal is the main region that producing the music. In conclusion, REST can reconstruct the true signals approximately, and it can be used to help to listen to the true voice of the neural singers in the brain. PMID:29593487

Lung function and exhaled nitric oxide in healthy unsedated African infants

PubMed Central

Gray, Diane; Willemse, Lauren; Visagie, Ane; Smith, Emilee; Czövek, Dorottya; Sly, Peter D; Hantos, Zoltán; Hall, Graham L; Zar, Heather J

2015-01-01

Background and objective Population-appropriate lung function reference data are essential to accurately identify respiratory disease and measure response to interventions. There are currently no reference data in African infants. The aim was to describe normal lung function in healthy African infants. Methods Lung function was performed on healthy South African infants enrolled in a birth cohort study, the Drakenstein child health study. Infants were excluded if they were born preterm or had a history of neonatal respiratory distress or prior respiratory tract infection. Measurements, made during natural sleep, included the forced oscillation technique, tidal breathing, exhaled nitric oxide and multiple breath washout measures. Results Three hundred sixty-three infants were tested. Acceptable and repeatable measurements were obtained in 356 (98%) and 352 (97%) infants for tidal breathing analysis and exhaled nitric oxide outcomes, 345 (95%) infants for multiple breath washout and 293 of the 333 (88%) infants for the forced oscillation technique. Age, sex and weight-for-age z score were significantly associated with lung function measures. Conclusions This study provides reference data for unsedated infant lung function in African infants and highlights the importance of using population-specific data. PMID:26134556

Comparison of osmolality and refractometric readings of Hispaniolan Amazon parrot (Amazona ventralis) urine.

PubMed

Brock, A Paige; Grunkemeyer, Vanessa L; Fry, Michael M; Hall, James S; Bartges, Joseph W

2013-12-01

To evaluate the relationship between osmolality and specific gravity of urine samples from clinically normal adult parrots and to determine a formula to convert urine specific gravity (USG) measured on a reference scale to a more accurate USG value for an avian species, urine samples were collected opportunistically from a colony of Hispaniolan Amazon parrots (Amazona ventralis). Samples were analyzed by using a veterinary refractometer, and specific gravity was measured on both canine and feline scales. Osmolality was measured by vapor pressure osmometry. Specific gravity and osmolality measurements were highly correlated (r = 0.96). The linear relationship between refractivity measurements on a reference scale and osmolality was determined. An equation was calculated to allow specific gravity results from a medical refractometer to be converted to specific gravity values of Hispaniolan Amazon parrots: USGHAp = 0.201 +0.798(USGref). Use of the reference-canine scale to approximate the osmolality of parrot urine leads to an overestimation of the true osmolality of the sample. In addition, this error increases as the concentration of urine increases. Compared with the human-canine scale, the feline scale provides a closer approximation to urine osmolality of Hispaniolan Amazon parrots but still results in overestimation of osmolality.

Quantitative determination and validation of octreotide acetate using 1 H-NMR spectroscopy with internal standard method.

PubMed

Yu, Chen; Zhang, Qian; Xu, Peng-Yao; Bai, Yin; Shen, Wen-Bin; Di, Bin; Su, Meng-Xiang

2018-01-01

Quantitative nuclear magnetic resonance (qNMR) is a well-established technique in quantitative analysis. We presented a validated 1 H-qNMR method for assay of octreotide acetate, a kind of cyclic octopeptide. Deuterium oxide was used to remove the undesired exchangeable peaks, which was referred to as proton exchange, in order to make the quantitative signals isolated in the crowded spectrum of the peptide and ensure precise quantitative analysis. Gemcitabine hydrochloride was chosen as the suitable internal standard. Experimental conditions, including relaxation delay time, the numbers of scans, and pulse angle, were optimized first. Then method validation was carried out in terms of selectivity, stability, linearity, precision, and robustness. The assay result was compared with that by means of high performance liquid chromatography, which is provided by Chinese Pharmacopoeia. The statistical F test, Student's t test, and nonparametric test at 95% confidence level indicate that there was no significant difference between these two methods. qNMR is a simple and accurate quantitative tool with no need for specific corresponding reference standards. It has the potential of the quantitative analysis of other peptide drugs and standardization of the corresponding reference standards. Copyright © 2017 John Wiley & Sons, Ltd.

Simple method for self-referenced and lable-free biosensing by using a capillary sensing element.

PubMed

Liu, Yun; Chen, Shimeng; Liu, Qiang; Liu, Zigeng; Wei, Peng

2017-05-15

We demonstrated a simple method for self-reference and label free biosensing based on a capillary sensing element and common optoelectronic devices. The capillary sensing element is illuminated by a light-emitting diode (LED) light source and detected by a webcam. Part of gold film that deposited on the tubing wall is functionalized to carry on the biological information in the excited SPR modes. The end face of the capillary was monitored and separate regions of interest (ROIs) were selected as the measurement channel and the reference channel. In the ROIs, the biological information can be accurately extracted from the image by simple image processing. Moreover, temperature fluctuation, bulk RI fluctuation, light source fluctuation and other factors can be effectively compensated during detection. Our biosensing device has a sensitivity of 1145%/RIU and a resolution better than 5.287 × 10 -4 RIU, considering a 0.79% noise level. We apply it for concanavalin A (Con A) biological measurement, which has an approximately linear response to the specific analyte concentration. This simple method provides a new approach for multichannel SPR sensing and reference-compensated calibration of SPR signal for label-free detection.

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

Wu, Hao; Garzoglio, Gabriele; Ren, Shangping

FermiCloud is a private cloud developed in Fermi National Accelerator Laboratory to provide elastic and on-demand resources for different scientific research experiments. The design goal of the FermiCloud is to automatically allocate resources for different scientific applications so that the QoS required by these applications is met and the operational cost of the FermiCloud is minimized. Our earlier research shows that VM launching overhead has large variations. If such variations are not taken into consideration when making resource allocation decisions, it may lead to poor performance and resource waste. In this paper, we show how we may use an VMmore » launching overhead reference model to minimize VM launching overhead. In particular, we first present a training algorithm that automatically tunes a given refer- ence model to accurately reflect FermiCloud environment. Based on the tuned reference model for virtual machine launching overhead, we develop an overhead-aware-best-fit resource allocation algorithm that decides where and when to allocate resources so that the average virtual machine launching overhead is minimized. The experimental results indicate that the developed overhead-aware-best-fit resource allocation algorithm can significantly improved the VM launching time when large number of VMs are simultaneously launched.« less

Methodological evaluation and comparison of five urinary albumin measurements.

PubMed

Liu, Rui; Li, Gang; Cui, Xiao-Fan; Zhang, Dong-Ling; Yang, Qing-Hong; Mu, Xiao-Yan; Pan, Wen-Jie

2011-01-01

Microalbuminuria is an indicator of kidney damage and a risk factor for the progression kidney disease, cardiovascular disease, and so on. Therefore, accurate and precise measurement of urinary albumin is critical. However, there are no reference measurement procedures and reference materials for urinary albumin. Nephelometry, turbidimetry, colloidal gold method, radioimmunoassay, and chemiluminescence immunoassay were performed for methodological evaluation, based on imprecision test, recovery rate, linearity, haemoglobin interference rate, and verified reference interval. Then we tested 40 urine samples from diabetic patients by each method, and compared the result between assays. The results indicate that nephelometry is the method with best analytical performance among the five methods, with an average intraassay coefficient of variation (CV) of 2.6%, an average interassay CV of 1.7%, a mean recovery of 99.6%, a linearity of R=1.00 from 2 to 250 mg/l, and an interference rate of <10% at haemoglobin concentrations of <1.82 g/l. The correlation (r) between assays was from 0.701 to 0.982, and the Bland-Altman plots indicated each assay provided significantly different results from each other. Nephelometry is the clinical urinary albumin method with best analytical performance in our study. © 2011 Wiley-Liss, Inc.

Reference standards for lean mass measures using GE dual energy x-ray absorptiometry in Caucasian adults.

PubMed

Imboden, Mary T; Swartz, Ann M; Finch, Holmes W; Harber, Matthew P; Kaminsky, Leonard A

2017-01-01

To develop reference values by age and sex for LM measures using GE-Healthcare DXA systems. A de-identified sample was obtained from Ball State University's Clinical Exercise Physiology Laboratory and University of Wisconsin-Milwaukee's Physical Activity & Health Research Laboratory. DXA scans of 2,076 women and 1,251 men were completed using a GE Lunar Prodigy or iDXA. Percentiles (%ile) were calculated for all variables of interest (LM, LMI, %LM, and ALMI) and a factorial ANOVA was used to assess differences for each variable between 10-year age groups and sex, as well as the interaction between age and sex. Men had higher mean total LM, %LM, LMI, and ALMI than women (p<0.01), across all age groups. All LM variables decreased significantly over the 5 decades in men, however in women only total LM, %LM, and ALMI decreased from the youngest to oldest age groups (p<0.01). These reference values provide for a more accurate interpretation of GE-Healthcare DXA-derived LM measurements offering clinicians and researchers with an initial resource to aid in the early detection and assessment of LM deficits.

Premature trial discontinuation often not accurately reflected in registries: comparison of registry records with publications.

PubMed

Alturki, Reem; Schandelmaier, Stefan; Olu, Kelechi Kalu; von Niederhäusern, Belinda; Agarwal, Arnav; Frei, Roy; Bhatnagar, Neera; Hooft, Lotty; von Elm, Erik; Briel, Matthias

2017-01-01

One quarter of randomized clinical trials (RCTs) are prematurely discontinued and frequently remain unpublished. Trial registries can document whether a trial is ongoing, suspended, discontinued, or completed and therefore represent an important source for trial status information. The accuracy of this information is unclear. To examine the accuracy of completion status and reasons for discontinuation documented in trial registries as compared to corresponding publications of discontinued RCTs and to investigate potential predictors for accurate trial status information in registries. We conducted a cross-sectional study comparing information provided in publications (reference standard) to corresponding registry entries. First, we reviewed publications of RCTs providing information on both discontinuation and registration. We identified eligible publications through systematic searches of MEDLINE and EMBASE (2010-2014) and an international cohort of 1,017 RCTs initiated between 2000 and 2003. Second, pairs of investigators independently and in duplicate extracted data from publications and corresponding registry records. Third, for each discontinued RCT, we compared publication information to registry information. We used multivariable regression to examine whether accurate labeling of trials as discontinued (vs. other status) in the registry was associated with recent initiation of RCT, industry sponsorship, multicenter design, or larger sample size. We identified 173 publications of RCTs that were discontinued due to slow recruitment (55%), harm (16%), futility (11%), benefit (5%), other reasons (3%), or multiple reasons (9%). Trials were registered with clinicaltrials.gov (77%), isrctn.com (14%), or other registries (8%). Of the 173 corresponding registry records, 77 (45%) trials were labeled as discontinued and 57 (33%) provided a reason for discontinuation (of which 53, 93%, provided the same reason as in the publication). Labeling of discontinued trials as discontinued (vs. other label) in corresponding trial registry records improved over time (adjusted odds ratio 1.16 per year, confidence interval 1.04-1.30) and was possibly associated with industry sponsorship (2.01, 0.99-4.07) but unlikely with multicenter status (0.81, 0.32-2.04) or sample size (1.07, 0.89-1.29). Less than half of published discontinued RCTs were accurately labelled as discontinued in corresponding registry records. One-third of registry records provided a reason for discontinuation. Current trial status information in registries should be viewed with caution. Copyright © 2016 Elsevier Inc. All rights reserved.

Identification of Appropriate Reference Genes for Normalization of miRNA Expression in Grafted Watermelon Plants under Different Nutrient Stresses

PubMed Central

Wu, Weifang; Deng, Qin; Shi, Pibiao; Yang, Jinghua; Hu, Zhongyuan; Zhang, Mingfang

2016-01-01

Watermelon (Citrullus lanatus) is a globally important crop belonging to the family Cucurbitaceae. The grafting technique is commonly used to improve its tolerance to stress, as well as to enhance its nutrient uptake and utilization. It is believed that miRNA is most likely involved in its nutrient-starvation response as a graft-transportable signal. The quantitative real-time reverse transcriptase polymerase chain reaction is the preferred method for miRNA functional analysis, in which reliable reference genes for normalization are crucial to ensure the accuracy. The purpose of this study was to select appropriate reference genes in scion (watermelon) and rootstocks (squash and bottle gourd) of grafted watermelon plants under normal growth conditions and nutrient stresses (nitrogen and phosphorus starvation). Under nutrient starvation, geNorm identified miR167c and miR167f as two most stable genes in both watermelon leaves and squash roots. miR166b was recommended by both geNorm and NormFinder as the best reference in bottle gourd roots under nutrient limitation. Expression of a new Cucurbitaceae miRNA, miR85, was used to validate the reliability of candidate reference genes under nutrient starvation. Moreover, by comparing several target genes expression in qRT-PCR analysis with those in RNA-seq data, miR166b and miR167c were proved to be the most suitable reference genes to normalize miRNA expression under normal growth condition in scion and rootstock tissues, respectively. This study represents the first comprehensive survey of the stability of miRNA reference genes in Cucurbitaceae and provides valuable information for investigating more accurate miRNA expression involving grafted watermelon plants. PMID:27749935

Identification of Appropriate Reference Genes for Normalization of miRNA Expression in Grafted Watermelon Plants under Different Nutrient Stresses.

