Sample records for accurate quantitative analyses

  1. Quantitative analyses for elucidating mechanisms of cell fate commitment in the mouse blastocyst

    NASA Astrophysics Data System (ADS)

    Saiz, Néstor; Kang, Minjung; Puliafito, Alberto; Schrode, Nadine; Xenopoulos, Panagiotis; Lou, Xinghua; Di Talia, Stefano; Hadjantonakis, Anna-Katerina

    2015-03-01

    In recent years we have witnessed a shift from qualitative image analysis towards higher resolution, quantitative analyses of imaging data in developmental biology. This shift has been fueled by technological advances in both imaging and analysis software. We have recently developed a tool for accurate, semi-automated nuclear segmentation of imaging data from early mouse embryos and embryonic stem cells. We have applied this software to the study of the first lineage decisions that take place during mouse development and established analysis pipelines for both static and time-lapse imaging experiments. In this paper we summarize the conclusions from these studies to illustrate how quantitative, single-cell level analysis of imaging data can unveil biological processes that cannot be revealed by traditional qualitative studies.

  2. Discrete sensors distribution for accurate plantar pressure analyses.

    PubMed

    Claverie, Laetitia; Ille, Anne; Moretto, Pierre

    2016-12-01

    The aim of this study was to determine the distribution of discrete sensors under the footprint for accurate plantar pressure analyses. For this purpose, two different sensor layouts have been tested and compared, to determine which was the most accurate to monitor plantar pressure with wireless devices in research and/or clinical practice. Ten healthy volunteers participated in the study (age range: 23-58 years). The barycenter of pressures (BoP) determined from the plantar pressure system (W-inshoe®) was compared to the center of pressures (CoP) determined from a force platform (AMTI) in the medial-lateral (ML) and anterior-posterior (AP) directions. Then, the vertical ground reaction force (vGRF) obtained from both W-inshoe® and force platform was compared for both layouts for each subject. The BoP and vGRF determined from the plantar pressure system data showed good correlation (SCC) with those determined from the force platform data, notably for the second sensor organization (ML SCC= 0.95; AP SCC=0.99; vGRF SCC=0.91). The study demonstrates that an adjusted placement of removable sensors is key to accurate plantar pressure analyses. These results are promising for a plantar pressure recording outside clinical or laboratory settings, for long time monitoring, real time feedback or for whatever activity requiring a low-cost system. Copyright © 2016 IPEM. Published by Elsevier Ltd. All rights reserved.

  3. Toward Accurate and Quantitative Comparative Metagenomics

    PubMed Central

    Nayfach, Stephen; Pollard, Katherine S.

    2016-01-01

    Shotgun metagenomics and computational analysis are used to compare the taxonomic and functional profiles of microbial communities. Leveraging this approach to understand roles of microbes in human biology and other environments requires quantitative data summaries whose values are comparable across samples and studies. Comparability is currently hampered by the use of abundance statistics that do not estimate a meaningful parameter of the microbial community and biases introduced by experimental protocols and data-cleaning approaches. Addressing these challenges, along with improving study design, data access, metadata standardization, and analysis tools, will enable accurate comparative metagenomics. We envision a future in which microbiome studies are replicable and new metagenomes are easily and rapidly integrated with existing data. Only then can the potential of metagenomics for predictive ecological modeling, well-powered association studies, and effective microbiome medicine be fully realized. PMID:27565341

  4. Accurate quantitation standards of glutathione via traceable sulfur measurement by inductively coupled plasma optical emission spectrometry and ion chromatography

    PubMed Central

    Rastogi, L.; Dash, K.; Arunachalam, J.

    2013-01-01

    The quantitative analysis of glutathione (GSH) is important in different fields like medicine, biology, and biotechnology. Accurate quantitative measurements of this analyte have been hampered by the lack of well characterized reference standards. The proposed procedure is intended to provide an accurate and definitive method for the quantitation of GSH for reference measurements. Measurement of the stoichiometrically existing sulfur content in purified GSH offers an approach for its quantitation and calibration through an appropriate characterized reference material (CRM) for sulfur would provide a methodology for the certification of GSH quantity, that is traceable to SI (International system of units). The inductively coupled plasma optical emission spectrometry (ICP-OES) approach negates the need for any sample digestion. The sulfur content of the purified GSH is quantitatively converted into sulfate ions by microwave-assisted UV digestion in the presence of hydrogen peroxide prior to ion chromatography (IC) measurements. The measurement of sulfur by ICP-OES and IC (as sulfate) using the “high performance” methodology could be useful for characterizing primary calibration standards and certified reference materials with low uncertainties. The relative expanded uncertainties (% U) expressed at 95% confidence interval for ICP-OES analyses varied from 0.1% to 0.3%, while in the case of IC, they were between 0.2% and 1.2%. The described methods are more suitable for characterizing primary calibration standards and certifying reference materials of GSH, than for routine measurements. PMID:29403814

  5. Toward Accurate and Quantitative Comparative Metagenomics.

    PubMed

    Nayfach, Stephen; Pollard, Katherine S

    2016-08-25

    Shotgun metagenomics and computational analysis are used to compare the taxonomic and functional profiles of microbial communities. Leveraging this approach to understand roles of microbes in human biology and other environments requires quantitative data summaries whose values are comparable across samples and studies. Comparability is currently hampered by the use of abundance statistics that do not estimate a meaningful parameter of the microbial community and biases introduced by experimental protocols and data-cleaning approaches. Addressing these challenges, along with improving study design, data access, metadata standardization, and analysis tools, will enable accurate comparative metagenomics. We envision a future in which microbiome studies are replicable and new metagenomes are easily and rapidly integrated with existing data. Only then can the potential of metagenomics for predictive ecological modeling, well-powered association studies, and effective microbiome medicine be fully realized. Copyright © 2016 Elsevier Inc. All rights reserved.

  6. Accurate Construction of Photoactivated Localization Microscopy (PALM) Images for Quantitative Measurements

    PubMed Central

    Coltharp, Carla; Kessler, Rene P.; Xiao, Jie

    2012-01-01

    Localization-based superresolution microscopy techniques such as Photoactivated Localization Microscopy (PALM) and Stochastic Optical Reconstruction Microscopy (STORM) have allowed investigations of cellular structures with unprecedented optical resolutions. One major obstacle to interpreting superresolution images, however, is the overcounting of molecule numbers caused by fluorophore photoblinking. Using both experimental and simulated images, we determined the effects of photoblinking on the accurate reconstruction of superresolution images and on quantitative measurements of structural dimension and molecule density made from those images. We found that structural dimension and relative density measurements can be made reliably from images that contain photoblinking-related overcounting, but accurate absolute density measurements, and consequently faithful representations of molecule counts and positions in cellular structures, require the application of a clustering algorithm to group localizations that originate from the same molecule. We analyzed how applying a simple algorithm with different clustering thresholds (tThresh and dThresh) affects the accuracy of reconstructed images, and developed an easy method to select optimal thresholds. We also identified an empirical criterion to evaluate whether an imaging condition is appropriate for accurate superresolution image reconstruction with the clustering algorithm. Both the threshold selection method and imaging condition criterion are easy to implement within existing PALM clustering algorithms and experimental conditions. The main advantage of our method is that it generates a superresolution image and molecule position list that faithfully represents molecule counts and positions within a cellular structure, rather than only summarizing structural properties into ensemble parameters. This feature makes it particularly useful for cellular structures of heterogeneous densities and irregular geometries, and

  7. Accurate Quantitative Sensing of Intracellular pH based on Self-ratiometric Upconversion Luminescent Nanoprobe.

    PubMed

    Li, Cuixia; Zuo, Jing; Zhang, Li; Chang, Yulei; Zhang, Youlin; Tu, Langping; Liu, Xiaomin; Xue, Bin; Li, Qiqing; Zhao, Huiying; Zhang, Hong; Kong, Xianggui

    2016-12-09

    Accurate quantitation of intracellular pH (pH i ) is of great importance in revealing the cellular activities and early warning of diseases. A series of fluorescence-based nano-bioprobes composed of different nanoparticles or/and dye pairs have already been developed for pH i sensing. Till now, biological auto-fluorescence background upon UV-Vis excitation and severe photo-bleaching of dyes are the two main factors impeding the accurate quantitative detection of pH i . Herein, we have developed a self-ratiometric luminescence nanoprobe based on förster resonant energy transfer (FRET) for probing pH i , in which pH-sensitive fluorescein isothiocyanate (FITC) and upconversion nanoparticles (UCNPs) were served as energy acceptor and donor, respectively. Under 980 nm excitation, upconversion emission bands at 475 nm and 645 nm of NaYF 4 :Yb 3+ , Tm 3+ UCNPs were used as pH i response and self-ratiometric reference signal, respectively. This direct quantitative sensing approach has circumvented the traditional software-based subsequent processing of images which may lead to relatively large uncertainty of the results. Due to efficient FRET and fluorescence background free, a highly-sensitive and accurate sensing has been achieved, featured by 3.56 per unit change in pH i value 3.0-7.0 with deviation less than 0.43. This approach shall facilitate the researches in pH i related areas and development of the intracellular drug delivery systems.

  8. Accurate Quantitative Sensing of Intracellular pH based on Self-ratiometric Upconversion Luminescent Nanoprobe

    NASA Astrophysics Data System (ADS)

    Li, Cuixia; Zuo, Jing; Zhang, Li; Chang, Yulei; Zhang, Youlin; Tu, Langping; Liu, Xiaomin; Xue, Bin; Li, Qiqing; Zhao, Huiying; Zhang, Hong; Kong, Xianggui

    2016-12-01

    Accurate quantitation of intracellular pH (pHi) is of great importance in revealing the cellular activities and early warning of diseases. A series of fluorescence-based nano-bioprobes composed of different nanoparticles or/and dye pairs have already been developed for pHi sensing. Till now, biological auto-fluorescence background upon UV-Vis excitation and severe photo-bleaching of dyes are the two main factors impeding the accurate quantitative detection of pHi. Herein, we have developed a self-ratiometric luminescence nanoprobe based on förster resonant energy transfer (FRET) for probing pHi, in which pH-sensitive fluorescein isothiocyanate (FITC) and upconversion nanoparticles (UCNPs) were served as energy acceptor and donor, respectively. Under 980 nm excitation, upconversion emission bands at 475 nm and 645 nm of NaYF4:Yb3+, Tm3+ UCNPs were used as pHi response and self-ratiometric reference signal, respectively. This direct quantitative sensing approach has circumvented the traditional software-based subsequent processing of images which may lead to relatively large uncertainty of the results. Due to efficient FRET and fluorescence background free, a highly-sensitive and accurate sensing has been achieved, featured by 3.56 per unit change in pHi value 3.0-7.0 with deviation less than 0.43. This approach shall facilitate the researches in pHi related areas and development of the intracellular drug delivery systems.

  9. Practicable methods for histological section thickness measurement in quantitative stereological analyses.

    PubMed

    Matenaers, Cyrill; Popper, Bastian; Rieger, Alexandra; Wanke, Rüdiger; Blutke, Andreas

    2018-01-01

    The accuracy of quantitative stereological analysis tools such as the (physical) disector method substantially depends on the precise determination of the thickness of the analyzed histological sections. One conventional method for measurement of histological section thickness is to re-embed the section of interest vertically to its original section plane. The section thickness is then measured in a subsequently prepared histological section of this orthogonally re-embedded sample. However, the orthogonal re-embedding (ORE) technique is quite work- and time-intensive and may produce inaccurate section thickness measurement values due to unintentional slightly oblique (non-orthogonal) positioning of the re-embedded sample-section. Here, an improved ORE method is presented, allowing for determination of the factual section plane angle of the re-embedded section, and correction of measured section thickness values for oblique (non-orthogonal) sectioning. For this, the analyzed section is mounted flat on a foil of known thickness (calibration foil) and both the section and the calibration foil are then vertically (re-)embedded. The section angle of the re-embedded section is then calculated from the deviation of the measured section thickness of the calibration foil and its factual thickness, using basic geometry. To find a practicable, fast, and accurate alternative to ORE, the suitability of spectral reflectance (SR) measurement for determination of plastic section thicknesses was evaluated. Using a commercially available optical reflectometer (F20, Filmetrics®, USA), the thicknesses of 0.5 μm thick semi-thin Epon (glycid ether)-sections and of 1-3 μm thick plastic sections (glycolmethacrylate/ methylmethacrylate, GMA/MMA), as regularly used in physical disector analyses, could precisely be measured within few seconds. Compared to the measured section thicknesses determined by ORE, SR measures displayed less than 1% deviation. Our results prove the applicability

  10. Practicable methods for histological section thickness measurement in quantitative stereological analyses

    PubMed Central

    Matenaers, Cyrill; Popper, Bastian; Rieger, Alexandra; Wanke, Rüdiger

    2018-01-01

    The accuracy of quantitative stereological analysis tools such as the (physical) disector method substantially depends on the precise determination of the thickness of the analyzed histological sections. One conventional method for measurement of histological section thickness is to re-embed the section of interest vertically to its original section plane. The section thickness is then measured in a subsequently prepared histological section of this orthogonally re-embedded sample. However, the orthogonal re-embedding (ORE) technique is quite work- and time-intensive and may produce inaccurate section thickness measurement values due to unintentional slightly oblique (non-orthogonal) positioning of the re-embedded sample-section. Here, an improved ORE method is presented, allowing for determination of the factual section plane angle of the re-embedded section, and correction of measured section thickness values for oblique (non-orthogonal) sectioning. For this, the analyzed section is mounted flat on a foil of known thickness (calibration foil) and both the section and the calibration foil are then vertically (re-)embedded. The section angle of the re-embedded section is then calculated from the deviation of the measured section thickness of the calibration foil and its factual thickness, using basic geometry. To find a practicable, fast, and accurate alternative to ORE, the suitability of spectral reflectance (SR) measurement for determination of plastic section thicknesses was evaluated. Using a commercially available optical reflectometer (F20, Filmetrics®, USA), the thicknesses of 0.5 μm thick semi-thin Epon (glycid ether)-sections and of 1–3 μm thick plastic sections (glycolmethacrylate/ methylmethacrylate, GMA/MMA), as regularly used in physical disector analyses, could precisely be measured within few seconds. Compared to the measured section thicknesses determined by ORE, SR measures displayed less than 1% deviation. Our results prove the applicability

  11. 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'.

  12. 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

  13. Accurate single-shot quantitative phase imaging of biological specimens with telecentric digital holographic microscopy.

    PubMed

    Doblas, Ana; Sánchez-Ortiga, Emilio; Martínez-Corral, Manuel; Saavedra, Genaro; Garcia-Sucerquia, Jorge

    2014-04-01

    The advantages of using a telecentric imaging system in digital holographic microscopy (DHM) to study biological specimens are highlighted. To this end, the performances of nontelecentric DHM and telecentric DHM are evaluated from the quantitative phase imaging (QPI) point of view. The evaluated stability of the microscope allows single-shot QPI in DHM by using telecentric imaging systems. Quantitative phase maps of a section of the head of the drosophila melanogaster fly and of red blood cells are obtained via single-shot DHM with no numerical postprocessing. With these maps we show that the use of telecentric DHM provides larger field of view for a given magnification and permits more accurate QPI measurements with less number of computational operations.

  14. 75 FR 29537 - Draft Transportation Conformity Guidance for Quantitative Hot-spot Analyses in PM2.5

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-26

    ... Quantitative Hot- spot Analyses in PM 2.5 and PM 10 Nonattainment and Maintenance Areas AGENCY: Environmental... finalized, this guidance would help state and local agencies complete quantitative PM 2.5 and PM 10 hot-spot...), EPA stated that quantitative PM 2.5 and PM 10 hot-spot analyses would not be required until EPA...

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

    PubMed

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

    2017-10-01

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

  16. Quantitative analyses of bifunctional molecules.

    PubMed

    Braun, Patrick D; Wandless, Thomas J

    2004-05-11

    Small molecules can be discovered or engineered to bind tightly to biologically relevant proteins, and these molecules have proven to be powerful tools for both basic research and therapeutic applications. In many cases, detailed biophysical analyses of the intermolecular binding events are essential for improving the activity of the small molecules. These interactions can often be characterized as straightforward bimolecular binding events, and a variety of experimental and analytical techniques have been developed and refined to facilitate these analyses. Several investigators have recently synthesized heterodimeric molecules that are designed to bind simultaneously with two different proteins to form ternary complexes. These heterodimeric molecules often display compelling biological activity; however, they are difficult to characterize. The bimolecular interaction between one protein and the heterodimeric ligand (primary dissociation constant) can be determined by a number of methods. However, the interaction between that protein-ligand complex and the second protein (secondary dissociation constant) is more difficult to measure due to the noncovalent nature of the original protein-ligand complex. Consequently, these heterodimeric compounds are often characterized in terms of their activity, which is an experimentally dependent metric. We have developed a general quantitative mathematical model that can be used to measure both the primary (protein + ligand) and secondary (protein-ligand + protein) dissociation constants for heterodimeric small molecules. These values are largely independent of the experimental technique used and furthermore provide a direct measure of the thermodynamic stability of the ternary complexes that are formed. Fluorescence polarization and this model were used to characterize the heterodimeric molecule, SLFpYEEI, which binds to both FKBP12 and the Fyn SH2 domain, demonstrating that the model is useful for both predictive as well as ex

  17. Searching for an Accurate Marker-Based Prediction of an Individual Quantitative Trait in Molecular Plant Breeding

    PubMed Central

    Fu, Yong-Bi; Yang, Mo-Hua; Zeng, Fangqin; Biligetu, Bill

    2017-01-01

    Molecular plant breeding with the aid of molecular markers has played an important role in modern plant breeding over the last two decades. Many marker-based predictions for quantitative traits have been made to enhance parental selection, but the trait prediction accuracy remains generally low, even with the aid of dense, genome-wide SNP markers. To search for more accurate trait-specific prediction with informative SNP markers, we conducted a literature review on the prediction issues in molecular plant breeding and on the applicability of an RNA-Seq technique for developing function-associated specific trait (FAST) SNP markers. To understand whether and how FAST SNP markers could enhance trait prediction, we also performed a theoretical reasoning on the effectiveness of these markers in a trait-specific prediction, and verified the reasoning through computer simulation. To the end, the search yielded an alternative to regular genomic selection with FAST SNP markers that could be explored to achieve more accurate trait-specific prediction. Continuous search for better alternatives is encouraged to enhance marker-based predictions for an individual quantitative trait in molecular plant breeding. PMID:28729875

  18. Qualitative and Quantitative Analyses of Glycogen in Human Milk.

    PubMed

    Matsui-Yatsuhashi, Hiroko; Furuyashiki, Takashi; Takata, Hiroki; Ishida, Miyuki; Takumi, Hiroko; Kakutani, Ryo; Kamasaka, Hiroshi; Nagao, Saeko; Hirose, Junko; Kuriki, Takashi

    2017-02-22

    Identification as well as a detailed analysis of glycogen in human milk has not been shown yet. The present study confirmed that glycogen is contained in human milk by qualitative and quantitative analyses. High-performance anion exchange chromatography (HPAEC) and high-performance size exclusion chromatography with a multiangle laser light scattering detector (HPSEC-MALLS) were used for qualitative analysis of glycogen in human milk. Quantitative analysis was carried out by using samples obtained from the individual milks. The result revealed that the concentration of human milk glycogen varied depending on the mother's condition-such as the period postpartum and inflammation. The amounts of glycogen in human milk collected at 0 and 1-2 months postpartum were higher than in milk collected at 3-14 months postpartum. In the milk from mothers with severe mastitis, the concentration of glycogen was about 40 times higher than that in normal milk.

  19. Accurate Virus Quantitation Using a Scanning Transmission Electron Microscopy (STEM) Detector in a Scanning Electron Microscope

    DTIC Science & Technology

    2017-06-29

    Accurate Virus Quantitation Using a Scanning Transmission Electron Microscopy (STEM) Detector in a Scanning Electron Microscope Candace D Blancett1...L Norris2, Cynthia A Rossi4 , Pamela J Glass3, Mei G Sun1,* 1 Pathology Division, United States Army Medical Research Institute of Infectious...Diseases (USAMRIID), 1425 Porter Street, Fort Detrick, Maryland, 21702 2Biostatistics Division, United States Army Medical Research Institute of

  20. A correlative imaging based methodology for accurate quantitative assessment of bone formation in additive manufactured implants.

    PubMed

    Geng, Hua; Todd, Naomi M; Devlin-Mullin, Aine; Poologasundarampillai, Gowsihan; Kim, Taek Bo; Madi, Kamel; Cartmell, Sarah; Mitchell, Christopher A; Jones, Julian R; Lee, Peter D

    2016-06-01

    A correlative imaging methodology was developed to accurately quantify bone formation in the complex lattice structure of additive manufactured implants. Micro computed tomography (μCT) and histomorphometry were combined, integrating the best features from both, while demonstrating the limitations of each imaging modality. This semi-automatic methodology registered each modality using a coarse graining technique to speed the registration of 2D histology sections to high resolution 3D μCT datasets. Once registered, histomorphometric qualitative and quantitative bone descriptors were directly correlated to 3D quantitative bone descriptors, such as bone ingrowth and bone contact. The correlative imaging allowed the significant volumetric shrinkage of histology sections to be quantified for the first time (~15 %). This technique demonstrated the importance of location of the histological section, demonstrating that up to a 30 % offset can be introduced. The results were used to quantitatively demonstrate the effectiveness of 3D printed titanium lattice implants.

  1. Highly Accurate Quantitative Analysis Of Enantiomeric Mixtures from Spatially Frequency Encoded 1H NMR Spectra.

    PubMed

    Plainchont, Bertrand; Pitoux, Daisy; Cyrille, Mathieu; Giraud, Nicolas

    2018-02-06

    We propose an original concept to measure accurately enantiomeric excesses on proton NMR spectra, which combines high-resolution techniques based on a spatial encoding of the sample, with the use of optically active weakly orienting solvents. We show that it is possible to simulate accurately dipolar edited spectra of enantiomers dissolved in a chiral liquid crystalline phase, and to use these simulations to calibrate integrations that can be measured on experimental data, in order to perform a quantitative chiral analysis. This approach is demonstrated on a chemical intermediate for which optical purity is an essential criterion. We find that there is a very good correlation between the experimental and calculated integration ratios extracted from G-SERF spectra, which paves the way to a general method of determination of enantiomeric excesses based on the observation of 1 H nuclei.

  2. Numerically accurate computational techniques for optimal estimator analyses of multi-parameter models

    NASA Astrophysics Data System (ADS)

    Berger, Lukas; Kleinheinz, Konstantin; Attili, Antonio; Bisetti, Fabrizio; Pitsch, Heinz; Mueller, Michael E.

    2018-05-01

    Modelling unclosed terms in partial differential equations typically involves two steps: First, a set of known quantities needs to be specified as input parameters for a model, and second, a specific functional form needs to be defined to model the unclosed terms by the input parameters. Both steps involve a certain modelling error, with the former known as the irreducible error and the latter referred to as the functional error. Typically, only the total modelling error, which is the sum of functional and irreducible error, is assessed, but the concept of the optimal estimator enables the separate analysis of the total and the irreducible errors, yielding a systematic modelling error decomposition. In this work, attention is paid to the techniques themselves required for the practical computation of irreducible errors. Typically, histograms are used for optimal estimator analyses, but this technique is found to add a non-negligible spurious contribution to the irreducible error if models with multiple input parameters are assessed. Thus, the error decomposition of an optimal estimator analysis becomes inaccurate, and misleading conclusions concerning modelling errors may be drawn. In this work, numerically accurate techniques for optimal estimator analyses are identified and a suitable evaluation of irreducible errors is presented. Four different computational techniques are considered: a histogram technique, artificial neural networks, multivariate adaptive regression splines, and an additive model based on a kernel method. For multiple input parameter models, only artificial neural networks and multivariate adaptive regression splines are found to yield satisfactorily accurate results. Beyond a certain number of input parameters, the assessment of models in an optimal estimator analysis even becomes practically infeasible if histograms are used. The optimal estimator analysis in this paper is applied to modelling the filtered soot intermittency in large eddy

  3. Restriction Site Tiling Analysis: accurate discovery and quantitative genotyping of genome-wide polymorphisms using nucleotide arrays

    PubMed Central

    2010-01-01

    High-throughput genotype data can be used to identify genes important for local adaptation in wild populations, phenotypes in lab stocks, or disease-related traits in human medicine. Here we advance microarray-based genotyping for population genomics with Restriction Site Tiling Analysis. The approach simultaneously discovers polymorphisms and provides quantitative genotype data at 10,000s of loci. It is highly accurate and free from ascertainment bias. We apply the approach to uncover genomic differentiation in the purple sea urchin. PMID:20403197

  4. Challenges in Higher Education Research: The Use of Quantitative Tools in Comparative Analyses

    ERIC Educational Resources Information Center

    Reale, Emanuela

    2014-01-01

    Despite the value of the comparative perspective for the study of higher education is widely recognised, there is little consensus about the specific methodological approaches. Quantitative tools outlined their relevance for addressing comparative analyses since they are supposed to reducing the complexity, finding out and graduating similarities…

  5. A unique charge-coupled device/xenon arc lamp based imaging system for the accurate detection and quantitation of multicolour fluorescence.

    PubMed

    Spibey, C A; Jackson, P; Herick, K

    2001-03-01

    In recent years the use of fluorescent dyes in biological applications has dramatically increased. The continual improvement in the capabilities of these fluorescent dyes demands increasingly sensitive detection systems that provide accurate quantitation over a wide linear dynamic range. In the field of proteomics, the detection, quantitation and identification of very low abundance proteins are of extreme importance in understanding cellular processes. Therefore, the instrumentation used to acquire an image of such samples, for spot picking and identification by mass spectrometry, must be sensitive enough to be able, not only, to maximise the sensitivity and dynamic range of the staining dyes but, as importantly, adapt to the ever changing portfolio of fluorescent dyes as they become available. Just as the available fluorescent probes are improving and evolving so are the users application requirements. Therefore, the instrumentation chosen must be flexible to address and adapt to those changing needs. As a result, a highly competitive market for the supply and production of such dyes and the instrumentation for their detection and quantitation have emerged. The instrumentation currently available is based on either laser/photomultiplier tube (PMT) scanning or lamp/charge-coupled device (CCD) based mechanisms. This review briefly discusses the advantages and disadvantages of both System types for fluorescence imaging, gives a technical overview of CCD technology and describes in detail a unique xenon/are lamp CCD based instrument, from PerkinElmer Life Sciences. The Wallac-1442 ARTHUR is unique in its ability to scan both large areas at high resolution and give accurate selectable excitation over the whole of the UV/visible range. It operates by filtering both the excitation and emission wavelengths, providing optimal and accurate measurement and quantitation of virtually any available dye and allows excellent spectral resolution between different fluorophores

  6. Recycling and Ambivalence: Quantitative and Qualitative Analyses of Household Recycling among Young Adults

    ERIC Educational Resources Information Center

    Ojala, Maria

    2008-01-01

    Theories about ambivalence, as well as quantitative and qualitative empirical approaches, are applied to obtain an understanding of recycling among young adults. A questionnaire was mailed to 422 Swedish young people. Regression analyses showed that a mix of negative emotions (worry) and positive emotions (hope and joy) about the environmental…

  7. Multidimensional quantitative analysis of mRNA expression within intact vertebrate embryos.

    PubMed

    Trivedi, Vikas; Choi, Harry M T; Fraser, Scott E; Pierce, Niles A

    2018-01-08

    For decades, in situ hybridization methods have been essential tools for studies of vertebrate development and disease, as they enable qualitative analyses of mRNA expression in an anatomical context. Quantitative mRNA analyses typically sacrifice the anatomy, relying on embryo microdissection, dissociation, cell sorting and/or homogenization. Here, we eliminate the trade-off between quantitation and anatomical context, using quantitative in situ hybridization chain reaction (qHCR) to perform accurate and precise relative quantitation of mRNA expression with subcellular resolution within whole-mount vertebrate embryos. Gene expression can be queried in two directions: read-out from anatomical space to expression space reveals co-expression relationships in selected regions of the specimen; conversely, read-in from multidimensional expression space to anatomical space reveals those anatomical locations in which selected gene co-expression relationships occur. As we demonstrate by examining gene circuits underlying somitogenesis, quantitative read-out and read-in analyses provide the strengths of flow cytometry expression analyses, but by preserving subcellular anatomical context, they enable bi-directional queries that open a new era for in situ hybridization. © 2018. Published by The Company of Biologists Ltd.

  8. Accurate quantitation of D+ fetomaternal hemorrhage by flow cytometry using a novel reagent to eliminate granulocytes from analysis.