PubMed

Wu, Weifang; Deng, Qin; Shi, Pibiao; Yang, Jinghua; Hu, Zhongyuan; Zhang, Mingfang

2016-01-01

Watermelon (Citrullus lanatus) is a globally important crop belonging to the family Cucurbitaceae. The grafting technique is commonly used to improve its tolerance to stress, as well as to enhance its nutrient uptake and utilization. It is believed that miRNA is most likely involved in its nutrient-starvation response as a graft-transportable signal. The quantitative real-time reverse transcriptase polymerase chain reaction is the preferred method for miRNA functional analysis, in which reliable reference genes for normalization are crucial to ensure the accuracy. The purpose of this study was to select appropriate reference genes in scion (watermelon) and rootstocks (squash and bottle gourd) of grafted watermelon plants under normal growth conditions and nutrient stresses (nitrogen and phosphorus starvation). Under nutrient starvation, geNorm identified miR167c and miR167f as two most stable genes in both watermelon leaves and squash roots. miR166b was recommended by both geNorm and NormFinder as the best reference in bottle gourd roots under nutrient limitation. Expression of a new Cucurbitaceae miRNA, miR85, was used to validate the reliability of candidate reference genes under nutrient starvation. Moreover, by comparing several target genes expression in qRT-PCR analysis with those in RNA-seq data, miR166b and miR167c were proved to be the most suitable reference genes to normalize miRNA expression under normal growth condition in scion and rootstock tissues, respectively. This study represents the first comprehensive survey of the stability of miRNA reference genes in Cucurbitaceae and provides valuable information for investigating more accurate miRNA expression involving grafted watermelon plants.

Adult Hematology and Clinical Chemistry Laboratory Reference Ranges in a Zimbabwean Population.

PubMed

Samaneka, Wadzanai P; Mandozana, Gibson; Tinago, Willard; Nhando, Nehemiah; Mgodi, Nyaradzo M; Bwakura-Dangarembizi, Mutsawashe F; Munjoma, Marshall W; Gomo, Zvenyika A R; Chirenje, Zvavahera M; Hakim, James G

2016-01-01

Laboratory reference ranges used for clinical care and clinical trials in various laboratories in Zimbabwe were derived from textbooks and research studies conducted more than ten years ago. Periodic verification of these ranges is essential to track changes over time. The purpose of this study was to establish hematology and chemistry laboratory reference ranges using more rigorous methods. A community-based cross-sectional study was carried out in Harare, Chitungwiza, and Mutoko. A multistage sampling technique was used. Samples were transported from the field for analysis at the ISO15189 certified University of Zimbabwe-University of California San Francisco Central Research Laboratory. Hematology and clinical chemistry reference ranges lower and upper reference limits were estimated at the 2.5th and 97.5th percentiles respectively. A total of 769 adults (54% males) aged 18 to 55 years were included in the analysis. Median age was 28 [IQR: 23-35] years. Males had significantly higher red cell counts, hemoglobin, hematocrit, and mean corpuscular hemoglobin compared to females. Females had higher white cell counts, platelets, absolute neutrophil counts, and absolute lymphocyte counts compared to males. There were no gender differences in eosinophils, monocytes, and absolute basophil count. Males had significantly higher levels of urea, sodium, potassium, calcium, creatinine, amylase, total protein, albumin and liver enzymes levels compared to females. Females had higher cholesterol and lipase compared with males. There are notable differences in the white cell counts, neutrophils, cholesterol, and creatinine kinase when compared with the currently used reference ranges. Data from this study provides new country specific reference ranges which should be immediately adopted for routine clinical care and accurate monitoring of adverse events in research studies.

CLSI-based transference and verification of CALIPER pediatric reference intervals for 29 Ortho VITROS 5600 chemistry assays.

PubMed

Higgins, Victoria; Truong, Dorothy; Woroch, Amy; Chan, Man Khun; Tahmasebi, Houman; Adeli, Khosrow

2018-03-01

Evidence-based reference intervals (RIs) are essential to accurately interpret pediatric laboratory test results. To fill gaps in pediatric RIs, the Canadian Laboratory Initiative on Pediatric Reference Intervals (CALIPER) project developed an age- and sex-specific pediatric RI database based on healthy pediatric subjects. Originally established for Abbott ARCHITECT assays, CALIPER RIs were transferred to assays on Beckman, Roche, Siemens, and Ortho analytical platforms. This study provides transferred reference intervals for 29 biochemical assays for the Ortho VITROS 5600 Chemistry System (Ortho). Based on Clinical Laboratory Standards Institute (CLSI) guidelines, a method comparison analysis was performed by measuring approximately 200 patient serum samples using Abbott and Ortho assays. The equation of the line of best fit was calculated and the appropriateness of the linear model was assessed. This equation was used to transfer RIs from Abbott to Ortho assays. Transferred RIs were verified using 84 healthy pediatric serum samples from the CALIPER cohort. RIs for most chemistry analytes successfully transferred from Abbott to Ortho assays. Calcium and CO 2 did not meet statistical criteria for transference (r 2 <0.70). Of the 32 transferred reference intervals, 29 successfully verified with approximately 90% of results from reference samples falling within transferred confidence limits. Transferred RIs for total bilirubin, magnesium, and LDH did not meet verification criteria and are not reported. This study broadens the utility of the CALIPER pediatric RI database to laboratories using Ortho VITROS 5600 biochemical assays. Clinical laboratories should verify CALIPER reference intervals for their specific analytical platform and local population as recommended by CLSI. Copyright © 2018 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

RAMICS: trainable, high-speed and biologically relevant alignment of high-throughput sequencing reads to coding DNA

PubMed Central

Wright, Imogen A.; Travers, Simon A.

2014-01-01

The challenge presented by high-throughput sequencing necessitates the development of novel tools for accurate alignment of reads to reference sequences. Current approaches focus on using heuristics to map reads quickly to large genomes, rather than generating highly accurate alignments in coding regions. Such approaches are, thus, unsuited for applications such as amplicon-based analysis and the realignment phase of exome sequencing and RNA-seq, where accurate and biologically relevant alignment of coding regions is critical. To facilitate such analyses, we have developed a novel tool, RAMICS, that is tailored to mapping large numbers of sequence reads to short lengths (<10 000 bp) of coding DNA. RAMICS utilizes profile hidden Markov models to discover the open reading frame of each sequence and aligns to the reference sequence in a biologically relevant manner, distinguishing between genuine codon-sized indels and frameshift mutations. This approach facilitates the generation of highly accurate alignments, accounting for the error biases of the sequencing machine used to generate reads, particularly at homopolymer regions. Performance improvements are gained through the use of graphics processing units, which increase the speed of mapping through parallelization. RAMICS substantially outperforms all other mapping approaches tested in terms of alignment quality while maintaining highly competitive speed performance. PMID:24861618

Comprehensive evaluation of candidate reference genes for gene expression studies in Lysiphlebia japonica (Hymenoptera: Aphidiidae) using RT-qPCR.

PubMed

Gao, Xue-Ke; Zhang, Shuai; Luo, Jun-Yu; Wang, Chun-Yi; Lü, Li-Min; Zhang, Li-Juan; Zhu, Xiang-Zhen; Wang, Li; Lu, Hui; Cui, Jin-Jie

2017-12-30

Lysiphlebia japonica (Ashmead) is a predominant parasitoid of cotton-melon aphids in the fields of northern China with a proven ability to effectively control cotton aphid populations in early summer. For accurate normalization of gene expression in L. japonica using quantitative reverse transcriptase-polymerase chain reaction (RT-qPCR), reference genes with stable gene expression patterns are essential. However, no appropriate reference genes is L. japonica have been investigated to date. In the present study, 12 selected housekeeping genes from L. japonica were cloned. We evaluated the stability of these genes under various experimental treatments by RT-qPCR using four independent (geNorm, NormFinder, BestKeeper and Delta Ct) and one comparative (RefFinder) algorithm. We identified genes showing the most stable levels of expression: DIMT, 18S rRNA, and RPL13 during different stages; AK, RPL13, and TBP among sexes; EF1A, PPI, and RPL27 in different tissues, and EF1A, RPL13, and PPI in adults fed on different diets. Moreover, the expression profile of a target gene (odorant receptor 1, OR1) studied during the developmental stages confirms the reliability of the chosen selected reference genes. This study provides for the first time a comprehensive list of suitable reference genes for gene expression studies in L. japonica and will benefit subsequent genomics and functional genomics research on this natural enemy. Copyright © 2017. Published by Elsevier B.V.

1983 international intercomparison of nuclear accident dosimetry systems at Oak Ridge National Laboratory

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

Swaja, R.E.; Greene, R.T.; Sims, C.S.

1985-04-01

An international intercomparison of nuclear accident dosimetry systems was conducted during September 12-16, 1983, at Oak Ridge National Laboratory (ORNL) using the Health Physics Research Reactor operated in the pulse mode to simulate criticality accidents. This study marked the twentieth in a series of annual accident dosimetry intercomparisons conducted at ORNL. Participants from ten organizations attended this intercomparison and measured neutron and gamma doses at area monitoring stations and on phantoms for three different shield conditions. Results of this study indicate that foil activation techniques are the most popular and accurate method of determining accident-level neutron doses at area monitoringmore » stations. For personnel monitoring, foil activation, blood sodium activation, and thermoluminescent (TL) methods are all capable of providing accurate dose estimates in a variety of radiation fields. All participants in this study used TLD's to determine gamma doses with very good results on the average. Chemical dosemeters were also shown to be capable of yielding accurate estimates of total neutron plus gamma doses in a variety of radiation fields. While 83% of all neutron measurements satisfied regulatory standards relative to reference values, only 39% of all gamma results satisfied corresponding guidelines for gamma measurements. These results indicate that continued improvement in accident dosimetry evaluation and measurement techniques is needed.« less

Accuracy of complete-arch dental impressions: a new method of measuring trueness and precision.

PubMed

Ender, Andreas; Mehl, Albert

2013-02-01

A new approach to both 3-dimensional (3D) trueness and precision is necessary to assess the accuracy of intraoral digital impressions and compare them to conventionally acquired impressions. The purpose of this in vitro study was to evaluate whether a new reference scanner is capable of measuring conventional and digital intraoral complete-arch impressions for 3D accuracy. A steel reference dentate model was fabricated and measured with a reference scanner (digital reference model). Conventional impressions were made from the reference model, poured with Type IV dental stone, scanned with the reference scanner, and exported as digital models. Additionally, digital impressions of the reference model were made and the digital models were exported. Precision was measured by superimposing the digital models within each group. Superimposing the digital models on the digital reference model assessed the trueness of each impression method. Statistical significance was assessed with an independent sample t test (α=.05). The reference scanner delivered high accuracy over the entire dental arch with a precision of 1.6 ±0.6 µm and a trueness of 5.3 ±1.1 µm. Conventional impressions showed significantly higher precision (12.5 ±2.5 µm) and trueness values (20.4 ±2.2 µm) with small deviations in the second molar region (P<.001). Digital impressions were significantly less accurate with a precision of 32.4 ±9.6 µm and a trueness of 58.6 ±15.8µm (P<.001). More systematic deviations of the digital models were visible across the entire dental arch. The new reference scanner is capable of measuring the precision and trueness of both digital and conventional complete-arch impressions. The digital impression is less accurate and shows a different pattern of deviation than the conventional impression. Copyright © 2013 The Editorial Council of the Journal of Prosthetic Dentistry. Published by Mosby, Inc. All rights reserved.

Predicting oropharyngeal tumor volume throughout the course of radiation therapy from pretreatment computed tomography data using general linear models.

PubMed

Yock, Adam D; Rao, Arvind; Dong, Lei; Beadle, Beth M; Garden, Adam S; Kudchadker, Rajat J; Court, Laurence E

2014-05-01

The purpose of this work was to develop and evaluate the accuracy of several predictive models of variation in tumor volume throughout the course of radiation therapy. Nineteen patients with oropharyngeal cancers were imaged daily with CT-on-rails for image-guided alignment per an institutional protocol. The daily volumes of 35 tumors in these 19 patients were determined and used to generate (1) a linear model in which tumor volume changed at a constant rate, (2) a general linear model that utilized the power fit relationship between the daily and initial tumor volumes, and (3) a functional general linear model that identified and exploited the primary modes of variation between time series describing the changing tumor volumes. Primary and nodal tumor volumes were examined separately. The accuracy of these models in predicting daily tumor volumes were compared with those of static and linear reference models using leave-one-out cross-validation. In predicting the daily volume of primary tumors, the general linear model and the functional general linear model were more accurate than the static reference model by 9.9% (range: -11.6%-23.8%) and 14.6% (range: -7.3%-27.5%), respectively, and were more accurate than the linear reference model by 14.2% (range: -6.8%-40.3%) and 13.1% (range: -1.5%-52.5%), respectively. In predicting the daily volume of nodal tumors, only the 14.4% (range: -11.1%-20.5%) improvement in accuracy of the functional general linear model compared to the static reference model was statistically significant. A general linear model and a functional general linear model trained on data from a small population of patients can predict the primary tumor volume throughout the course of radiation therapy with greater accuracy than standard reference models. These more accurate models may increase the prognostic value of information about the tumor garnered from pretreatment computed tomography images and facilitate improved treatment management.

Learning-based automatic detection of severe coronary stenoses in CT angiographies

NASA Astrophysics Data System (ADS)

Melki, Imen; Cardon, Cyril; Gogin, Nicolas; Talbot, Hugues; Najman, Laurent

2014-03-01

3D cardiac computed tomography angiography (CCTA) is becoming a standard routine for non-invasive heart diseases diagnosis. Thanks to its high negative predictive value, CCTA is increasingly used to decide whether or not the patient should be considered for invasive angiography. However, an accurate assessment of cardiac lesions using this modality is still a time consuming task and needs a high degree of clinical expertise. Thus, providing automatic tool to assist clinicians during the diagnosis task is highly desirable. In this work, we propose a fully automatic approach for accurate severe cardiac stenoses detection. Our algorithm uses the Random Forest classi cation to detect stenotic areas. First, the classi er is trained on 18 CT cardiac exams with CTA reference standard. Then, then classi cation result is used to detect severe stenoses (with a narrowing degree higher than 50%) in a 30 cardiac CT exam database. Features that best captures the di erent stenoses con guration are extracted along the vessel centerlines at di erent scales. To ensure the accuracy against the vessel direction and scale changes, we extract features inside cylindrical patterns with variable directions and radii. Thus, we make sure that the ROIs contains only the vessel walls. The algorithm is evaluated using the Rotterdam Coronary Artery Stenoses Detection and Quantication Evaluation Framework. The evaluation is performed using reference standard quanti cations obtained from quantitative coronary angiography (QCA) and consensus reading of CTA. The obtained results show that we can reliably detect severe stenosis with a sensitivity of 64%.