    PubMed

    Kumpel, Belinda; Hazell, Matthew; Guest, Alan; Dixey, Jonathan; Mushens, Rosey; Bishop, Debbie; Wreford-Bush, Tim; Lee, Edmond

    2014-05-01

    Quantitation of fetomaternal hemorrhage (FMH) is performed to determine the dose of prophylactic anti-D (RhIG) required to prevent D immunization of D- women. Flow cytometry (FC) is the most accurate method. However, maternal white blood cells (WBCs) can give high background by binding anti-D nonspecifically, compromising accuracy. Maternal blood samples (69) were sent for FC quantitation of FMH after positive Kleihauer-Betke test (KBT) analysis and RhIG administration. Reagents used were BRAD-3-fluorescein isothiocyanate (FITC; anti-D), AEVZ5.3-FITC (anti-varicella zoster [anti-VZ], negative control), anti-fetal hemoglobin (HbF)-FITC, blended two-color reagents, BRAD-3-FITC/anti-CD45-phycoerythrin (PE; anti-D/L), and BRAD-3-FITC/anti-CD66b-PE (anti-D/G). PE-positive WBCs were eliminated from analysis by gating. Full blood counts were performed on maternal samples and female donors. Elevated numbers of neutrophils were present in 80% of patients. Red blood cell (RBC) indices varied widely in maternal blood. D+ FMH values obtained with anti-D/L, anti-D/G, and anti-HbF-FITC were very similar (r = 0.99, p < 0.001). Correlation between KBT and anti-HbF-FITC FMH results was low (r = 0.716). Inaccurate FMH quantitation using the current method (anti-D minus anti-VZ) occurred with 71% samples having less than 15 mL of D+ FMH (RBCs) and insufficient RhIG calculated for 9%. Using two-color reagents and anti-HbF-FITC, approximately 30% patients had elevated F cells, 26% had no fetal cells, 6% had D- FMH, 26% had 4 to 15 mL of D+ FMH, and 12% patients had more than 15 mL of D+ FMH (RBCs) requiring more than 300 μg of RhIG. Without accurate quantitation of D+ FMH by FC, some women would receive inappropriate or inadequate anti-D prophylaxis. The latter may be at risk of immunization leading to hemolytic disease of the newborn. © 2013 American Association of Blood Banks.

  9. Accurate and quantitative polarization-sensitive OCT by unbiased birefringence estimator with noise-stochastic correction

    NASA Astrophysics Data System (ADS)

    Kasaragod, Deepa; Sugiyama, Satoshi; Ikuno, Yasushi; Alonso-Caneiro, David; Yamanari, Masahiro; Fukuda, Shinichi; Oshika, Tetsuro; Hong, Young-Joo; Li, En; Makita, Shuichi; Miura, Masahiro; Yasuno, Yoshiaki

    2016-03-01

    Polarization sensitive optical coherence tomography (PS-OCT) is a functional extension of OCT that contrasts the polarization properties of tissues. It has been applied to ophthalmology, cardiology, etc. Proper quantitative imaging is required for a widespread clinical utility. However, the conventional method of averaging to improve the signal to noise ratio (SNR) and the contrast of the phase retardation (or birefringence) images introduce a noise bias offset from the true value. This bias reduces the effectiveness of birefringence contrast for a quantitative study. Although coherent averaging of Jones matrix tomography has been widely utilized and has improved the image quality, the fundamental limitation of nonlinear dependency of phase retardation and birefringence to the SNR was not overcome. So the birefringence obtained by PS-OCT was still not accurate for a quantitative imaging. The nonlinear effect of SNR to phase retardation and birefringence measurement was previously formulated in detail for a Jones matrix OCT (JM-OCT) [1]. Based on this, we had developed a maximum a-posteriori (MAP) estimator and quantitative birefringence imaging was demonstrated [2]. However, this first version of estimator had a theoretical shortcoming. It did not take into account the stochastic nature of SNR of OCT signal. In this paper, we present an improved version of the MAP estimator which takes into account the stochastic property of SNR. This estimator uses a probability distribution function (PDF) of true local retardation, which is proportional to birefringence, under a specific set of measurements of the birefringence and SNR. The PDF was pre-computed by a Monte-Carlo (MC) simulation based on the mathematical model of JM-OCT before the measurement. A comparison between this new MAP estimator, our previous MAP estimator [2], and the standard mean estimator is presented. The comparisons are performed both by numerical simulation and in vivo measurements of anterior and

  10. Quantitative analyses of cell behaviors underlying notochord formation and extension in mouse embryos.

    PubMed

    Sausedo, R A; Schoenwolf, G C

    1994-05-01

    Formation and extension of the notochord (i.e., notogenesis) is one of the earliest and most obvious events of axis development in vertebrate embryos. In birds and mammals, prospective notochord cells arise from Hensen's node and come to lie beneath the midline of the neural plate. Throughout the period of neurulation, the notochord retains its close spatial relationship with the developing neural tube and undergoes rapid extension in concert with the overlying neuroepithelium. In the present study, we examined notochord development quantitatively in mouse embryos. C57BL/6 mouse embryos were collected at 8, 8.5, 9, 9.5, and 10 days of gestation. They were then embedded in paraffin and sectioned transversely. Serial sections from 21 embryos were stained with Schiff's reagent according to the Feulgen-Rossenbeck procedure and used for quantitative analyses of notochord extension. Quantitative analyses revealed that extension of the notochord involves cell division within the notochord proper and cell rearrangement within the notochordal plate (the immediate precursor of the notochord). In addition, extension of the notochord involves cell accretion, that is, the addition of cells to the notochord's caudal end, a process that involves considerable cell rearrangement at the notochordal plate-node interface. Extension of the mouse notochord occurs similarly to that described previously for birds (Sausedo and Schoenwolf, 1993 Anat. Rec. 237:58-70). That is, in both birds (i.e., quail and chick) and mouse embryos, notochord extension involves cell division, cell rearrangement, and cell accretion. Thus higher vertebrates utilize similar morphogenetic movements to effect notogenesis.

  11. Quantitative analysis of naphthenic acids in water by liquid chromatography-accurate mass time-of-flight mass spectrometry.

    PubMed

    Hindle, Ralph; Noestheden, Matthew; Peru, Kerry; Headley, John

    2013-04-19

    This study details the development of a routine method for quantitative analysis of oil sands naphthenic acids, which are a complex class of compounds found naturally and as contaminants in oil sands process waters from Alberta's Athabasca region. Expanding beyond classical naphthenic acids (CnH2n-zO2), those compounds conforming to the formula CnH2n-zOx (where 2≥x≤4) were examined in commercial naphthenic acid and environmental water samples. HPLC facilitated a five-fold reduction in ion suppression when compared to the more commonly used flow injection analysis. A comparison of 39 model naphthenic acids revealed significant variability in response factors, demonstrating the necessity of using naphthenic acid mixtures for quantitation, rather than model compounds. It was also demonstrated that naphthenic acidic heterogeneity (commercial and environmental) necessitates establishing a single NA mix as the standard against which all quantitation is performed. The authors present the first ISO17025 accredited method for the analysis of naphthenic acids in water using HPLC high resolution accurate mass time-of-flight mass spectrometry. The method detection limit was 1mg/L total oxy-naphthenic acids (Sigma technical mix). Copyright © 2013 Elsevier B.V. All rights reserved.

  12. Accurate ECG diagnosis of atrial tachyarrhythmias using quantitative analysis: a prospective diagnostic and cost-effectiveness study.

    PubMed

    Krummen, David E; Patel, Mitul; Nguyen, Hong; Ho, Gordon; Kazi, Dhruv S; Clopton, Paul; Holland, Marian C; Greenberg, Scott L; Feld, Gregory K; Faddis, Mitchell N; Narayan, Sanjiv M

    2010-11-01

    Quantitative ECG Analysis. Optimal atrial tachyarrhythmia management is facilitated by accurate electrocardiogram interpretation, yet typical atrial flutter (AFl) may present without sawtooth F-waves or RR regularity, and atrial fibrillation (AF) may be difficult to separate from atypical AFl or rapid focal atrial tachycardia (AT). We analyzed whether improved diagnostic accuracy using a validated analysis tool significantly impacts costs and patient care. We performed a prospective, blinded, multicenter study using a novel quantitative computerized algorithm to identify atrial tachyarrhythmia mechanism from the surface ECG in patients referred for electrophysiology study (EPS). In 122 consecutive patients (age 60 ± 12 years) referred for EPS, 91 sustained atrial tachyarrhythmias were studied. ECGs were also interpreted by 9 physicians from 3 specialties for comparison and to allow healthcare system modeling. Diagnostic accuracy was compared to the diagnosis at EPS. A Markov model was used to estimate the impact of improved arrhythmia diagnosis. We found 13% of typical AFl ECGs had neither sawtooth flutter waves nor RR regularity, and were misdiagnosed by the majority of clinicians (0/6 correctly diagnosed by consensus visual interpretation) but correctly by quantitative analysis in 83% (5/6, P = 0.03). AF diagnosis was also improved through use of the algorithm (92%) versus visual interpretation (primary care: 76%, P < 0.01). Economically, we found that these improvements in diagnostic accuracy resulted in an average cost-savings of $1,303 and 0.007 quality-adjusted-life-years per patient. Typical AFl and AF are frequently misdiagnosed using visual criteria. Quantitative analysis improves diagnostic accuracy and results in improved healthcare costs and patient outcomes. © 2010 Wiley Periodicals, Inc.

  13. Linear Quantitative Profiling Method Fast Monitors Alkaloids of Sophora Flavescens That Was Verified by Tri-Marker Analyses.

    PubMed

    Hou, Zhifei; Sun, Guoxiang; Guo, Yong

    2016-01-01

    The present study demonstrated the use of the Linear Quantitative Profiling Method (LQPM) to evaluate the quality of Alkaloids of Sophora flavescens (ASF) based on chromatographic fingerprints in an accurate, economical and fast way. Both linear qualitative and quantitative similarities were calculated in order to monitor the consistency of the samples. The results indicate that the linear qualitative similarity (LQLS) is not sufficiently discriminating due to the predominant presence of three alkaloid compounds (matrine, sophoridine and oxymatrine) in the test samples; however, the linear quantitative similarity (LQTS) was shown to be able to obviously identify the samples based on the difference in the quantitative content of all the chemical components. In addition, the fingerprint analysis was also supported by the quantitative analysis of three marker compounds. The LQTS was found to be highly correlated to the contents of the marker compounds, indicating that quantitative analysis of the marker compounds may be substituted with the LQPM based on the chromatographic fingerprints for the purpose of quantifying all chemicals of a complex sample system. Furthermore, once reference fingerprint (RFP) developed from a standard preparation in an immediate detection way and the composition similarities calculated out, LQPM could employ the classical mathematical model to effectively quantify the multiple components of ASF samples without any chemical standard.

  14. Linear Quantitative Profiling Method Fast Monitors Alkaloids of Sophora Flavescens That Was Verified by Tri-Marker Analyses

    PubMed Central

    Hou, Zhifei; Sun, Guoxiang; Guo, Yong

    2016-01-01

    The present study demonstrated the use of the Linear Quantitative Profiling Method (LQPM) to evaluate the quality of Alkaloids of Sophora flavescens (ASF) based on chromatographic fingerprints in an accurate, economical and fast way. Both linear qualitative and quantitative similarities were calculated in order to monitor the consistency of the samples. The results indicate that the linear qualitative similarity (LQLS) is not sufficiently discriminating due to the predominant presence of three alkaloid compounds (matrine, sophoridine and oxymatrine) in the test samples; however, the linear quantitative similarity (LQTS) was shown to be able to obviously identify the samples based on the difference in the quantitative content of all the chemical components. In addition, the fingerprint analysis was also supported by the quantitative analysis of three marker compounds. The LQTS was found to be highly correlated to the contents of the marker compounds, indicating that quantitative analysis of the marker compounds may be substituted with the LQPM based on the chromatographic fingerprints for the purpose of quantifying all chemicals of a complex sample system. Furthermore, once reference fingerprint (RFP) developed from a standard preparation in an immediate detection way and the composition similarities calculated out, LQPM could employ the classical mathematical model to effectively quantify the multiple components of ASF samples without any chemical standard. PMID:27529425

  15. Analytical method for the accurate determination of tricothecenes in grains using LC-MS/MS: a comparison between MRM transition and MS3 quantitation.

    PubMed

    Lim, Chee Wei; Tai, Siew Hoon; Lee, Lin Min; Chan, Sheot Harn

    2012-07-01

    The current food crisis demands unambiguous determination of mycotoxin contamination in staple foods to achieve safer food for consumption. This paper describes the first accurate LC-MS/MS method developed to analyze tricothecenes in grains by applying multiple reaction monitoring (MRM) transition and MS(3) quantitation strategies in tandem. The tricothecenes are nivalenol, deoxynivalenol, deoxynivalenol-3-glucoside, fusarenon X, 3-acetyl-deoxynivalenol, 15-acetyldeoxynivalenol, diacetoxyscirpenol, and HT-2 and T-2 toxins. Acetic acid and ammonium acetate were used to convert the analytes into their respective acetate adducts and ammonium adducts under negative and positive MS polarity conditions, respectively. The mycotoxins were separated by reversed-phase LC in a 13.5-min run, ionized using electrospray ionization, and detected by tandem mass spectrometry. Analyte-specific mass-to-charge (m/z) ratios were used to perform quantitation under MRM transition and MS(3) (linear ion trap) modes. Three experiments were made for each quantitation mode and matrix in batches over 6 days for recovery studies. The matrix effect was investigated at concentration levels of 20, 40, 80, 120, 160, and 200 μg kg(-1) (n = 3) in 5 g corn flour and rice flour. Extraction with acetonitrile provided a good overall recovery range of 90-108% (n = 3) at three levels of spiking concentration of 40, 80, and 120 μg kg(-1). A quantitation limit of 2-6 μg kg(-1) was achieved by applying an MRM transition quantitation strategy. Under MS(3) mode, a quantitation limit of 4-10 μg kg(-1) was achieved. Relative standard deviations of 2-10% and 2-11% were reported for MRM transition and MS(3) quantitation, respectively. The successful utilization of MS(3) enabled accurate analyte fragmentation pattern matching and its quantitation, leading to the development of analytical methods in fields that demand both analyte specificity and fragmentation fingerprint-matching capabilities that are

  16. Quantitative methods for analysing cumulative effects on fish migration success: a review.

    PubMed

    Johnson, J E; Patterson, D A; Martins, E G; Cooke, S J; Hinch, S G

    2012-07-01

    It is often recognized, but seldom addressed, that a quantitative assessment of the cumulative effects, both additive and non-additive, of multiple stressors on fish survival would provide a more realistic representation of the factors that influence fish migration. This review presents a compilation of analytical methods applied to a well-studied fish migration, a more general review of quantitative multivariable methods, and a synthesis on how to apply new analytical techniques in fish migration studies. A compilation of adult migration papers from Fraser River sockeye salmon Oncorhynchus nerka revealed a limited number of multivariable methods being applied and the sub-optimal reliance on univariable methods for multivariable problems. The literature review of fisheries science, general biology and medicine identified a large number of alternative methods for dealing with cumulative effects, with a limited number of techniques being used in fish migration studies. An evaluation of the different methods revealed that certain classes of multivariable analyses will probably prove useful in future assessments of cumulative effects on fish migration. This overview and evaluation of quantitative methods gathered from the disparate fields should serve as a primer for anyone seeking to quantify cumulative effects on fish migration survival. © 2012 The Authors. Journal of Fish Biology © 2012 The Fisheries Society of the British Isles.

  17. Application of the accurate mass and time tag approach in studies of the human blood lipidome

    PubMed Central

    Ding, Jie; Sorensen, Christina M.; Jaitly, Navdeep; Jiang, Hongliang; Orton, Daniel J.; Monroe, Matthew E.; Moore, Ronald J.; Smith, Richard D.; Metz, Thomas O.

    2008-01-01

    We report a preliminary demonstration of the accurate mass and time (AMT) tag approach for lipidomics. Initial data-dependent LC-MS/MS analyses of human plasma, erythrocyte, and lymphocyte lipids were performed in order to identify lipid molecular species in conjunction with complementary accurate mass and isotopic distribution information. Identified lipids were used to populate initial lipid AMT tag databases containing 250 and 45 entries for those species detected in positive and negative electrospray ionization (ESI) modes, respectively. The positive ESI database was then utilized to identify human plasma, erythrocyte, and lymphocyte lipids in high-throughput LC-MS analyses based on the AMT tag approach. We were able to define the lipid profiles of human plasma, erythrocytes, and lymphocytes based on qualitative and quantitative differences in lipid abundance. PMID:18502191

  18. Toward Quantitative Small Animal Pinhole SPECT: Assessment of Quantitation Accuracy Prior to Image Compensations

    PubMed Central

    Chen, Chia-Lin; Wang, Yuchuan; Lee, Jason J. S.; Tsui, Benjamin M. W.

    2011-01-01

    Purpose We assessed the quantitation accuracy of small animal pinhole single photon emission computed tomography (SPECT) under the current preclinical settings, where image compensations are not routinely applied. Procedures The effects of several common image-degrading factors and imaging parameters on quantitation accuracy were evaluated using Monte-Carlo simulation methods. Typical preclinical imaging configurations were modeled, and quantitative analyses were performed based on image reconstructions without compensating for attenuation, scatter, and limited system resolution. Results Using mouse-sized phantom studies as examples, attenuation effects alone degraded quantitation accuracy by up to −18% (Tc-99m or In-111) or −41% (I-125). The inclusion of scatter effects changed the above numbers to −12% (Tc-99m or In-111) and −21% (I-125), respectively, indicating the significance of scatter in quantitative I-125 imaging. Region-of-interest (ROI) definitions have greater impacts on regional quantitation accuracy for small sphere sources as compared to attenuation and scatter effects. For the same ROI, SPECT acquisitions using pinhole apertures of different sizes could significantly affect the outcome, whereas the use of different radii-of-rotation yielded negligible differences in quantitation accuracy for the imaging configurations simulated. Conclusions We have systematically quantified the influence of several factors affecting the quantitation accuracy of small animal pinhole SPECT. In order to consistently achieve accurate quantitation within 5% of the truth, comprehensive image compensation methods are needed. PMID:19048346

  19. Analyser-based phase contrast image reconstruction using geometrical optics.

    PubMed

    Kitchen, M J; Pavlov, K M; Siu, K K W; Menk, R H; Tromba, G; Lewis, R A

    2007-07-21

    Analyser-based phase contrast imaging can provide radiographs of exceptional contrast at high resolution (<100 microm), whilst quantitative phase and attenuation information can be extracted using just two images when the approximations of geometrical optics are satisfied. Analytical phase retrieval can be performed by fitting the analyser rocking curve with a symmetric Pearson type VII function. The Pearson VII function provided at least a 10% better fit to experimentally measured rocking curves than linear or Gaussian functions. A test phantom, a hollow nylon cylinder, was imaged at 20 keV using a Si(1 1 1) analyser at the ELETTRA synchrotron radiation facility. Our phase retrieval method yielded a more accurate object reconstruction than methods based on a linear fit to the rocking curve. Where reconstructions failed to map expected values, calculations of the Takagi number permitted distinction between the violation of the geometrical optics conditions and the failure of curve fitting procedures. The need for synchronized object/detector translation stages was removed by using a large, divergent beam and imaging the object in segments. Our image acquisition and reconstruction procedure enables quantitative phase retrieval for systems with a divergent source and accounts for imperfections in the analyser.

  20. Novel Autism Subtype-Dependent Genetic Variants Are Revealed by Quantitative Trait and Subphenotype Association Analyses of Published GWAS Data

    PubMed Central

    Hu, Valerie W.; Addington, Anjene; Hyman, Alexander

    2011-01-01

    The heterogeneity of symptoms associated with autism spectrum disorders (ASDs) has presented a significant challenge to genetic analyses. Even when associations with genetic variants have been identified, it has been difficult to associate them with a specific trait or characteristic of autism. Here, we report that quantitative trait analyses of ASD symptoms combined with case-control association analyses using distinct ASD subphenotypes identified on the basis of symptomatic profiles result in the identification of highly significant associations with 18 novel single nucleotide polymorphisms (SNPs). The symptom categories included deficits in language usage, non-verbal communication, social development, and play skills, as well as insistence on sameness or ritualistic behaviors. Ten of the trait-associated SNPs, or quantitative trait loci (QTL), were associated with more than one subtype, providing partial replication of the identified QTL. Notably, none of the novel SNPs is located within an exonic region, suggesting that these hereditary components of ASDs are more likely related to gene regulatory processes (or gene expression) than to structural or functional changes in gene products. Seven of the QTL reside within intergenic chromosomal regions associated with rare copy number variants that have been previously reported in autistic samples. Pathway analyses of the genes associated with the QTL identified in this study implicate neurological functions and disorders associated with autism pathophysiology. This study underscores the advantage of incorporating both quantitative traits as well as subphenotypes into large-scale genome-wide analyses of complex disorders. PMID:21556359

  1. Preferential access to genetic information from endogenous hominin ancient DNA and accurate quantitative SNP-typing via SPEX

    PubMed Central

    Brotherton, Paul; Sanchez, Juan J.; Cooper, Alan; Endicott, Phillip

    2010-01-01

    The analysis of targeted genetic loci from ancient, forensic and clinical samples is usually built upon polymerase chain reaction (PCR)-generated sequence data. However, many studies have shown that PCR amplification from poor-quality DNA templates can create sequence artefacts at significant levels. With hominin (human and other hominid) samples, the pervasive presence of highly PCR-amplifiable human DNA contaminants in the vast majority of samples can lead to the creation of recombinant hybrids and other non-authentic artefacts. The resulting PCR-generated sequences can then be difficult, if not impossible, to authenticate. In contrast, single primer extension (SPEX)-based approaches can genotype single nucleotide polymorphisms from ancient fragments of DNA as accurately as modern DNA. A single SPEX-type assay can amplify just one of the duplex DNA strands at target loci and generate a multi-fold depth-of-coverage, with non-authentic recombinant hybrids reduced to undetectable levels. Crucially, SPEX-type approaches can preferentially access genetic information from damaged and degraded endogenous ancient DNA templates over modern human DNA contaminants. The development of SPEX-type assays offers the potential for highly accurate, quantitative genotyping from ancient hominin samples. PMID:19864251

  2. NEW TARGET AND CONTROL ASSAYS FOR QUANTITATIVE POLYMERASE CHAIN REACTION (QPCR) ANALYSIS OF ENTEROCOCCI IN WATER

    EPA Science Inventory

    Enterococci are frequently monitored in water samples as indicators of fecal pollution. Attention is now shifting from culture based methods for enumerating these organisms to more rapid molecular methods such as QPCR. Accurate quantitative analyses by this method requires highly...

  3. A New Material Mapping Procedure for Quantitative Computed Tomography-Based, Continuum Finite Element Analyses of the Vertebra

    PubMed Central

    Unnikrishnan, Ginu U.; Morgan, Elise F.

    2011-01-01

    Inaccuracies in the estimation of material properties and errors in the assignment of these properties into finite element models limit the reliability, accuracy, and precision of quantitative computed tomography (QCT)-based finite element analyses of the vertebra. In this work, a new mesh-independent, material mapping procedure was developed to improve the quality of predictions of vertebral mechanical behavior from QCT-based finite element models. In this procedure, an intermediate step, called the material block model, was introduced to determine the distribution of material properties based on bone mineral density, and these properties were then mapped onto the finite element mesh. A sensitivity study was first conducted on a calibration phantom to understand the influence of the size of the material blocks on the computed bone mineral density. It was observed that varying the material block size produced only marginal changes in the predictions of mineral density. Finite element (FE) analyses were then conducted on a square column-shaped region of the vertebra and also on the entire vertebra in order to study the effect of material block size on the FE-derived outcomes. The predicted values of stiffness for the column and the vertebra decreased with decreasing block size. When these results were compared to those of a mesh convergence analysis, it was found that the influence of element size on vertebral stiffness was less than that of the material block size. This mapping procedure allows the material properties in a finite element study to be determined based on the block size required for an accurate representation of the material field, while the size of the finite elements can be selected independently and based on the required numerical accuracy of the finite element solution. The mesh-independent, material mapping procedure developed in this study could be particularly helpful in improving the accuracy of finite element analyses of

  4. Elastic fibers in human skin: quantitation of elastic fibers by computerized digital image analyses and determination of elastin by radioimmunoassay of desmosine.

    PubMed

    Uitto, J; Paul, J L; Brockley, K; Pearce, R H; Clark, J G

    1983-10-01

    The elastic fibers in the skin and other organs can be affected in several disease processes. In this study, we have developed morphometric techniques that allow accurate quantitation of the elastic fibers in punch biopsy specimens of skin. In this procedure, the elastic fibers, visualized by elastin-specific stains, are examined through a camera unit attached to the microscope. The black and white images sensing various gray levels are then converted to binary images after selecting a threshold with an analog threshold selection device. The binary images are digitized and the data analyzed by a computer program designed to express the properties of the image, thus allowing determination of the volume fraction occupied by the elastic fibers. As an independent measure of the elastic fibers, alternate tissue sections were used for assay of desmosine, an elastin-specific cross-link compound, by a radioimmunoassay. The clinical applicability of the computerized morphometric analyses was tested by examining the elastic fibers in the skin of five patients with pseudoxanthoma elasticum or Buschke-Ollendorff syndrome. In the skin of 10 healthy control subjects, the elastic fibers occupied 2.1 +/- 1.1% (mean +/- SD) of the dermis. The volume fractions occupied by the elastic fibers in the lesions of pseudoxanthoma elasticum or Buschke-Ollendorff syndrome were increased as much as 6-fold, whereas the values in the unaffected areas of the skin in the same patients were within normal limits. A significant correlation between the volume fraction of elastic fibers, determined by computerized morphometric analyses, and the concentration of desmosine, quantitated by radioimmunoassay, was noted in the total material. These results demonstrate that computerized morphometric techniques are helpful in characterizing disease processes affecting skin. This methodology should also be applicable to other tissues that contain elastic fibers and that are affected in various heritable and

  5. Accurate quantitation of circulating cell-free mitochondrial DNA in plasma by droplet digital PCR.

    PubMed

    Ye, Wei; Tang, Xiaojun; Liu, Chu; Wen, Chaowei; Li, Wei; Lyu, Jianxin

    2017-04-01

    To establish a method for accurate quantitation of circulating cell-free mitochondrial DNA (ccf-mtDNA) in plasma by droplet digital PCR (ddPCR), we designed a ddPCR method to determine the copy number of ccf-mtDNA by amplifying mitochondrial ND1 (MT-ND1). To evaluate the sensitivity and specificity of the method, a recombinant pMD18-T plasmid containing MT-ND1 sequences and mtDNA-deleted (ρ 0 ) HeLa cells were used, respectively. Subsequently, different plasma samples were prepared for ddPCR to evaluate the feasibility of detecting plasma ccf-mtDNA. In the results, the ddPCR method showed high sensitivity and specificity. When the DNA was extracted from plasma prior to ddPCR, the ccf-mtDNA copy number was higher than that measured without extraction. This difference was not due to a PCR inhibitor, such as EDTA-Na 2 , an anti-coagulant in plasma, because standard EDTA-Na 2 concentration (5 mM) did not significantly inhibit ddPCR reactions. The difference might be attributable to plasma exosomal mtDNA, which was 4.21 ± 0.38 copies/μL of plasma, accounting for ∼19% of plasma ccf-mtDNA. Therefore, ddPCR can quickly and reliably detect ccf-mtDNA from plasma with a prior DNA extraction step, providing for a more accurate detection of ccf-mtDNA. The direct use of plasma as a template in ddPCR is suitable for the detection of exogenous cell-free nucleic acids within plasma, but not of nucleic acids that have a vesicle-associated form, such as exosomal mtDNA. Graphical Abstract Designs of the present work. *: Module 1, #: Module 2, &: Module 3.

  6. Study Quality in SLA: An Assessment of Designs, Analyses, and Reporting Practices in Quantitative L2 Research

    ERIC Educational Resources Information Center

    Plonsky, Luke

    2013-01-01

    This study assesses research and reporting practices in quantitative second language (L2) research. A sample of 606 primary studies, published from 1990 to 2010 in "Language Learning and Studies in Second Language Acquisition," was collected and coded for designs, statistical analyses, reporting practices, and outcomes (i.e., effect…

  7. Quantitative Phase Microscopy for Accurate Characterization of Microlens Arrays

    NASA Astrophysics Data System (ADS)

    Grilli, Simonetta; Miccio, Lisa; Merola, Francesco; Finizio, Andrea; Paturzo, Melania; Coppola, Sara; Vespini, Veronica; Ferraro, Pietro

    Microlens arrays are of fundamental importance in a wide variety of applications in optics and photonics. This chapter deals with an accurate digital holography-based characterization of both liquid and polymeric microlenses fabricated by an innovative pyro-electrowetting process. The actuation of liquid and polymeric films is obtained through the use of pyroelectric charges generated into polar dielectric lithium niobate crystals.

  8. Accurate quantitative CF-LIBS analysis of both major and minor elements in alloys via iterative correction of plasma temperature and spectral intensity

    NASA Astrophysics Data System (ADS)

    Shuxia, ZHAO; Lei, ZHANG; Jiajia, HOU; Yang, ZHAO; Wangbao, YIN; Weiguang, MA; Lei, DONG; Liantuan, XIAO; Suotang, JIA

    2018-03-01

    The chemical composition of alloys directly determines their mechanical behaviors and application fields. Accurate and rapid analysis of both major and minor elements in alloys plays a key role in metallurgy quality control and material classification processes. A quantitative calibration-free laser-induced breakdown spectroscopy (CF-LIBS) analysis method, which carries out combined correction of plasma temperature and spectral intensity by using a second-order iterative algorithm and two boundary standard samples, is proposed to realize accurate composition measurements. Experimental results show that, compared to conventional CF-LIBS analysis, the relative errors for major elements Cu and Zn and minor element Pb in the copper-lead alloys has been reduced from 12%, 26% and 32% to 1.8%, 2.7% and 13.4%, respectively. The measurement accuracy for all elements has been improved substantially.