Improving the Conservation of Mediterranean Chondrichthyans: The ELASMOMED DNA Barcode Reference Library

PubMed Central

Arculeo, Marco; Bonello, Juan J.; Bonnici, Leanne; Cannas, Rita; Carbonara, Pierluigi; Cau, Alessandro; Charilaou, Charis; El Ouamari, Najib; Fiorentino, Fabio; Follesa, Maria Cristina; Garofalo, Germana; Golani, Daniel; Guarniero, Ilaria; Hanner, Robert; Hemida, Farid; Kada, Omar; Lo Brutto, Sabrina; Mancusi, Cecilia; Morey, Gabriel; Schembri, Patrick J.; Serena, Fabrizio; Sion, Letizia; Stagioni, Marco; Tursi, Angelo; Vrgoc, Nedo; Steinke, Dirk; Tinti, Fausto

2017-01-01

Cartilaginous fish are particularly vulnerable to anthropogenic stressors and environmental change because of their K-selected reproductive strategy. Accurate data from scientific surveys and landings are essential to assess conservation status and to develop robust protection and management plans. Currently available data are often incomplete or incorrect as a result of inaccurate species identifications, due to a high level of morphological stasis, especially among closely related taxa. Moreover, several diagnostic characters clearly visible in adult specimens are less evident in juveniles. Here we present results generated by the ELASMOMED Consortium, a regional network aiming to sample and DNA-barcode the Mediterranean Chondrichthyans with the ultimate goal to provide a comprehensive DNA barcode reference library. This library will support and improve the molecular taxonomy of this group and the effectiveness of management and conservation measures. We successfully barcoded 882 individuals belonging to 42 species (17 sharks, 24 batoids and one chimaera), including four endemic and several threatened ones. Morphological misidentifications were found across most orders, further confirming the need for a comprehensive DNA barcoding library as a valuable tool for the reliable identification of specimens in support of taxonomist who are reviewing current identification keys. Despite low intraspecific variation among their barcode sequences and reduced samples size, five species showed preliminary evidence of phylogeographic structure. Overall, the ELASMOMED initiative further emphasizes the key role accurate DNA barcoding libraries play in establishing reliable diagnostic species specific features in otherwise taxonomically problematic groups for biodiversity management and conservation actions. PMID:28107413

Additivity rules using similarity models for chemical reactivity: calculation and interpretation of electrofugality and nucleofugality.

PubMed

Bentley, T William

2006-08-25

A recently proposed, multi-parameter correlation: log k (25 degrees C)=s(f) (Ef + Nf), where Ef is electrofugality and Nf is nucleofugality, for the substituent and solvent effects on the rate constants for solvolyses of benzhydryl and substituted benzhydryl substrates, is re-evaluated. A new formula (Ef=log k (RCl/EtOH/25 degrees C) -1.87), where RCl/EtOH refers to ethanolysis of chlorides, reproduces published values of Ef satisfactorily, avoids multi-parameter optimisations and provides additional values of Ef. From the formula for Ef, it is shown that the term (sfxEf) is compatible with the Hammett-Brown (rho+sigma+) equation for substituent effects. However, the previously published values of N(f) do not accurately account for solvent and leaving group effects (e.g. nucleofuge Cl or X), even for benzhydryl solvolyses; alternatively, if the more exact, two-parameter term, (sfxNf) is used, calculated effects are less accurate. A new formula (Nf=6.14 + log k(BX/any solvent/25 degrees C)), where BX refers to solvolysis of the parent benzhydryl as electrofuge, defines improved Nf values for benzhydryl substrates. The new formulae for Ef and Nf are consistent with an assumption that sf=1.00(,) and so improved correlations for benzhydryl substrates can be obtained from the additive formula: log k(RX/any solvent/25 degrees C)=(Ef + Nf). Possible extensions of this approach are also discussed.

Cometary Astrometry

NASA Technical Reports Server (NTRS)

Yeomans, D. K. (Editor); West, R. M. (Editor); Harrington, R. S. (Editor); Marsden, B. G. (Editor)

1984-01-01

Modern techniques for making cometary astrometric observations, reducing these observations, using accurate reference star catalogs, and computing precise orbits and ephemerides are discussed in detail and recommendations and suggestions are given in each area.

New ab initio adiabatic potential energy surfaces and bound state calculations for the singlet ground X˜ 1A1 and excited C˜ 1B2(21A') states of SO2

NASA Astrophysics Data System (ADS)

Kłos, Jacek; Alexander, Millard H.; Kumar, Praveen; Poirier, Bill; Jiang, Bin; Guo, Hua

2016-05-01

We report new and more accurate adiabatic potential energy surfaces (PESs) for the ground X˜ 1A1 and electronically excited C˜ 1B2(21A') states of the SO2 molecule. Ab initio points are calculated using the explicitly correlated internally contracted multi-reference configuration interaction (icMRCI-F12) method. A second less accurate PES for the ground X ˜ state is also calculated using an explicitly correlated single-reference coupled-cluster method with single, double, and non-iterative triple excitations [CCSD(T)-F12]. With these new three-dimensional PESs, we determine energies of the vibrational bound states and compare these values to existing literature data and experiment.

Plasma Processes for Semiconductor Fabrication

NASA Astrophysics Data System (ADS)

Hitchon, W. N. G.

1999-01-01

Plasma processing is a central technique in the fabrication of semiconductor devices. This self-contained book provides an up-to-date description of plasma etching and deposition in semiconductor fabrication. It presents the basic physics and chemistry of these processes, and shows how they can be accurately modeled. The author begins with an overview of plasma reactors and discusses the various models for understanding plasma processes. He then covers plasma chemistry, addressing the effects of different chemicals on the features being etched. Having presented the relevant background material, he then describes in detail the modeling of complex plasma systems, with reference to experimental results. The book closes with a useful glossary of technical terms. No prior knowledge of plasma physics is assumed in the book. It contains many homework exercises and serves as an ideal introduction to plasma processing and technology for graduate students of electrical engineering and materials science. It will also be a useful reference for practicing engineers in the semiconductor industry.

Automatic creation of three-dimensional avatars

NASA Astrophysics Data System (ADS)

Villa-Uriol, Maria-Cruz; Sainz, Miguel; Kuester, Falko; Bagherzadeh, Nader

2003-01-01

Highly accurate avatars of humans promise a new level of realism in engineering and entertainment applications, including areas such as computer animated movies, computer game development interactive virtual environments and tele-presence. In order to provide high-quality avatars, new techniques for the automatic acquisition and creation are required. A framework for the capture and construction of arbitrary avatars from image data is presented in this paper. Avatars are automatically reconstructed from multiple static images of a human subject by utilizing image information to reshape a synthetic three-dimensional articulated reference model. A pipeline is presented that combines a set of hardware-accelerated stages into one seamless system. Primary stages in this pipeline include pose estimation, skeleton fitting, body part segmentation, geometry construction and coloring, leading to avatars that can be animated and included into interactive environments. The presented system removes traditional constraints in the initial pose of the captured subject by using silhouette-based modification techniques in combination with a reference model. Results can be obtained in near-real time with very limited user intervention.

Distortion-free diffusion MRI using an MRI-guided Tri-Cobalt 60 radiotherapy system: Sequence verification and preliminary clinical experience.

PubMed

Gao, Yu; Han, Fei; Zhou, Ziwu; Cao, Minsong; Kaprealian, Tania; Kamrava, Mitchell; Wang, Chenyang; Neylon, John; Low, Daniel A; Yang, Yingli; Hu, Peng

2017-10-01

Monitoring tumor response during the course of treatment and adaptively modifying treatment plan based on tumor biological feedback may represent a new paradigm for radiotherapy. Diffusion MRI has shown great promises in assessing and predicting tumor response to radiotherapy. However, the conventional diffusion-weighted single-shot echo-planar-imaging (DW-ssEPI) technique suffers from limited resolution, severe distortion, and possibly inaccurate ADC at low field strength. The purpose of this work was to develop a reliable, accurate and distortion-free diffusion MRI technique that is practicable for longitudinal tumor response evaluation and adaptive radiotherapy on a 0.35 T MRI-guided radiotherapy system. A diffusion-prepared turbo spin echo readout (DP-TSE) sequence was developed and compared with the conventional diffusion-weighted single-shot echo-planar-imaging sequence on a 0.35 T MRI-guided radiotherapy system (ViewRay). A spatial integrity phantom was used to quantitate and compare the geometric accuracy of the two diffusion sequences for three orthogonal orientations. The apparent diffusion coefficient (ADC) accuracy was evaluated on a diffusion phantom under both 0 °C and room temperature to cover a diffusivity range between 0.40 × 10 -3 and 2.10 × 10 -3 mm 2 /s. Ten room temperature measurements repeated on five different days were conducted to assess the ADC reproducibility of DP-TSE. Two glioblastoma (GBM) and six sarcoma patients were included to examine the in vivo feasibility. The target registration error (TRE) was calculated to quantitate the geometric accuracy where structural CT or MR images were co-registered to the diffusion images as references. ADC maps from DP-TSE and DW-ssEPI were calculated and compared. A tube phantom was placed next to patients not treated on ViewRay, and ADCs of this reference tube were also compared. The proposed DP-TSE passed the spatial integrity test (< 1 mm within 100 mm radius and < 2 mm within 175 mm radius) under the three orthogonal orientations. The detected errors were 0.474 ± 0.355 mm, 0.475 ± 0.287 mm, and 0.546 ± 0.336 mm in the axial, coronal, and sagittal plane. DW-ssEPI, however, failed the tests due to severe distortion and low signal intensity. Noise correction must be performed for the DW-ssEPI to avoid ADC quantitation errors, whereas it is optional for DP-TSE. At 0 °C, the two sequences provided accurate quantitation with < 3% variation with the reference. In the room temperature study, discrepancies between ADCs from DP-TSE and the reference were within 4%, but could be as high as 8% for DW-ssEPI after the noise correction. Excellent ADC reproducibility with a coefficient of variation < 5% was observed among the 10 measurements of DP-TSE, indicating desirable robustness for ADC-based tumor response assessment. In vivo TRE in DP-TSE was less than 1.6 mm overall, whereas it could be greater than 12 mm in DW-ssEPI. For GBM patients, the CSF and brain tissue ADCs from DP-TSE were within the ranges found in literature. ADC differences between the two techniques were within 8% among the six sarcoma patients. For the reference tube that had a relatively low diffusivity, the two diffusion sequences provided matched measurements. A diffusion technique with excellent geometric fidelity, accurate, and reproducible ADC measurement was demonstrated for longitudinal tumor response assessment using a low-field MRI-guided radiotherapy system. © 2017 American Association of Physicists in Medicine.

Generating Ground Reference Data for a Global Impervious Surface Survey

NASA Technical Reports Server (NTRS)

Tilton, James C.; deColstoun, Eric Brown; Wolfe, Robert E.; Tan, Bin; Huang, Chengquan

2012-01-01

We are engaged in a project to produce a 30m impervious cover data set of the entire Earth for the years 2000 and 2010 based on the Landsat Global Land Survey (GLS) data set. The GLS data from Landsat provide an unprecedented opportunity to map global urbanization at this resolution for the first time, with unprecedented detail and accuracy. Moreover, the spatial resolution of Landsat is absolutely essential to accurately resolve urban targets such as buildings, roads and parking lots. Finally, with GLS data available for the 1975, 1990, 2000, and 2005 time periods, and soon for the 2010 period, the land cover/use changes due to urbanization can now be quantified at this spatial scale as well. Our approach works across spatial scales using very high spatial resolution commercial satellite data to both produce and evaluate continental scale products at the 30m spatial resolution of Landsat data. We are developing continental scale training data at 1m or so resolution and aggregating these to 30m for training a regression tree algorithm. Because the quality of the input training data are critical, we have developed an interactive software tool, called HSegLearn, to facilitate the photo-interpretation of high resolution imagery data, such as Quickbird or Ikonos data, into an impervious versus non-impervious map. Previous work has shown that photo-interpretation of high resolution data at 1 meter resolution will generate an accurate 30m resolution ground reference when coarsened to that resolution. Since this process can be very time consuming when using standard clustering classification algorithms, we are looking at image segmentation as a potential avenue to not only improve the training process but also provide a semi-automated approach for generating the ground reference data. HSegLearn takes as its input a hierarchical set of image segmentations produced by the HSeg image segmentation program [1, 2]. HSegLearn lets an analyst specify pixel locations as being either positive or negative examples, and displays a classification of the study area based on these examples. For our study, the positive examples are examples of impervious surfaces and negative examples are examples of non-impervious surfaces. HSegLearn searches the hierarchical segmentation from HSeg for the coarsest level of segmentation at which selected positive example locations do not conflict with negative example locations and labels the image accordingly. The negative example regions are always defined at the finest level of segmentation detail. The resulting classification map can be then further edited at a region object level using the previously developed HSegViewer tool [3]. After providing an overview of the HSeg image segmentation program, we provide a detailed description of the HSegLearn software tool. We then give examples of using HSegLearn to generate ground reference data and conclude with comments on the effectiveness of the HSegLearn tool.

Documentation for the machine-readable version of the lick Saturn-Voyager Reference Star Catalogue

NASA Technical Reports Server (NTRS)

Warren, W. H., Jr.

1982-01-01

The machine-readable version of the catalog is described. The catalog was prepared in order to determine accurate equatorial coordinates for reference stars in a band of sky against which cameras of the Voyager spacecraft were aligned for observations in the region of Saturn during the flyby. Tape contents and characteristics are described and a sample listing presented.

Diffusion-Weighted PROPELLER MRI for Quantitative Assessment of Liver Tumor Necrotic Fraction and Viable Tumor Volume in VX2 Rabbits

PubMed Central

Deng, Jie; Virmani, Sumeet; Young, Joseph; Harris, Kathleen; Yang, Guang-Yu; Rademaker, Alfred; Woloschak, Gayle; Omary, Reed A.; Larson, Andrew C.

2010-01-01

Purpose To test the hypothesis that diffusion-weighted (DW)-PROPELLER (periodically rotated overlapping parallel lines with enhanced reconstruction) MRI provides more accurate liver tumor necrotic fraction (NF) and viable tumor volume (VTV) measurements than conventional DW-SE-EPI (spin echo echo-planar imaging) methods. Materials and Methods Our institutional Animal Care and Use Committee approved all experiments. In six rabbits implanted with 10 VX2 liver tumors, DW-PROPELLER and DW-SE-EPI scans were performed at contiguous axial slice positions covering each tumor volume. Apparent diffusion coefficient maps of each tumor were used to generate spatially resolved tumor viability maps for NF and VTV measurements. We compared NF, whole tumor volume (WTV), and VTV measurements to corresponding reference standard histological measurements based on correlation and concordance coefficients and the Bland–Altman analysis. Results DW-PROPELLER generally improved image quality with less distortion compared to DW-SE-EPI. DW-PROPELLER NF, WTV, and VTV measurements were strongly correlated and satisfactorily concordant with histological measurements. DW-SE-EPI NF measurements were weakly correlated and poorly concordant with histological measurements. Bland–Altman analysis demonstrated that DWPROPELLER WTV and VTV measurements were less biased from histological measurements than the corresponding DW-SE-EPI measurements. Conclusion DW-PROPELLER MRI can provide spatially resolved liver tumor viability maps for accurate NF and VTV measurements, superior to DW-SE-EPI approaches. DWPROPELLER measurements may serve as a noninvasive surrogate for pathology, offering the potential for more accurate assessments of therapy response than conventional anatomic size measurements. PMID:18407540

MR diffusion-weighted imaging-based subcutaneous tumour volumetry in a xenografted nude mouse model using 3D Slicer: an accurate and repeatable method

PubMed Central

Ma, Zelan; Chen, Xin; Huang, Yanqi; He, Lan; Liang, Cuishan; Liang, Changhong; Liu, Zaiyi

2015-01-01

Accurate and repeatable measurement of the gross tumour volume(GTV) of subcutaneous xenografts is crucial in the evaluation of anti-tumour therapy. Formula and image-based manual segmentation methods are commonly used for GTV measurement but are hindered by low accuracy and reproducibility. 3D Slicer is open-source software that provides semiautomatic segmentation for GTV measurements. In our study, subcutaneous GTVs from nude mouse xenografts were measured by semiautomatic segmentation with 3D Slicer based on morphological magnetic resonance imaging(mMRI) or diffusion-weighted imaging(DWI)(b = 0,20,800 s/mm2) . These GTVs were then compared with those obtained via the formula and image-based manual segmentation methods with ITK software using the true tumour volume as the standard reference. The effects of tumour size and shape on GTVs measurements were also investigated. Our results showed that, when compared with the true tumour volume, segmentation for DWI(P = 0.060–0.671) resulted in better accuracy than that mMRI(P < 0.001) and the formula method(P < 0.001). Furthermore, semiautomatic segmentation for DWI(intraclass correlation coefficient, ICC = 0.9999) resulted in higher reliability than manual segmentation(ICC = 0.9996–0.9998). Tumour size and shape had no effects on GTV measurement across all methods. Therefore, DWI-based semiautomatic segmentation, which is accurate and reproducible and also provides biological information, is the optimal GTV measurement method in the assessment of anti-tumour treatments. PMID:26489359

Application of droplet digital PCR to determine copy number of endogenous genes and transgenes in sugarcane.

PubMed

Sun, Yue; Joyce, Priya Aiyar

2017-11-01

Droplet digital PCR combined with the low copy ACT allele as endogenous reference gene, makes accurate and rapid estimation of gene copy number in Q208 A and Q240 A attainable. Sugarcane is an important cultivated crop with both high polyploidy and aneuploidy in its 10 Gb genome. Without a known copy number reference gene, it is difficult to accurately estimate the copy number of any gene of interest by PCR-based methods in sugarcane. Recently, a new technology, known as droplet digital PCR (ddPCR) has been developed which can measure the absolute amount of the target DNA in a given sample. In this study, we deduced the true copy number of three endogenous genes, actin depolymerizing factor (ADF), adenine phosphoribosyltransferase (APRT) and actin (ACT) in three Australian sugarcane varieties, using ddPCR by comparing the absolute amounts of the above genes with a transgene of known copy number. A single copy of the ACT allele was detected in Q208 A , two copies in Q240 A , but was absent in Q117. Copy number variation was also observed for both APRT and ADF, and ranged from 9 to 11 in the three tested varieties. Using this newly developed ddPCR method, transgene copy number was successfully determined in 19 transgenic Q208 A and Q240 A events using ACT as the reference endogenous gene. Our study demonstrates that ddPCR can be used for high-throughput genetic analysis and is a quick, accurate and reliable alternative method for gene copy number determination in sugarcane. This discovered ACT allele would be a suitable endogenous reference gene for future gene copy number variation and dosage studies of functional genes in Q208 A and Q240 A .

U.S. Department of Energy Reference Model Program RM1: Experimental Results.

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

Hill, Craig; Neary, Vincent Sinclair; Gunawan, Budi

The Reference Model Project (RMP), sponsored by the U.S. Department of Energy’s (DOE) Wind and Water Power Technologies Program within the Office of Energy Efficiency & Renewable Energy (EERE), aims at expediting industry growth and efficiency by providing nonproprietary Reference Models (RM) of MHK technology designs as study objects for opensource research and development (Neary et al. 2014a,b). As part of this program, MHK turbine models were tested in a large open channel facility at the University of Minnesota’s St. Anthony Falls Laboratory (UMN-SAFL). Reference Model 1 (RM1) is a 1:40 geometric scale dual-rotor axial flow horizontal axis device withmore » counter-rotating rotors, each with a rotor diameter dT = 0.5m. Precise blade angular position and torque measurements were synchronized with three acoustic Doppler velocimeters (ADVs) aligned with each rotor and the midpoint for RM1. Flow conditions for each case were controlled such that depth, h = 1m, and volumetric flow rate, Qw = 2.425m3s-1, resulting in a hub height velocity of approximately Uhub = 1.05ms-1 and blade chord length Reynolds numbers of Rec ≈ 3.0x105. Vertical velocity profiles collected in the wake of each device from 1 to 10 rotor diameters are used to estimate the velocity recovery and turbulent characteristics in the wake, as well as the interaction of the counter-rotating rotor wakes. The development of this high resolution laboratory investigation provides a robust dataset that enables assessing turbulence performance models and their ability to accurately predict device performance metrics, including computational fluid dynamics (CFD) models that can be used to predict turbulent inflow environments, reproduce wake velocity deficit, recovery and higher order turbulent statistics, as well as device performance metrics.« less

Toward Automatic Georeferencing of Archival Aerial Photogrammetric Surveys

NASA Astrophysics Data System (ADS)

Giordano, S.; Le Bris, A.; Mallet, C.

2018-05-01

Images from archival aerial photogrammetric surveys are a unique and relatively unexplored means to chronicle 3D land-cover changes over the past 100 years. They provide a relatively dense temporal sampling of the territories with very high spatial resolution. Such time series image analysis is a mandatory baseline for a large variety of long-term environmental monitoring studies. The current bottleneck for accurate comparison between epochs is their fine georeferencing step. No fully automatic method has been proposed yet and existing studies are rather limited in terms of area and number of dates. State-of-the art shows that the major challenge is the identification of ground references: cartographic coordinates and their position in the archival images. This task is manually performed, and extremely time-consuming. This paper proposes to use a photogrammetric approach, and states that the 3D information that can be computed is the key to full automation. Its original idea lies in a 2-step approach: (i) the computation of a coarse absolute image orientation; (ii) the use of the coarse Digital Surface Model (DSM) information for automatic absolute image orientation. It only relies on a recent orthoimage+DSM, used as master reference for all epochs. The coarse orthoimage, compared with such a reference, allows the identification of dense ground references and the coarse DSM provides their position in the archival images. Results on two areas and 5 dates show that this method is compatible with long and dense archival aerial image series. Satisfactory planimetric and altimetric accuracies are reported, with variations depending on the ground sampling distance of the images and the location of the Ground Control Points.

Accurate registration of temporal CT images for pulmonary nodules detection

NASA Astrophysics Data System (ADS)

Yan, Jichao; Jiang, Luan; Li, Qiang

2017-02-01

Interpretation of temporal CT images could help the radiologists to detect some subtle interval changes in the sequential examinations. The purpose of this study was to develop a fully automated scheme for accurate registration of temporal CT images for pulmonary nodule detection. Our method consisted of three major registration steps. Firstly, affine transformation was applied in the segmented lung region to obtain global coarse registration images. Secondly, B-splines based free-form deformation (FFD) was used to refine the coarse registration images. Thirdly, Demons algorithm was performed to align the feature points extracted from the registered images in the second step and the reference images. Our database consisted of 91 temporal CT cases obtained from Beijing 301 Hospital and Shanghai Changzheng Hospital. The preliminary results showed that approximately 96.7% cases could obtain accurate registration based on subjective observation. The subtraction images of the reference images and the rigid and non-rigid registered images could effectively remove the normal structures (i.e. blood vessels) and retain the abnormalities (i.e. pulmonary nodules). This would be useful for the screening of lung cancer in our future study.

Ray Effect Mitigation Through Reference Frame Rotation

DOE PAGES

Tencer, John

2016-05-01

The discrete ordinates method is a popular and versatile technique for solving the radiative transport equation, a major drawback of which is the presence of ray effects. Mitigation of ray effects can yield significantly more accurate results and enhanced numerical stability for combined mode codes. Moreover, when ray effects are present, the solution is seen to be highly dependent upon the relative orientation of the geometry and the global reference frame. It is an undesirable property. A novel ray effect mitigation technique of averaging the computed solution for various reference frame orientations is proposed.

Accurate determination of the geoid undulation N

NASA Astrophysics Data System (ADS)

Lambrou, E.; Pantazis, G.; Balodimos, D. D.

2003-04-01

This work is related to the activities of the CERGOP Study Group Geodynamics of the Balkan Peninsula, presents a method for the determination of the variation ΔN and, indirectly, of the geoid undulation N with an accuracy of a few millimeters. It is based on the determination of the components xi, eta of the deflection of the vertical using modern geodetic instruments (digital total station and GPS receiver). An analysis of the method is given. Accuracy of the order of 0.01arcsec in the estimated values of the astronomical coordinates Φ and Δ is achieved. The result of applying the proposed method in an area around Athens is presented. In this test application, a system is used which takes advantage of the capabilities of modern geodetic instruments. The GPS receiver permits the determination of the geodetic coordinates at a chosen reference system and, in addition, provides accurate timing information. The astronomical observations are performed through a digital total station with electronic registering of angles and time. The required accuracy of the values of the coordinates is achieved in about four hours of fieldwork. In addition, the instrumentation is lightweight, easily transportable and can be setup in the field very quickly. Combined with a stream-lined data reduction procedure and the use of up-to-date astrometric data, the values of the components xi, eta of the deflection of the vertical and, eventually, the changes ΔN of the geoid undulation are determined easily and accurately. In conclusion, this work demonstrates that it is quite feasible to create an accurate map of the geoid undulation, especially in areas that present large geoid variations and other methods are not capable to give accurate and reliable results.

Reference values for developing responsive functional outcome measures across the lifespan.

PubMed

McKay, Marnee J; Baldwin, Jennifer N; Ferreira, Paulo; Simic, Milena; Vanicek, Natalie; Burns, Joshua

2017-04-18

To generate a reference dataset of commonly performed functional outcome measures in 1,000 children and adults and investigate the influence of demographic, anthropometric, strength, and flexibility characteristics. Twelve functional outcome measures were collected from 1,000 healthy individuals aged 3-101 years: 6-minute walk test, 30-second chair stand test, timed stairs test, long jump, vertical jump, choice stepping reaction time, balance (Star Excursion Balance Test, tandem stance eyes open and closed, single-leg stance eyes closed), and dexterity (9-hole peg test, Functional Dexterity Test). Correlation and multiple regression analyses were performed to identify factors independently associated with each measure. Age- and sex-stratified reference values for functional outcome measures were generated. Functional performance increased through childhood and adolescence, plateaued during adulthood, and declined in older adulthood. While balance did not differ between the sexes, male participants generally performed better at gross motor tasks while female participants performed better at dexterous tasks. Height was the most consistent correlate of functional performance in children, while lower limb muscle strength was a major determinant in adolescents and adults. In older adults, age, lower limb strength, and joint flexibility explained up to 63% of the variance in functional measures. These normative reference values provide a framework to accurately track functional decline associated with neuromuscular disorders and assist development and validation of responsive outcome measures for therapeutic trials. © 2017 American Academy of Neurology.

Achievements and Future Directions of the APFCB Mass Spectrometry Harmonisation Project on Serum Testosterone.