  9. Quantitative analysis of periodontal pathogens by ELISA and real-time polymerase chain reaction.

    PubMed

    Hamlet, Stephen M

    2010-01-01

    The development of analytical methods enabling the accurate identification and enumeration of bacterial species colonizing the oral cavity has led to the identification of a small number of bacterial pathogens that are major factors in the etiology of periodontal disease. Further, these methods also underpin more recent epidemiological analyses of the impact of periodontal disease on general health. Given the complex milieu of over 700 species of microorganisms known to exist within the complex biofilms found in the oral cavity, the identification and enumeration of oral periodontopathogens has not been an easy task. In recent years however, some of the intrinsic limitations of the more traditional microbiological analyses previously used have been overcome with the advent of immunological and molecular analytical methods. Of the plethora of methodologies reported in the literature, the enzyme-linked immunosorbent assay (ELISA), which combines the specificity of antibody with the sensitivity of simple enzyme assays and the polymerase chain reaction (PCR), has been widely utilized in both laboratory and clinical applications. Although conventional PCR does not allow quantitation of the target organism, real-time PCR (rtPCR) has the ability to detect amplicons as they accumulate in "real time" allowing subsequent quantitation. These methods enable the accurate quantitation of as few as 10(2) (using rtPCR) to 10(4) (using ELISA) periodontopathogens in dental plaque samples.

  10. Supramolecular assembly affording a ratiometric two-photon fluorescent nanoprobe for quantitative detection and bioimaging.

    PubMed

    Wang, Peng; Zhang, Cheng; Liu, Hong-Wen; Xiong, Mengyi; Yin, Sheng-Yan; Yang, Yue; Hu, Xiao-Xiao; Yin, Xia; Zhang, Xiao-Bing; Tan, Weihong

    2017-12-01

    Fluorescence quantitative analyses for vital biomolecules are in great demand in biomedical science owing to their unique detection advantages with rapid, sensitive, non-damaging and specific identification. However, available fluorescence strategies for quantitative detection are usually hard to design and achieve. Inspired by supramolecular chemistry, a two-photon-excited fluorescent supramolecular nanoplatform ( TPSNP ) was designed for quantitative analysis with three parts: host molecules (β-CD polymers), a guest fluorophore of sensing probes (Np-Ad) and a guest internal reference (NpRh-Ad). In this strategy, the TPSNP possesses the merits of (i) improved water-solubility and biocompatibility; (ii) increased tissue penetration depth for bioimaging by two-photon excitation; (iii) quantitative and tunable assembly of functional guest molecules to obtain optimized detection conditions; (iv) a common approach to avoid the limitation of complicated design by adjustment of sensing probes; and (v) accurate quantitative analysis by virtue of reference molecules. As a proof-of-concept, we utilized the two-photon fluorescent probe NHS-Ad-based TPSNP-1 to realize accurate quantitative analysis of hydrogen sulfide (H 2 S), with high sensitivity and good selectivity in live cells, deep tissues and ex vivo -dissected organs, suggesting that the TPSNP is an ideal quantitative indicator for clinical samples. What's more, TPSNP will pave the way for designing and preparing advanced supramolecular sensors for biosensing and biomedicine.

  11. Spotsizer: High-throughput quantitative analysis of microbial growth.

    PubMed

    Bischof, Leanne; Převorovský, Martin; Rallis, Charalampos; Jeffares, Daniel C; Arzhaeva, Yulia; Bähler, Jürg

    2016-10-01

    Microbial colony growth can serve as a useful readout in assays for studying complex genetic interactions or the effects of chemical compounds. Although computational tools for acquiring quantitative measurements of microbial colonies have been developed, their utility can be compromised by inflexible input image requirements, non-trivial installation procedures, or complicated operation. Here, we present the Spotsizer software tool for automated colony size measurements in images of robotically arrayed microbial colonies. Spotsizer features a convenient graphical user interface (GUI), has both single-image and batch-processing capabilities, and works with multiple input image formats and different colony grid types. We demonstrate how Spotsizer can be used for high-throughput quantitative analysis of fission yeast growth. The user-friendly Spotsizer tool provides rapid, accurate, and robust quantitative analyses of microbial growth in a high-throughput format. Spotsizer is freely available at https://data.csiro.au/dap/landingpage?pid=csiro:15330 under a proprietary CSIRO license.

  12. OdorMapComparer: an application for quantitative analyses and comparisons of fMRI brain odor maps.

    PubMed

    Liu, Nian; Xu, Fuqiang; Miller, Perry L; Shepherd, Gordon M

    2007-01-01

    Brain odor maps are reconstructed flat images that describe the spatial activity patterns in the glomerular layer of the olfactory bulbs in animals exposed to different odor stimuli. We have developed a software application, OdorMapComparer, to carry out quantitative analyses and comparisons of the fMRI odor maps. This application is an open-source window program that first loads two odor map images being compared. It allows image transformations including scaling, flipping, rotating, and warping so that the two images can be appropriately aligned to each other. It performs simple subtraction, addition, and average of signals in the two images. It also provides comparative statistics including the normalized correlation (NC) and spatial correlation coefficient. Experimental studies showed that the rodent fMRI odor maps for aliphatic aldehydes displayed spatial activity patterns that are similar in gross outlines but somewhat different in specific subregions. Analyses with OdorMapComparer indicate that the similarity between odor maps decreases with increasing difference in the length of carbon chains. For example, the map of butanal is more closely related to that of pentanal (with a NC = 0.617) than to that of octanal (NC = 0.082), which is consistent with animal behavioral studies. The study also indicates that fMRI odor maps are statistically odor-specific and repeatable across both the intra- and intersubject trials. OdorMapComparer thus provides a tool for quantitative, statistical analyses and comparisons of fMRI odor maps in a fashion that is integrated with the overall odor mapping techniques.

  13. Qualitative and quantitative analyses of flavonoids in Spirodela polyrrhiza by high-performance liquid chromatography coupled with mass spectrometry.

    PubMed

    Qiao, Xue; He, Wen-ni; Xiang, Cheng; Han, Jian; Wu, Li-jun; Guo, De-an; Ye, Min

    2011-01-01

    Spirodela polyrrhiza (L.) Schleid. is a traditional Chinese herbal medicine for the treatment of influenza. Despite its wide use in Chinese medicine, no report on quality control of this herb is available so far. To establish qualitative and quantitative analytical methods by high-performance liquid chromatography (HPLC) coupled with mass spectrometry (MS) for the quality control of S. polyrrhiza. The methanol extract of S. polyrrhiza was analysed by HPLC/ESI-MS(n). Flavonoids were identified by comparing with reference standards or according to their MS(n) (n = 2-4) fragmentation behaviours. Based on LC/MS data, a standardised HPLC fingerprint was established by analysing 15 batches of commercial herbal samples. Furthermore, quantitative analysis was conducted by determining five major flavonoids, namely luteolin 8-C-glucoside, apigenin 8-C-glucoside, luteolin 7-O-glucoside, apigenin 7-O-glucoside and luteolin. A total of 18 flavonoids were identified by LC/MS, and 14 of them were reported from this herb for the first time. The HPLC fingerprints contained 10 common peaks, and could differentiate good quality batches from counterfeits. The total contents of five major flavonoids in S. polyrrhiza varied significantly from 4.28 to 19.87 mg/g. Qualitative LC/MS and quantitative HPLC analytical methods were established for the comprehensive quality control of S. polyrrhiza. Copyright © 2011 John Wiley & Sons, Ltd.

  14. A quantitative test of population genetics using spatiogenetic patterns in bacterial colonies.

    PubMed

    Korolev, Kirill S; Xavier, João B; Nelson, David R; Foster, Kevin R

    2011-10-01

    It is widely accepted that population-genetics theory is the cornerstone of evolutionary analyses. Empirical tests of the theory, however, are challenging because of the complex relationships between space, dispersal, and evolution. Critically, we lack quantitative validation of the spatial models of population genetics. Here we combine analytics, on- and off-lattice simulations, and experiments with bacteria to perform quantitative tests of the theory. We study two bacterial species, the gut microbe Escherichia coli and the opportunistic pathogen Pseudomonas aeruginosa, and show that spatiogenetic patterns in colony biofilms of both species are accurately described by an extension of the one-dimensional stepping-stone model. We use one empirical measure, genetic diversity at the colony periphery, to parameterize our models and show that we can then accurately predict another key variable: the degree of short-range cell migration along an edge. Moreover, the model allows us to estimate other key parameters, including effective population size (density) at the expansion frontier. While our experimental system is a simplification of natural microbial community, we argue that it constitutes proof of principle that the spatial models of population genetics can quantitatively capture organismal evolution.

  15. Rigour in quantitative research.

    PubMed

    Claydon, Leica Sarah

    2015-07-22

    This article which forms part of the research series addresses scientific rigour in quantitative research. It explores the basis and use of quantitative research and the nature of scientific rigour. It examines how the reader may determine whether quantitative research results are accurate, the questions that should be asked to determine accuracy and the checklists that may be used in this process. Quantitative research has advantages in nursing, since it can provide numerical data to help answer questions encountered in everyday practice.

  16. Who Let the CAT Out of the Bag? Accurately Dealing with Substitutional Heterogeneity in Phylogenomic Analyses.

    PubMed

    Whelan, Nathan V; Halanych, Kenneth M

    2017-03-01

    As phylogenetic datasets have increased in size, site-heterogeneous substitution models such as CAT-F81 and CAT-GTR have been advocated in favor of other models because they purportedly suppress long-branch attraction (LBA). These models are two of the most commonly used models in phylogenomics, and they have been applied to a variety of taxa, ranging from Drosophila to land plants. However, many arguments in favor of CAT models have been based on tenuous assumptions about the true phylogeny, rather than rigorous testing with known trees via simulation. Moreover, CAT models have not been compared to other approaches for handling substitutional heterogeneity such as data partitioning with site-homogeneous substitution models. We simulated amino acid sequence datasets with substitutional heterogeneity on a variety of tree shapes including those susceptible to LBA. Data were analyzed with both CAT models and partitioning to explore model performance; in total over 670,000 CPU hours were used, of which over 97% was spent running analyses with CAT models. In many cases, all models recovered branching patterns that were identical to the known tree. However, CAT-F81 consistently performed worse than other models in inferring the correct branching patterns, and both CAT models often overestimated substitutional heterogeneity. Additionally, reanalysis of two empirical metazoan datasets supports the notion that CAT-F81 tends to recover less accurate trees than data partitioning and CAT-GTR. Given these results, we conclude that partitioning and CAT-GTR perform similarly in recovering accurate branching patterns. However, computation time can be orders of magnitude less for data partitioning, with commonly used implementations of CAT-GTR often failing to reach completion in a reasonable time frame (i.e., for Bayesian analyses to converge). Practices such as removing constant sites and parsimony uninformative characters, or using CAT-F81 when CAT-GTR is deemed too

  17. Quantitative Analyse und Visualisierung der Herzfunktionen

    NASA Astrophysics Data System (ADS)

    Sauer, Anne; Schwarz, Tobias; Engel, Nicole; Seitel, Mathias; Kenngott, Hannes; Mohrhardt, Carsten; Loßnitzer, Dirk; Giannitsis, Evangelos; Katus, Hugo A.; Meinzer, Hans-Peter

    Die computergestützte bildbasierte Analyse der Herzfunktionen ist mittlerweile Standard in der Kardiologie. Die verfügbaren Produkte erfordern meist ein hohes Maß an Benutzerinteraktion und somit einen erhöhten Zeitaufwand. In dieser Arbeit wird ein Ansatz vorgestellt, der dem Kardiologen eine größtenteils automatische Analyse der Herzfunktionen mittels MRT-Bilddaten ermöglicht und damit Zeitersparnis schafft. Hierbei werden alle relevanten herzphysiologsichen Parameter berechnet und mithilfe von Diagrammen und Graphen visualisiert. Diese Berechnungen werden evaluiert, indem die ermittelten Werte mit manuell vermessenen verglichen werden. Der hierbei berechnete mittlere Fehler liegt mit 2,85 mm für die Wanddicke und 1,61 mm für die Wanddickenzunahme immer noch im Bereich einer Pixelgrösse der verwendeten Bilder.

  18. Method for accurate quantitation of background tissue optical properties in the presence of emission from a strong fluorescence marker

    NASA Astrophysics Data System (ADS)

    Bravo, Jaime; Davis, Scott C.; Roberts, David W.; Paulsen, Keith D.; Kanick, Stephen C.

    2015-03-01

    Quantification of targeted fluorescence markers during neurosurgery has the potential to improve and standardize surgical distinction between normal and cancerous tissues. However, quantitative analysis of marker fluorescence is complicated by tissue background absorption and scattering properties. Correction algorithms that transform raw fluorescence intensity into quantitative units, independent of absorption and scattering, require a paired measurement of localized white light reflectance to provide estimates of the optical properties. This study focuses on the unique problem of developing a spectral analysis algorithm to extract tissue absorption and scattering properties from white light spectra that contain contributions from both elastically scattered photons and fluorescence emission from a strong fluorophore (i.e. fluorescein). A fiber-optic reflectance device was used to perform measurements in a small set of optical phantoms, constructed with Intralipid (1% lipid), whole blood (1% volume fraction) and fluorescein (0.16-10 μg/mL). Results show that the novel spectral analysis algorithm yields accurate estimates of tissue parameters independent of fluorescein concentration, with relative errors of blood volume fraction, blood oxygenation fraction (BOF), and the reduced scattering coefficient (at 521 nm) of <7%, <1%, and <22%, respectively. These data represent a first step towards quantification of fluorescein in tissue in vivo.

  19. New ventures require accurate risk analyses and adjustments.

    PubMed

    Eastaugh, S R

    2000-01-01

    For new business ventures to succeed, healthcare executives need to conduct robust risk analyses and develop new approaches to balance risk and return. Risk analysis involves examination of objective risks and harder-to-quantify subjective risks. Mathematical principles applied to investment portfolios also can be applied to a portfolio of departments or strategic business units within an organization. The ideal business investment would have a high expected return and a low standard deviation. Nonetheless, both conservative and speculative strategies should be considered in determining an organization's optimal service line and helping the organization manage risk.

  20. Quantitative analyses of the 3D nuclear landscape recorded with super-resolved fluorescence microscopy.

    PubMed

    Schmid, Volker J; Cremer, Marion; Cremer, Thomas

    2017-07-01

    Recent advancements of super-resolved fluorescence microscopy have revolutionized microscopic studies of cells, including the exceedingly complex structural organization of cell nuclei in space and time. In this paper we describe and discuss tools for (semi-) automated, quantitative 3D analyses of the spatial nuclear organization. These tools allow the quantitative assessment of highly resolved different chromatin compaction levels in individual cell nuclei, which reflect functionally different regions or sub-compartments of the 3D nuclear landscape, and measurements of absolute distances between sites of different chromatin compaction. In addition, these tools allow 3D mapping of specific DNA/RNA sequences and nuclear proteins relative to the 3D chromatin compaction maps and comparisons of multiple cell nuclei. The tools are available in the free and open source R packages nucim and bioimagetools. We discuss the use of masks for the segmentation of nuclei and the use of DNA stains, such as DAPI, as a proxy for local differences in chromatin compaction. We further discuss the limitations of 3D maps of the nuclear landscape as well as problems of the biological interpretation of such data. Copyright © 2017 Elsevier Inc. All rights reserved.

  1. Improving Short Term Instability for Quantitative Analyses with Portable Electronic Noses

    PubMed Central

    Macías, Miguel Macías; Agudo, J. Enrique; Manso, Antonio García; Orellana, Carlos Javier García; Velasco, Horacio Manuel González; Caballero, Ramón Gallardo

    2014-01-01

    One of the main problems when working with electronic noses is the lack of reproducibility or repeatability of the sensor response, so that, if this problem is not properly considered, electronic noses can be useless, especially for quantitative analyses. On the other hand, irreproducibility is increased with portable and low cost electronic noses where laboratory equipment like gas zero generators cannot be used. In this work, we study the reproducibility of two portable electronic noses, the PEN3 (commercial) and CAPINose (a proprietary design) by using synthetic wine samples. We show that in both cases short term instability associated to the sensors' response to the same sample and under the same conditions represents a major problem and we propose an internal normalization technique that, in both cases, reduces the variability of the sensors' response. Finally, we show that the normalization proposed seems to be more effective in the CAPINose case, reducing, for example, the variability associated to the TGS2602 sensor from 12.19% to 2.2%. PMID:24932869

  2. An accurate method of extracting fat droplets in liver images for quantitative evaluation

    NASA Astrophysics Data System (ADS)

    Ishikawa, Masahiro; Kobayashi, Naoki; Komagata, Hideki; Shinoda, Kazuma; Yamaguchi, Masahiro; Abe, Tokiya; Hashiguchi, Akinori; Sakamoto, Michiie

    2015-03-01

    The steatosis in liver pathological tissue images is a promising indicator of nonalcoholic fatty liver disease (NAFLD) and the possible risk of hepatocellular carcinoma (HCC). The resulting values are also important for ensuring the automatic and accurate classification of HCC images, because the existence of many fat droplets is likely to create errors in quantifying the morphological features used in the process. In this study we propose a method that can automatically detect, and exclude regions with many fat droplets by using the feature values of colors, shapes and the arrangement of cell nuclei. We implement the method and confirm that it can accurately detect fat droplets and quantify the fat droplet ratio of actual images. This investigation also clarifies the effective characteristics that contribute to accurate detection.

  3. Quantitative and comparative liquid chromatography-electrospray ionization-mass spectrometry analyses of hydrogen sulfide and thiol metabolites derivaitized with 2-iodoacetanilide isotopologues.

    PubMed

    Lee, Der-Yen; Huang, Wei-Chieh; Gu, Ting-Jia; Chang, Geen-Dong

    2018-06-01

    Hydrogen sulfide (H 2 S), previously known as a toxic gas, is now recognized as a gasotransmitter along with nitric oxide and carbon monoxide. However, only few methods are available for quantitative determination of H 2 S in biological samples. 2-Iodoacetanilide (2-IAN), a thiol-reacting agent, has been used to tag the reduced cysteine residues of proteins for quantitative proteomics and for detection of cysteine oxidation modification. In this article, we proposed a new method for quantitative analyses of H 2 S and thiol metabolites using the procedure of pre-column 2-IAN derivatization coupled with liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS). 13 C 6 -Labeled and label-free 2-IAN efficiently react with H 2 S and thiol compounds at pH 9.5 and 65 °C. The derivatives exhibit excellent stability at alkaline conditions, high resolution on reverse phase liquid chromatography and great sensitivity for ESI-MS detection. The measurement of H 2 S, l-cysteine, glutathione, and DL-homocysteine derivatives was validated using 13 C 6 -labeled standard in LC-ESI-MS analyses and exhibited 10 nM-1 μM linear ranges for DL-homocysteine and glutathione and 1 nM-1 μM linear ranges for l-cysteine and H 2 S. In addition, the sequence of derivatization and extraction of metabolites is important in the quantification of thiol metabolites suggesting the presence of matrix effects. Most importantly, labeling with 2-IAN and 13 C 6 -2-IAN isotopologues could achieve quantitative and matched sample comparative analyses with minimal bias using our extraction and labeling procedures before LC-MS analysis. Copyright © 2018 Elsevier B.V. All rights reserved.

  4. A simplified and accurate detection of the genetically modified wheat MON71800 with one calibrator plasmid.

    PubMed

    Kim, Jae-Hwan; Park, Saet-Byul; Roh, Hyo-Jeong; Park, Sunghoon; Shin, Min-Ki; Moon, Gui Im; Hong, Jin-Hwan; Kim, Hae-Yeong

    2015-06-01

    With the increasing number of genetically modified (GM) events, unauthorized GMO releases into the food market have increased dramatically, and many countries have developed detection tools for them. This study described the qualitative and quantitative detection methods of unauthorized the GM wheat MON71800 with a reference plasmid (pGEM-M71800). The wheat acetyl-CoA carboxylase (acc) gene was used as the endogenous gene. The plasmid pGEM-M71800, which contains both the acc gene and the event-specific target MON71800, was constructed as a positive control for the qualitative and quantitative analyses. The limit of detection in the qualitative PCR assay was approximately 10 copies. In the quantitative PCR assay, the standard deviation and relative standard deviation repeatability values ranged from 0.06 to 0.25 and from 0.23% to 1.12%, respectively. This study supplies a powerful and very simple but accurate detection strategy for unauthorized GM wheat MON71800 that utilizes a single calibrator plasmid. Copyright © 2014 Elsevier Ltd. All rights reserved.

  5. A general method for bead-enhanced quantitation by flow cytometry

    PubMed Central

    Montes, Martin; Jaensson, Elin A.; Orozco, Aaron F.; Lewis, Dorothy E.; Corry, David B.

    2009-01-01

    Flow cytometry provides accurate relative cellular quantitation (percent abundance) of cells from diverse samples, but technical limitations of most flow cytometers preclude accurate absolute quantitation. Several quantitation standards are now commercially available which, when added to samples, permit absolute quantitation of CD4+ T cells. However, these reagents are limited by their cost, technical complexity, requirement for additional software and/or limited applicability. Moreover, few studies have validated the use of such reagents in complex biological samples, especially for quantitation of non-T cells. Here we show that addition to samples of known quantities of polystyrene fluorescence standardization beads permits accurate quantitation of CD4+ T cells from complex cell samples. This procedure, here termed single bead-enhanced cytofluorimetry (SBEC), was equally capable of enumerating eosinophils as well as subcellular fragments of apoptotic cells, moieties with very different optical and fluorescent characteristics. Relative to other proprietary products, SBEC is simple, inexpensive and requires no special software, suggesting that the method is suitable for the routine quantitation of most cells and other particles by flow cytometry. PMID:17067632

  6. A High Resolution/Accurate Mass (HRAM) Data-Dependent MS3 Neutral Loss Screening, Classification, and Relative Quantitation Methodology for Carbonyl Compounds in Saliva

    NASA Astrophysics Data System (ADS)

    Dator, Romel; Carrà, Andrea; Maertens, Laura; Guidolin, Valeria; Villalta, Peter W.; Balbo, Silvia

    2017-04-01

    Reactive carbonyl compounds (RCCs) are ubiquitous in the environment and are generated endogenously as a result of various physiological and pathological processes. These compounds can react with biological molecules inducing deleterious processes believed to be at the basis of their toxic effects. Several of these compounds are implicated in neurotoxic processes, aging disorders, and cancer. Therefore, a method characterizing exposures to these chemicals will provide insights into how they may influence overall health and contribute to disease pathogenesis. Here, we have developed a high resolution accurate mass (HRAM) screening strategy allowing simultaneous identification and relative quantitation of DNPH-derivatized carbonyls in human biological fluids. The screening strategy involves the diagnostic neutral loss of hydroxyl radical triggering MS3 fragmentation, which is only observed in positive ionization mode of DNPH-derivatized carbonyls. Unique fragmentation pathways were used to develop a classification scheme for characterizing known and unanticipated/unknown carbonyl compounds present in saliva. Furthermore, a relative quantitation strategy was implemented to assess variations in the levels of carbonyl compounds before and after exposure using deuterated d 3 -DNPH. This relative quantitation method was tested on human samples before and after exposure to specific amounts of alcohol. The nano-electrospray ionization (nano-ESI) in positive mode afforded excellent sensitivity with detection limits on-column in the high-attomole levels. To the best of our knowledge, this is the first report of a method using HRAM neutral loss screening of carbonyl compounds. In addition, the method allows simultaneous characterization and relative quantitation of DNPH-derivatized compounds using nano-ESI in positive mode.

  7. A quantitative reconstruction software suite for SPECT imaging

    NASA Astrophysics Data System (ADS)

    Namías, Mauro; Jeraj, Robert

    2017-11-01

    Quantitative Single Photon Emission Tomography (SPECT) imaging allows for measurement of activity concentrations of a given radiotracer in vivo. Although SPECT has usually been perceived as non-quantitative by the medical community, the introduction of accurate CT based attenuation correction and scatter correction from hybrid SPECT/CT scanners has enabled SPECT systems to be as quantitative as Positron Emission Tomography (PET) systems. We implemented a software suite to reconstruct quantitative SPECT images from hybrid or dedicated SPECT systems with a separate CT scanner. Attenuation, scatter and collimator response corrections were included in an Ordered Subset Expectation Maximization (OSEM) algorithm. A novel scatter fraction estimation technique was introduced. The SPECT/CT system was calibrated with a cylindrical phantom and quantitative accuracy was assessed with an anthropomorphic phantom and a NEMA/IEC image quality phantom. Accurate activity measurements were achieved at an organ level. This software suite helps increasing quantitative accuracy of SPECT scanners.

  8. Stability Test and Quantitative and Qualitative Analyses of the Amino Acids in Pharmacopuncture Extracted from Scolopendra subspinipes mutilans.

    PubMed

    Cho, GyeYoon; Han, KyuChul; Yoon, JinYoung

    2015-03-01

    Scolopendra subspinipes mutilans (S. subspinipes mutilans) is known as a traditional medicine and includes various amino acids, peptides and proteins. The amino acids in the pharmacopuncture extracted from S. subspinipes mutilans by using derivatization methods were analyzed quantitatively and qualitatively by using high performance liquid chromatography (HPLC) over a 12 month period to confirm its stability. Amino acids of pharmacopuncture extracted from S. subspinipes mutilans were derived by using O-phthaldialdehyde (OPA) & 9-fluorenyl methoxy carbonyl chloride (FMOC) reagent and were analyzed using HPLC. The amino acids were detected by using a diode array detector (DAD) and a fluorescence detector (FLD) to compare a mixed amino acid standard (STD) to the pharmacopuncture from centipedes. The stability tests on the pharmacopuncture from centipedes were done using HPLC for three conditions: a room temperature test chamber, an acceleration test chamber, and a cold test chamber. The pharmacopuncture from centipedes was prepared by using the method of the Korean Pharmacopuncture Institute (KPI) and through quantitative analyses was shown to contain 9 amino acids of the 16 amino acids in the mixed amino acid STD. The amounts of the amino acids in the pharmacopuncture from centipedes were 34.37 ppm of aspartate, 123.72 ppm of arginine, 170.63 ppm of alanine, 59.55 ppm of leucine and 57 ppm of lysine. The relative standard deviation (RSD %) results for the pharmacopuncture from centipedes had a maximum value of 14.95% and minimum value of 1.795% on the room temperature test chamber, the acceleration test chamber and the cold test chamber stability tests. Stability tests on and quantitative and qualitative analyses of the amino acids in the pharmacopuncture extracted from centipedes by using derivatization methods were performed by using HPLC. Through research, we hope to determine the relationship between time and the concentrations of the amino acids in the

  9. Digital PCR Quantitation of Muscle Mitochondrial DNA: Age, Fiber Type, and Mutation-Induced Changes.

    PubMed

    Herbst, Allen; Widjaja, Kevin; Nguy, Beatrice; Lushaj, Entela B; Moore, Timothy M; Hevener, Andrea L; McKenzie, Debbie; Aiken, Judd M; Wanagat, Jonathan

    2017-10-01

    Definitive quantitation of mitochondrial DNA (mtDNA) and mtDNA deletion mutation abundances would help clarify the role of mtDNA instability in aging. To more accurately quantify mtDNA, we applied the emerging technique of digital polymerase chain reaction to individual muscle fibers and muscle homogenates from aged rodents. Individual fiber mtDNA content correlated with fiber type and decreased with age. We adapted a digital polymerase chain reaction deletion assay that was accurate in mixing experiments to a mutation frequency of 0.03% and quantitated an age-induced increase in deletion frequency from rat muscle homogenates. Importantly, the deletion frequency measured in muscle homogenates strongly correlated with electron transport chain-deficient fiber abundance determined by histochemical analyses. These data clarify the temporal accumulation of mtDNA deletions that lead to electron chain-deficient fibers, a process culminating in muscle fiber loss. © The Author 2017. Published by Oxford University Press on behalf of The Gerontological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  10. The importance of accurate muscle modelling for biomechanical analyses: a case study with a lizard skull

    PubMed Central

    Gröning, Flora; Jones, Marc E. H.; Curtis, Neil; Herrel, Anthony; O'Higgins, Paul; Evans, Susan E.; Fagan, Michael J.

    2013-01-01

    Computer-based simulation techniques such as multi-body dynamics analysis are becoming increasingly popular in the field of skull mechanics. Multi-body models can be used for studying the relationships between skull architecture, muscle morphology and feeding performance. However, to be confident in the modelling results, models need to be validated against experimental data, and the effects of uncertainties or inaccuracies in the chosen model attributes need to be assessed with sensitivity analyses. Here, we compare the bite forces predicted by a multi-body model of a lizard (Tupinambis merianae) with in vivo measurements, using anatomical data collected from the same specimen. This subject-specific model predicts bite forces that are very close to the in vivo measurements and also shows a consistent increase in bite force as the bite position is moved posteriorly on the jaw. However, the model is very sensitive to changes in muscle attributes such as fibre length, intrinsic muscle strength and force orientation, with bite force predictions varying considerably when these three variables are altered. We conclude that accurate muscle measurements are crucial to building realistic multi-body models and that subject-specific data should be used whenever possible. PMID:23614944

  11. A highly sensitive and accurate gene expression analysis by sequencing ("bead-seq") for a single cell.

    PubMed

    Matsunaga, Hiroko; Goto, Mari; Arikawa, Koji; Shirai, Masataka; Tsunoda, Hiroyuki; Huang, Huan; Kambara, Hideki

    2015-02-15

    Analyses of gene expressions in single cells are important for understanding detailed biological phenomena. Here, a highly sensitive and accurate method by sequencing (called "bead-seq") to obtain a whole gene expression profile for a single cell is proposed. A key feature of the method is to use a complementary DNA (cDNA) library on magnetic beads, which enables adding washing steps to remove residual reagents in a sample preparation process. By adding the washing steps, the next steps can be carried out under the optimal conditions without losing cDNAs. Error sources were carefully evaluated to conclude that the first several steps were the key steps. It is demonstrated that bead-seq is superior to the conventional methods for single-cell gene expression analyses in terms of reproducibility, quantitative accuracy, and biases caused during sample preparation and sequencing processes. Copyright © 2014 Elsevier Inc. All rights reserved.

  12. Quantitating Organoleptic Volatile Phenols in Smoke-Exposed Vitis vinifera Berries.

    PubMed

    Noestheden, Matthew; Thiessen, Katelyn; Dennis, Eric G; Tiet, Ben; Zandberg, Wesley F

    2017-09-27

    Accurate methods for quantitating volatile phenols (i.e., guaiacol, syringol, 4-ethylphenol, etc.) in smoke-exposed Vitis vinifera berries prior to fermentation are needed to predict the likelihood of perceptible smoke taint following vinification. Reported here is a complete, cross-validated analytical workflow to accurately quantitate free and glycosidically bound volatile phenols in smoke-exposed berries using liquid-liquid extraction, acid-mediated hydrolysis, and gas chromatography-tandem mass spectrometry. The reported workflow addresses critical gaps in existing methods for volatile phenols that impact quantitative accuracy, most notably the effect of injection port temperature and the variability in acid-mediated hydrolytic procedures currently used. Addressing these deficiencies will help the wine industry make accurate, informed decisions when producing wines from smoke-exposed berries.

  13. Quantitation and Identification of Intact Major Milk Proteins for High-Throughput LC-ESI-Q-TOF MS Analyses

    PubMed Central

    Vincent, Delphine; Elkins, Aaron; Condina, Mark R.; Ezernieks, Vilnis; Rochfort, Simone

    2016-01-01

    Cow’s milk is an important source of proteins in human nutrition. On average, cow’s milk contains 3.5% protein. The most abundant proteins in bovine milk are caseins and some of the whey proteins, namely beta-lactoglobulin, alpha-lactalbumin, and serum albumin. A number of allelic variants and post-translationally modified forms of these proteins have been identified. Their occurrence varies with breed, individuality, stage of lactation, and health and nutritional status of the animal. It is therefore essential to have reliable methods of detection and quantitation of these proteins. Traditionally, major milk proteins are quantified using liquid chromatography (LC) and ultra violet detection method. However, as these protein variants co-elute to some degree, another dimension of separation is beneficial to accurately measure their amounts. Mass spectrometry (MS) offers such a tool. In this study, we tested several RP-HPLC and MS parameters to optimise the analysis of intact bovine proteins from milk. From our tests, we developed an optimum method that includes a 20-28-40% phase B gradient with 0.02% TFA in both mobile phases, at 0.2 mL/min flow rate, using 75°C for the C8 column temperature, scanning every 3 sec over a 600–3000 m/z window. The optimisations were performed using external standards commercially purchased for which ionisation efficiency, linearity of calibration, LOD, LOQ, sensitivity, selectivity, precision, reproducibility, and mass accuracy were demonstrated. From the MS analysis, we can use extracted ion chromatograms (EICs) of specific ion series of known proteins and integrate peaks at defined retention time (RT) window for quantitation purposes. This optimum quantitative method was successfully applied to two bulk milk samples from different breeds, Holstein-Friesian and Jersey, to assess differences in protein variant levels. PMID:27749892

  14. Quantitation and Identification of Intact Major Milk Proteins for High-Throughput LC-ESI-Q-TOF MS Analyses.

    PubMed

    Vincent, Delphine; Elkins, Aaron; Condina, Mark R; Ezernieks, Vilnis; Rochfort, Simone

    2016-01-01

    Cow's milk is an important source of proteins in human nutrition. On average, cow's milk contains 3.5% protein. The most abundant proteins in bovine milk are caseins and some of the whey proteins, namely beta-lactoglobulin, alpha-lactalbumin, and serum albumin. A number of allelic variants and post-translationally modified forms of these proteins have been identified. Their occurrence varies with breed, individuality, stage of lactation, and health and nutritional status of the animal. It is therefore essential to have reliable methods of detection and quantitation of these proteins. Traditionally, major milk proteins are quantified using liquid chromatography (LC) and ultra violet detection method. However, as these protein variants co-elute to some degree, another dimension of separation is beneficial to accurately measure their amounts. Mass spectrometry (MS) offers such a tool. In this study, we tested several RP-HPLC and MS parameters to optimise the analysis of intact bovine proteins from milk. From our tests, we developed an optimum method that includes a 20-28-40% phase B gradient with 0.02% TFA in both mobile phases, at 0.2 mL/min flow rate, using 75°C for the C8 column temperature, scanning every 3 sec over a 600-3000 m/z window. The optimisations were performed using external standards commercially purchased for which ionisation efficiency, linearity of calibration, LOD, LOQ, sensitivity, selectivity, precision, reproducibility, and mass accuracy were demonstrated. From the MS analysis, we can use extracted ion chromatograms (EICs) of specific ion series of known proteins and integrate peaks at defined retention time (RT) window for quantitation purposes. This optimum quantitative method was successfully applied to two bulk milk samples from different breeds, Holstein-Friesian and Jersey, to assess differences in protein variant levels.

  15. Comparison of multipoint linkage analyses for quantitative traits in the CEPH data: parametric LOD scores, variance components LOD scores, and Bayes factors.

    PubMed

    Sung, Yun Ju; Di, Yanming; Fu, Audrey Q; Rothstein, Joseph H; Sieh, Weiva; Tong, Liping; Thompson, Elizabeth A; Wijsman, Ellen M

    2007-01-01

    We performed multipoint linkage analyses with multiple programs and models for several gene expression traits in the Centre d'Etude du Polymorphisme Humain families. All analyses provided consistent results for both peak location and shape. Variance-components (VC) analysis gave wider peaks and Bayes factors gave fewer peaks. Among programs from the MORGAN package, lm_multiple performed better than lm_markers, resulting in less Markov-chain Monte Carlo (MCMC) variability between runs, and the program lm_twoqtl provided higher LOD scores by also including either a polygenic component or an additional quantitative trait locus.

  16. Impact of reconstruction parameters on quantitative I-131 SPECT

    NASA Astrophysics Data System (ADS)

    van Gils, C. A. J.; Beijst, C.; van Rooij, R.; de Jong, H. W. A. M.

    2016-07-01

    Radioiodine therapy using I-131 is widely used for treatment of thyroid disease or neuroendocrine tumors. Monitoring treatment by accurate dosimetry requires quantitative imaging. The high energy photons however render quantitative SPECT reconstruction challenging, potentially requiring accurate correction for scatter and collimator effects. The goal of this work is to assess the effectiveness of various correction methods on these effects using phantom studies. A SPECT/CT acquisition of the NEMA IEC body phantom was performed. Images were reconstructed using the following parameters: (1) without scatter correction, (2) with triple energy window (TEW) scatter correction and (3) with Monte Carlo-based scatter correction. For modelling the collimator-detector response (CDR), both (a) geometric Gaussian CDRs as well as (b) Monte Carlo simulated CDRs were compared. Quantitative accuracy, contrast to noise ratios and recovery coefficients were calculated, as well as the background variability and the residual count error in the lung insert. The Monte Carlo scatter corrected reconstruction method was shown to be intrinsically quantitative, requiring no experimentally acquired calibration factor. It resulted in a more accurate quantification of the background compartment activity density compared with TEW or no scatter correction. The quantification error relative to a dose calibrator derived measurement was found to be  <1%,-26% and 33%, respectively. The adverse effects of partial volume were significantly smaller with the Monte Carlo simulated CDR correction compared with geometric Gaussian or no CDR modelling. Scatter correction showed a small effect on quantification of small volumes. When using a weighting factor, TEW correction was comparable to Monte Carlo reconstruction in all measured parameters, although this approach is clinically impractical since this factor may be patient dependent. Monte Carlo based scatter correction including accurately simulated CDR

  17. Stability Test and Quantitative and Qualitative Analyses of the Amino Acids in Pharmacopuncture Extracted from Scolopendra subspinipes mutilans

    PubMed Central

    Cho, GyeYoon; Han, KyuChul; Yoon, JinYoung

    2015-01-01

    Objectives: Scolopendra subspinipes mutilans (S. subspinipes mutilans) is known as a traditional medicine and includes various amino acids, peptides and proteins. The amino acids in the pharmacopuncture extracted from S. subspinipes mutilans by using derivatization methods were analyzed quantitatively and qualitatively by using high performance liquid chromatography (HPLC) over a 12 month period to confirm its stability. Methods: Amino acids of pharmacopuncture extracted from S. subspinipes mutilans were derived by using O-phthaldialdehyde (OPA) & 9-fluorenyl methoxy carbonyl chloride (FMOC) reagent and were analyzed using HPLC. The amino acids were detected by using a diode array detector (DAD) and a fluorescence detector (FLD) to compare a mixed amino acid standard (STD) to the pharmacopuncture from centipedes. The stability tests on the pharmacopuncture from centipedes were done using HPLC for three conditions: a room temperature test chamber, an acceleration test chamber, and a cold test chamber. Results: The pharmacopuncture from centipedes was prepared by using the method of the Korean Pharmacopuncture Institute (KPI) and through quantitative analyses was shown to contain 9 amino acids of the 16 amino acids in the mixed amino acid STD. The amounts of the amino acids in the pharmacopuncture from centipedes were 34.37 ppm of aspartate, 123.72 ppm of arginine, 170.63 ppm of alanine, 59.55 ppm of leucine and 57 ppm of lysine. The relative standard deviation (RSD %) results for the pharmacopuncture from centipedes had a maximum value of 14.95% and minimum value of 1.795% on the room temperature test chamber, the acceleration test chamber and the cold test chamber stability tests. Conclusion: Stability tests on and quantitative and qualitative analyses of the amino acids in the pharmacopuncture extracted from centipedes by using derivatization methods were performed by using HPLC. Through research, we hope to determine the relationship between time and the

  18. Landslide inventories: The essential part of seismic landslide hazard analyses

    USGS Publications Warehouse

    Harp, E.L.; Keefer, D.K.; Sato, H.P.; Yagi, H.

    2011-01-01

    A detailed and accurate landslide inventory is an essential part of seismic landslide hazard analysis. An ideal inventory would cover the entire area affected by an earthquake and include all of the landslides that are possible to detect down to sizes of 1-5. m in length. The landslides must also be located accurately and mapped as polygons depicting their true shapes. Such mapped landslide distributions can then be used to perform seismic landslide hazard analysis and other quantitative analyses. Detailed inventory maps of landslide triggered by earthquakes began in the early 1960s with the use of aerial photography. In recent years, advances in technology have resulted in the accessibility of satellite imagery with sufficiently high resolution to identify and map all but the smallest of landslides triggered by a seismic event. With this ability to view any area of the globe, we can acquire imagery for any earthquake that triggers significant numbers of landslides. However, a common problem of incomplete coverage of the full distributions of landslides has emerged along with the advent of high resolution satellite imagery. ?? 2010.

  19. Cloning, characterisation, and comparative quantitative expression analyses of receptor for advanced glycation end products (RAGE) transcript forms.

    PubMed

    Sterenczak, Katharina A; Willenbrock, Saskia; Barann, Matthias; Klemke, Markus; Soller, Jan T; Eberle, Nina; Nolte, Ingo; Bullerdiek, Jörn; Murua Escobar, Hugo

    2009-04-01

    RAGE is a member of the immunoglobulin superfamily of cell surface molecules playing key roles in pathophysiological processes, e.g. immune/inflammatory disorders, Alzheimer's disease, diabetic arteriosclerosis and tumourigenesis. In humans 19 naturally occurring RAGE splicing variants resulting in either N-terminally or C-terminally truncated proteins were identified and are lately discussed as mechanisms for receptor regulation. Accordingly, deregulation of sRAGE levels has been associated with several diseases e.g. Alzheimer's disease, Type 1 diabetes, and rheumatoid arthritis. Administration of recombinant sRAGE to animal models of cancer blocked tumour growth successfully. In spite of its obvious relationship to cancer and metastasis data focusing sRAGE deregulation and tumours is rare. In this study we screened a set of tumours, healthy tissues and various cancer cell lines for RAGE splicing variants and analysed their structure. Additionally, we analysed the ratio of the mainly found transcript variants using quantitative Real-Time PCR. In total we characterised 24 previously not described canine and 4 human RAGE splicing variants, analysed their structure, classified their characteristics, and derived their respective protein forms. Interestingly, the healthy and the neoplastic tissue samples showed in majority RAGE transcripts coding for the complete receptor and transcripts showing insertions of intron 1.

  20. Quantitative analyses and modelling to support achievement of the 2020 goals for nine neglected tropical diseases.

    PubMed

    Hollingsworth, T Déirdre; Adams, Emily R; Anderson, Roy M; Atkins, Katherine; Bartsch, Sarah; Basáñez, María-Gloria; Behrend, Matthew; Blok, David J; Chapman, Lloyd A C; Coffeng, Luc; Courtenay, Orin; Crump, Ron E; de Vlas, Sake J; Dobson, Andy; Dyson, Louise; Farkas, Hajnal; Galvani, Alison P; Gambhir, Manoj; Gurarie, David; Irvine, Michael A; Jervis, Sarah; Keeling, Matt J; Kelly-Hope, Louise; King, Charles; Lee, Bruce Y; Le Rutte, Epke A; Lietman, Thomas M; Ndeffo-Mbah, Martial; Medley, Graham F; Michael, Edwin; Pandey, Abhishek; Peterson, Jennifer K; Pinsent, Amy; Porco, Travis C; Richardus, Jan Hendrik; Reimer, Lisa; Rock, Kat S; Singh, Brajendra K; Stolk, Wilma; Swaminathan, Subramanian; Torr, Steve J; Townsend, Jeffrey; Truscott, James; Walker, Martin; Zoueva, Alexandra

    2015-12-09

    Quantitative analysis and mathematical models are useful tools in informing strategies to control or eliminate disease. Currently, there is an urgent need to develop these tools to inform policy to achieve the 2020 goals for neglected tropical diseases (NTDs). In this paper we give an overview of a collection of novel model-based analyses which aim to address key questions on the dynamics of transmission and control of nine NTDs: Chagas disease, visceral leishmaniasis, human African trypanosomiasis, leprosy, soil-transmitted helminths, schistosomiasis, lymphatic filariasis, onchocerciasis and trachoma. Several common themes resonate throughout these analyses, including: the importance of epidemiological setting on the success of interventions; targeting groups who are at highest risk of infection or re-infection; and reaching populations who are not accessing interventions and may act as a reservoir for infection,. The results also highlight the challenge of maintaining elimination 'as a public health problem' when true elimination is not reached. The models elucidate the factors that may be contributing most to persistence of disease and discuss the requirements for eventually achieving true elimination, if that is possible. Overall this collection presents new analyses to inform current control initiatives. These papers form a base from which further development of the models and more rigorous validation against a variety of datasets can help to give more detailed advice. At the moment, the models' predictions are being considered as the world prepares for a final push towards control or elimination of neglected tropical diseases by 2020.

  1. Comparison of multipoint linkage analyses for quantitative traits in the CEPH data: parametric LOD scores, variance components LOD scores, and Bayes factors

    PubMed Central

    Sung, Yun Ju; Di, Yanming; Fu, Audrey Q; Rothstein, Joseph H; Sieh, Weiva; Tong, Liping; Thompson, Elizabeth A; Wijsman, Ellen M

    2007-01-01

    We performed multipoint linkage analyses with multiple programs and models for several gene expression traits in the Centre d'Etude du Polymorphisme Humain families. All analyses provided consistent results for both peak location and shape. Variance-components (VC) analysis gave wider peaks and Bayes factors gave fewer peaks. Among programs from the MORGAN package, lm_multiple performed better than lm_markers, resulting in less Markov-chain Monte Carlo (MCMC) variability between runs, and the program lm_twoqtl provided higher LOD scores by also including either a polygenic component or an additional quantitative trait locus. PMID:18466597

  2. [A new method of processing quantitative PCR data].

    PubMed

    Ke, Bing-Shen; Li, Guang-Yun; Chen, Shi-Min; Huang, Xiang-Yan; Chen, Ying-Jian; Xu, Jun

    2003-05-01

    Today standard PCR can't satisfy the need of biotechnique development and clinical research any more. After numerous dynamic research, PE company found there is a linear relation between initial template number and cycling time when the accumulating fluorescent product is detectable.Therefore,they developed a quantitative PCR technique to be used in PE7700 and PE5700. But the error of this technique is too great to satisfy the need of biotechnique development and clinical research. A better quantitative PCR technique is needed. The mathematical model submitted here is combined with the achievement of relative science,and based on the PCR principle and careful analysis of molecular relationship of main members in PCR reaction system. This model describes the function relation between product quantity or fluorescence intensity and initial template number and other reaction conditions, and can reflect the accumulating rule of PCR product molecule accurately. Accurate quantitative PCR analysis can be made use this function relation. Accumulated PCR product quantity can be obtained from initial template number. Using this model to do quantitative PCR analysis,result error is only related to the accuracy of fluorescence intensity or the instrument used. For an example, when the fluorescence intensity is accurate to 6 digits and the template size is between 100 to 1,000,000, the quantitative result accuracy will be more than 99%. The difference of result error is distinct using same condition,same instrument but different analysis method. Moreover,if the PCR quantitative analysis system is used to process data, it will get result 80 times of accuracy than using CT method.

  3. A Radioactivity Based Quantitative Analysis of the Amount of Thorium Present in Ores and Metallurgical Products; ANALYSE QUANTITATIVE DU THORIUM DANS LES MINERAIS ET LES PRODUITS THORIFERES PAR UNE METHODE BASEE SUR LA RADIOACTIVITE

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

    Collee, R.; Govaerts, J.; Winand, L.

    1959-10-31

    A brief resume of the classical methods of quantitative determination of thorium in ores and thoriferous products is given to show that a rapid, accurate, and precise physical method based on the radioactivity of thorium would be of great utility. A method based on the utilization of the characteristic spectrum of the thorium gamma radiation is presented. The preparation of the samples and the instruments needed for the measurements is discussed. The experimental results show that the reproducibility is very satisfactory and that it is possible to detect Th contents of 1% or smaller. (J.S.R.)

  4. Quantitative LC-MS of polymers: determining accurate molecular weight distributions by combined size exclusion chromatography and electrospray mass spectrometry with maximum entropy data processing.

    PubMed

    Gruendling, Till; Guilhaus, Michael; Barner-Kowollik, Christopher

    2008-09-15

    We report on the successful application of size exclusion chromatography (SEC) combined with electrospray ionization mass spectrometry (ESI-MS) and refractive index (RI) detection for the determination of accurate molecular weight distributions of synthetic polymers, corrected for chromatographic band broadening. The presented method makes use of the ability of ESI-MS to accurately depict the peak profiles and retention volumes of individual oligomers eluting from the SEC column, whereas quantitative information on the absolute concentration of oligomers is obtained from the RI-detector only. A sophisticated computational algorithm based on the maximum entropy principle is used to process the data gained by both detectors, yielding an accurate molecular weight distribution, corrected for chromatographic band broadening. Poly(methyl methacrylate) standards with molecular weights up to 10 kDa serve as model compounds. Molecular weight distributions (MWDs) obtained by the maximum entropy procedure are compared to MWDs, which were calculated by a conventional calibration of the SEC-retention time axis with peak retention data obtained from the mass spectrometer. Comparison showed that for the employed chromatographic system, distributions below 7 kDa were only weakly influenced by chromatographic band broadening. However, the maximum entropy algorithm could successfully correct the MWD of a 10 kDa standard for band broadening effects. Molecular weight averages were between 5 and 14% lower than the manufacturer stated data obtained by classical means of calibration. The presented method demonstrates a consistent approach for analyzing data obtained by coupling mass spectrometric detectors and concentration sensitive detectors to polymer liquid chromatography.

  5. Quantitative Graphics in Newspapers.

    ERIC Educational Resources Information Center

    Tankard, James W., Jr.

    The use of quantitative graphics in newspapers requires achieving a balance between being accurate and getting the attention of the reader. The statistical representations in newspapers are drawn by graphic designers whose key technique is fusion--the striking combination of two visual images. This technique often results in visual puns,…

  6. Accurate radiation temperature and chemical potential from quantitative photoluminescence analysis of hot carrier populations.

    PubMed

    Gibelli, François; Lombez, Laurent; Guillemoles, Jean-François

    2017-02-15

    In order to characterize hot carrier populations in semiconductors, photoluminescence measurement is a convenient tool, enabling us to probe the carrier thermodynamical properties in a contactless way. However, the analysis of the photoluminescence spectra is based on some assumptions which will be discussed in this work. We especially emphasize the importance of the variation of the material absorptivity that should be considered to access accurate thermodynamical properties of the carriers, especially by varying the excitation power. The proposed method enables us to obtain more accurate results of thermodynamical properties by taking into account a rigorous physical description and finds direct application in investigating hot carrier solar cells, which are an adequate concept for achieving high conversion efficiencies with a relatively simple device architecture.

  7. Quantitative Residual Strain Analyses on Strain Hardened Nickel Based Alloy

    NASA Astrophysics Data System (ADS)

    Yonezawa, Toshio; Maeguchi, Takaharu; Goto, Toru; Juan, Hou

    Many papers have reported about the effects of strain hardening by cold rolling, grinding, welding, etc. on stress corrosion cracking susceptibility of nickel based alloys and austenitic stainless steels for LWR pipings and components. But, the residual strain value due to cold rolling, grinding, welding, etc. is not so quantitatively evaluated.

  8. The influence of the design matrix on treatment effect estimates in the quantitative analyses of single-subject experimental design research.

    PubMed

    Moeyaert, Mariola; Ugille, Maaike; Ferron, John M; Beretvas, S Natasha; Van den Noortgate, Wim

    2014-09-01

    The quantitative methods for analyzing single-subject experimental data have expanded during the last decade, including the use of regression models to statistically analyze the data, but still a lot of questions remain. One question is how to specify predictors in a regression model to account for the specifics of the design and estimate the effect size of interest. These quantitative effect sizes are used in retrospective analyses and allow synthesis of single-subject experimental study results which is informative for evidence-based decision making, research and theory building, and policy discussions. We discuss different design matrices that can be used for the most common single-subject experimental designs (SSEDs), namely, the multiple-baseline designs, reversal designs, and alternating treatment designs, and provide empirical illustrations. The purpose of this article is to guide single-subject experimental data analysts interested in analyzing and meta-analyzing SSED data. © The Author(s) 2014.

  9. Quantitative research.

    PubMed

    Watson, Roger

    2015-04-01

    This article describes the basic tenets of quantitative research. The concepts of dependent and independent variables are addressed and the concept of measurement and its associated issues, such as error, reliability and validity, are explored. Experiments and surveys – the principal research designs in quantitative research – are described and key features explained. The importance of the double-blind randomised controlled trial is emphasised, alongside the importance of longitudinal surveys, as opposed to cross-sectional surveys. Essential features of data storage are covered, with an emphasis on safe, anonymous storage. Finally, the article explores the analysis of quantitative data, considering what may be analysed and the main uses of statistics in analysis.

  10. Quantitative profiling of immune repertoires for minor lymphocyte counts using unique molecular identifiers.

    PubMed

    Egorov, Evgeny S; Merzlyak, Ekaterina M; Shelenkov, Andrew A; Britanova, Olga V; Sharonov, George V; Staroverov, Dmitriy B; Bolotin, Dmitriy A; Davydov, Alexey N; Barsova, Ekaterina; Lebedev, Yuriy B; Shugay, Mikhail; Chudakov, Dmitriy M

    2015-06-15

    Emerging high-throughput sequencing methods for the analyses of complex structure of TCR and BCR repertoires give a powerful impulse to adaptive immunity studies. However, there are still essential technical obstacles for performing a truly quantitative analysis. Specifically, it remains challenging to obtain comprehensive information on the clonal composition of small lymphocyte populations, such as Ag-specific, functional, or tissue-resident cell subsets isolated by sorting, microdissection, or fine needle aspirates. In this study, we report a robust approach based on unique molecular identifiers that allows profiling Ag receptors for several hundred to thousand lymphocytes while preserving qualitative and quantitative information on clonal composition of the sample. We also describe several general features regarding the data analysis with unique molecular identifiers that are critical for accurate counting of starting molecules in high-throughput sequencing applications. Copyright © 2015 by The American Association of Immunologists, Inc.

  11. Multiplexed and Microparticle-based Analyses: Quantitative Tools for the Large-Scale Analysis of Biological Systems

    PubMed Central

    Nolan, John P.; Mandy, Francis

    2008-01-01

    While the term flow cytometry refers to the measurement of cells, the approach of making sensitive multiparameter optical measurements in a flowing sample stream is a very general analytical approach. The past few years have seen an explosion in the application of flow cytometry technology for molecular analysis and measurements using micro-particles as solid supports. While microsphere-based molecular analyses using flow cytometry date back three decades, the need for highly parallel quantitative molecular measurements that has arisen from various genomic and proteomic advances has driven the development in particle encoding technology to enable highly multiplexed assays. Multiplexed particle-based immunoassays are now common place, and new assays to study genes, protein function, and molecular assembly. Numerous efforts are underway to extend the multiplexing capabilities of microparticle-based assays through new approaches to particle encoding and analyte reporting. The impact of these developments will be seen in the basic research and clinical laboratories, as well as in drug development. PMID:16604537

  12. Multiphase Method for Analysing Online Discussions

    ERIC Educational Resources Information Center

    Häkkinen, P.

    2013-01-01

    Several studies have analysed and assessed online performance and discourse using quantitative and qualitative methods. Quantitative measures have typically included the analysis of participation rates and learning outcomes in terms of grades. Qualitative measures of postings, discussions and context features aim to give insights into the nature…

  13. Precocious quantitative cognition in monkeys.

    PubMed

    Ferrigno, Stephen; Hughes, Kelly D; Cantlon, Jessica F

    2016-02-01

    Basic quantitative abilities are thought to have an innate basis in humans partly because the ability to discriminate quantities emerges early in child development. If humans and nonhuman primates share this developmentally primitive foundation of quantitative reasoning, then this ability should be present early in development across species and should emerge earlier in monkeys than in humans because monkeys mature faster than humans. We report that monkeys spontaneously make accurate quantity choices by 1 year of age in a task that human children begin to perform only at 2.5 to 3 years of age. Additionally, we report that the quantitative sensitivity of infant monkeys is equal to that of the adult animals in their group and that rates of learning do not differ between infant and adult animals. This novel evidence of precocious quantitative reasoning in infant monkeys suggests that human quantitative reasoning shares its early developing foundation with other primates. The data further suggest that early developing components of primate quantitative reasoning are constrained by maturational factors related to genetic development as opposed to learning experience alone.

  14. Fluorescence correlation spectroscopy analysis for accurate determination of proportion of doubly labeled DNA in fluorescent DNA pool for quantitative biochemical assays.

    PubMed

    Hou, Sen; Sun, Lili; Wieczorek, Stefan A; Kalwarczyk, Tomasz; Kaminski, Tomasz S; Holyst, Robert

    2014-01-15

    Fluorescent double-stranded DNA (dsDNA) molecules labeled at both ends are commonly produced by annealing of complementary single-stranded DNA (ssDNA) molecules, labeled with fluorescent dyes at the same (3' or 5') end. Because the labeling efficiency of ssDNA is smaller than 100%, the resulting dsDNA have two, one or are without a dye. Existing methods are insufficient to measure the percentage of the doubly-labeled dsDNA component in the fluorescent DNA sample and it is even difficult to distinguish the doubly-labeled DNA component from the singly-labeled component. Accurate measurement of the percentage of such doubly labeled dsDNA component is a critical prerequisite for quantitative biochemical measurements, which has puzzled scientists for decades. We established a fluorescence correlation spectroscopy (FCS) system to measure the percentage of doubly labeled dsDNA (PDL) in the total fluorescent dsDNA pool. The method is based on comparative analysis of the given sample and a reference dsDNA sample prepared by adding certain amount of unlabeled ssDNA into the original ssDNA solution. From FCS autocorrelation functions, we obtain the number of fluorescent dsDNA molecules in the focal volume of the confocal microscope and PDL. We also calculate the labeling efficiency of ssDNA. The method requires minimal amount of material. The samples have the concentration of DNA in the nano-molar/L range and the volume of tens of microliters. We verify our method by using restriction enzyme Hind III to cleave the fluorescent dsDNA. The kinetics of the reaction depends strongly on PDL, a critical parameter for quantitative biochemical measurements. Copyright © 2013 Elsevier B.V. All rights reserved.