PubMed

Greaves, Ronda F; Ho, Chung S; Hoad, Kirsten E; Joseph, John; McWhinney, Brett; Gill, Janice P; Koal, Therese; Fouracre, Chris; Iu, Heidi P; Cooke, Brian R; Boyder, Conchita; Pham, Hai T; Jolly, Lisa M

2016-05-01

As an outcome of the 2010 Asian Pacific Conference for Chromatography and Mass Spectrometry in Hong Kong, a collaborative working group was formed to promote the harmonisation of mass spectrometry methods. The Mass Spectrometry Harmonisation Working Group resides under the combined auspices of the Asia-Pacific Federation for Clinical Biochemistry and Laboratory Medicine (APFCB) and the Australasian Association of Clinical Biochemists (AACB). A decision was made to initially focus attention on serum steroids due to the common interest of members in this area; with the first steroid to assess being testosterone. In principle, full standardisation with traceability should be achievable for all steroids as they are small compounds with defined molecular weight and structure. In order to achieve this we need certified reference materials, reference methods, reference laboratories, reference intervals and external quality assurance programs; each being an important pillar in the process. When all the pillars are present, such as for serum testosterone, it is feasible to fully standardise the liquid chromatography - tandem mass spectrometry (LC-MS/MS) methods. In a collaborative process with interested stakeholders, we commenced on a pathway to provide ongoing assessment and seek opportunities for improvement in the LC-MS/MS methods for serum steroids. Here we discuss the outcomes to date and major challenges related to the accurate measurement of serum steroids with a focus on serum testosterone.

Portable digital lock-in instrument to determine chemical constituents with single-color absorption measurements for Global Health Initiatives

NASA Astrophysics Data System (ADS)

Vacas-Jacques, Paulino; Linnes, Jacqueline; Young, Anna; Gerrard, Victoria; Gomez-Marquez, Jose

2014-03-01

Innovations in international health require the use of state-of-the-art technology to enable clinical chemistry for diagnostics of bodily fluids. We propose the implementation of a portable and affordable lock-in amplifier-based instrument that employs digital technology to perform biochemical diagnostics on blood, urine, and other fluids. The digital instrument is composed of light source and optoelectronic sensor, lock-in detection electronics, microcontroller unit, and user interface components working with either power supply or batteries. The instrument performs lock-in detection provided that three conditions are met. First, the optoelectronic signal of interest needs be encoded in the envelope of an amplitude-modulated waveform. Second, the reference signal required in the demodulation channel has to be frequency and phase locked with respect to the optoelectronic carrier signal. Third, the reference signal should be conditioned appropriately. We present three approaches to condition the signal appropriately: high-pass filtering the reference signal, precise offset tuning the reference level by low-pass filtering, and by using a voltage divider network. We assess the performance of the lock-in instrument by comparing it to a benchmark device and by determining protein concentration with single-color absorption measurements. We validate the concentration values obtained with the proposed instrument using chemical concentration measurements. Finally, we demonstrate that accurate retrieval of phase information can be achieved by using the same instrument.

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

Vacas-Jacques, Paulino; Wellman Center for Photomedicine and Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts 02114; Linnes, Jacqueline

Innovations in international health require the use of state-of-the-art technology to enable clinical chemistry for diagnostics of bodily fluids. We propose the implementation of a portable and affordable lock-in amplifier-based instrument that employs digital technology to perform biochemical diagnostics on blood, urine, and other fluids. The digital instrument is composed of light source and optoelectronic sensor, lock-in detection electronics, microcontroller unit, and user interface components working with either power supply or batteries. The instrument performs lock-in detection provided that three conditions are met. First, the optoelectronic signal of interest needs be encoded in the envelope of an amplitude-modulated waveform. Second,more » the reference signal required in the demodulation channel has to be frequency and phase locked with respect to the optoelectronic carrier signal. Third, the reference signal should be conditioned appropriately. We present three approaches to condition the signal appropriately: high-pass filtering the reference signal, precise offset tuning the reference level by low-pass filtering, and by using a voltage divider network. We assess the performance of the lock-in instrument by comparing it to a benchmark device and by determining protein concentration with single-color absorption measurements. We validate the concentration values obtained with the proposed instrument using chemical concentration measurements. Finally, we demonstrate that accurate retrieval of phase information can be achieved by using the same instrument.« less

The distribution of the bats of South Carolina

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

Menzel, Jennifer M.; Menzel, Michael A.; Ford, W. Mark

Menzel. J.M., M.A. Menzel, W.M. Ford, J.W. Edwards, S.R. Sheffield, J.C. Kilgo, and M.S. Bunch. 2003. The distribution of the bats of South Carolina. Southeastern Nat. 2(1): 121-152. There is a paucity of information available about the distribution of bats in the southeastern United States. We synthesized records from museums, bat captures, and bats submitted for rabies testing to provide a more accurate and useful distribution for natural resource managers and those planning to research bats in South Carolina. Distributional information, including maps, collection localities within counties, and literature references, for all 14 species of bats that occur in Southmore » Carolina, has never been synthesized. To provide better information on the state's bat fauna, we have updated distributions for all species that occur in South Carolina.« less

Magnetic Resonance-Guided High-Intensity Focused Ultrasound (MR-HIFU) in Treatment of Symptomatic Uterine Myomas

PubMed Central

Filipowska, Justyna; Łoziński, Tomasz

2014-01-01

Summary Magnetic Resonance-guided High-Intensity Focused Ultrasound (MR-HIFU) is a noninvasive technique for ablation therapy for uterine myomas, where focused ultrasound energy beam generates localized high temperature in the selected area and coagulates chosen tissue, leaving the skin and tissues in between unharmed. Magnetic resonance imaging enables accurate targeting for HIFU as well as temperature monitoring during treatment. MR guidance with 3D anatomical imaging provides reference data for treatment planning, while real-time temperature monitoring aids in controlling ablation process. This review provides basic information regarding methodology, clinical indications for this kind of treatment, expected outcome and patient management during MR-HIFU procedure. The aim of this work is to introduce a new, noninvasive treatment method for uterine leiomyomas and to present a comparison with other currently used methods. PMID:25469176

Magnetic Resonance-Guided High-Intensity Focused Ultrasound (MR-HIFU) in Treatment of Symptomatic Uterine Myomas.

PubMed

Filipowska, Justyna; Loziński, Tomasz

2014-01-01

Magnetic Resonance-guided High-Intensity Focused Ultrasound (MR-HIFU) is a noninvasive technique for ablation therapy for uterine myomas, where focused ultrasound energy beam generates localized high temperature in the selected area and coagulates chosen tissue, leaving the skin and tissues in between unharmed. Magnetic resonance imaging enables accurate targeting for HIFU as well as temperature monitoring during treatment. MR guidance with 3D anatomical imaging provides reference data for treatment planning, while real-time temperature monitoring aids in controlling ablation process. This review provides basic information regarding methodology, clinical indications for this kind of treatment, expected outcome and patient management during MR-HIFU procedure. The aim of this work is to introduce a new, noninvasive treatment method for uterine leiomyomas and to present a comparison with other currently used methods.

orthoFind Facilitates the Discovery of Homologous and Orthologous Proteins.

PubMed

Mier, Pablo; Andrade-Navarro, Miguel A; Pérez-Pulido, Antonio J

2015-01-01

Finding homologous and orthologous protein sequences is often the first step in evolutionary studies, annotation projects, and experiments of functional complementation. Despite all currently available computational tools, there is a requirement for easy-to-use tools that provide functional information. Here, a new web application called orthoFind is presented, which allows a quick search for homologous and orthologous proteins given one or more query sequences, allowing a recurrent and exhaustive search against reference proteomes, and being able to include user databases. It addresses the protein multidomain problem, searching for homologs with the same domain architecture, and gives a simple functional analysis of the results to help in the annotation process. orthoFind is easy to use and has been proven to provide accurate results with different datasets. Availability: http://www.bioinfocabd.upo.es/orthofind/.

Faculty development for the evaluation system: a dual agenda

PubMed Central

Oller, Kellee L; Mai, Cuc T; Ledford, Robert J; O’Brien, Kevin E

2017-01-01

Faculty development for the evaluation process serves two distinct goals. The first goal is to improve the quality of the evaluations submitted by the faculty. Providing an accurate assessment of a learner’s capabilities is a skill and, similar to other skills, can be developed with training. Frame-of-reference training serves to calibrate the faculty’s standard of performance and build a uniform language of the evaluation. Second, areas for faculty professional growth can be identified from data generated from learners’ evaluations of the faculty using narrative comments, item-level comparison reports, and comparative rank list information. This paper presents an innovative model, grounded in institutional experience and review of the literature, to provide feedback to faculty evaluators, thereby improving the reliability of the evaluation process, and motivating the professional growth of faculty as educators. PMID:28331382

Echo

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

Harvey, Dustin Yewell

This document is a white paper marketing proposal for Echo™ is a data analysis platform designed for efficient, robust, and scalable creation and execution of complex workflows. Echo’s analysis management system refers to the ability to track, understand, and reproduce workflows used for arriving at results and decisions. Echo improves on traditional scripted data analysis in MATLAB, Python, R, and other languages to allow analysts to make better use of their time. Additionally, the Echo platform provides a powerful data management and curation solution allowing analysts to quickly find, access, and consume datasets. After two years of development and amore » first release in early 2016, Echo is now available for use with many data types in a wide range of application domains. Echo provides tools that allow users to focus on data analysis and decisions with confidence that results are reported accurately.« less

JSC almanac

NASA Technical Reports Server (NTRS)

1993-01-01

During America's space shuttle flights, press and public attention focuses on the Johnson Space Center in Houston. The press and public often put questions to JSC technical and management staff. This fourth JSC Almanac supplies answers for many such questions, and provide an informational resource for speeches to general interest groups. This Almanac is not necessarily comprehensive or definitive. It is not intended as a statement of JSC or NASA policy. However, it does provide a much needed compilation of information from diverse sources. These sources are given as references, permitting the reader to obtain additional information as required. While every effort has been made to ensure accuracy and to reconcile statistics, users requiring the most up-to-date and accurate information should contact the office supplying the information at issue. The Almanac is updated periodically as needed. The following offices were responsible for supplying material for this update.

Interferometric scanning optical microscope for surface characterization.

PubMed

Offside, M J; Somekh, M G

1992-11-01

A phase-sensitive scanning optical microscope is described that can measure surface height changes down to 0.1 nm. This is achieved by using two heterodyne Michelson interferometers in parallel. One interferometer probes the sample with a tightly focused beam, and the second has a collimated beam that illuminates a large area of the surface, providing a large area on sample reference. This is facilitated by using a specially constructed objective lens that permits the relative areas illuminated by the two probe beams to be varied both arbitrarily and independently, thus ensuring an accurate absolute phase measurement. We subtracted the phase outputs from each interferometer to provide the sample phase information, canceling the phase noise resulting from microphonics in the process. Results from a prototype version of the microscope are presented that demonstrate the advantages of the system over existing techniques.

How accurate are quotations and references in medical journals?

PubMed

de Lacey, G; Record, C; Wade, J

1985-09-28

The accuracy of quotations and references in six medical journals published during January 1984 was assessed. The original author was misquoted in 15% of all references, and most of the errors would have misled readers. Errors in citation of references occurred in 24%, of which 8% were major errors--that is, they prevented immediate identification of the source of the reference. Inaccurate quotations and citations are displeasing for the original author, misleading for the reader, and mean that untruths become "accepted fact." Some suggestions for reducing these high levels of inaccuracy are that papers scheduled for publication with errors of citation should be returned to the author and checked completely and a permanent column specifically for misquotations could be inserted into the journal.

How accurate are quotations and references in medical journals?

PubMed Central

de Lacey, G; Record, C; Wade, J

1985-01-01

The accuracy of quotations and references in six medical journals published during January 1984 was assessed. The original author was misquoted in 15% of all references, and most of the errors would have misled readers. Errors in citation of references occurred in 24%, of which 8% were major errors--that is, they prevented immediate identification of the source of the reference. Inaccurate quotations and citations are displeasing for the original author, misleading for the reader, and mean that untruths become "accepted fact." Some suggestions for reducing these high levels of inaccuracy are that papers scheduled for publication with errors of citation should be returned to the author and checked completely and a permanent column specifically for misquotations could be inserted into the journal. PMID:3931753

[Rapidly identify oligosaccharides in Morinda officinalis by UPLC-Q-TOF-MSE].

PubMed

Hao, Qing-Xiu; Kang, Li-Ping; Zhu, Shou-Dong; Yu, Yi; Hu, Ming-Hua; Ma, Fang-Li; Zhou, Jie; Guo, Lan-Ping

2018-03-01

In this paper, an approach was applied for separation and identification of oligosaccharides in Morinda officinalis How by Ultra performance liquid chromatography/quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS) with collision energy. The separation was carried out on an ACQUITY UPLC BEH Amide C₁₈(2.1mm×100 mm，1.7 μm) with gradient elution using acetonitrile(A) and water(B) containing 0.1% ammonia as mobile phase at a flow rate of 0.2 mL·min⁻¹. The column temperature was maintained at 40 °C. The information of accurate mass and characteristic fragment ion were acquired by MSE in ESI negative mode in low and high collision energy. The chemical structures and formula of oligosaccharides were obtained and identified by the software of UNIFI and Masslynx 4.1 based on the accurate mass, fragment ions, neutral losses, mass error, reference substance, isotope information, the intensity of fragments, and retention time. A total of 19 inulin oligosaccharide structures were identified including D(+)-sucrose, 1-kestose, nystose, 1F-fructofuranosyl nystose and other inulin oligosaccharides (DP 5-18). This research provided important information about the inulin oligosaccharides in M. officinalis. The results would provide scientific basis for innovative utilization of M. officinalis. Copyright© by the Chinese Pharmaceutical Association.

A Fiber Bragg Grating-Based Monitoring System for Roof Safety Control in Underground Coal Mining

PubMed Central

Zhao, Yiming; Zhang, Nong; Si, Guangyao

2016-01-01

Monitoring of roof activity is a primary measure adopted in the prevention of roof collapse accidents and functions to optimize and support the design of roadways in underground coalmines. However, traditional monitoring measures, such as using mechanical extensometers or electronic gauges, either require arduous underground labor or cannot function properly in the harsh underground environment. Therefore, in this paper, in order to break through this technological barrier, a novel monitoring system for roof safety control in underground coal mining, using fiber Bragg grating (FBG) material as a perceived element and transmission medium, has been developed. Compared with traditional monitoring equipment, the developed, novel monitoring system has the advantages of providing accurate, reliable, and continuous online monitoring of roof activities in underground coal mining. This is expected to further enable the prevention of catastrophic roof collapse accidents. The system has been successfully implemented at a deep hazardous roadway in Zhuji Coal Mine, China. Monitoring results from the study site have demonstrated the advantages of FBG-based sensors over traditional monitoring approaches. The dynamic impacts of progressive face advance on roof displacement and stress have been accurately captured by the novel roadway roof activity and safety monitoring system, which provided essential references for roadway support and design of the mine. PMID:27775657

Review of Advances in Cobb Angle Calculation and Image-Based Modelling Techniques for Spinal Deformities

NASA Astrophysics Data System (ADS)

Giannoglou, V.; Stylianidis, E.