  15. Mitochondrial DNA as a non-invasive biomarker: Accurate quantification using real time quantitative PCR without co-amplification of pseudogenes and dilution bias

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

    Malik, Afshan N., E-mail: afshan.malik@kcl.ac.uk; Shahni, Rojeen; Rodriguez-de-Ledesma, Ana

    2011-08-19

    Highlights: {yields} Mitochondrial dysfunction is central to many diseases of oxidative stress. {yields} 95% of the mitochondrial genome is duplicated in the nuclear genome. {yields} Dilution of untreated genomic DNA leads to dilution bias. {yields} Unique primers and template pretreatment are needed to accurately measure mitochondrial DNA content. -- Abstract: Circulating mitochondrial DNA (MtDNA) is a potential non-invasive biomarker of cellular mitochondrial dysfunction, the latter known to be central to a wide range of human diseases. Changes in MtDNA are usually determined by quantification of MtDNA relative to nuclear DNA (Mt/N) using real time quantitative PCR. We propose that themore » methodology for measuring Mt/N needs to be improved and we have identified that current methods have at least one of the following three problems: (1) As much of the mitochondrial genome is duplicated in the nuclear genome, many commonly used MtDNA primers co-amplify homologous pseudogenes found in the nuclear genome; (2) use of regions from genes such as {beta}-actin and 18S rRNA which are repetitive and/or highly variable for qPCR of the nuclear genome leads to errors; and (3) the size difference of mitochondrial and nuclear genomes cause a 'dilution bias' when template DNA is diluted. We describe a PCR-based method using unique regions in the human mitochondrial genome not duplicated in the nuclear genome; unique single copy region in the nuclear genome and template treatment to remove dilution bias, to accurately quantify MtDNA from human samples.« less

  16. Sensitivity analyses of exposure estimates from a quantitative job-exposure matrix (SYN-JEM) for use in community-based studies.

    PubMed

    Peters, Susan; Kromhout, Hans; Portengen, Lützen; Olsson, Ann; Kendzia, Benjamin; Vincent, Raymond; Savary, Barbara; Lavoué, Jérôme; Cavallo, Domenico; Cattaneo, Andrea; Mirabelli, Dario; Plato, Nils; Fevotte, Joelle; Pesch, Beate; Brüning, Thomas; Straif, Kurt; Vermeulen, Roel

    2013-01-01

    We describe the elaboration and sensitivity analyses of a quantitative job-exposure matrix (SYN-JEM) for respirable crystalline silica (RCS). The aim was to gain insight into the robustness of the SYN-JEM RCS estimates based on critical decisions taken in the elaboration process. SYN-JEM for RCS exposure consists of three axes (job, region, and year) based on estimates derived from a previously developed statistical model. To elaborate SYN-JEM, several decisions were taken: i.e. the application of (i) a single time trend; (ii) region-specific adjustments in RCS exposure; and (iii) a prior job-specific exposure level (by the semi-quantitative DOM-JEM), with an override of 0 mg/m(3) for jobs a priori defined as non-exposed. Furthermore, we assumed that exposure levels reached a ceiling in 1960 and remained constant prior to this date. We applied SYN-JEM to the occupational histories of subjects from a large international pooled community-based case-control study. Cumulative exposure levels derived with SYN-JEM were compared with those from alternative models, described by Pearson correlation ((Rp)) and differences in unit of exposure (mg/m(3)-year). Alternative models concerned changes in application of job- and region-specific estimates and exposure ceiling, and omitting the a priori exposure ranking. Cumulative exposure levels for the study subjects ranged from 0.01 to 60 mg/m(3)-years, with a median of 1.76 mg/m(3)-years. Exposure levels derived from SYN-JEM and alternative models were overall highly correlated (R(p) > 0.90), although somewhat lower when omitting the region estimate ((Rp) = 0.80) or not taking into account the assigned semi-quantitative exposure level (R(p) = 0.65). Modification of the time trend (i.e. exposure ceiling at 1950 or 1970, or assuming a decline before 1960) caused the largest changes in absolute exposure levels (26-33% difference), but without changing the relative ranking ((Rp) = 0.99). Exposure estimates derived from SYN

  17. Effects of detector dead-time on quantitative analyses involving boron and multi-hit detection events in atom probe tomography.

    PubMed

    Meisenkothen, Frederick; Steel, Eric B; Prosa, Ty J; Henry, Karen T; Prakash Kolli, R

    2015-12-01

    In atom probe tomography (APT), some elements tend to field evaporate preferentially in multi-hit detection events. Boron (B) is one such element. It is thought that a large fraction of the B signal may be lost during data acquisition and is not reported in the mass spectrum or in the 3-D APT reconstruction. Understanding the relationship between the field evaporation behavior of B and the limitations for detecting multi-hit events can provide insight into the signal loss mechanism for B and may suggest ways to improve B detection accuracy. The present work reports data for nominally pure B and for B-implanted silicon (Si) (NIST-SRM2137) at dose levels two-orders of magnitude lower than previously studied by Da Costa, et al. in 2012. Boron concentration profiles collected from SRM2137 specimens qualitatively confirmed a signal loss mechanism is at work in laser pulsed atom probe measurements of B in Si. Ion correlation analysis was used to graphically demonstrate that the detector dead-time results in few same isotope, same charge-state (SISCS) ion pairs being properly recorded in the multi-hit data, explaining why B is consistently under-represented in quantitative analyses. Given the important role of detector dead-time as a signal loss mechanism, the results from three different methods of estimating the detector dead-time are presented. The findings of this study apply to all quantitative analyses that involve multi-hit data, but the dead-time will have the greatest effect on the elements that have a significant quantity of ions detected in multi-hit events. Published by Elsevier B.V.

  18. A new high-resolution 3-D quantitative method for analysing small morphological features: an example using a Cambrian trilobite.

    PubMed

    Esteve, Jorge; Zhao, Yuan-Long; Maté-González, Miguel Ángel; Gómez-Heras, Miguel; Peng, Jin

    2018-02-12

    Taphonomic processes play an important role in the preservation of small morphological features such as granulation or pits. However, the assessment of these features may face the issue of the small size of the specimens and, sometimes, the destructiveness of these analyses, which makes impossible carrying them out in singular specimen, such as holotypes or lectotypes. This paper takes a new approach to analysing small-morphological features, by using an optical surface roughness (OSR) meter to create a high-resolution three-dimensional digital-elevation model (DEM). This non-destructive technique allows analysing quantitatively the DEM using geometric morphometric methods (GMM). We created a number of DEMs from three populations putatively belonging to the same species of trilobite (Oryctocephalus indicus) that present the same cranidial outline, but differ in the presence or absence of the second and third transglabellar furrows. Profile analysis of the DEMs demonstrate that all three populations show similar preservation variation in the glabellar furrows and lobes. The GMM shows that all populations exhibit the same range of variation. Differences in preservation are a consequence of different degrees of cementation and rates of dissolution. Fast cementation enhances the preservation of glabellar furrows and lobes, while fast dissolution hampers preservation of the same structures.

  19. Performing statistical analyses on quantitative data in Taverna workflows: an example using R and maxdBrowse to identify differentially-expressed genes from microarray data.

    PubMed

    Li, Peter; Castrillo, Juan I; Velarde, Giles; Wassink, Ingo; Soiland-Reyes, Stian; Owen, Stuart; Withers, David; Oinn, Tom; Pocock, Matthew R; Goble, Carole A; Oliver, Stephen G; Kell, Douglas B

    2008-08-07

    There has been a dramatic increase in the amount of quantitative data derived from the measurement of changes at different levels of biological complexity during the post-genomic era. However, there are a number of issues associated with the use of computational tools employed for the analysis of such data. For example, computational tools such as R and MATLAB require prior knowledge of their programming languages in order to implement statistical analyses on data. Combining two or more tools in an analysis may also be problematic since data may have to be manually copied and pasted between separate user interfaces for each tool. Furthermore, this transfer of data may require a reconciliation step in order for there to be interoperability between computational tools. Developments in the Taverna workflow system have enabled pipelines to be constructed and enacted for generic and ad hoc analyses of quantitative data. Here, we present an example of such a workflow involving the statistical identification of differentially-expressed genes from microarray data followed by the annotation of their relationships to cellular processes. This workflow makes use of customised maxdBrowse web services, a system that allows Taverna to query and retrieve gene expression data from the maxdLoad2 microarray database. These data are then analysed by R to identify differentially-expressed genes using the Taverna RShell processor which has been developed for invoking this tool when it has been deployed as a service using the RServe library. In addition, the workflow uses Beanshell scripts to reconcile mismatches of data between services as well as to implement a form of user interaction for selecting subsets of microarray data for analysis as part of the workflow execution. A new plugin system in the Taverna software architecture is demonstrated by the use of renderers for displaying PDF files and CSV formatted data within the Taverna workbench. Taverna can be used by data analysis

  20. Performing statistical analyses on quantitative data in Taverna workflows: An example using R and maxdBrowse to identify differentially-expressed genes from microarray data

    PubMed Central

    Li, Peter; Castrillo, Juan I; Velarde, Giles; Wassink, Ingo; Soiland-Reyes, Stian; Owen, Stuart; Withers, David; Oinn, Tom; Pocock, Matthew R; Goble, Carole A; Oliver, Stephen G; Kell, Douglas B

    2008-01-01

    Background There has been a dramatic increase in the amount of quantitative data derived from the measurement of changes at different levels of biological complexity during the post-genomic era. However, there are a number of issues associated with the use of computational tools employed for the analysis of such data. For example, computational tools such as R and MATLAB require prior knowledge of their programming languages in order to implement statistical analyses on data. Combining two or more tools in an analysis may also be problematic since data may have to be manually copied and pasted between separate user interfaces for each tool. Furthermore, this transfer of data may require a reconciliation step in order for there to be interoperability between computational tools. Results Developments in the Taverna workflow system have enabled pipelines to be constructed and enacted for generic and ad hoc analyses of quantitative data. Here, we present an example of such a workflow involving the statistical identification of differentially-expressed genes from microarray data followed by the annotation of their relationships to cellular processes. This workflow makes use of customised maxdBrowse web services, a system that allows Taverna to query and retrieve gene expression data from the maxdLoad2 microarray database. These data are then analysed by R to identify differentially-expressed genes using the Taverna RShell processor which has been developed for invoking this tool when it has been deployed as a service using the RServe library. In addition, the workflow uses Beanshell scripts to reconcile mismatches of data between services as well as to implement a form of user interaction for selecting subsets of microarray data for analysis as part of the workflow execution. A new plugin system in the Taverna software architecture is demonstrated by the use of renderers for displaying PDF files and CSV formatted data within the Taverna workbench. Conclusion Taverna can

  1. Quantitative and qualitative analyses of subacromial impingement by kinematic open MRI.

    PubMed

    Tasaki, Atsushi; Nimura, Akimoto; Nozaki, Taiki; Yamakawa, Akira; Niitsu, Mamoru; Morita, Wataru; Hoshikawa, Yoshimitsu; Akita, Keiichi

    2015-05-01

    Quantitative and qualitative kinematic analyses of subacromial impingement by 1.2T open MRI were performed to determine the location of impingement and the involvement of the acromioclavicular joint. In 20 healthy shoulders, 10 sequential images in the scapular plane were taken in a 10-s pause at equal intervals from 30° to maximum abduction in neutral and internal rotation. The distances between the rotator cuff (RC) and the acromion and the acromioclavicular joint were measured. To comprehend the positional relationships, cadaveric specimens were also observed. Although asymptomatic, the RC came into contact with the acromion and the acromioclavicular joint in six and five cases, respectively. The superior RC acted as a depressor for the humeral head against the acromion as the shoulder elevated. The mean elevation angle and distance at the closest position between the RC and the acromion in neutral rotation were 93.5° and 1.6 mm, respectively, while those between the RC and the acromioclavicular joint were 86.7° and 2.0 mm. When comparing this distance and angle, there was no significant difference between the RC to the acromion and to the acromioclavicular joint. The minimum distance between the RC and the acromion was significantly shorter than that between the greater tuberosity and the acromion. The location of RC closest to the acromion and the acromioclavicular joint differed significantly. Although asymptomatic, contact was found between the RC and the acromion and the acromioclavicular joint. The important role of the RC to prevent impingement was observed, and hence, dysfunction of the RC could lead to impingement that could result in a RC lesion. The RC lesions may differ when they are caused by impingement from either the acromion or the acromioclavicular joint.

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

    PubMed

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

    2012-07-06

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

  3. Quantitative characterization of colloidal assembly of graphene oxide-silver nanoparticle hybrids using aerosol differential mobility-coupled mass analyses.

    PubMed

    Nguyen, Thai Phuong; Chang, Wei-Chang; Lai, Yen-Chih; Hsiao, Ta-Chih; Tsai, De-Hao

    2017-10-01

    In this work, we develop an aerosol-based, time-resolved ion mobility-coupled mass characterization method to investigate colloidal assembly of graphene oxide (GO)-silver nanoparticle (AgNP) hybrid nanostructure on a quantitative basis. Transmission electron microscopy (TEM) and zeta potential (ZP) analysis were used to provide visual information and elemental-based particle size distributions, respectively. Results clearly show a successful controlled assembly of GO-AgNP by electrostatic-directed heterogeneous aggregation between GO and bovine serum albumin (BSA)-functionalized AgNP under an acidic environment. Additionally, physical size, mass, and conformation (i.e., number of AgNP per nanohybrid) of GO-AgNP were shown to be proportional to the number concentration ratio of AgNP to GO (R) and the selected electrical mobility diameter. An analysis of colloidal stability of GO-AgNP indicates that the stability increased with its absolute ZP, which was dependent on R and environmental pH. The work presented here provides a proof of concept for systematically synthesizing hybrid colloidal nanomaterials through the tuning of surface chemistry in aqueous phase with the ability in quantitative characterization. Graphical Abstract Colloidal assembly of graphene oxide-silver nanoparticle hybrids characterized by aerosol differential mobility-coupled mass analyses.

  4. A Second-Generation Device for Automated Training and Quantitative Behavior Analyses of Molecularly-Tractable Model Organisms

    PubMed Central

    Blackiston, Douglas; Shomrat, Tal; Nicolas, Cindy L.; Granata, Christopher; Levin, Michael

    2010-01-01

    A deep understanding of cognitive processes requires functional, quantitative analyses of the steps leading from genetics and the development of nervous system structure to behavior. Molecularly-tractable model systems such as Xenopus laevis and planaria offer an unprecedented opportunity to dissect the mechanisms determining the complex structure of the brain and CNS. A standardized platform that facilitated quantitative analysis of behavior would make a significant impact on evolutionary ethology, neuropharmacology, and cognitive science. While some animal tracking systems exist, the available systems do not allow automated training (feedback to individual subjects in real time, which is necessary for operant conditioning assays). The lack of standardization in the field, and the numerous technical challenges that face the development of a versatile system with the necessary capabilities, comprise a significant barrier keeping molecular developmental biology labs from integrating behavior analysis endpoints into their pharmacological and genetic perturbations. Here we report the development of a second-generation system that is a highly flexible, powerful machine vision and environmental control platform. In order to enable multidisciplinary studies aimed at understanding the roles of genes in brain function and behavior, and aid other laboratories that do not have the facilities to undergo complex engineering development, we describe the device and the problems that it overcomes. We also present sample data using frog tadpoles and flatworms to illustrate its use. Having solved significant engineering challenges in its construction, the resulting design is a relatively inexpensive instrument of wide relevance for several fields, and will accelerate interdisciplinary discovery in pharmacology, neurobiology, regenerative medicine, and cognitive science. PMID:21179424

  5. Mass spectrometry-based protein identification with accurate statistical significance assignment.

    PubMed

    Alves, Gelio; Yu, Yi-Kuo

    2015-03-01

    Assigning statistical significance accurately has become increasingly important as metadata of many types, often assembled in hierarchies, are constructed and combined for further biological analyses. Statistical inaccuracy of metadata at any level may propagate to downstream analyses, undermining the validity of scientific conclusions thus drawn. From the perspective of mass spectrometry-based proteomics, even though accurate statistics for peptide identification can now be achieved, accurate protein level statistics remain challenging. We have constructed a protein ID method that combines peptide evidences of a candidate protein based on a rigorous formula derived earlier; in this formula the database P-value of every peptide is weighted, prior to the final combination, according to the number of proteins it maps to. We have also shown that this protein ID method provides accurate protein level E-value, eliminating the need of using empirical post-processing methods for type-I error control. Using a known protein mixture, we find that this protein ID method, when combined with the Sorić formula, yields accurate values for the proportion of false discoveries. In terms of retrieval efficacy, the results from our method are comparable with other methods tested. The source code, implemented in C++ on a linux system, is available for download at ftp://ftp.ncbi.nlm.nih.gov/pub/qmbp/qmbp_ms/RAId/RAId_Linux_64Bit. Published by Oxford University Press 2014. This work is written by US Government employees and is in the public domain in the US.

  6. Quantitative Analysis of Venus Radar Backscatter Data in ArcGIS

    NASA Technical Reports Server (NTRS)

    Long, S. M.; Grosfils, E. B.

    2005-01-01

    Ongoing mapping of the Ganiki Planitia (V14) quadrangle of Venus and definition of material units has involved an integrated but qualitative analysis of Magellan radar backscatter images and topography using standard geomorphological mapping techniques. However, such analyses do not take full advantage of the quantitative information contained within the images. Analysis of the backscatter coefficient allows a much more rigorous statistical comparison between mapped units, permitting first order selfsimilarity tests of geographically separated materials assigned identical geomorphological labels. Such analyses cannot be performed directly on pixel (DN) values from Magellan backscatter images, because the pixels are scaled to the Muhleman law for radar echoes on Venus and are not corrected for latitudinal variations in incidence angle. Therefore, DN values must be converted based on pixel latitude back to their backscatter coefficient values before accurate statistical analysis can occur. Here we present a method for performing the conversions and analysis of Magellan backscatter data using commonly available ArcGIS software and illustrate the advantages of the process for geological mapping.

  7. Accurate atomistic first-principles calculations of electronic stopping

    DOE PAGES

    Schleife, André; Kanai, Yosuke; Correa, Alfredo A.

    2015-01-20

    In this paper, we show that atomistic first-principles calculations based on real-time propagation within time-dependent density functional theory are capable of accurately describing electronic stopping of light projectile atoms in metal hosts over a wide range of projectile velocities. In particular, we employ a plane-wave pseudopotential scheme to solve time-dependent Kohn-Sham equations for representative systems of H and He projectiles in crystalline aluminum. This approach to simulate nonadiabatic electron-ion interaction provides an accurate framework that allows for quantitative comparison with experiment without introducing ad hoc parameters such as effective charges, or assumptions about the dielectric function. Finally, our work clearlymore » shows that this atomistic first-principles description of electronic stopping is able to disentangle contributions due to tightly bound semicore electrons and geometric aspects of the stopping geometry (channeling versus off-channeling) in a wide range of projectile velocities.« less

  8. Generation of accurate peptide retention data for targeted and data independent quantitative LC-MS analysis: Chromatographic lessons in proteomics.

    PubMed

    Krokhin, Oleg V; Spicer, Vic

    2016-12-01

    The emergence of data-independent quantitative LC-MS/MS analysis protocols further highlights the importance of high-quality reproducible chromatographic procedures. Knowing, controlling and being able to predict the effect of multiple factors that alter peptide RP-HPLC separation selectivity is critical for successful data collection for the construction of ion libraries. Proteomic researchers have often regarded RP-HPLC as a "black box", while vast amount of research on peptide separation is readily available. In addition to obvious parameters, such as the type of ion-pairing modifier, stationary phase and column temperature, we describe the "mysterious" effects of gradient slope, column size and flow rate on peptide separation selectivity. Retention time variations due to these parameters are governed by the linear solvent strength (LSS) theory on a peptide level by the value of its slope S in the basic LSS equation-a parameter that can be accurately predicted. Thus, the application of shallower gradients, higher flow rates, or smaller columns will each increases the relative retention of peptides with higher S-values (long species with multiple positively charged groups). Simultaneous changes to these parameters that each drive shifts in separation selectivity in the same direction should be avoided. The unification of terminology represents another pressing issue in this field of applied proteomics that should be addressed to facilitate further progress. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Multicenter Evaluation of a Commercial Cytomegalovirus Quantitative Standard: Effects of Commutability on Interlaboratory Concordance

    PubMed Central

    Shahbazian, M. D.; Valsamakis, A.; Boonyaratanakornkit, J.; Cook, L.; Pang, X. L.; Preiksaitis, J. K.; Schönbrunner, E. R.; Caliendo, A. M.

    2013-01-01

    Commutability of quantitative reference materials has proven important for reliable and accurate results in clinical chemistry. As international reference standards and commercially produced calibration material have become available to address the variability of viral load assays, the degree to which such materials are commutable and the effect of commutability on assay concordance have been questioned. To investigate this, 60 archived clinical plasma samples, which previously tested positive for cytomegalovirus (CMV), were retested by five different laboratories, each using a different quantitative CMV PCR assay. Results from each laboratory were calibrated both with lab-specific quantitative CMV standards (“lab standards”) and with common, commercially available standards (“CMV panel”). Pairwise analyses among laboratories were performed using mean results from each clinical sample, calibrated first with lab standards and then with the CMV panel. Commutability of the CMV panel was determined based on difference plots for each laboratory pair showing plotted values of standards that were within the 95% prediction intervals for the clinical specimens. Commutability was demonstrated for 6 of 10 laboratory pairs using the CMV panel. In half of these pairs, use of the CMV panel improved quantitative agreement compared to use of lab standards. Two of four laboratory pairs for which the CMV panel was noncommutable showed reduced quantitative agreement when that panel was used as a common calibrator. Commutability of calibration material varies across different quantitative PCR methods. Use of a common, commutable quantitative standard can improve agreement across different assays; use of a noncommutable calibrator can reduce agreement among laboratories. PMID:24025907

  10. Multivariate Quantitative Chemical Analysis

    NASA Technical Reports Server (NTRS)

    Kinchen, David G.; Capezza, Mary

    1995-01-01

    Technique of multivariate quantitative chemical analysis devised for use in determining relative proportions of two components mixed and sprayed together onto object to form thermally insulating foam. Potentially adaptable to other materials, especially in process-monitoring applications in which necessary to know and control critical properties of products via quantitative chemical analyses of products. In addition to chemical composition, also used to determine such physical properties as densities and strengths.

  11. Application of Mixed-Methods Approaches to Higher Education and Intersectional Analyses

    ERIC Educational Resources Information Center

    Griffin, Kimberly A.; Museus, Samuel D.

    2011-01-01

    In this article, the authors discuss the utility of combining quantitative and qualitative methods in conducting intersectional analyses. First, they discuss some of the paradigmatic underpinnings of qualitative and quantitative research, and how these methods can be used in intersectional analyses. They then consider how paradigmatic pragmatism…

  12. Analyzing the impacts of global trade and investment on non-communicable diseases and risk factors: a critical review of methodological approaches used in quantitative analyses.

    PubMed

    Cowling, Krycia; Thow, Anne Marie; Pollack Porter, Keshia

    2018-05-24

    A key mechanism through which globalization has impacted health is the liberalization of trade and investment, yet relatively few studies to date have used quantitative methods to investigate the impacts of global trade and investment policies on non-communicable diseases and risk factors. Recent reviews of this literature have found heterogeneity in results and a range of quality across studies, which may be in part attributable to a lack of conceptual clarity and methodological inconsistencies. This study is a critical review of methodological approaches used in the quantitative literature on global trade and investment and diet, tobacco, alcohol, and related health outcomes, with the objective of developing recommendations and providing resources to guide future robust, policy relevant research. A review of reviews, expert review, and reference tracing were employed to identify relevant studies, which were evaluated using a novel quality assessment tool designed for this research. Eight review articles and 34 quantitative studies were identified for inclusion. Important ways to improve this literature were identified and discussed: clearly defining exposures of interest and not conflating trade and investment; exploring mechanisms of broader relationships; increasing the use of individual-level data; ensuring consensus and consistency in key confounding variables; utilizing more sector-specific versus economy-wide trade and investment indicators; testing and adequately adjusting for autocorrelation and endogeneity when using longitudinal data; and presenting results from alternative statistical models and sensitivity analyses. To guide the development of future analyses, recommendations for international data sources for selected trade and investment indicators, as well as key gaps in the literature, are presented. More methodologically rigorous and consistent approaches in future quantitative studies on the impacts of global trade and investment policies on non

  13. Accurate phase measurements for thick spherical objects using optical quadrature microscopy

    NASA Astrophysics Data System (ADS)

    Warger, William C., II; DiMarzio, Charles A.

    2009-02-01

    In vitro fertilization (IVF) procedures have resulted in the birth of over three million babies since 1978. Yet the live birth rate in the United States was only 34% in 2005, with 32% of the successful pregnancies resulting in multiple births. These multiple pregnancies were directly attributed to the transfer of multiple embryos to increase the probability that a single, healthy embryo was included. Current viability markers used for IVF, such as the cell number, symmetry, size, and fragmentation, are analyzed qualitatively with differential interference contrast (DIC) microscopy. However, this method is not ideal for quantitative measures beyond the 8-cell stage of development because the cells overlap and obstruct the view within and below the cluster of cells. We have developed the phase-subtraction cell-counting method that uses the combination of DIC and optical quadrature microscopy (OQM) to count the number of cells accurately in live mouse embryos beyond the 8-cell stage. We have also created a preliminary analysis to measure the cell symmetry, size, and fragmentation quantitatively by analyzing the relative dry mass from the OQM image in conjunction with the phase-subtraction count. In this paper, we will discuss the characterization of OQM with respect to measuring the phase accurately for spherical samples that are much larger than the depth of field. Once fully characterized and verified with human embryos, this methodology could provide the means for a more accurate method to score embryo viability.

  14. MsViz: A Graphical Software Tool for In-Depth Manual Validation and Quantitation of Post-translational Modifications.

    PubMed

    Martín-Campos, Trinidad; Mylonas, Roman; Masselot, Alexandre; Waridel, Patrice; Petricevic, Tanja; Xenarios, Ioannis; Quadroni, Manfredo

    2017-08-04

    Mass spectrometry (MS) has become the tool of choice for the large scale identification and quantitation of proteins and their post-translational modifications (PTMs). This development has been enabled by powerful software packages for the automated analysis of MS data. While data on PTMs of thousands of proteins can nowadays be readily obtained, fully deciphering the complexity and combinatorics of modification patterns even on a single protein often remains challenging. Moreover, functional investigation of PTMs on a protein of interest requires validation of the localization and the accurate quantitation of its changes across several conditions, tasks that often still require human evaluation. Software tools for large scale analyses are highly efficient but are rarely conceived for interactive, in-depth exploration of data on individual proteins. We here describe MsViz, a web-based and interactive software tool that supports manual validation of PTMs and their relative quantitation in small- and medium-size experiments. The tool displays sequence coverage information, peptide-spectrum matches, tandem MS spectra and extracted ion chromatograms through a single, highly intuitive interface. We found that MsViz greatly facilitates manual data inspection to validate PTM location and quantitate modified species across multiple samples.

  15. Quantitative analysis of tympanic membrane perforation: a simple and reliable method.

    PubMed

    Ibekwe, T S; Adeosun, A A; Nwaorgu, O G

    2009-01-01

    Accurate assessment of the features of tympanic membrane perforation, especially size, site, duration and aetiology, is important, as it enables optimum management. To describe a simple, cheap and effective method of quantitatively analysing tympanic membrane perforations. The system described comprises a video-otoscope (capable of generating still and video images of the tympanic membrane), adapted via a universal serial bus box to a computer screen, with images analysed using the Image J geometrical analysis software package. The reproducibility of results and their correlation with conventional otoscopic methods of estimation were tested statistically with the paired t-test and correlational tests, using the Statistical Package for the Social Sciences version 11 software. The following equation was generated: P/T x 100 per cent = percentage perforation, where P is the area (in pixels2) of the tympanic membrane perforation and T is the total area (in pixels2) for the entire tympanic membrane (including the perforation). Illustrations are shown. Comparison of blinded data on tympanic membrane perforation area obtained independently from assessments by two trained otologists, of comparative years of experience, using the video-otoscopy system described, showed similar findings, with strong correlations devoid of inter-observer error (p = 0.000, r = 1). Comparison with conventional otoscopic assessment also indicated significant correlation, comparing results for two trained otologists, but some inter-observer variation was present (p = 0.000, r = 0.896). Correlation between the two methods for each of the otologists was also highly significant (p = 0.000). A computer-adapted video-otoscope, with images analysed by Image J software, represents a cheap, reliable, technology-driven, clinical method of quantitative analysis of tympanic membrane perforations and injuries.

  16. A quantitative image cytometry technique for time series or population analyses of signaling networks.

    PubMed

    Ozaki, Yu-ichi; Uda, Shinsuke; Saito, Takeshi H; Chung, Jaehoon; Kubota, Hiroyuki; Kuroda, Shinya

    2010-04-01

    Modeling of cellular functions on the basis of experimental observation is increasingly common in the field of cellular signaling. However, such modeling requires a large amount of quantitative data of signaling events with high spatio-temporal resolution. A novel technique which allows us to obtain such data is needed for systems biology of cellular signaling. We developed a fully automatable assay technique, termed quantitative image cytometry (QIC), which integrates a quantitative immunostaining technique and a high precision image-processing algorithm for cell identification. With the aid of an automated sample preparation system, this device can quantify protein expression, phosphorylation and localization with subcellular resolution at one-minute intervals. The signaling activities quantified by the assay system showed good correlation with, as well as comparable reproducibility to, western blot analysis. Taking advantage of the high spatio-temporal resolution, we investigated the signaling dynamics of the ERK pathway in PC12 cells. The QIC technique appears as a highly quantitative and versatile technique, which can be a convenient replacement for the most conventional techniques including western blot, flow cytometry and live cell imaging. Thus, the QIC technique can be a powerful tool for investigating the systems biology of cellular signaling.

  17. Improving the Linkages between Air Pollution Epidemiology and Quantitative Risk Assessment

    PubMed Central

    Bell, Michelle L.; Walker, Katy; Hubbell, Bryan

    2011-01-01

    Background: Air pollution epidemiology plays an integral role in both identifying the hazards of air pollution as well as supplying the risk coefficients that are used in quantitative risk assessments. Evidence from both epidemiology and risk assessments has historically supported critical environmental policy decisions. The extent to which risk assessors can properly specify a quantitative risk assessment and characterize key sources of uncertainty depends in part on the availability, and clarity, of data and assumptions in the epidemiological studies. Objectives: We discuss the interests shared by air pollution epidemiology and risk assessment communities in ensuring that the findings of epidemiological studies are appropriately characterized and applied correctly in risk assessments. We highlight the key input parameters for risk assessments and consider how modest changes in the characterization of these data might enable more accurate risk assessments that better represent the findings of epidemiological studies. Discussion: We argue that more complete information regarding the methodological choices and input data used in epidemiological studies would support more accurate risk assessments—to the benefit of both disciplines. In particular, we suggest including additional details regarding air quality, demographic, and health data, as well as certain types of data-rich graphics. Conclusions: Relatively modest changes to the data reported in epidemiological studies will improve the quality of risk assessments and help prevent the misinterpretation and mischaracterization of the results of epidemiological studies. Such changes may also benefit epidemiologists undertaking meta-analyses. We suggest workshops as a way to improve the dialogue between the two communities. PMID:21816702

  18. Quantitative imaging methods in osteoporosis.

    PubMed

    Oei, Ling; Koromani, Fjorda; Rivadeneira, Fernando; Zillikens, M Carola; Oei, Edwin H G

    2016-12-01

    Osteoporosis is characterized by a decreased bone mass and quality resulting in an increased fracture risk. Quantitative imaging methods are critical in the diagnosis and follow-up of treatment effects in osteoporosis. Prior radiographic vertebral fractures and bone mineral density (BMD) as a quantitative parameter derived from dual-energy X-ray absorptiometry (DXA) are among the strongest known predictors of future osteoporotic fractures. Therefore, current clinical decision making relies heavily on accurate assessment of these imaging features. Further, novel quantitative techniques are being developed to appraise additional characteristics of osteoporosis including three-dimensional bone architecture with quantitative computed tomography (QCT). Dedicated high-resolution (HR) CT equipment is available to enhance image quality. At the other end of the spectrum, by utilizing post-processing techniques such as the trabecular bone score (TBS) information on three-dimensional architecture can be derived from DXA images. Further developments in magnetic resonance imaging (MRI) seem promising to not only capture bone micro-architecture but also characterize processes at the molecular level. This review provides an overview of various quantitative imaging techniques based on different radiological modalities utilized in clinical osteoporosis care and research.

  19. Arctic Stratospheric Temperature In The Winters 1999/2000 and 2000/2001: A Quantitative Assessment and Microphysical Implications

    NASA Astrophysics Data System (ADS)

    Buss, S.; Wernli, H.; Peter, T.; Kivi, R.; Bui, T. P.; Kleinböhl, A.; Schiller, C.

    Stratospheric winter temperatures play a key role in the chain of microphysical and chemical processes that lead to the formation of polar stratospheric clouds (PSCs), chlorine activation and eventually to stratospheric ozone depletion. Here the tempera- ture conditions during the Arctic winters 1999/2000 and 2000/2001 are quantitatively investigated using observed profiles of water vapour and nitric acid, and tempera- tures from high-resolution radiosondes and aircraft observations, global ECMWF and UKMO analyses and mesoscale model simulations over Scandinavia and Greenland. The ECMWF model resolves parts of the gravity wave activity and generally agrees well with the observations. However, for the very cold temperatures near the ice frost point the ECMWF analyses have a warm bias of 1-6 K compared to radiosondes. For the mesoscale model HRM, this bias is generally reduced due to a more accurate rep- resentation of gravity waves. Quantitative estimates of the impact of the mesoscale temperature perturbations indicates that over Scandinavia and Greenland the wave- induced stratospheric cooling (as simulated by the HRM) affects only moderately the estimated chlorine activation and homogeneous NAT particle formation, but strongly enhances the potential for ice formation.

  20. Accurate determination of reference materials and natural isolates by means of quantitative (1)h NMR spectroscopy.

    PubMed

    Frank, Oliver; Kreissl, Johanna Karoline; Daschner, Andreas; Hofmann, Thomas

    2014-03-26

    A fast and precise proton nuclear magnetic resonance (qHNMR) method for the quantitative determination of low molecular weight target molecules in reference materials and natural isolates has been validated using ERETIC 2 (Electronic REference To access In vivo Concentrations) based on the PULCON (PULse length based CONcentration determination) methodology and compared to the gravimetric results. Using an Avance III NMR spectrometer (400 MHz) equipped with a broad band observe (BBO) probe, the qHNMR method was validated by determining its linearity, range, precision, and accuracy as well as robustness and limit of quantitation. The linearity of the method was assessed by measuring samples of l-tyrosine, caffeine, or benzoic acid in a concentration range between 0.3 and 16.5 mmol/L (r(2) ≥ 0.99), whereas the interday and intraday precisions were found to be ≤2%. The recovery of a range of reference compounds was ≥98.5%, thus demonstrating the qHNMR method as a precise tool for the rapid quantitation (~15 min) of food-related target compounds in reference materials and natural isolates such as nucleotides, polyphenols, or cyclic peptides.

  1. QUESP and QUEST revisited - fast and accurate quantitative CEST experiments.

    PubMed

    Zaiss, Moritz; Angelovski, Goran; Demetriou, Eleni; McMahon, Michael T; Golay, Xavier; Scheffler, Klaus

    2018-03-01

    Chemical exchange saturation transfer (CEST) NMR or MRI experiments allow detection of low concentrated molecules with enhanced sensitivity via their proton exchange with the abundant water pool. Be it endogenous metabolites or exogenous contrast agents, an exact quantification of the actual exchange rate is required to design optimal pulse sequences and/or specific sensitive agents. Refined analytical expressions allow deeper insight and improvement of accuracy for common quantification techniques. The accuracy of standard quantification methodologies, such as quantification of exchange rate using varying saturation power or varying saturation time, is improved especially for the case of nonequilibrium initial conditions and weak labeling conditions, meaning the saturation amplitude is smaller than the exchange rate (γB 1  < k). The improved analytical 'quantification of exchange rate using varying saturation power/time' (QUESP/QUEST) equations allow for more accurate exchange rate determination, and provide clear insights on the general principles to execute the experiments and to perform numerical evaluation. The proposed methodology was evaluated on the large-shift regime of paramagnetic chemical-exchange-saturation-transfer agents using simulated data and data of the paramagnetic Eu(III) complex of DOTA-tetraglycineamide. The refined formulas yield improved exchange rate estimation. General convergence intervals of the methods that would apply for smaller shift agents are also discussed. Magn Reson Med 79:1708-1721, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

  2. Quantitative Analysis of Radar Returns from Insects

    NASA Technical Reports Server (NTRS)

    Riley, J. R.

    1979-01-01

    When a number of flying insects is low enough to permit their resolution as individual radar targets, quantitative estimates of their aerial density are developed. Accurate measurements of heading distribution using a rotating polarization radar to enhance the wingbeat frequency method of identification are presented.

  3. Quantitative analyses of tartaric acid based on terahertz time domain spectroscopy

    NASA Astrophysics Data System (ADS)

    Cao, Binghua; Fan, Mengbao

    2010-10-01

    Terahertz wave is the electromagnetic spectrum situated between microwave and infrared wave. Quantitative analysis based on terahertz spectroscopy is very important for the application of terahertz techniques. But how to realize it is still under study. L-tartaric acid is widely used as acidulant in beverage, and other food, such as soft drinks, wine, candy, bread and some colloidal sweetmeats. In this paper, terahertz time-domain spectroscopy is applied to quantify the tartaric acid. Two methods are employed to process the terahertz spectra of different samples with different content of tartaric acid. The first one is linear regression combining correlation analysis. The second is partial least square (PLS), in which the absorption spectra in the 0.8-1.4THz region are used to quantify the tartaric acid. To compare the performance of these two principles, the relative error of the two methods is analyzed. For this experiment, the first method does better than the second one. But the first method is suitable for the quantitative analysis of materials which has obvious terahertz absorption peaks, while for material which has no obvious terahertz absorption peaks, the second one is more appropriate.

  4. ICSH recommendations for assessing automated high-performance liquid chromatography and capillary electrophoresis equipment for the quantitation of HbA2.

    PubMed

    Stephens, A D; Colah, R; Fucharoen, S; Hoyer, J; Keren, D; McFarlane, A; Perrett, D; Wild, B J

    2015-10-01

    Automated high performance liquid chromatography and Capillary electrophoresis are used to quantitate the proportion of Hemoglobin A2 (HbA2 ) in blood samples order to enable screening and diagnosis of carriers of β-thalassemia. Since there is only a very small difference in HbA2 levels between people who are carriers and people who are not carriers such analyses need to be both precise and accurate. This paper examines the different parameters of such equipment and discusses how they should be assessed. © 2015 John Wiley & Sons Ltd.

  5. A high seroprevalence of antibodies to pertussis toxin among Japanese adults: Qualitative and quantitative analyses

    PubMed Central

    Moriuchi, Takumi; Otsuka, Nao; Hiramatsu, Yukihiro; Shibayama, Keigo

    2017-01-01

    In 2013, national serosurveillance detected a high seroprevalence of antibodies to pertussis toxin (PT) from Bordetella pertussis among Japanese adults. Thus, we aimed to determine the cause(s) of this high seroprevalence, and analyzed the titers of antibodies to PT and filamentous hemagglutinin (FHA) among adults (35–44 years old), young children (4–7 years old), and older children (10–14 years old). Our quantitative analyses revealed that adults had higher seroprevalences of anti-PT IgG and PT-neutralizing antibodies, and similar titers of anti-FHA IgG, compared to the young and older children. Positive correlations were observed between the titers of PT-neutralizing antibodies and anti-PT IgG in all age groups (rs values of 0.326–0.522), although the correlation tended to decrease with age. The ratio of PT-neutralizing antibodies to anti-PT IgG was significantly different when we compared the serum and purified IgG fractions among adults (p = 0.016), although this result was not observed among young and older children. Thus, it appears that some adults had non-IgG immunoglobulins to PT. Our analyses also revealed that adults had high-avidity anti-PT IgG (avidity index: 63.5%, similar results were observed among the children); however, the adults had lower-avidity anti-FHA IgG (37.9%, p < 0.05). It is possible that low-avidity anti-FHA IgG is related to infection with other respiratory pathogens (e.g., Bordetella parapertussis, Haemophilus influenzae, or Mycoplasma pneumoniae), which produces antibodies to FHA-like proteins. Our observations suggest that these adults had been infected with B. pertussis and other pathogen(s) during their adulthood. PMID:28700751

  6. Quantitative protein localization signatures reveal an association between spatial and functional divergences of proteins.

    PubMed

    Loo, Lit-Hsin; Laksameethanasan, Danai; Tung, Yi-Ling

    2014-03-01

    Protein subcellular localization is a major determinant of protein function. However, this important protein feature is often described in terms of discrete and qualitative categories of subcellular compartments, and therefore it has limited applications in quantitative protein function analyses. Here, we present Protein Localization Analysis and Search Tools (PLAST), an automated analysis framework for constructing and comparing quantitative signatures of protein subcellular localization patterns based on microscopy images. PLAST produces human-interpretable protein localization maps that quantitatively describe the similarities in the localization patterns of proteins and major subcellular compartments, without requiring manual assignment or supervised learning of these compartments. Using the budding yeast Saccharomyces cerevisiae as a model system, we show that PLAST is more accurate than existing, qualitative protein localization annotations in identifying known co-localized proteins. Furthermore, we demonstrate that PLAST can reveal protein localization-function relationships that are not obvious from these annotations. First, we identified proteins that have similar localization patterns and participate in closely-related biological processes, but do not necessarily form stable complexes with each other or localize at the same organelles. Second, we found an association between spatial and functional divergences of proteins during evolution. Surprisingly, as proteins with common ancestors evolve, they tend to develop more diverged subcellular localization patterns, but still occupy similar numbers of compartments. This suggests that divergence of protein localization might be more frequently due to the development of more specific localization patterns over ancestral compartments than the occupation of new compartments. PLAST enables systematic and quantitative analyses of protein localization-function relationships, and will be useful to elucidate protein

  7. Quantitative Protein Localization Signatures Reveal an Association between Spatial and Functional Divergences of Proteins

    PubMed Central

    Loo, Lit-Hsin; Laksameethanasan, Danai; Tung, Yi-Ling

    2014-01-01

    Protein subcellular localization is a major determinant of protein function. However, this important protein feature is often described in terms of discrete and qualitative categories of subcellular compartments, and therefore it has limited applications in quantitative protein function analyses. Here, we present Protein Localization Analysis and Search Tools (PLAST), an automated analysis framework for constructing and comparing quantitative signatures of protein subcellular localization patterns based on microscopy images. PLAST produces human-interpretable protein localization maps that quantitatively describe the similarities in the localization patterns of proteins and major subcellular compartments, without requiring manual assignment or supervised learning of these compartments. Using the budding yeast Saccharomyces cerevisiae as a model system, we show that PLAST is more accurate than existing, qualitative protein localization annotations in identifying known co-localized proteins. Furthermore, we demonstrate that PLAST can reveal protein localization-function relationships that are not obvious from these annotations. First, we identified proteins that have similar localization patterns and participate in closely-related biological processes, but do not necessarily form stable complexes with each other or localize at the same organelles. Second, we found an association between spatial and functional divergences of proteins during evolution. Surprisingly, as proteins with common ancestors evolve, they tend to develop more diverged subcellular localization patterns, but still occupy similar numbers of compartments. This suggests that divergence of protein localization might be more frequently due to the development of more specific localization patterns over ancestral compartments than the occupation of new compartments. PLAST enables systematic and quantitative analyses of protein localization-function relationships, and will be useful to elucidate protein

  8. Quantitative characterisation of sedimentary grains

    NASA Astrophysics Data System (ADS)

    Tunwal, Mohit; Mulchrone, Kieran F.; Meere, Patrick A.

    2016-04-01

    Analysis of sedimentary texture helps in determining the formation, transportation and deposition processes of sedimentary rocks. Grain size analysis is traditionally quantitative, whereas grain shape analysis is largely qualitative. A semi-automated approach to quantitatively analyse shape and size of sand sized sedimentary grains is presented. Grain boundaries are manually traced from thin section microphotographs in the case of lithified samples and are automatically identified in the case of loose sediments. Shape and size paramters can then be estimated using a software package written on the Mathematica platform. While automated methodology already exists for loose sediment analysis, the available techniques for the case of lithified samples are limited to cases of high definition thin section microphotographs showing clear contrast between framework grains and matrix. Along with the size of grain, shape parameters such as roundness, angularity, circularity, irregularity and fractal dimension are measured. A new grain shape parameter developed using Fourier descriptors has also been developed. To test this new approach theoretical examples were analysed and produce high quality results supporting the accuracy of the algorithm. Furthermore sandstone samples from known aeolian and fluvial environments from the Dingle Basin, County Kerry, Ireland were collected and analysed. Modern loose sediments from glacial till from County Cork, Ireland and aeolian sediments from Rajasthan, India have also been collected and analysed. A graphical summary of the data is presented and allows for quantitative distinction between samples extracted from different sedimentary environments.

  9. pyQms enables universal and accurate quantification of mass spectrometry data.

    PubMed

    Leufken, Johannes; Niehues, Anna; Sarin, L Peter; Wessel, Florian; Hippler, Michael; Leidel, Sebastian A; Fufezan, Christian

    2017-10-01

    Quantitative mass spectrometry (MS) is a key technique in many research areas (1), including proteomics, metabolomics, glycomics, and lipidomics. Because all of the corresponding molecules can be described by chemical formulas, universal quantification tools are highly desirable. Here, we present pyQms, an open-source software for accurate quantification of all types of molecules measurable by MS. pyQms uses isotope pattern matching that offers an accurate quality assessment of all quantifications and the ability to directly incorporate mass spectrometer accuracy. pyQms is, due to its universal design, applicable to every research field, labeling strategy, and acquisition technique. This opens ultimate flexibility for researchers to design experiments employing innovative and hitherto unexplored labeling strategies. Importantly, pyQms performs very well to accurately quantify partially labeled proteomes in large scale and high throughput, the most challenging task for a quantification algorithm. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  10. Linkage disequilibrium interval mapping of quantitative trait loci.

    PubMed

    Boitard, Simon; Abdallah, Jihad; de Rochambeau, Hubert; Cierco-Ayrolles, Christine; Mangin, Brigitte

    2006-03-16

    For many years gene mapping studies have been performed through linkage analyses based on pedigree data. Recently, linkage disequilibrium methods based on unrelated individuals have been advocated as powerful tools to refine estimates of gene location. Many strategies have been proposed to deal with simply inherited disease traits. However, locating quantitative trait loci is statistically more challenging and considerable research is needed to provide robust and computationally efficient methods. Under a three-locus Wright-Fisher model, we derived approximate expressions for the expected haplotype frequencies in a population. We considered haplotypes comprising one trait locus and two flanking markers. Using these theoretical expressions, we built a likelihood-maximization method, called HAPim, for estimating the location of a quantitative trait locus. For each postulated position, the method only requires information from the two flanking markers. Over a wide range of simulation scenarios it was found to be more accurate than a two-marker composite likelihood method. It also performed as well as identity by descent methods, whilst being valuable in a wider range of populations. Our method makes efficient use of marker information, and can be valuable for fine mapping purposes. Its performance is increased if multiallelic markers are available. Several improvements can be developed to account for more complex evolution scenarios or provide robust confidence intervals for the location estimates.

  11. Graded Interface Models for more accurate Determination of van der Waals-London Dispersion Interactions across Grain Boundaries

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

    van Benthem, Klaus; Tan, Guolong; French, Roger H

    2006-01-01

    Attractive van der Waals V London dispersion interactions between two half crystals arise from local physical property gradients within the interface layer separating the crystals. Hamaker coefficients and London dispersion energies were quantitatively determined for 5 and near- 13 grain boundaries in SrTiO3 by analysis of spatially resolved valence electron energy-loss spectroscopy (VEELS) data. From the experimental data, local complex dielectric functions were determined, from which optical properties can be locally analysed. Both local electronic structures and optical properties revealed gradients within the grain boundary cores of both investigated interfaces. The obtained results show that even in the presence ofmore » atomically structured grain boundary cores with widths of less than 1 nm, optical properties have to be represented with gradual changes across the grain boundary structures to quantitatively reproduce accurate van der Waals V London dispersion interactions. London dispersion energies of the order of 10% of the apparent interface energies of SrTiO3 were observed, demonstrating their significance in the grain boundary formation process. The application of different models to represent optical property gradients shows that long-range van der Waals V London dispersion interactions scale significantly with local, i.e atomic length scale property variations.« less

  12. Quantitative X-ray Map Analyser (Q-XRMA): A new GIS-based statistical approach to Mineral Image Analysis

    NASA Astrophysics Data System (ADS)

    Ortolano, Gaetano; Visalli, Roberto; Godard, Gaston; Cirrincione, Rosolino

    2018-06-01

    We present a new ArcGIS®-based tool developed in the Python programming language for calibrating EDS/WDS X-ray element maps, with the aim of acquiring quantitative information of petrological interest. The calibration procedure is based on a multiple linear regression technique that takes into account interdependence among elements and is constrained by the stoichiometry of minerals. The procedure requires an appropriate number of spot analyses for use as internal standards and provides several test indexes for a rapid check of calibration accuracy. The code is based on an earlier image-processing tool designed primarily for classifying minerals in X-ray element maps; the original Python code has now been enhanced to yield calibrated maps of mineral end-members or the chemical parameters of each classified mineral. The semi-automated procedure can be used to extract a dataset that is automatically stored within queryable tables. As a case study, the software was applied to an amphibolite-facies garnet-bearing micaschist. The calibrated images obtained for both anhydrous (i.e., garnet and plagioclase) and hydrous (i.e., biotite) phases show a good fit with corresponding electron microprobe analyses. This new GIS-based tool package can thus find useful application in petrology and materials science research. Moreover, the huge quantity of data extracted opens new opportunities for the development of a thin-section microchemical database that, using a GIS platform, can be linked with other major global geoscience databases.

  13. Joint analyses of open comments and quantitative data: Added value in a job satisfaction survey of hospital professionals.

    PubMed

    Gilles, Ingrid; Mayer, Mauro; Courvoisier, Nelly; Peytremann-Bridevaux, Isabelle

    2017-01-01

    To obtain a comprehensive understanding of the job opinions of hospital professionals by conducting qualitative analyses of the open comments included in a job satisfaction survey and combining these results with the quantitative results. A cross-sectional survey targeting all Lausanne University Hospital professionals was performed in the fall of 2013. The survey considered ten job satisfaction dimensions (e.g. self-fulfilment, workload, management, work-related burnout, organisational commitment, intent to stay) and included an open comment section. Computer-assisted qualitative analyses were conducted on these comments. Satisfaction rates on the included dimensions and professional groups were entered as predictive variables in the qualitative analyses. Of 10 838 hospital professionals, 4978 participated in the survey and 1067 provided open comments. Data from 1045 respondents with usable comments constituted the analytic sample (133 physicians, 393 nurses, 135 laboratory technicians, 247 administrative staff, including researchers, 67 logistic staff, 44 psycho-social workers, and 26 unspecified). Almost a third of the comments addressed scheduling issues, mostly related to problems and exhaustion linked to shifts, work-life balance, and difficulties with colleagues' absences and the consequences for quality of care and patient safety. The other two-thirds related to classic themes included in job satisfaction surveys. Although some comments were provided equally by all professional groups, others were group specific: work and hierarchy pressures for physicians, healthcare quality and patient safety for nurses, skill recognition for administrative staff. Overall, respondents' comments were consistent with their job satisfaction ratings. Open comment analysis provides a comprehensive understanding of hospital professionals' job experiences, allowing better consideration of quality initiatives that match the needs of professionals with reality.

  14. 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

  15. 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

  16. Quantitative Phase Imaging in a Volume Holographic Microscope

    NASA Astrophysics Data System (ADS)

    Waller, Laura; Luo, Yuan; Barbastathis, George

    2010-04-01

    We demonstrate a method for quantitative phase imaging in a Volume Holographic Microscope (VHM) from a single exposure, describe the properties of the system and show experimental results. The VHM system uses a multiplexed volume hologram (VH) to laterally separate images from different focal planes. This 3D intensity information is then used to solve the transport of intensity (TIE) equation and recover phase quantitatively. We discuss the modifications to the technique that were made in order to give accurate results.

  17. A gold nanoparticle-based semi-quantitative and quantitative ultrasensitive paper sensor for the detection of twenty mycotoxins

    NASA Astrophysics Data System (ADS)

    Kong, Dezhao; Liu, Liqiang; Song, Shanshan; Suryoprabowo, Steven; Li, Aike; Kuang, Hua; Wang, Libing; Xu, Chuanlai

    2016-02-01

    A semi-quantitative and quantitative multi-immunochromatographic (ICA) strip detection assay was developed for the simultaneous detection of twenty types of mycotoxins from five classes, including zearalenones (ZEAs), deoxynivalenols (DONs), T-2 toxins (T-2s), aflatoxins (AFs), and fumonisins (FBs), in cereal food samples. Sensitive and specific monoclonal antibodies were selected for this assay. The semi-quantitative results were obtained within 20 min by the naked eye, with visual limits of detection for ZEAs, DONs, T-2s, AFs and FBs of 0.1-0.5, 2.5-250, 0.5-1, 0.25-1 and 2.5-10 μg kg-1, and cut-off values of 0.25-1, 5-500, 1-10, 0.5-2.5 and 5-25 μg kg-1, respectively. The quantitative results were obtained using a hand-held strip scan reader, with the calculated limits of detection for ZEAs, DONs, T-2s, AFs and FBs of 0.04-0.17, 0.06-49, 0.15-0.22, 0.056-0.49 and 0.53-1.05 μg kg-1, respectively. The analytical results of spiked samples were in accordance with the accurate content in the simultaneous detection analysis. This newly developed ICA strip assay is suitable for the on-site detection and rapid initial screening of mycotoxins in cereal samples, facilitating both semi-quantitative and quantitative determination.A semi-quantitative and quantitative multi-immunochromatographic (ICA) strip detection assay was developed for the simultaneous detection of twenty types of mycotoxins from five classes, including zearalenones (ZEAs), deoxynivalenols (DONs), T-2 toxins (T-2s), aflatoxins (AFs), and fumonisins (FBs), in cereal food samples. Sensitive and specific monoclonal antibodies were selected for this assay. The semi-quantitative results were obtained within 20 min by the naked eye, with visual limits of detection for ZEAs, DONs, T-2s, AFs and FBs of 0.1-0.5, 2.5-250, 0.5-1, 0.25-1 and 2.5-10 μg kg-1, and cut-off values of 0.25-1, 5-500, 1-10, 0.5-2.5 and 5-25 μg kg-1, respectively. The quantitative results were obtained using a hand-held strip scan

  18. Partial differential equation techniques for analysing animal movement: A comparison of different methods.

    PubMed

    Wang, Yi-Shan; Potts, Jonathan R

    2017-03-07

    Recent advances in animal tracking have allowed us to uncover the drivers of movement in unprecedented detail. This has enabled modellers to construct ever more realistic models of animal movement, which aid in uncovering detailed patterns of space use in animal populations. Partial differential equations (PDEs) provide a popular tool for mathematically analysing such models. However, their construction often relies on simplifying assumptions which may greatly affect the model outcomes. Here, we analyse the effect of various PDE approximations on the analysis of some simple movement models, including a biased random walk, central-place foraging processes and movement in heterogeneous landscapes. Perhaps the most commonly-used PDE method dates back to a seminal paper of Patlak from 1953. However, our results show that this can be a very poor approximation in even quite simple models. On the other hand, more recent methods, based on transport equation formalisms, can provide more accurate results, as long as the kernel describing the animal's movement is sufficiently smooth. When the movement kernel is not smooth, we show that both the older and newer methods can lead to quantitatively misleading results. Our detailed analysis will aid future researchers in the appropriate choice of PDE approximation for analysing models of animal movement. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. Identification and Quantitation of Flavanols and Proanthocyanidins in Foods: How Good are the Datas?

    PubMed Central

    Kelm, Mark A.; Hammerstone, John F.; Schmitz, Harold H.

    2005-01-01

    Evidence suggesting that dietary polyphenols, flavanols, and proanthocyanidins in particular offer significant cardiovascular health benefits is rapidly increasing. Accordingly, reliable and accurate methods are needed to provide qualitative and quantitative food composition data necessary for high quality epidemiological and clinical research. Measurements for flavonoids and proanthocyanidins have employed a range of analytical techniques, with various colorimetric assays still being popular for estimating total polyphenolic content in foods and other biological samples despite advances made with more sophisticated analyses. More crudely, estimations of polyphenol content as well as antioxidant activity are also reported with values relating to radical scavenging activity. High-performance liquid chromatography (HPLC) is the method of choice for quantitative analysis of individual polyphenols such as flavanols and proanthocyanidins. Qualitative information regarding proanthocyanidin structure has been determined by chemical methods such as thiolysis and by HPLC-mass spectrometry (MS) techniques at present. The lack of appropriate standards is the single most important factor that limits the aforementioned analyses. However, with ever expanding research in the arena of flavanols, proanthocyanidins, and health and the importance of their future inclusion in food composition databases, the need for standards becomes more critical. At present, sufficiently well-characterized standard material is available for selective flavanols and proanthocyanidins, and construction of at least a limited food composition database is feasible. PMID:15712597

  20. Fast and accurate mock catalogue generation for low-mass galaxies

    NASA Astrophysics Data System (ADS)

    Koda, Jun; Blake, Chris; Beutler, Florian; Kazin, Eyal; Marin, Felipe

    2016-06-01

    We present an accurate and fast framework for generating mock catalogues including low-mass haloes, based on an implementation of the COmoving Lagrangian Acceleration (COLA) technique. Multiple realisations of mock catalogues are crucial for analyses of large-scale structure, but conventional N-body simulations are too computationally expensive for the production of thousands of realizations. We show that COLA simulations can produce accurate mock catalogues with a moderate computation resource for low- to intermediate-mass galaxies in 1012 M⊙ haloes, both in real and redshift space. COLA simulations have accurate peculiar velocities, without systematic errors in the velocity power spectra for k ≤ 0.15 h Mpc-1, and with only 3-per cent error for k ≤ 0.2 h Mpc-1. We use COLA with 10 time steps and a Halo Occupation Distribution to produce 600 mock galaxy catalogues of the WiggleZ Dark Energy Survey. Our parallelized code for efficient generation of accurate halo catalogues is publicly available at github.com/junkoda/cola_halo.

  1. Using an Educational Electronic Documentation System to Help Nursing Students Accurately Identify Nursing Diagnoses

    ERIC Educational Resources Information Center

    Pobocik, Tamara J.

    2013-01-01

    The use of technology and electronic medical records in healthcare has exponentially increased. This quantitative research project used a pretest/posttest design, and reviewed how an educational electronic documentation system helped nursing students to identify the accurate related to statement of the nursing diagnosis for the patient in the case…

  2. Using Inequality Measures to Incorporate Environmental Justice into Regulatory Analyses

    EPA Science Inventory

    Abstract: Formally evaluating how specific policy measures influence environmental justice is challenging, especially in the context of regulatory analyses in which quantitative comparisons are the norm. However, there is a large literature on developing and applying quantitative...