2016-06-01

Scoliosis is a 3D deformity of the human spinal column that is caused from the bending of the latter, causing pain, aesthetic and respiratory problems. This internal deformation is reflected in the outer shape of the human back. The golden standard for diagnosis and monitoring of scoliosis is the Cobb angle, which refers to the internal curvature of the trunk. This work is the first part of a post-doctoral research, presenting the most important researches that have been done in the field of scoliosis, concerning its digital visualisation, in order to provide a more precise and robust identification and monitoring of scoliosis. The research is divided in four fields, namely, the X-ray processing, the automatic Cobb angle(s) calculation, the 3D modelling of the spine that provides a more accurate representation of the trunk and the reduction of X-ray radiation exposure throughout the monitoring of scoliosis. Despite the fact that many researchers have been working on the field for the last decade at least, there is no reliable and universal tool to automatically calculate the Cobb angle(s) and successfully perform proper 3D modelling of the spinal column that would assist a more accurate detection and monitoring of scoliosis.

Laryngeal High-Speed Videoendoscopy: Rationale and Recommendation for Accurate and Consistent Terminology

PubMed Central

Deliyski, Dimitar D.; Hillman, Robert E.

2015-01-01

Purpose The authors discuss the rationale behind the term laryngeal high-speed videoendoscopy to describe the application of high-speed endoscopic imaging techniques to the visualization of vocal fold vibration. Method Commentary on the advantages of using accurate and consistent terminology in the field of voice research is provided. Specific justification is described for each component of the term high-speed videoendoscopy, which is compared and contrasted with alternative terminologies in the literature. Results In addition to the ubiquitous high-speed descriptor, the term endoscopy is necessary to specify the appropriate imaging technology and distinguish among modalities such as ultrasound, magnetic resonance imaging, and nonendoscopic optical imaging. Furthermore, the term video critically indicates the electronic recording of a sequence of optical still images representing scenes in motion, in contrast to strobed images using high-speed photography and non-optical high-speed magnetic resonance imaging. High-speed videoendoscopy thus concisely describes the technology and can be appended by the desired anatomical nomenclature such as laryngeal. Conclusions Laryngeal high-speed videoendoscopy strikes a balance between conciseness and specificity when referring to the typical high-speed imaging method performed on human participants. Guidance for the creation of future terminology provides clarity and context for current and future experiments and the dissemination of results among researchers. PMID:26375398

Accuracy of buffered-force QM/MM simulations of silica

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

Peguiron, Anke; Moras, Gianpietro; Colombi Ciacchi, Lucio

2015-02-14

We report comparisons between energy-based quantum mechanics/molecular mechanics (QM/MM) and buffered force-based QM/MM simulations in silica. Local quantities—such as density of states, charges, forces, and geometries—calculated with both QM/MM approaches are compared to the results of full QM simulations. We find the length scale over which forces computed using a finite QM region converge to reference values obtained in full quantum-mechanical calculations is ∼10 Å rather than the ∼5 Å previously reported for covalent materials such as silicon. Electrostatic embedding of the QM region in the surrounding classical point charges gives only a minor contribution to the force convergence. Whilemore » the energy-based approach provides accurate results in geometry optimizations of point defects, we find that the removal of large force errors at the QM/MM boundary provided by the buffered force-based scheme is necessary for accurate constrained geometry optimizations where Si–O bonds are elongated and for finite-temperature molecular dynamics simulations of crack propagation. Moreover, the buffered approach allows for more flexibility, since special-purpose QM/MM coupling terms that link QM and MM atoms are not required and the region that is treated at the QM level can be adaptively redefined during the course of a dynamical simulation.« less

Development of a Star Tracker-Based Reference System for Accurate Attitude Determination of a Simulated Spacecraft

DTIC Science & Technology

2012-03-01

the mathematical pretext for quaternions, which summarizes as: In three- dimensional space , any displacement of a rigid body such that a ...for the patch board was selected, with a uniform 8 mm spacing between LED centers. Figure 33 is schematic of the patch board layout, and Fig. 34 shows...attitude determination since the dawn of the space age. Without accurate attitude determination, a “Lost- in-

Hematology of camelids.

PubMed

Vap, Linda; Bohn, Andrea A

2015-01-01

Interpretation of camelid hematology results is similar to that of other mammals. Obtaining accurate results and using appropriate reference intervals can be a bit problematic, particularly when evaluating the erythron. Camelid erythrocytes vary from other mammals in that they are small, flat, and elliptical. This variation makes data obtained from samples collected from these species prone to error when using some automated instruments. Normal and abnormal findings in camelid blood are reviewed as well as how to ensure accurate results.

Engaging Australian Aboriginal narratives to challenge attitudes and create empathy in health care: a methodological perspective.

PubMed

Wain, Toni; Sim, Moira; Bessarab, Dawn; Mak, Donna; Hayward, Colleen; Rudd, Cobie

2016-06-02

Unconscious bias and negative attitudes towards minority groups have detrimental effects on the way health care is, or is not, provided to these groups. Recognition of racist attitudes and behaviours as well as understanding clients' experiences of health and health care are pivotal to developing better health care strategies to positively impact on the quality and safety of care provided to Indigenous people. Indigenous research demands inclusive research processes and the use of culturally appropriate methodologies. This paper presents a methodological account of collecting narratives which accurately and respectfully reflect Aboriginal Australians' experiences with health care in Western Australia. The purpose of these narratives is to provide health students and professionals with an opportunity to 'walk-in the shoes' of Aboriginal people where face-to-face interaction is not feasible. With the incorporation of Indigenous peoples' voices being an important link in cultural safety, the project was led by an Indigenous Reference group, who encouraged active participation of Aboriginal people in all areas of the project. Using a phenomenological approach and guided by the Indigenous Reference group, yarning data collection was implemented to collect stories focusing on Aboriginal people's experiences with health care services. An open-access, on-line website was established to host education resources developed from these "yarns". Yarning provided a rich source of information on personal experiences and encouraged the story provider to recognise their facilitative role in the research process. While the methodology used in this project was lengthy and labour-intensive it afforded a respectful manner for story collection and highlighted several innate flaws when Western methods are applied to an Indigenous context. Engagement of an Indigenous Reference Group was pivotal to designing an appropriate methodology that incorporated the voices of Aboriginal people in a multimedia resource of Aboriginal narratives. However further research is warranted to understand how the resources are being used and integrated into curricula, and their impact on students and health care outcomes.

GNSS Radio Occultation Excess Phase Processing with Integrated Uncertainty Estimation for Thermodynamic Cal/Val of Passive Atmospheric Sounders and Climate Science

NASA Astrophysics Data System (ADS)

Innerkofler, J.; Pock, C.; Kirchengast, G.; Schwaerz, M.; Jaeggi, A.; Andres, Y.; Marquardt, C.; Hunt, D.; Schreiner, W. S.; Schwarz, J.

2017-12-01

Global Navigation Satellite System (GNSS) radio occultation (RO) is a highly valuable satellite remote sensing technique for atmospheric and climate sciences, including calibration and validation (cal/val) of passive sounding instruments such as radiometers. It is providing accurate and precise measurements in the troposphere and stratosphere regions with global coverage, long-term stability, and virtually all-weather capability since 2001. For fully exploiting the potential of RO data as a cal/val reference and climate data record, uncertainties attributed to the data need to be assessed. Here we focus on the atmospheric excess phase data, based on the raw occultation tracking and orbit data, and its integrated uncertainty estimation within the new Reference Occultation Processing System (rOPS) developed at the WEGC. These excess phases correspond to integrated refractivity, proportional to pressure/temperature and water vapor, and are therefore highly valuable reference data for thermodynamic cal/val of passive (radiometric) sounder data. In order to enable high accuracy of the excess phase profiles, accurate orbit positions and velocities as well as clock estimates of the GNSS transmitter satellites and RO receiver satellites are determined using the Bernese and Napeos orbit determination software packages. We find orbit uncertainty estimates of about 5 cm (position) / 0.05 mm/s (velocity) for daily orbits for the MetOp, GRACE, and CHAMP RO missions, and decreased uncertainty estimates near 20 cm (position) / 0.2 mm/s (velocity) for the COSMIC RO mission. The strict evaluation and quality control of the position, velocity, and clock accuracies of the daily LEO and GNSS orbits assure smallest achievable uncertainties in the excess phase data. We compared the excess phase profiles from WEGC against profiles from EUMETSAT and UCAR. Results show good agreement in line with the estimated uncertainties, with millimetric differences in the upper stratosphere and mesosphere and centimetric differences in the troposphere, where the excess phases amount to beyond 100 m. This underlines the potential for a new fundamental cal/val reference and climate data record based on atmospheric excess phases from RO, given their narrow uncertainty and independence from background data.

Comparison of the accuracy of cone beam computed tomography and medical computed tomography: implications for clinical diagnostics with guided surgery.

PubMed

Abboud, Marcus; Calvo-Guirado, Jose Luis; Orentlicher, Gary; Wahl, Gerhard

2013-01-01

This study compared the accuracy of cone beam computed tomography (CBCT) and medical-grade CT in the context of evaluating the diagnostic value and accuracy of fiducial marker localization for reference marker-based guided surgery systems. Cadaver mandibles with attached radiopaque gutta-percha markers, as well as glass balls and composite cylinders of known dimensions, were measured manually with a highly accurate digital caliper. The objects were then scanned using a medical-grade CT scanner (Philips Brilliance 64) and five different CBCT scanners (Sirona Galileos, Morita 3D Accuitomo 80, Vatech PaX-Reve3D, 3M Imtech Iluma, and Planmeca ProMax 3D). The data were then imported into commercially available software, and measurements were made of the scanned markers and objects. CT and CBCT measurements were compared to each other and to the caliper measurements. The difference between the CBCT measurements and the caliper measurements was larger than the difference between the CT measurements and the caliper measurements. Measurements of the cadaver mandible and the geometric reference markers were highly accurate with CT. The average absolute errors of the human mandible measurements were 0.03 mm for CT and 0.23 mm for CBCT. The measurement errors of the geometric objects based on CT ranged between 0.00 and 0.12 mm, compared to an error range between 0.00 and 2.17 mm with the CBCT scanners. CT provided the most accurate images in this study, closely followed by one CBCT of the five tested. Although there were differences in the distance measurements of the hard tissue of the human mandible between CT and CBCT, these differences may not be of clinical significance for most diagnostic purposes. The fiducial marker localization error caused by some CBCT scanners may be a problem for guided surgery systems.

A comparative study on different methods of automatic mesh generation of human femurs.

PubMed

Viceconti, M; Bellingeri, L; Cristofolini, L; Toni, A

1998-01-01

The aim of this study was to evaluate comparatively five methods for automating mesh generation (AMG) when used to mesh a human femur. The five AMG methods considered were: mapped mesh, which provides hexahedral elements through a direct mapping of the element onto the geometry; tetra mesh, which generates tetrahedral elements from a solid model of the object geometry; voxel mesh which builds cubic 8-node elements directly from CT images; and hexa mesh that automatically generated hexahedral elements from a surface definition of the femur geometry. The various methods were tested against two reference models: a simplified geometric model and a proximal femur model. The first model was useful to assess the inherent accuracy of the meshes created by the AMG methods, since an analytical solution was available for the elastic problem of the simplified geometric model. The femur model was used to test the AMG methods in a more realistic condition. The femoral geometry was derived from a reference model (the "standardized femur") and the finite element analyses predictions were compared to experimental measurements. All methods were evaluated in terms of human and computer effort needed to carry out the complete analysis, and in terms of accuracy. The comparison demonstrated that each tested method deserves attention and may be the best for specific situations. The mapped AMG method requires a significant human effort but is very accurate and it allows a tight control of the mesh structure. The tetra AMG method requires a solid model of the object to be analysed but is widely available and accurate. The hexa AMG method requires a significant computer effort but can also be used on polygonal models and is very accurate. The voxel AMG method requires a huge number of elements to reach an accuracy comparable to that of the other methods, but it does not require any pre-processing of the CT dataset to extract the geometry and in some cases may be the only viable solution.

Identification and Validation of Reference Genes and Their Impact on Normalized Gene Expression Studies across Cultivated and Wild Cicer Species

PubMed Central

Reddy, Palakolanu Sudhakar; Sri Cindhuri, Katamreddy; Sivaji Ganesh, Adusumalli; Sharma, Kiran Kumar

2016-01-01

Quantitative Real-Time PCR (qPCR) is a preferred and reliable method for accurate quantification of gene expression to understand precise gene functions. A total of 25 candidate reference genes including traditional and new generation reference genes were selected and evaluated in a diverse set of chickpea samples. The samples used in this study included nine chickpea genotypes (Cicer spp.) comprising of cultivated and wild species, six abiotic stress treatments (drought, salinity, high vapor pressure deficit, abscisic acid, cold and heat shock), and five diverse tissues (leaf, root, flower, seedlings and seed). The geNorm, NormFinder and RefFinder algorithms used to identify stably expressed genes in four sample sets revealed stable expression of UCP and G6PD genes across genotypes, while TIP41 and CAC were highly stable under abiotic stress conditions. While PP2A and ABCT genes were ranked as best for different tissues, ABCT, UCP and CAC were most stable across all samples. This study demonstrated the usefulness of new generation reference genes for more accurate qPCR based gene expression quantification in cultivated as well as wild chickpea species. Validation of the best reference genes was carried out by studying their impact on normalization of aquaporin genes PIP1;4 and TIP3;1, in three contrasting chickpea genotypes under high vapor pressure deficit (VPD) treatment. The chickpea TIP3;1 gene got significantly up regulated under high VPD conditions with higher relative expression in the drought susceptible genotype, confirming the suitability of the selected reference genes for expression analysis. This is the first comprehensive study on the stability of the new generation reference genes for qPCR studies in chickpea across species, different tissues and abiotic stresses. PMID:26863232

Identification and Validation of Reference Genes and Their Impact on Normalized Gene Expression Studies across Cultivated and Wild Cicer Species.

PubMed

Reddy, Dumbala Srinivas; Bhatnagar-Mathur, Pooja; Reddy, Palakolanu Sudhakar; Sri Cindhuri, Katamreddy; Sivaji Ganesh, Adusumalli; Sharma, Kiran Kumar

2016-01-01

Quantitative Real-Time PCR (qPCR) is a preferred and reliable method for accurate quantification of gene expression to understand precise gene functions. A total of 25 candidate reference genes including traditional and new generation reference genes were selected and evaluated in a diverse set of chickpea samples. The samples used in this study included nine chickpea genotypes (Cicer spp.) comprising of cultivated and wild species, six abiotic stress treatments (drought, salinity, high vapor pressure deficit, abscisic acid, cold and heat shock), and five diverse tissues (leaf, root, flower, seedlings and seed). The geNorm, NormFinder and RefFinder algorithms used to identify stably expressed genes in four sample sets revealed stable expression of UCP and G6PD genes across genotypes, while TIP41 and CAC were highly stable under abiotic stress conditions. While PP2A and ABCT genes were ranked as best for different tissues, ABCT, UCP and CAC were most stable across all samples. This study demonstrated the usefulness of new generation reference genes for more accurate qPCR based gene expression quantification in cultivated as well as wild chickpea species. Validation of the best reference genes was carried out by studying their impact on normalization of aquaporin genes PIP1;4 and TIP3;1, in three contrasting chickpea genotypes under high vapor pressure deficit (VPD) treatment. The chickpea TIP3;1 gene got significantly up regulated under high VPD conditions with higher relative expression in the drought susceptible genotype, confirming the suitability of the selected reference genes for expression analysis. This is the first comprehensive study on the stability of the new generation reference genes for qPCR studies in chickpea across species, different tissues and abiotic stresses.

Candidate Reference Genes Selection and Application for RT-qPCR Analysis in Kenaf with Cytoplasmic Male Sterility Background

PubMed Central

Zhou, Bujin; Chen, Peng; Khan, Aziz; Zhao, Yanhong; Chen, Lihong; Liu, Dongmei; Liao, Xiaofang; Kong, Xiangjun; Zhou, Ruiyang

2017-01-01

Cytoplasmic male sterility (CMS) is a maternally inherited trait that results in the production of dysfunctional pollen. Based on reliable reference gene-normalized real-time quantitative PCR (RT-qPCR) data, examining gene expression profile can provide valuable information on the molecular mechanism of kenaf CMS. However, studies have not been conducted regarding selection of reference genes for normalizing RT-qPCR data in the CMS and maintainer lines of kenaf crop. Therefore, we studied 10 candidate reference genes (ACT3, ELF1A, G6PD, PEPKR1, TUB, TUA, CYP, GAPDH, H3, and 18S) to assess their expression stability at three stages of pollen development in CMS line 722A and maintainer line 722B of kenaf. Five computational statistical approaches (GeNorm, NormFinder, ΔCt, BestKeeper, and RefFinder) were used to evaluate the expression stability levels of these genes. According to RefFinder and GeNorm, the combination of TUB, CYP, and PEPKR1 was identified as an internal control for the accurate normalization across all sample set, which was further confirmed by validating the expression of HcPDIL5-2a. Furthermore, the combination of TUB, CYP, and PEPKR1 was used to differentiate the expression pattern of five mitochondria F1F0-ATPase subunit genes (atp1, atp4, atp6, atp8, and atp9) by RT-qPCR during pollen development in CMS line 722A and maintainer line 722B. We found that atp1, atp6, and atp9 exhibited significantly different expression patterns during pollen development in line 722A compared with line 722B. This is the first systematic study of reference genes selection for CMS and will provide useful information for future research on the gene expressions and molecular mechanisms underlying CMS in kenaf. PMID:28919905

Selection of stable reference genes for quantitative rt-PCR comparisons of mouse embryonic and extra-embryonic stem cells.

PubMed

Veazey, Kylee J; Golding, Michael C

2011-01-01

Isolation and culture of both embryonic and tissue specific stem cells provide an enormous opportunity to study the molecular processes driving development. To gain insight into the initial events underpinning mammalian embryogenesis, pluripotent stem cells from each of the three distinct lineages present within the preimplantation blastocyst have been derived. Embryonic (ES), trophectoderm (TS) and extraembryonic endoderm (XEN) stem cells possess the developmental potential of their founding lineages and seemingly utilize distinct epigenetic modalities to program gene expression. However, the basis for these differing cellular identities and epigenetic properties remain poorly defined.Quantitative reverse transcription-polymerase chain reaction (qPCR) is a powerful and efficient means of rapidly comparing patterns of gene expression between different developmental stages and experimental conditions. However, careful, empirical selection of appropriate reference genes is essential to accurately measuring transcriptional differences. Here we report the quantitation and evaluation of fourteen commonly used references genes between ES, TS and XEN stem cells. These included: Actb, B2m, Hsp70, Gapdh, Gusb, H2afz, Hk2, Hprt, Pgk1, Ppia, Rn7sk, Sdha, Tbp and Ywhaz. Utilizing three independent statistical analysis, we identify Pgk1, Sdha and Tbp as the most stable reference genes between each of these stem cell types. Furthermore, we identify Sdha, Tbp and Ywhaz as well as Ywhaz, Pgk1 and Hk2 as the three most stable reference genes through the in vitro differentiation of embryonic and trophectoderm stem cells respectively.Understanding the transcriptional and epigenetic regulatory mechanisms controlling cellular identity within these distinct stem cell types provides essential insight into cellular processes controlling both embryogenesis and stem cell biology. Normalizing quantitative RT-PCR measurements using the geometric mean CT values obtained for the identified mRNAs, offers a reliable method to assess differing patterns of gene expression between the three founding stem cell lineages present within the mammalian preimplantation embryo.

Japanese Society for Laboratory Hematology flow cytometric reference method of determining the differential leukocyte count: external quality assurance using fresh blood samples.

PubMed

Kawai, Y; Nagai, Y; Ogawa, E; Kondo, H

2017-04-01

To provide target values for the manufacturers' survey of the Japanese Society for Laboratory Hematology (JSLH), accurate standard data from healthy volunteers were needed for the five-part differential leukocyte count. To obtain such data, JSLH required an antibody panel that achieved high specificity (particularly for mononuclear cells) using simple gating procedures. We developed a flow cytometric method for determining the differential leukocyte count (JSLH-Diff) and validated it by comparison with the flow cytometric differential leukocyte count of the International Council for Standardization in Haematology (ICSH-Diff) and the manual differential count obtained by microscopy (Manual-Diff). First, the reference laboratory performed an imprecision study of JSLH-Diff and ICSH-Diff, as well as performing comparison among JSLH-Diff, Manual-Diff, and ICSH-Diff. Then two reference laboratories and seven participating laboratories performed imprecision and accuracy studies of JSLH-Diff, Manual-Diff, and ICSH-Diff. Simultaneously, six manufacturers' laboratories provided their own representative values by using automated hematology analyzers. The precision of both JSLH-Diff and ICSH-Diff methods was adequate. Comparison by the reference laboratory showed that all correlation coefficients, slopes and intercepts obtained by the JSLH-Diff, ICSH-Diff, and Manual-Diff methods conformed to the criteria. When the imprecision and accuracy of JSLH-Diff were assessed at seven laboratories, the CV% for lymphocytes, neutrophils, monocytes, eosinophils, and basophils was 0.5~0.9%, 0.3~0.7%, 1.7~2.6%, 3.0~7.9%, and 3.8~10.4%, respectively. More than 99% of CD45 positive leukocytes were identified as normal leukocytes by JSLH-Diff. When JSLH-Diff method were validated by comparison with Manual-Diff and ICSH-Diff, JSLH-Diff showed good performance as a reference method. © 2016 John Wiley & Sons Ltd.

The Superior Lambert Algorithm

NASA Astrophysics Data System (ADS)

der, G.

2011-09-01

Lambert algorithms are used extensively for initial orbit determination, mission planning, space debris correlation, and missile targeting, just to name a few applications. Due to the significance of the Lambert problem in Astrodynamics, Gauss, Battin, Godal, Lancaster, Gooding, Sun and many others (References 1 to 15) have provided numerous formulations leading to various analytic solutions and iterative methods. Most Lambert algorithms and their computer programs can only work within one revolution, break down or converge slowly when the transfer angle is near zero or 180 degrees, and their multi-revolution limitations are either ignored or barely addressed. Despite claims of robustness, many Lambert algorithms fail without notice, and the users seldom have a clue why. The DerAstrodynamics lambert2 algorithm, which is based on the analytic solution formulated by Sun, works for any number of revolutions and converges rapidly at any transfer angle. It provides significant capability enhancements over every other Lambert algorithm in use today. These include improved speed, accuracy, robustness, and multirevolution capabilities as well as implementation simplicity. Additionally, the lambert2 algorithm provides a powerful tool for solving the angles-only problem without artificial singularities (pointed out by Gooding in Reference 16), which involves 3 lines of sight captured by optical sensors, or systems such as the Air Force Space Surveillance System (AFSSS). The analytic solution is derived from the extended Godal’s time equation by Sun, while the iterative method of solution is that of Laguerre, modified for robustness. The Keplerian solution of a Lambert algorithm can be extended to include the non-Keplerian terms of the Vinti algorithm via a simple targeting technique (References 17 to 19). Accurate analytic non-Keplerian trajectories can be predicted for satellites and ballistic missiles, while performing at least 100 times faster in speed than most numerical integration methods.

Robust tracking of a virtual electrode on a coronary sinus catheter for atrial fibrillation ablation procedures

NASA Astrophysics Data System (ADS)

Wu, Wen; Chen, Terrence; Strobel, Norbert; Comaniciu, Dorin

2012-02-01

Catheter tracking in X-ray fluoroscopic images has become more important in interventional applications for atrial fibrillation (AF) ablation procedures. It provides real-time guidance for the physicians and can be used as reference for motion compensation applications. In this paper, we propose a novel approach to track a virtual electrode (VE), which is a non-existing electrode on the coronary sinus (CS) catheter at a more proximal location than any real electrodes. Successful tracking of the VE can provide more accurate motion information than tracking of real electrodes. To achieve VE tracking, we first model the CS catheter as a set of electrodes which are detected by our previously published learning-based approach.1 The tracked electrodes are then used to generate the hypotheses for tracking the VE. Model-based hypotheses are fused and evaluated by a Bayesian framework. Evaluation has been conducted on a database of clinical AF ablation data including challenging scenarios such as low signal-to-noise ratio (SNR), occlusion and nonrigid deformation. Our approach obtains 0.54mm median error and 90% of evaluated data have errors less than 1.67mm. The speed of our tracking algorithm reaches 6 frames-per-second on most data. Our study on motion compensation shows that using the VE as reference provides a good point to detect non-physiological catheter motion during the AF ablation procedures.2

Assessment of the Accuracy of the Bethe-Salpeter (BSE/GW) Oscillator Strengths.

PubMed

Jacquemin, Denis; Duchemin, Ivan; Blondel, Aymeric; Blase, Xavier

2016-08-09

Aiming to assess the accuracy of the oscillator strengths determined at the BSE/GW level, we performed benchmark calculations using three complementary sets of molecules. In the first, we considered ∼80 states in Thiel's set of compounds and compared the BSE/GW oscillator strengths to recently determined ADC(3/2) and CC3 reference values. The second set includes the oscillator strengths of the low-lying states of 80 medium to large dyes for which we have determined CC2/aug-cc-pVTZ values. The third set contains 30 anthraquinones for which experimental oscillator strengths are available. We find that BSE/GW accurately reproduces the trends for all series with excellent correlation coefficients to the benchmark data and generally very small errors. Indeed, for Thiel's sets, the BSE/GW values are more accurate (using CC3 references) than both CC2 and ADC(3/2) values on both absolute and relative scales. For all three sets, BSE/GW errors also tend to be nicely spread with almost equal numbers of positive and negative deviations as compared to reference values.

Practical wavelength calibration considerations for UV-visible Fourier-transform spectroscopy.

PubMed

Salit, M L; Travis, J C; Winchester, M R

1996-06-01

The intrinsic wavelength scale in a modern reference laser-controlled Michelson interferometer-sometimes referred to as the Connes advantage-offers excellent wavelength accuracy with relative ease. Truly superb wavelength accuracy, with total relative uncertainty in line position of the order of several parts in 10(8), should be within reach with single-point, multiplicative calibration. The need for correction of the wavelength scale arises from two practical effects: the use of a finite aperture, from which off-axis rays propagate through the interferometer, and imperfect geometric alignment of the sample beam with the reference beam and the optical axis of the moving mirror. Although an analytical correction can be made for the finite-aperture effect, calibration with a trusted wavelength standard is typically used to accomplish both corrections. Practical aspects of accurate calibration of an interferometer in the UV-visible region are discussed. Critical issues regarding accurate use of a standard external to the sample source and the evaluation and selection of an appropriate standard are addressed. Anomalous results for two different potential wavelength standards measured by Fabry-Perot interferometry (Ar II and (198)Hg I) are observed.