  3. Ultra-fast quantitative imaging using ptychographic iterative engine based digital micro-mirror device

    NASA Astrophysics Data System (ADS)

    Sun, Aihui; Tian, Xiaolin; Kong, Yan; Jiang, Zhilong; Liu, Fei; Xue, Liang; Wang, Shouyu; Liu, Cheng

    2018-01-01

    As a lensfree imaging technique, ptychographic iterative engine (PIE) method can provide both quantitative sample amplitude and phase distributions avoiding aberration. However, it requires field of view (FoV) scanning often relying on mechanical translation, which not only slows down measuring speed, but also introduces mechanical errors decreasing both resolution and accuracy in retrieved information. In order to achieve high-accurate quantitative imaging with fast speed, digital micromirror device (DMD) is adopted in PIE for large FoV scanning controlled by on/off state coding by DMD. Measurements were implemented using biological samples as well as USAF resolution target, proving high resolution in quantitative imaging using the proposed system. Considering its fast and accurate imaging capability, it is believed the DMD based PIE technique provides a potential solution for medical observation and measurements.

  4. Highly accurate quantitative spectroscopy of massive stars in the Galaxy

    NASA Astrophysics Data System (ADS)

    Nieva, María-Fernanda; Przybilla, Norbert

    2017-11-01

    Achieving high accuracy and precision in stellar parameter and chemical composition determinations is challenging in massive star spectroscopy. On one hand, the target selection for an unbiased sample build-up is complicated by several types of peculiarities that can occur in individual objects. On the other hand, composite spectra are often not recognized as such even at medium-high spectral resolution and typical signal-to-noise ratios, despite multiplicity among massive stars is widespread. In particular, surveys that produce large amounts of automatically reduced data are prone to oversight of details that turn hazardous for the analysis with techniques that have been developed for a set of standard assumptions applicable to a spectrum of a single star. Much larger systematic errors than anticipated may therefore result because of the unrecognized true nature of the investigated objects, or much smaller sample sizes of objects for the analysis than initially planned, if recognized. More factors to be taken care of are the multiple steps from the choice of instrument over the details of the data reduction chain to the choice of modelling code, input data, analysis technique and the selection of the spectral lines to be analyzed. Only when avoiding all the possible pitfalls, a precise and accurate characterization of the stars in terms of fundamental parameters and chemical fingerprints can be achieved that form the basis for further investigations regarding e.g. stellar structure and evolution or the chemical evolution of the Galaxy. The scope of the present work is to provide the massive star and also other astrophysical communities with criteria to evaluate the quality of spectroscopic investigations of massive stars before interpreting them in a broader context. The discussion is guided by our experiences made in the course of over a decade of studies of massive star spectroscopy ranging from the simplest single objects to multiple systems.

  5. Quantitative prediction of phase transformations in silicon during nanoindentation

    NASA Astrophysics Data System (ADS)

    Zhang, Liangchi; Basak, Animesh

    2013-08-01

    This paper establishes the first quantitative relationship between the phases transformed in silicon and the shape characteristics of nanoindentation curves. Based on an integrated analysis using TEM and unit cell properties of phases, the volumes of the phases emerged in a nanoindentation are formulated as a function of pop-out size and depth of nanoindentation impression. This simple formula enables a fast, accurate and quantitative prediction of the phases in a nanoindentation cycle, which has been impossible before.

  6. Diagnostic accuracy of semi-automatic quantitative metrics as an alternative to expert reading of CT myocardial perfusion in the CORE320 study.

    PubMed

    Ostovaneh, Mohammad R; Vavere, Andrea L; Mehra, Vishal C; Kofoed, Klaus F; Matheson, Matthew B; Arbab-Zadeh, Armin; Fujisawa, Yasuko; Schuijf, Joanne D; Rochitte, Carlos E; Scholte, Arthur J; Kitagawa, Kakuya; Dewey, Marc; Cox, Christopher; DiCarli, Marcelo F; George, Richard T; Lima, Joao A C

    To determine the diagnostic accuracy of semi-automatic quantitative metrics compared to expert reading for interpretation of computed tomography perfusion (CTP) imaging. The CORE320 multicenter diagnostic accuracy clinical study enrolled patients between 45 and 85 years of age who were clinically referred for invasive coronary angiography (ICA). Computed tomography angiography (CTA), CTP, single photon emission computed tomography (SPECT), and ICA images were interpreted manually in blinded core laboratories by two experienced readers. Additionally, eight quantitative CTP metrics as continuous values were computed semi-automatically from myocardial and blood attenuation and were combined using logistic regression to derive a final quantitative CTP metric score. For the reference standard, hemodynamically significant coronary artery disease (CAD) was defined as a quantitative ICA stenosis of 50% or greater and a corresponding perfusion defect by SPECT. Diagnostic accuracy was determined by area under the receiver operating characteristic curve (AUC). Of the total 377 included patients, 66% were male, median age was 62 (IQR: 56, 68) years, and 27% had prior myocardial infarction. In patient based analysis, the AUC (95% CI) for combined CTA-CTP expert reading and combined CTA-CTP semi-automatic quantitative metrics was 0.87(0.84-0.91) and 0.86 (0.83-0.9), respectively. In vessel based analyses the AUC's were 0.85 (0.82-0.88) and 0.84 (0.81-0.87), respectively. No significant difference in AUC was found between combined CTA-CTP expert reading and CTA-CTP semi-automatic quantitative metrics in patient based or vessel based analyses(p > 0.05 for all). Combined CTA-CTP semi-automatic quantitative metrics is as accurate as CTA-CTP expert reading to detect hemodynamically significant CAD. Copyright © 2018 Society of Cardiovascular Computed Tomography. Published by Elsevier Inc. All rights reserved.

  7. A versatile pipeline for the multi-scale digital reconstruction and quantitative analysis of 3D tissue architecture

    PubMed Central

    Morales-Navarrete, Hernán; Segovia-Miranda, Fabián; Klukowski, Piotr; Meyer, Kirstin; Nonaka, Hidenori; Marsico, Giovanni; Chernykh, Mikhail; Kalaidzidis, Alexander; Zerial, Marino; Kalaidzidis, Yannis

    2015-01-01

    A prerequisite for the systems biology analysis of tissues is an accurate digital three-dimensional reconstruction of tissue structure based on images of markers covering multiple scales. Here, we designed a flexible pipeline for the multi-scale reconstruction and quantitative morphological analysis of tissue architecture from microscopy images. Our pipeline includes newly developed algorithms that address specific challenges of thick dense tissue reconstruction. Our implementation allows for a flexible workflow, scalable to high-throughput analysis and applicable to various mammalian tissues. We applied it to the analysis of liver tissue and extracted quantitative parameters of sinusoids, bile canaliculi and cell shapes, recognizing different liver cell types with high accuracy. Using our platform, we uncovered an unexpected zonation pattern of hepatocytes with different size, nuclei and DNA content, thus revealing new features of liver tissue organization. The pipeline also proved effective to analyse lung and kidney tissue, demonstrating its generality and robustness. DOI: http://dx.doi.org/10.7554/eLife.11214.001 PMID:26673893

  8. Analytical performance of reciprocal isotope labeling of proteome digests for quantitative proteomics and its application for comparative studies of aerobic and anaerobic Escherichia coli proteomes.

    PubMed

    Lo, Andy; Weiner, Joel H; Li, Liang

    2013-09-17

    Due to limited sample amounts, instrument time considerations, and reagent costs, only a small number of replicate experiments are typically performed for quantitative proteome analyses. Generation of reproducible data that can be readily assessed for consistency within a small number of datasets is critical for accurate quantification. We report our investigation of a strategy using reciprocal isotope labeling of two comparative samples as a tool for determining proteome changes. Reciprocal labeling was evaluated to determine the internal consistency of quantified proteome changes from Escherichia coli grown under aerobic and anaerobic conditions. Qualitatively, the peptide overlap between replicate analyses of the same sample and reverse labeled samples were found to be within 8%. Quantitatively, reciprocal analyses showed only a slight increase in average overall inconsistency when compared with replicate analyses (1.29 vs. 1.24-fold difference). Most importantly, reverse labeling was successfully used to identify spurious values resulting from incorrect peptide identifications and poor peak fitting. After removal of 5% of the peptide data with low reproducibility, a total of 275 differentially expressed proteins (>1.50-fold difference) were consistently identified and were then subjected to bioinformatics analysis. General considerations and guidelines for reciprocal labeling experimental design and biological significance of obtained results are discussed. Copyright © 2013 Elsevier B.V. All rights reserved.

  9. Joint analyses of open comments and quantitative data: Added value in a job satisfaction survey of hospital professionals

    PubMed Central

    Gilles, Ingrid; Mayer, Mauro; Courvoisier, Nelly; Peytremann-Bridevaux, Isabelle

    2017-01-01

    Objective To obtain a comprehensive understanding of the job opinions of hospital professionals by conducting qualitative analyses of the open comments included in a job satisfaction survey and combining these results with the quantitative results. Design A cross-sectional survey targeting all Lausanne University Hospital professionals was performed in the fall of 2013. Material and methods The survey considered ten job satisfaction dimensions (e.g. self-fulfilment, workload, management, work-related burnout, organisational commitment, intent to stay) and included an open comment section. Computer-assisted qualitative analyses were conducted on these comments. Satisfaction rates on the included dimensions and professional groups were entered as predictive variables in the qualitative analyses. Participants Of 10 838 hospital professionals, 4978 participated in the survey and 1067 provided open comments. Data from 1045 respondents with usable comments constituted the analytic sample (133 physicians, 393 nurses, 135 laboratory technicians, 247 administrative staff, including researchers, 67 logistic staff, 44 psycho-social workers, and 26 unspecified). Results Almost a third of the comments addressed scheduling issues, mostly related to problems and exhaustion linked to shifts, work-life balance, and difficulties with colleagues’ absences and the consequences for quality of care and patient safety. The other two-thirds related to classic themes included in job satisfaction surveys. Although some comments were provided equally by all professional groups, others were group specific: work and hierarchy pressures for physicians, healthcare quality and patient safety for nurses, skill recognition for administrative staff. Overall, respondents’ comments were consistent with their job satisfaction ratings. Conclusion Open comment analysis provides a comprehensive understanding of hospital professionals’ job experiences, allowing better consideration of quality

  10. Highly accurate nephelometric titrimetry.

    PubMed

    Zhan, Xiancheng; Li, Chengrong; Li, Zhiyi; Yang, Xiucen; Zhong, Shuguang; Yi, Tao

    2004-02-01

    A method that accurately indicates the end-point of precipitation reactions by the measurement of the relative intensity of the scattered light in the titrate is presented. A new nephelometric titrator with an internal nephelometric sensor has been devised. The work of the titrator including the sensor and change in the turbidity of the titrate and intensity of the scattered light are described. The accuracy of the nephelometric titrimetry is discussed theoretically. The titration of NaCl with AgNO(3) serves as a model. A relative error as well as deviation is within 0.2% under the experimental conditions. The applicability of the titrimetry in pharmaceutical analyses, for example, phenytoin sodium and procaine hydrochloride, is generally illustrated. Copyright 2004 Wiley-Liss, Inc. and the American Pharmacists Association

  11. Detection and quantitation of trace phenolphthalein (in pharmaceutical preparations and in forensic exhibits) by liquid chromatography-tandem mass spectrometry, a sensitive and accurate method.

    PubMed

    Sharma, Kakali; Sharma, Shiba P; Lahiri, Sujit C

    2013-01-01

    Phenolphthalein, an acid-base indicator and laxative, is important as a constituent of widely used weight-reducing multicomponent food formulations. Phenolphthalein is an useful reagent in forensic science for the identification of blood stains of suspected victims and for apprehending erring officials accepting bribes in graft or trap cases. The pink-colored alkaline hand washes originating from the phenolphthalein-smeared notes can easily be determined spectrophotometrically. But in many cases, colored solution turns colorless with time, which renders the genuineness of bribe cases doubtful to the judiciary. No method is known till now for the detection and identification of phenolphthalein in colorless forensic exhibits with positive proof. Liquid chromatography-tandem mass spectrometry had been found to be most sensitive, accurate method capable of detection and quantitation of trace phenolphthalein in commercial formulations and colorless forensic exhibits with positive proof. The detection limit of phenolphthalein was found to be 1.66 pg/L or ng/mL, and the calibration curve shows good linearity (r(2) = 0.9974). © 2012 American Academy of Forensic Sciences.

  12. Pentobarbital quantitation using EMIT serum barbiturate assay reagents: application to monitoring of high-dose pentobarbital therapy.

    PubMed

    Pape, B E; Cary, P L; Clay, L C; Godolphin, W

    1983-01-01

    Pentobarbital serum concentrations associated with a high-dose therapeutic regimen were determined using EMIT immunoassay reagents. Replicate analyses of serum controls resulted in a within-assay coefficient of variation of 5.0% and a between-assay coefficient of variation of 10%. Regression analysis of 44 serum samples analyzed by this technique (y) and a reference procedure (x) were y = 0.98x + 3.6 (r = 0.98; x = ultraviolet spectroscopy) and y = 1.04x + 2.4 (r = 0.96; x = high-performance liquid chromatography). Clinical evaluation of the results indicates the immunoassay is sufficiently sensitive and selective for pentobarbital to allow accurate quantitation within the therapeutic range associated with high-dose therapy.

  13. Quantitative DNA Analyses for Airborne Birch Pollen

    PubMed Central

    Müller-Germann, Isabell; Vogel, Bernhard; Vogel, Heike; Pauling, Andreas; Fröhlich-Nowoisky, Janine; Pöschl, Ulrich; Després, Viviane R.

    2015-01-01

    Birch trees produce large amounts of highly allergenic pollen grains that are distributed by wind and impact human health by causing seasonal hay fever, pollen-related asthma, and other allergic diseases. Traditionally, pollen forecasts are based on conventional microscopic counting techniques that are labor-intensive and limited in the reliable identification of species. Molecular biological techniques provide an alternative approach that is less labor-intensive and enables identification of any species by its genetic fingerprint. A particularly promising method is quantitative Real-Time polymerase chain reaction (qPCR), which can be used to determine the number of DNA copies and thus pollen grains in air filter samples. During the birch pollination season in 2010 in Mainz, Germany, we collected air filter samples of fine (<3 μm) and coarse air particulate matter. These were analyzed by qPCR using two different primer pairs: one for a single-copy gene (BP8) and the other for a multi-copy gene (ITS). The BP8 gene was better suitable for reliable qPCR results, and the qPCR results obtained for coarse particulate matter were well correlated with the birch pollen forecasting results of the regional air quality model COSMO-ART. As expected due to the size of birch pollen grains (~23 μm), the concentration of DNA in fine particulate matter was lower than in the coarse particle fraction. For the ITS region the factor was 64, while for the single-copy gene BP8 only 51. The possible presence of so-called sub-pollen particles in the fine particle fraction is, however, interesting even in low concentrations. These particles are known to be highly allergenic, reach deep into airways and cause often severe health problems. In conclusion, the results of this exploratory study open up the possibility of predicting and quantifying the pollen concentration in the atmosphere more precisely in the future. PMID:26492534

  14. Role Of Social Networks In Resilience Of Naval Recruits: A Quantitative Analysis

    DTIC Science & Technology

    2016-06-01

    comprises 1,297 total surveys from a total of eight divisions of recruits at two different time periods. Quantitative analyses using surveys and network... surveys from a total of eight divisions of recruits at two different time periods. Quantitative analyses using surveys and network data examine the effects...NETWORKS IN RESILIENCE OF NAVAL RECRUITS: A QUANTITATIVE ANALYSIS by Andrea M. Watling June 2016 Thesis Advisor: Edward H. Powley Co

  15. Semi-quantitative prediction of a multiple API solid dosage form with a combination of vibrational spectroscopy methods.

    PubMed

    Hertrampf, A; Sousa, R M; Menezes, J C; Herdling, T

    2016-05-30

    Quality control (QC) in the pharmaceutical industry is a key activity in ensuring medicines have the required quality, safety and efficacy for their intended use. QC departments at pharmaceutical companies are responsible for all release testing of final products but also all incoming raw materials. Near-infrared spectroscopy (NIRS) and Raman spectroscopy are important techniques for fast and accurate identification and qualification of pharmaceutical samples. Tablets containing two different active pharmaceutical ingredients (API) [bisoprolol, hydrochlorothiazide] in different commercially available dosages were analysed using Raman- and NIR Spectroscopy. The goal was to define multivariate models based on each vibrational spectroscopy to discriminate between different dosages (identity) and predict their dosage (semi-quantitative). Furthermore the combination of spectroscopic techniques was investigated. Therefore, two different multiblock techniques based on PLS have been applied: multiblock PLS (MB-PLS) and sequential-orthogonalised PLS (SO-PLS). NIRS showed better results compared to Raman spectroscopy for both identification and quantitation. The multiblock techniques investigated showed that each spectroscopy contains information not present or captured with the other spectroscopic technique, thus demonstrating that there is a potential benefit in their combined use for both identification and quantitation purposes. Copyright © 2016 Elsevier B.V. All rights reserved.

  16. Simultaneous Qualitative and Quantitative Analyses of Triterpenoids in Ilex pubescens by Ultra-High-Performance Liquid Chromatography Coupled with Quadrupole Time-of-Flight Mass Spectrometry.

    PubMed

    Cao, Di; Wang, Qing; Jin, Jing; Qiu, Maosong; Zhou, Lian; Zhou, Xinghong; Li, Hui; Zhao, Zhongxiang

    2018-03-01

    Ilex pubescens Hook et Arn mainly contains triterpenoids that possess antithrombotic, anti-inflammatory and analgesic effects. Quantitative and qualitative analyses of the triterpenoids in I. pubescens can be useful for determining the authenticity and quality of raw materials and guiding its clinical preparation. To establish a method for rapid and comprehensive analysis of triterpenoids in I. pubescens using ultra-high-performance liquid chromatography coupled to electrospray ionisation and quadrupole time-of-flight-mass spectrometry (UPLC-ESI-QTOF-MS), which will also be applied to evaluate the contents of nine triterpenoids among root, root heartwood and root bark of I. pubescens to judge the value of the root bark to avoid wastage. UPLC-ESI-QTOF-MS data from the extracts of I. pubescens in negative mode were analysed using Peakview and Masterview software that provided molecular weight, mass errors, isotope pattern fit and MS/MS fragments for the identification of triterpenoids. The quantification of nine investigated compounds of I. pubescens was accomplished using MultiQuant software. A total of 33 triterpenoids, five phenolic acids, two lignans and a flavonol were characterised in only 14 min. The total content of the nine compounds in the root bark was generally slightly higher than that of the root and root heartwood, which has not been reported before. The developed UPLC-ESI-QTOF-MS method was proven to be rapid and comprehensive for simultaneous qualitative and quantitative analyses of the characteristic triterpenoids in I. pubescens. The results may provide a basis for holistic quality control and metabolic studies of I. pubescens, as well as serve as a reference for the analysis of other Ilex plants. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

  17. A NOVEL TECHNIQUE FOR QUANTITATIVE ESTIMATION OF UPTAKE OF DIESEL EXHAUST PARTICLES BY LUNG CELLS

    EPA Science Inventory

    While airborne particulates like diesel exhaust particulates (DEP) exert significant toxicological effects on lungs, quantitative estimation of accumulation of DEP inside lung cells has not been reported due to a lack of an accurate and quantitative technique for this purpose. I...

  18. METHODS TO CLASSIFY ENVIRONMENTAL SAMPLES BASED ON MOLD ANALYSES BY QPCR

    EPA Science Inventory

    Quantitative PCR (QPCR) analysis of molds in indoor environmental samples produces highly accurate speciation and enumeration data. In a number of studies, eighty of the most common or potentially problematic indoor molds were identified and quantified in dust samples from homes...

  19. Leadership and Culture-Building in Schools: Quantitative and Qualitative Understandings.

    ERIC Educational Resources Information Center

    Sashkin, Marshall; Sashkin, Molly G.

    Understanding effective school leadership as a function of culture building through quantitative and qualitative analyses is the purpose of this paper. The two-part quantitative phase of the research focused on statistical measures of culture and leadership behavior directed toward culture building in the school. The first quantitative part…

  20. The effects of AVIRIS atmospheric calibration methodology on identification and quantitative mapping of surface mineralogy, Drum Mountains, Utah

    NASA Technical Reports Server (NTRS)

    Kruse, Fred A.; Dwyer, John L.

    1993-01-01

    The Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) measures reflected light in 224 contiguous spectra bands in the 0.4 to 2.45 micron region of the electromagnetic spectrum. Numerous studies have used these data for mineralogic identification and mapping based on the presence of diagnostic spectral features. Quantitative mapping requires conversion of the AVIRIS data to physical units (usually reflectance) so that analysis results can be compared and validated with field and laboratory measurements. This study evaluated two different AVIRIS calibration techniques to ground reflectance: an empirically-based method and an atmospheric model based method to determine their effects on quantitative scientific analyses. Expert system analysis and linear spectral unmixing were applied to both calibrated data sets to determine the effect of the calibration on the mineral identification and quantitative mapping results. Comparison of the image-map results and image reflectance spectra indicate that the model-based calibrated data can be used with automated mapping techniques to produce accurate maps showing the spatial distribution and abundance of surface mineralogy. This has positive implications for future operational mapping using AVIRIS or similar imaging spectrometer data sets without requiring a priori knowledge.

  1. Quantitative, spectrally-resolved intraoperative fluorescence imaging

    PubMed Central

    Valdés, Pablo A.; Leblond, Frederic; Jacobs, Valerie L.; Wilson, Brian C.; Paulsen, Keith D.; Roberts, David W.

    2012-01-01

    Intraoperative visual fluorescence imaging (vFI) has emerged as a promising aid to surgical guidance, but does not fully exploit the potential of the fluorescent agents that are currently available. Here, we introduce a quantitative fluorescence imaging (qFI) approach that converts spectrally-resolved data into images of absolute fluorophore concentration pixel-by-pixel across the surgical field of view (FOV). The resulting estimates are linear, accurate, and precise relative to true values, and spectral decomposition of multiple fluorophores is also achieved. Experiments with protoporphyrin IX in a glioma rodent model demonstrate in vivo quantitative and spectrally-resolved fluorescence imaging of infiltrating tumor margins for the first time. Moreover, we present images from human surgery which detect residual tumor not evident with state-of-the-art vFI. The wide-field qFI technique has broad implications for intraoperative surgical guidance because it provides near real-time quantitative assessment of multiple fluorescent biomarkers across the operative field. PMID:23152935

  2. Quantitative three-dimensional microtextural analyses of tooth wear as a tool for dietary discrimination in fishes

    PubMed Central

    Purnell, Mark; Seehausen, Ole; Galis, Frietson

    2012-01-01

    Resource polymorphisms and competition for resources are significant factors in speciation. Many examples come from fishes, and cichlids are of particular importance because of their role as model organisms at the interface of ecology, development, genetics and evolution. However, analysis of trophic resource use in fishes can be difficult and time-consuming, and for fossil fish species it is particularly problematic. Here, we present evidence from cichlids that analysis of tooth microwear based on high-resolution (sub-micrometre scale) three-dimensional data and new ISO standards for quantification of surface textures provides a powerful tool for dietary discrimination and investigation of trophic resource exploitation. Our results suggest that three-dimensional approaches to analysis offer significant advantages over two-dimensional operator-scored methods of microwear analysis, including applicability to rough tooth surfaces that lack distinct scratches and pits. Tooth microwear textures develop over a longer period of time than is represented by stomach contents, and analyses based on textures are less prone to biases introduced by opportunistic feeding. They are more sensitive to subtle dietary differences than isotopic analysis. Quantitative textural analysis of tooth microwear has a useful role to play, complementing existing approaches, in trophic analysis of fishes—both extant and extinct. PMID:22491979

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

    PubMed

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

    2018-06-01

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

  4. [Evaluation of intraventricular dyssynchrony by quantitative tissue velocity imaging in rats of post-infarction heart failure].

    PubMed

    Wang, Yan; Zhu, Wenhui; Duan, Xingxing; Zhao, Yongfeng; Liu, Wengang; Li, Ruizhen

    2011-04-01

    To evaluate intraventricular systolic dyssynchrony in rats with post-infarction heart failure by quantitative tissue velocity imaging combining synchronous electrocardiograph. A total of 60 male SD rats were randomly assigned to 3 groups: a 4 week post-operative group and an 8 week post-operation group (each n=25, with anterior descending branch of the left coronary artery ligated), and a sham operation group (n=10, with thoracotomy and open pericardium, but no ligation of the artery). The time to peak systolic velocity of regional myocardial in the rats was measured and the index of the left intraventricular dyssynchrony was calculated. All indexes of the heart function became lower as the heart failure worsened except the left ventricle index in the post-operative groups. All indexes of the dyssynchrony got longer in the post-operative groups (P<0.05), while the changes in the sham operation group were not significantly different (P>0.05). Quantitative tissue velocity imaging combining synchronous electrocardiograph can analyse the intraventricular systolic dyssynchrony accurately.

  5. Knowledge gaps in host-parasite interaction preclude accurate assessment of meat-borne exposure to Toxoplasma gondii.

    PubMed

    Crotta, M; Limon, G; Blake, D P; Guitian, J

    2017-11-16

    Toxoplasma gondii is recognized as a widely prevalent zoonotic parasite worldwide. Although several studies clearly identified meat products as an important source of T. gondii infections in humans, quantitative understanding of the risk posed to humans through the food chain is surprisingly scant. While probabilistic risk assessments for pathogens such as Campylobacter jejuni, Listeria monocytogenes or Escherichia coli have been well established, attempts to quantify the probability of human exposure to T. gondii through consumption of food products of animal origin are at early stages. The biological complexity of the life cycle of T. gondii and limited understanding of several fundamental aspects of the host/parasite interaction, require the adoption of numerous critical assumptions and significant simplifications. In this study, we present a hypothetical quantitative model for the assessment of human exposure to T. gondii through meat products. The model has been conceptualized to capture the dynamics leading to the presence of parasite in meat and, for illustrative purposes, used to estimate the probability of at least one viable cyst occurring in 100g of fresh pork meat in England. Available data, including the results of a serological survey in pigs raised in England were used as a starting point to implement a probabilistic model and assess the fate of the parasite along the food chain. Uncertainty distributions were included to describe and account for the lack of knowledge where necessary. To quantify the impact of the key model inputs, sensitivity and scenario analyses were performed. The overall probability of 100g of a hypothetical edible tissue containing at least 1 cyst was 5.54%. Sensitivity analysis indicated that the variables exerting the greater effect on the output mean were the number of cysts and number of bradyzoites per cyst. Under the best and the worst scenarios, the probability of a single portion of fresh pork meat containing at least 1

  6. An easy and inexpensive method for quantitative analysis of endothelial damage by using vital dye staining and Adobe Photoshop software.

    PubMed

    Saad, Hisham A; Terry, Mark A; Shamie, Neda; Chen, Edwin S; Friend, Daniel F; Holiman, Jeffrey D; Stoeger, Christopher

    2008-08-01

    We developed a simple, practical, and inexpensive technique to analyze areas of endothelial cell loss and/or damage over the entire corneal area after vital dye staining by using a readily available, off-the-shelf, consumer software program, Adobe Photoshop. The purpose of this article is to convey a method of quantifying areas of cell loss and/or damage. Descemet-stripping automated endothelial keratoplasty corneal transplant surgery was performed by using 5 precut corneas on a human cadaver eye. Corneas were removed and stained with trypan blue and alizarin red S and subsequently photographed. Quantitative assessment of endothelial damage was performed by using Adobe Photoshop 7.0 software. The average difference for cell area damage for analyses performed by 1 observer twice was 1.41%. For analyses performed by 2 observers, the average difference was 1.71%. Three masked observers were 100% successful in matching the randomized stained corneas to their randomized processed Adobe images. Vital dye staining of corneal endothelial cells can be combined with Adobe Photoshop software to yield a quantitative assessment of areas of acute endothelial cell loss and/or damage. This described technique holds promise for a more consistent and accurate method to evaluate the surgical trauma to the endothelial cell layer in laboratory models. This method of quantitative analysis can probably be generalized to any area of research that involves areas that are differentiated by color or contrast.

  7. An overview of technical considerations when using quantitative real-time PCR analysis of gene expression in human exercise research

    PubMed Central

    Yan, Xu; Bishop, David J.