Real-time 3D change detection of IEDs

NASA Astrophysics Data System (ADS)

Wathen, Mitch; Link, Norah; Iles, Peter; Jinkerson, John; Mrstik, Paul; Kusevic, Kresimir; Kovats, David

2012-06-01

Road-side bombs are a real and continuing threat to soldiers in theater. CAE USA recently developed a prototype Volume based Intelligence Surveillance Reconnaissance (VISR) sensor platform for IED detection. This vehicle-mounted, prototype sensor system uses a high data rate LiDAR (1.33 million range measurements per second) to generate a 3D mapping of roadways. The mapped data is used as a reference to generate real-time change detection on future trips on the same roadways. The prototype VISR system is briefly described. The focus of this paper is the methodology used to process the 3D LiDAR data, in real-time, to detect small changes on and near the roadway ahead of a vehicle traveling at moderate speeds with sufficient warning to stop the vehicle at a safe distance from the threat. The system relies on accurate navigation equipment to geo-reference the reference run and the change-detection run. Since it was recognized early in the project that detection of small changes could not be achieved with accurate navigation solutions alone, a scene alignment algorithm was developed to register the reference run with the change detection run prior to applying the change detection algorithm. Good success was achieved in simultaneous real time processing of scene alignment plus change detection.

High precision UTDR measurements by sonic velocity compensation with reference transducer.

PubMed

Stade, Sam; Kallioinen, Mari; Mänttäri, Mika; Tuuva, Tuure

2014-07-02

An ultrasonic sensor design with sonic velocity compensation is developed to improve the accuracy of distance measurement in membrane modules. High accuracy real-time distance measurements are needed in membrane fouling and compaction studies. The benefits of the sonic velocity compensation with a reference transducer are compared to the sonic velocity calculated with the measured temperature and pressure using the model by Belogol'skii, Sekoyan et al. In the experiments the temperature was changed from 25 to 60 °C at pressures of 0.1, 0.3 and 0.5 MPa. The set measurement distance was 17.8 mm. Distance measurements with sonic velocity compensation were over ten times more accurate than the ones calculated based on the model. Using the reference transducer measured sonic velocity, the standard deviations for the distance measurements varied from 0.6 to 2.0 µm, while using the calculated sonic velocity the standard deviations were 21-39 µm. In industrial liquors, not only the temperature and the pressure, which were studied in this paper, but also the properties of the filtered solution, such as solute concentration, density, viscosity, etc., may vary greatly, leading to inaccuracy in the use of the Belogol'skii, Sekoyan et al. model. Therefore, calibration of the sonic velocity with reference transducers is needed for accurate distance measurements.

[Analysis and countermeasure for quality risk in process of traditional Chinese medicine preparations].

PubMed

Yang, Ming; Yang, Yuan-Zhen; Wang, Ya-Qi; Wu, Zhen-Feng; Wang, Xue-Cheng; Luo, Jing

2017-03-01

Product quality relies on not only testing methods,but also the design and development, production control and product manufacturing all aspects of logistics management. Quality comes from the process control level.Therefore, it is very important to accurately identify the factors that may induce quality risk in the production process and quality control measures correspondingly.This article systematically analyzes the source of the quality risk of all aspects of the production process in traditional Chinese medicine preparation. Discussing ways and methods of quality risk identification of traditional Chinese medicine preparation and providing references for perfecting the whole process quality management of traditional Chinese medicine preparation. Copyright© by the Chinese Pharmaceutical Association.

Cat-Map: putting cataract on the map

PubMed Central

Bennett, Thomas M.; Hejtmancik, J. Fielding

2010-01-01

Lens opacities, or cataract(s), may be inherited as a classic Mendelian disorder usually with early-onset or, more commonly, acquired with age as a multi-factorial or complex trait. Many genetic forms of cataract have been described in mice and other animal models. Considerable progress has been made in mapping and identifying the genes and mutations responsible for inherited forms of cataract, and genetic determinants of age-related cataract are beginning to be discovered. To provide a convenient and accurate summary of current information focused on the increasing genetic complexity of Mendelian and age-related cataract we have created an online chromosome map and reference database for cataract in humans and mice (Cat-Map). PMID:21042563

Statistical Significance of Optical Map Alignments

PubMed Central

Sarkar, Deepayan; Goldstein, Steve; Schwartz, David C.

2012-01-01

Abstract The Optical Mapping System constructs ordered restriction maps spanning entire genomes through the assembly and analysis of large datasets comprising individually analyzed genomic DNA molecules. Such restriction maps uniquely reveal mammalian genome structure and variation, but also raise computational and statistical questions beyond those that have been solved in the analysis of smaller, microbial genomes. We address the problem of how to filter maps that align poorly to a reference genome. We obtain map-specific thresholds that control errors and improve iterative assembly. We also show how an optimal self-alignment score provides an accurate approximation to the probability of alignment, which is useful in applications seeking to identify structural genomic abnormalities. PMID:22506568

Blood vessels segmentation of hatching eggs based on fully convolutional networks

NASA Astrophysics Data System (ADS)

Geng, Lei; Qiu, Ling; Wu, Jun; Xiao, Zhitao

2018-04-01

FCN, trained end-to-end, pixels-to-pixels, predict result of each pixel. It has been widely used for semantic segmentation. In order to realize the blood vessels segmentation of hatching eggs, a method based on FCN is proposed in this paper. The training datasets are composed of patches extracted from very few images to augment data. The network combines with lower layer and deconvolution to enables precise segmentation. The proposed method frees from the problem that training deep networks need large scale samples. Experimental results on hatching eggs demonstrate that this method can yield more accurate segmentation outputs than previous researches. It provides a convenient reference for fertility detection subsequently.

Proteome-scale human interactomics

PubMed Central

Luck, Katja; Sheynkman, Gloria M.; Zhang, Ivy; Vidal, Marc

2017-01-01

Cellular functions are mediated by complex interactome networks of physical, biochemical, and functional interactions between DNA sequences, RNA molecules, proteins, lipids, and small metabolites. A thorough understanding of cellular organization requires accurate and relatively complete models of interactome networks at proteome-scale. The recent publication of four human protein-protein interaction (PPI) maps represents a technological breakthrough and an unprecedented resource for the scientific community, heralding a new era of proteome-scale human interactomics. Our knowledge gained from these and complementary studies provides fresh insights into the opportunities and challenges when analyzing systematically generated interactome data, defines a clear roadmap towards the generation of a first reference interactome, and reveals new perspectives on the organization of cellular life. PMID:28284537

Cutting Edge Methods for Non-Invasive Disease Diagnosis Using E-Tongue and E-Nose Devices

PubMed Central

Fitzgerald, Jessica

2017-01-01

Biomimetic cross-reactive sensor arrays (B-CRSAs) have been used to detect and diagnose a wide variety of diseases including metabolic disorders, mental health diseases, and cancer by analyzing both vapor and liquid patient samples. Technological advancements over the past decade have made these systems selective, sensitive, and affordable. To date, devices for non-invasive and accurate disease diagnosis have seen rapid improvement, suggesting a feasible alternative to current standards for medical diagnostics. This review provides an overview of the most recent B-CRSAs for diagnostics (also referred to electronic noses and tongues in the literature) and an outlook for future technological development. PMID:29215588

De novo assembly of human genomes with massively parallel short read sequencing.

PubMed

Li, Ruiqiang; Zhu, Hongmei; Ruan, Jue; Qian, Wubin; Fang, Xiaodong; Shi, Zhongbin; Li, Yingrui; Li, Shengting; Shan, Gao; Kristiansen, Karsten; Li, Songgang; Yang, Huanming; Wang, Jian; Wang, Jun

2010-02-01

Next-generation massively parallel DNA sequencing technologies provide ultrahigh throughput at a substantially lower unit data cost; however, the data are very short read length sequences, making de novo assembly extremely challenging. Here, we describe a novel method for de novo assembly of large genomes from short read sequences. We successfully assembled both the Asian and African human genome sequences, achieving an N50 contig size of 7.4 and 5.9 kilobases (kb) and scaffold of 446.3 and 61.9 kb, respectively. The development of this de novo short read assembly method creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost-effective way.

[HPLC fingerprint of the antiarrhythmic fraction of Valeriana officinalis].

PubMed

Duan, Xue-Yun; Gong, Zhan-Feng; Chen, Shu-He; Fang, Ying; Liu, Yan-Wen

2009-06-01

To establish HPLC fingerprints of the Antiarrhythmic fraction of Valeriana officinalis. Agilent C18 (250 mm x 4.6 mm, 5 microm) column was used and the acetonitrile-water was chosen as the mobile phase in a gradient mode. The column temperature was 380 degrees C and the detection wavelength was 218 nm. The detection time was 70 min, and the flow rate was 1.0 mL/ min. Fifteen characteristic peaks were indicated in HPLC fingerprints. The relative retention time and the ranges of relative areas of the common peaks were also determined. This method is simple and accurate with a good reproducibility and provides a reference standard for the quality control of Valeriana officinalis.

On the nature of unintentional action: a study of force/moment drifts during multifinger tasks.

PubMed

Parsa, Behnoosh; O'Shea, Daniel J; Zatsiorsky, Vladimir M; Latash, Mark L

2016-08-01

We explored the origins of unintentional changes in performance during accurate force production in isometric conditions seen after turning visual feedback off. The idea of control with referent spatial coordinates suggests that these phenomena could result from drifts of the referent coordinate for the effector. Subjects performed accurate force/moment production tasks by pressing with the fingers of a hand on force sensors. Turning the visual feedback off resulted in slow drifts of both total force and total moment to lower magnitudes of these variables; these drifts were more pronounced in the right hand of the right-handed subjects. Drifts in individual finger forces could be in different direction; in particular, fingers that produced moments of force against the required total moment showed an increase in their forces. The force/moment drift was associated with a drop in the index of synergy stabilizing performance under visual feedback. The drifts in directions that changed performance (non-motor equivalent) and in directions that did not (motor equivalent) were of about the same magnitude. The results suggest that control with referent coordinates is associated with drifts of those referent coordinates toward the corresponding actual coordinates of the hand, a reflection of the natural tendency of physical systems to move toward a minimum of potential energy. The interaction between drifts of the hand referent coordinate and referent orientation leads to counterdirectional drifts in individual finger forces. The results also demonstrate that the sensory information used to create multifinger synergies is necessary for their presence over the task duration. Copyright © 2016 the American Physiological Society.

Airborne gravity measurement over sea-ice: The western Weddel Sea

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

Brozena, J.; Peters, M.; LaBrecque, J.

1990-10-01

An airborne gravity study of the western Weddel Sea, east of the Antarctic Peninsula, has shown that floating pack-ice provides a useful radar altimetric reference surface for altitude and vertical acceleration corrections surface for alititude and vertical acceleration corrections to airborne gravimetry. Airborne gravimetry provides an important alternative to satellite altimetry for the sea-ice covered regions of the world since satellite alimeters are not designed or intended to provide accurate geoidal heights in areas where significant sea-ice is present within the radar footprint. Errors in radar corrected airborne gravimetry are primarily sensitive to the variations in the second derivative ofmore » the sea-ice reference surface in the frequency pass-band of interest. With the exception of imbedded icebergs the second derivative of the pack-ice surface closely approximates that of the mean sea-level surface at wavelengths > 10-20 km. With the airborne method the percentage of ice coverage, the mixture of first and multi-year ice and the existence of leads and pressure ridges prove to be unimportant in determining gravity anomalies at scales of geophysical and geodetic interest, provided that the ice is floating and not grounded. In the Weddell study an analysis of 85 crosstrack miss-ties distributed over 25 data tracks yields an rms error of 2.2 mGals. Significant structural anomalies including the continental shelf and offsets and lineations interpreted as fracture zones recording the early spreading directions within the Weddell Sea are observed in the gravity map.« less

Identification of appropriate reference genes for human mesenchymal stem cell analysis by quantitative real-time PCR.

PubMed

Li, Xiuying; Yang, Qiwei; Bai, Jinping; Xuan, Yali; Wang, Yimin

2015-01-01

Normalization to a reference gene is the method of choice for quantitative reverse transcription-PCR (RT-qPCR) analysis. The stability of reference genes is critical for accurate experimental results and conclusions. We have evaluated the expression stability of eight commonly used reference genes found in four different human mesenchymal stem cells (MSC). Using geNorm, NormFinder and BestKeeper algorithms, we show that beta-2-microglobulin and peptidyl-prolylisomerase A were the optimal reference genes for normalizing RT-qPCR data obtained from MSC, whereas the TATA box binding protein was not suitable due to its extensive variability in expression. Our findings emphasize the significance of validating reference genes for qPCR analyses. We offer a short list of reference genes to use for normalization and recommend some commercially-available software programs as a rapid approach to validate reference genes. We also demonstrate that the two reference genes, β-actin and glyceraldehyde-3-phosphate dehydrogenase, are frequently used are not always successful in many cases.

Reduction of astrometric plates

NASA Technical Reports Server (NTRS)

Stock, J.

1984-01-01

A rapid and accurate method for the reduction of comet or asteroid plates is described. Projection equations, scale length correction, rotation of coordinates, linearization, the search for additional reference stars, and the final solution are examined.

Research on maximum level noise contaminated of remote reference magnetotelluric measurements using synthesized data

NASA Astrophysics Data System (ADS)

Gang, Zhang; Fansong, Meng; Jianzhong, Wang; Mingtao, Ding

2018-02-01

Determining magnetotelluric impedance precisely and accurately is fundamental to valid inversion and geological interpretation. This study aims to determine the minimum value of signal-to-noise ratio (SNR) which maintains the effectiveness of remote reference technique. Results of standard time series simulation, addition of different Gaussian noises to obtain the different SNR time series, and analysis of the intermediate data, such as polarization direction, correlation coefficient, and impedance tensor, show that when the SNR value is larger than 23.5743, the polarization direction disorder at morphology and a smooth and accurate sounding carve value can be obtained. At this condition, the correlation coefficient value of nearly complete segments between the base and remote station is larger than 0.9, and impedance tensor Zxy presents only one aggregation, which meet the natural magnetotelluric signal characteristic.