    2018-01-01

    Gene expression analysis by quantitative PCR in skeletal muscle is routine in exercise studies. The reproducibility and reliability of the data fundamentally depend on how the experiments are performed and interpreted. Despite the popularity of the assay, there is a considerable variation in experimental protocols and data analyses from different laboratories, and there is a lack of consistency of proper quality control steps throughout the assay. In this study, we present a number of experiments on various steps of quantitative PCR workflow, and demonstrate how to perform a quantitative PCR experiment with human skeletal muscle samples in an exercise study. We also tested some common mistakes in performing qPCR. Interestingly, we found that mishandling of muscle for a short time span (10 mins) before RNA extraction did not affect RNA quality, and isolated total RNA was preserved for up to one week at room temperature. Demonstrated by our data, use of unstable reference genes lead to substantial differences in the final results. Alternatively, cDNA content can be used for data normalisation; however, complete removal of RNA from cDNA samples is essential for obtaining accurate cDNA content. PMID:29746477

  8. Accurate and fast multiple-testing correction in eQTL studies.

    PubMed

    Sul, Jae Hoon; Raj, Towfique; de Jong, Simone; de Bakker, Paul I W; Raychaudhuri, Soumya; Ophoff, Roel A; Stranger, Barbara E; Eskin, Eleazar; Han, Buhm

    2015-06-04

    In studies of expression quantitative trait loci (eQTLs), it is of increasing interest to identify eGenes, the genes whose expression levels are associated with variation at a particular genetic variant. Detecting eGenes is important for follow-up analyses and prioritization because genes are the main entities in biological processes. To detect eGenes, one typically focuses on the genetic variant with the minimum p value among all variants in cis with a gene and corrects for multiple testing to obtain a gene-level p value. For performing multiple-testing correction, a permutation test is widely used. Because of growing sample sizes of eQTL studies, however, the permutation test has become a computational bottleneck in eQTL studies. In this paper, we propose an efficient approach for correcting for multiple testing and assess eGene p values by utilizing a multivariate normal distribution. Our approach properly takes into account the linkage-disequilibrium structure among variants, and its time complexity is independent of sample size. By applying our small-sample correction techniques, our method achieves high accuracy in both small and large studies. We have shown that our method consistently produces extremely accurate p values (accuracy > 98%) for three human eQTL datasets with different sample sizes and SNP densities: the Genotype-Tissue Expression pilot dataset, the multi-region brain dataset, and the HapMap 3 dataset. Copyright © 2015 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

  9. Transcriptomic and Quantitative Proteomic Analyses Provide Insights Into the Phagocytic Killing of Hemocytes in the Oyster Crassostrea gigas

    PubMed Central

    Jiang, Shuai; Qiu, Limei; Wang, Lingling; Jia, Zhihao; Lv, Zhao; Wang, Mengqiang; Liu, Conghui; Xu, Jiachao; Song, Linsheng

    2018-01-01

    As invertebrates lack an adaptive immune system, they depend to a large extent on their innate immune system to recognize and clear invading pathogens. Although phagocytes play pivotal roles in invertebrate innate immunity, the molecular mechanisms underlying this killing remain unclear. Cells of this type from the Pacific oyster Crassostrea gigas were classified efficiently in this study via fluorescence-activated cell sorting (FACS) based on their phagocytosis of FITC-labeled latex beads. Transcriptomic and quantitative proteomic analyses revealed a series of differentially expressed genes (DEGs) and proteins present in phagocytes; of the 352 significantly high expressed proteins identified here within the phagocyte proteome, 262 corresponding genes were similarly high expressed in the transcriptome, while 140 of 205 significantly low expressed proteins within the proteome were transcriptionally low expressed. A pathway crosstalk network analysis of these significantly high expressed proteins revealed that phagocytes were highly activated in a number of antimicrobial-related biological processes, including oxidation–reduction and lysosomal proteolysis processes. A number of DEGs, including oxidase, lysosomal protease, and immune receptors, were also validated in this study using quantitative PCR, while seven lysosomal cysteine proteases, referred to as cathepsin Ls, were significantly high expressed in phagocytes. Results show that the expression level of cathepsin L protein in phagocytes [mean fluorescence intensity (MFI): 327 ± 51] was significantly higher (p < 0.01) than that in non-phagocytic hemocytes (MFI: 83 ± 26), while the cathepsin L protein was colocalized with the phagocytosed Vibrio splendidus in oyster hemocytes during this process. The results of this study collectively suggest that oyster phagocytes possess both potent oxidative killing and microbial disintegration capacities; these findings provide important insights into hemocyte

  10. Tandem mass spectrometry measurement of the collision products of carbamate anions derived from CO2 capture sorbents: paving the way for accurate quantitation.

    PubMed

    Jackson, Phil; Fisher, Keith J; Attalla, Moetaz Ibrahim

    2011-08-01

    The reaction between CO(2) and aqueous amines to produce a charged carbamate product plays a crucial role in post-combustion capture chemistry when primary and secondary amines are used. In this paper, we report the low energy negative-ion CID results for several anionic carbamates derived from primary and secondary amines commonly used as post-combustion capture solvents. The study was performed using the modern equivalent of a triple quadrupole instrument equipped with a T-wave collision cell. Deuterium labeling of 2-aminoethanol (1,1,2,2,-d(4)-2-aminoethanol) and computations at the M06-2X/6-311++G(d,p) level were used to confirm the identity of the fragmentation products for 2-hydroxyethylcarbamate (derived from 2-aminoethanol), in particular the ions CN(-), NCO(-) and facile neutral losses of CO(2) and water; there is precedent for the latter in condensed phase isocyanate chemistry. The fragmentations of 2-hydroxyethylcarbamate were generalized for carbamate anions derived from other capture amines, including ethylenediamine, diethanolamine, and piperazine. We also report unequivocal evidence for the existence of carbamate anions derived from sterically hindered amines (Tris(2-hydroxymethyl)aminomethane and 2-methyl-2-aminopropanol). For the suite of carbamates investigated, diagnostic losses include the decarboxylation product (-CO(2), 44 mass units), loss of 46 mass units and the fragments NCO(-) (m/z 42) and CN(-) (m/z 26). We also report low energy CID results for the dicarbamate dianion ((-)O(2)CNHC(2)H(4)NHCO(2)(-)) commonly encountered in CO(2) capture solution utilizing ethylenediamine. Finally, we demonstrate a promising ion chromatography-MS based procedure for the separation and quantitation of aqueous anionic carbamates, which is based on the reported CID findings. The availability of accurate quantitation methods for ionic CO(2) capture products could lead to dynamic operational tuning of CO(2) capture-plants and, thus, cost-savings via real

  11. A field instrument for quantitative determination of beryllium by activation analysis

    USGS Publications Warehouse

    Vaughn, William W.; Wilson, E.E.; Ohm, J.M.

    1960-01-01

    A low-cost instrument has been developed for quantitative determinations of beryllium in the field by activation analysis. The instrument makes use of the gamma-neutron reaction between gammas emitted by an artificially radioactive source (Sb124) and beryllium as it occurs in nature. The instrument and power source are mounted in a panel-type vehicle. Samples are prepared by hand-crushing the rock to approximately ?-inch mesh size and smaller. Sample volumes are kept constant by means of a standard measuring cup. Instrument calibration, made by using standards of known BeO content, indicates the analyses are reproducible and accurate to within ? 0.25 percent BeO in the range from 1 to 20 percent BeO with a sample counting time of 5 minutes. Sensitivity of the instrument maybe increased somewhat by increasing the source size, the sample size, or by enlarging the cross-sectional area of the neutron-sensitive phosphor normal to the neutron flux.

  12. A bottom-up approach in estimating the measurement uncertainty and other important considerations for quantitative analyses in drug testing for horses.

    PubMed

    Leung, Gary N W; Ho, Emmie N M; Kwok, W Him; Leung, David K K; Tang, Francis P W; Wan, Terence S M; Wong, April S Y; Wong, Colton H F; Wong, Jenny K Y; Yu, Nola H

    2007-09-07

    derive the combined standard uncertainty. Finally, an expanded uncertainty is calculated at 99% one-tailed confidence level by multiplying the standard uncertainty with an appropriate coverage factor (k). A sample is considered positive if the determined concentration of the threshold substance exceeds its threshold by the expanded uncertainty. In addition, other important considerations, which can have a significant impact on quantitative analyses, will be presented.

  13. Towards in vivo focal cortical dysplasia phenotyping using quantitative MRI.

    PubMed

    Adler, Sophie; Lorio, Sara; Jacques, Thomas S; Benova, Barbora; Gunny, Roxana; Cross, J Helen; Baldeweg, Torsten; Carmichael, David W

    2017-01-01

    Focal cortical dysplasias (FCDs) are a range of malformations of cortical development each with specific histopathological features. Conventional radiological assessment of standard structural MRI is useful for the localization of lesions but is unable to accurately predict the histopathological features. Quantitative MRI offers the possibility to probe tissue biophysical properties in vivo and may bridge the gap between radiological assessment and ex-vivo histology. This review will cover histological, genetic and radiological features of FCD following the ILAE classification and will explain how quantitative voxel- and surface-based techniques can characterise these features. We will provide an overview of the quantitative MRI measures available, their link with biophysical properties and finally the potential application of quantitative MRI to the problem of FCD subtyping. Future research linking quantitative MRI to FCD histological properties should improve clinical protocols, allow better characterisation of lesions in vivo and tailored surgical planning to the individual.

  14. Quantitative proteomics in biological research.

    PubMed

    Wilm, Matthias

    2009-10-01

    Proteomics has enabled the direct investigation of biological material, at first through the analysis of individual proteins, then of lysates from cell cultures, and finally of extracts from tissues and biopsies from entire organisms. Its latest manifestation - quantitative proteomics - allows deeper insight into biological systems. This article reviews the different methods used to extract quantitative information from mass spectra. It follows the technical developments aimed toward global proteomics, the attempt to characterize every expressed protein in a cell by at least one peptide. When applications of the technology are discussed, the focus is placed on yeast biology. In particular, differential quantitative proteomics, the comparison between an experiment and its control, is very discriminating for proteins involved in the process being studied. When trying to understand biological processes on a molecular level, differential quantitative proteomics tends to give a clearer picture than global transcription analyses. As a result, MS has become an even more indispensable tool for biochemically motivated biological research.

  15. Quantitative interpretation of the magnetic susceptibility frequency dependence

    NASA Astrophysics Data System (ADS)

    Ustra, Andrea; Mendonça, Carlos A.; Leite, Aruã; Jovane, Luigi; Trindade, Ricardo I. F.

    2018-05-01

    Low-field mass-specific magnetic susceptibility (MS) measurements using multifrequency alternating fields are commonly used to evaluate concentration of ferrimagnetic particles in the transition of superparamagnetic (SP) to stable single domain (SSD). In classical palaeomagnetic analyses, this measurement serves as a preliminary assessment of rock samples providing rapid, non-destructive, economical and easy information of magnetic properties. The SP-SSD transition is relevant in environmental studies because it has been associated with several geological and biogeochemical processes affecting magnetic mineralogy. MS is a complex function of mineral-type and grain-size distribution, as well as measuring parameters such as external field magnitude and frequency. In this work, we propose a new technique to obtain quantitative information on grain-size variations of magnetic particles in the SP-SSD transition by inverting frequency-dependent susceptibility. We introduce a descriptive parameter named as `limiting frequency effect' that provides an accurate estimation of MS loss with frequency. Numerical simulations show the methodology capability in providing data fitting and model parameters in many practical situations. Real-data applications with magnetite nanoparticles and core samples from sediments of Poggio le Guaine section of Umbria-Marche Basin (Italy) provide additional information not clearly recognized when interpreting cruder MS data. Caution is needed when interpreting frequency dependence in terms of single relaxation processes, which are not universally applicable and depend upon the nature of magnetic mineral in the material. Nevertheless, the proposed technique is a promising tool for SP-SSD content analyses.

  16. Using Inequality Measures to Incorporate Environmental Justice into Regulatory Analyses

    PubMed Central

    Harper, Sam; Ruder, Eric; Roman, Henry A.; Geggel, Amelia; Nweke, Onyemaechi; Payne-Sturges, Devon; Levy, Jonathan I.

    2013-01-01

    Formally evaluating how specific policy measures influence environmental justice is challenging, especially in the context of regulatory analyses in which quantitative comparisons are the norm. However, there is a large literature on developing and applying quantitative measures of health inequality in other settings, and these measures may be applicable to environmental regulatory analyses. In this paper, we provide information to assist policy decision makers in determining the viability of using measures of health inequality in the context of environmental regulatory analyses. We conclude that quantification of the distribution of inequalities in health outcomes across social groups of concern, considering both within-group and between-group comparisons, would be consistent with both the structure of regulatory analysis and the core definition of environmental justice. Appropriate application of inequality indicators requires thorough characterization of the baseline distribution of exposures and risks, leveraging data generally available within regulatory analyses. Multiple inequality indicators may be applicable to regulatory analyses, and the choice among indicators should be based on explicit value judgments regarding the dimensions of environmental justice of greatest interest. PMID:23999551

  17. Quantitative single-photon emission computed tomography/computed tomography for technetium pertechnetate thyroid uptake measurement

    PubMed Central

    Lee, Hyunjong; Kim, Ji Hyun; Kang, Yeon-koo; Moon, Jae Hoon; So, Young; Lee, Won Woo

    2016-01-01

    Abstract Objectives: Technetium pertechnetate (99mTcO4) is a radioactive tracer used to assess thyroid function by thyroid uptake system (TUS). However, the TUS often fails to deliver accurate measurements of the percent of thyroid uptake (%thyroid uptake) of 99mTcO4. Here, we investigated the usefulness of quantitative single-photon emission computed tomography/computed tomography (SPECT/CT) after injection of 99mTcO4 in detecting thyroid function abnormalities. Materials and methods: We retrospectively reviewed data from 50 patients (male:female = 15:35; age, 46.2 ± 16.3 years; 17 Graves disease, 13 thyroiditis, and 20 euthyroid). All patients underwent 99mTcO4 quantitative SPECT/CT (185 MBq = 5 mCi), which yielded %thyroid uptake and standardized uptake value (SUV). Twenty-one (10 Graves disease and 11 thyroiditis) of the 50 patients also underwent conventional %thyroid uptake measurements using a TUS. Results: Quantitative SPECT/CT parameters (%thyroid uptake, SUVmean, and SUVmax) were the highest in Graves disease, second highest in euthyroid, and lowest in thyroiditis (P < 0.0001, Kruskal–Wallis test). TUS significantly overestimated the %thyroid uptake compared with SPECT/CT (P < 0.0001, paired t test) because other 99mTcO4 sources in addition to thyroid, such as salivary glands and saliva, contributed to the %thyroid uptake result by TUS, whereas %thyroid uptake, SUVmean and SUVmax from the SPECT/CT were associated with the functional status of thyroid. Conclusions: Quantitative SPECT/CT is more accurate than conventional TUS for measuring 99mTcO4 %thyroid uptake. Quantitative measurements using SPECT/CT may facilitate more accurate assessment of thyroid tracer uptake. PMID:27399139

  18. Analyses of Mobilization Manpower Supply and Demand.

    DTIC Science & Technology

    1982-03-01

    7AD-AI30 148 ANALYSES OF MOBIL ZATION MANPOWER SUPPLY AND DEMAND U) l1 . ADMINISTRATIVE SCIENCES CORP SPRINOFIELD VA BREAU EAL MAR82 ASCR134...79-C-0527 for use in identifying and quantifying issues in the CPAM process, and to employ the model for selected quantitative ard qualitative analyses...nurses and corpsmen) to operate on a Commander FX Microcomputer, to be used by 2 the Bureau of Medicine and Surgery to develop inputs for Navy-wide

  19. An analytic model for accurate spring constant calibration of rectangular atomic force microscope cantilevers.

    PubMed

    Li, Rui; Ye, Hongfei; Zhang, Weisheng; Ma, Guojun; Su, Yewang

    2015-10-29

    Spring constant calibration of the atomic force microscope (AFM) cantilever is of fundamental importance for quantifying the force between the AFM cantilever tip and the sample. The calibration within the framework of thin plate theory undoubtedly has a higher accuracy and broader scope than that within the well-established beam theory. However, thin plate theory-based accurate analytic determination of the constant has been perceived as an extremely difficult issue. In this paper, we implement the thin plate theory-based analytic modeling for the static behavior of rectangular AFM cantilevers, which reveals that the three-dimensional effect and Poisson effect play important roles in accurate determination of the spring constants. A quantitative scaling law is found that the normalized spring constant depends only on the Poisson's ratio, normalized dimension and normalized load coordinate. Both the literature and our refined finite element model validate the present results. The developed model is expected to serve as the benchmark for accurate calibration of rectangular AFM cantilevers.

  20. Quantitative self-assembly prediction yields targeted nanomedicines

    NASA Astrophysics Data System (ADS)

    Shamay, Yosi; Shah, Janki; Işık, Mehtap; Mizrachi, Aviram; Leibold, Josef; Tschaharganeh, Darjus F.; Roxbury, Daniel; Budhathoki-Uprety, Januka; Nawaly, Karla; Sugarman, James L.; Baut, Emily; Neiman, Michelle R.; Dacek, Megan; Ganesh, Kripa S.; Johnson, Darren C.; Sridharan, Ramya; Chu, Karen L.; Rajasekhar, Vinagolu K.; Lowe, Scott W.; Chodera, John D.; Heller, Daniel A.

    2018-02-01

    Development of targeted nanoparticle drug carriers often requires complex synthetic schemes involving both supramolecular self-assembly and chemical modification. These processes are generally difficult to predict, execute, and control. We describe herein a targeted drug delivery system that is accurately and quantitatively predicted to self-assemble into nanoparticles based on the molecular structures of precursor molecules, which are the drugs themselves. The drugs assemble with the aid of sulfated indocyanines into particles with ultrahigh drug loadings of up to 90%. We devised quantitative structure-nanoparticle assembly prediction (QSNAP) models to identify and validate electrotopological molecular descriptors as highly predictive indicators of nano-assembly and nanoparticle size. The resulting nanoparticles selectively targeted kinase inhibitors to caveolin-1-expressing human colon cancer and autochthonous liver cancer models to yield striking therapeutic effects while avoiding pERK inhibition in healthy skin. This finding enables the computational design of nanomedicines based on quantitative models for drug payload selection.

  1. Quantitative fluorescence tomography using a trimodality system: in vivo validation

    PubMed Central

    Lin, Yuting; Barber, William C.; Iwanczyk, Jan S.; Roeck, Werner W.; Nalcioglu, Orhan; Gulsen, Gultekin

    2010-01-01

    A fully integrated trimodality fluorescence, diffuse optical, and x-ray computed tomography (FT∕DOT∕XCT) system for small animal imaging is reported in this work. The main purpose of this system is to obtain quantitatively accurate fluorescence concentration images using a multimodality approach. XCT offers anatomical information, while DOT provides the necessary background optical property map to improve FT image accuracy. The quantitative accuracy of this trimodality system is demonstrated in vivo. In particular, we show that a 2-mm-diam fluorescence inclusion located 8 mm deep in a nude mouse can only be localized when functional a priori information from DOT is available. However, the error in the recovered fluorophore concentration is nearly 87%. On the other hand, the fluorophore concentration can be accurately recovered within 2% error when both DOT functional and XCT structural a priori information are utilized together to guide and constrain the FT reconstruction algorithm. PMID:20799770

  2. Accurate Phylogenetic Tree Reconstruction from Quartets: A Heuristic Approach

    PubMed Central

    Reaz, Rezwana; Bayzid, Md. Shamsuzzoha; Rahman, M. Sohel

    2014-01-01

    Supertree methods construct trees on a set of taxa (species) combining many smaller trees on the overlapping subsets of the entire set of taxa. A ‘quartet’ is an unrooted tree over taxa, hence the quartet-based supertree methods combine many -taxon unrooted trees into a single and coherent tree over the complete set of taxa. Quartet-based phylogeny reconstruction methods have been receiving considerable attentions in the recent years. An accurate and efficient quartet-based method might be competitive with the current best phylogenetic tree reconstruction methods (such as maximum likelihood or Bayesian MCMC analyses), without being as computationally intensive. In this paper, we present a novel and highly accurate quartet-based phylogenetic tree reconstruction method. We performed an extensive experimental study to evaluate the accuracy and scalability of our approach on both simulated and biological datasets. PMID:25117474

  3. Quantitative Characterisation and Analysis of Siliciclastic Fluvial Depositional Systems Using 3D Digital Outcrop Models

    NASA Astrophysics Data System (ADS)

    Burnham, Brian Scott

    Outcrop analogue studies of fluvial sedimentary systems are often undertaken to identify spatial and temporal characteristics (e.g. stacking patterns, lateral continuity, lithofacies proportions). However, the lateral extent typically exceeds that of the exposure, and/or the true width and thickness are not apparent. Accurate characterisation of fluvial sand bodies is integral for accurate identification and subsequent modelling of aquifer and hydrocarbon reservoir architecture. The studies presented in this thesis utilise techniques that integrate lidar, highresolution photography and differential geospatial measurements, to create accurate three-dimensional (3D) digital outcrop models (DOMs) of continuous 3D and laterally extensive 2D outcrop exposures. The sedimentary architecture of outcrops in the medial portion of a large Distributive Fluvial System (DFS) (Huesca fluvial fan) in the Ebro Basin, north-east Spain, and in the fluvio-deltaic succession of the Breathitt Group in the eastern Appalachian Basin, USA, are evaluated using traditional sedimentological and digital outcrop analytical techniques. The major sand bodies in the study areas are quantitatively analysed to accurately characterise spatial and temporal changes in sand body architecture, from two different outcrop exposure types and scales. Several stochastic reservoir simulations were created to approximate fluvial sand body lithological component and connectivity within the medial portion of the Huesca DFS. Results demonstrate a workflow and current methodology adaptation of digital outcrop techniques required for each study to approximate true geobody widths, thickness and characterise architectural patterns (internal and external) of major fluvial sand bodies interpreted as products of DFSs in the Huesca fluvial fan, and both palaeovalleys and progradational DFSs in the Pikeville and Hyden Formations in the Breathitt Group. The results suggest key geostatistical metrics, which are translatable

  4. Fluvial drainage networks: the fractal approach as an improvement of quantitative geomorphic analyses

    NASA Astrophysics Data System (ADS)

    Melelli, Laura; Liucci, Luisa; Vergari, Francesca; Ciccacci, Sirio; Del Monte, Maurizio

    2014-05-01

    Drainage basins are primary landscape units for geomorphological investigations. Both hillslopes and river drainage system are fundamental components in drainage basins analysis. As other geomorphological systems, also the drainage basins aim to an equilibrium condition where the sequence of erosion, transport and sedimentation approach to a condition of minimum energy effort. This state is revealed by a typical geometry of landforms and of drainage net. Several morphometric indexes can measure how much a drainage basin is far from the theoretical equilibrium configuration, revealing possible external disarray. In active tectonic areas, the drainage basins have a primary importance in order to highlight style, amount and rate of tectonic impulses, and morphometric indexes allow to estimate the tectonic activity classes of different sectors in a study area. Moreover, drainage rivers are characterized by a self-similarity structure; this promotes the use of fractals theory to investigate the system. In this study, fractals techniques are employed together with quantitative geomorphological analysis to study the Upper Tiber Valley (UTV), a tectonic intermontane basin located in northern Apennines (Umbria, central Italy). The area is the result of different tectonic phases. From Late Pliocene until present time the UTV is strongly controlled by a regional uplift and by an extensional phase with different sets of normal faults playing a fundamental role in basin morphology. Thirty-four basins are taken into account for the quantitative analysis, twenty on the left side of the basin, the others on the right side. Using fractals dimension of drainage networks, Horton's laws results, concavity and steepness indexes, and hypsometric curves, this study aims to obtain an evolutionary model of the UTV, where the uplift is compared to local subsidence induced by normal fault activity. The results highlight a well defined difference between western and eastern tributary basins

  5. Quantifying Forest Soil Physical Variables Potentially Important for Site Growth Analyses

    Treesearch

    John S. Kush; Douglas G. Pitt; Phillip J. Craul; William D. Boyer

    2004-01-01

    Accurate mean plot values of forest soil factors are required for use as independent variables in site-growth analyses. Adequate accuracy is often difficult to attain because soils are inherently widely variable. Estimates of the variability of appropriate soil factors influencing growth can be used to determine the sampling intensity required to secure accurate mean...

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

    NASA Astrophysics Data System (ADS)

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

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

  7. The accurate assessment of small-angle X-ray scattering data

    DOE PAGES

    Grant, Thomas D.; Luft, Joseph R.; Carter, Lester G.; ...

    2015-01-23

    Small-angle X-ray scattering (SAXS) has grown in popularity in recent times with the advent of bright synchrotron X-ray sources, powerful computational resources and algorithms enabling the calculation of increasingly complex models. However, the lack of standardized data-quality metrics presents difficulties for the growing user community in accurately assessing the quality of experimental SAXS data. Here, a series of metrics to quantitatively describe SAXS data in an objective manner using statistical evaluations are defined. These metrics are applied to identify the effects of radiation damage, concentration dependence and interparticle interactions on SAXS data from a set of 27 previously described targetsmore » for which high-resolution structures have been determined via X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. Studies show that these metrics are sufficient to characterize SAXS data quality on a small sample set with statistical rigor and sensitivity similar to or better than manual analysis. The development of data-quality analysis strategies such as these initial efforts is needed to enable the accurate and unbiased assessment of SAXS data quality.« less

  8. USING MICROSOFT OFFICE EXCEL® 2007 TO CONDUCT GENERALIZED MATCHING ANALYSES

    PubMed Central

    Reed, Derek D

    2009-01-01

    The generalized matching equation is a robust and empirically supported means of analyzing relations between reinforcement and behavior. Unfortunately, no simple task analysis is available to behavior analysts interested in using the matching equation to evaluate data in clinical or applied settings. This technical article presents a task analysis for the use of Microsoft Excel to analyze and plot the generalized matching equation. Using a data-based case example and a step-by-step guide for completing the analysis, these instructions are intended to promote the use of quantitative analyses by researchers with little to no experience in quantitative analyses or the matching law. PMID:20514196

  9. Using Microsoft Office Excel 2007 to conduct generalized matching analyses.

    PubMed

    Reed, Derek D

    2009-01-01

    The generalized matching equation is a robust and empirically supported means of analyzing relations between reinforcement and behavior. Unfortunately, no simple task analysis is available to behavior analysts interested in using the matching equation to evaluate data in clinical or applied settings. This technical article presents a task analysis for the use of Microsoft Excel to analyze and plot the generalized matching equation. Using a data-based case example and a step-by-step guide for completing the analysis, these instructions are intended to promote the use of quantitative analyses by researchers with little to no experience in quantitative analyses or the matching law.

  10. Genomic Quantitative Genetics to Study Evolution in the Wild.

    PubMed

    Gienapp, Phillip; Fior, Simone; Guillaume, Frédéric; Lasky, Jesse R; Sork, Victoria L; Csilléry, Katalin

    2017-12-01

    Quantitative genetic theory provides a means of estimating the evolutionary potential of natural populations. However, this approach was previously only feasible in systems where the genetic relatedness between individuals could be inferred from pedigrees or experimental crosses. The genomic revolution opened up the possibility of obtaining the realized proportion of genome shared among individuals in natural populations of virtually any species, which could promise (more) accurate estimates of quantitative genetic parameters in virtually any species. Such a 'genomic' quantitative genetics approach relies on fewer assumptions, offers a greater methodological flexibility, and is thus expected to greatly enhance our understanding of evolution in natural populations, for example, in the context of adaptation to environmental change, eco-evolutionary dynamics, and biodiversity conservation. Copyright © 2017 Elsevier Ltd. All rights reserved.

  11. Accuracy of quantitative visual soil assessment

    NASA Astrophysics Data System (ADS)

    van Leeuwen, Maricke; Heuvelink, Gerard; Stoorvogel, Jetse; Wallinga, Jakob; de Boer, Imke; van Dam, Jos; van Essen, Everhard; Moolenaar, Simon; Verhoeven, Frank; Stoof, Cathelijne

    2016-04-01

    farmers carried out quantitative visual observations all independently from each other. All observers assessed five sites, having a sand, peat or clay soil. For almost all quantitative visual observations the spread of observed values was low (coefficient of variation < 1.0), except for the number of biopores and gley mottles. Furthermore, farmers' observed mean values were significantly higher than soil scientists' mean values, for soil structure, amount of gley mottles and compaction. This study showed that VSA could be a valuable tool to assess soil quality. Subjectivity, due to the background of the observer, might influence the outcome of visual assessment of some soil properties. In countries where soil analyses can easily be carried out, VSA might be a good replenishment to available soil chemical analyses, and in countries where it is not feasible to carry out soil analyses, VSA might be a good start to assess soil quality.

  12. Investigating the Validity of Two Widely Used Quantitative Text Tools

    ERIC Educational Resources Information Center

    Cunningham, James W.; Hiebert, Elfrieda H.; Mesmer, Heidi Anne

    2018-01-01

    In recent years, readability formulas have gained new prominence as a basis for selecting texts for learning and assessment. Variables that quantitative tools count (e.g., word frequency, sentence length) provide valid measures of text complexity insofar as they accurately predict representative and high-quality criteria. The longstanding…

  13. Single-Cell Based Quantitative Assay of Chromosome Transmission Fidelity

    PubMed Central

    Zhu, Jin; Heinecke, Dominic; Mulla, Wahid A.; Bradford, William D.; Rubinstein, Boris; Box, Andrew; Haug, Jeffrey S.; Li, Rong

    2015-01-01

    Errors in mitosis are a primary cause of chromosome instability (CIN), generating aneuploid progeny cells. Whereas a variety of factors can influence CIN, under most conditions mitotic errors are rare events that have been difficult to measure accurately. Here we report a green fluorescent protein−based quantitative chromosome transmission fidelity (qCTF) assay in budding yeast that allows sensitive and quantitative detection of CIN and can be easily adapted to high-throughput analysis. Using the qCTF assay, we performed genome-wide quantitative profiling of genes that affect CIN in a dosage-dependent manner and identified genes that elevate CIN when either increased (icCIN) or decreased in copy number (dcCIN). Unexpectedly, qCTF screening also revealed genes whose change in copy number quantitatively suppress CIN, suggesting that the basal error rate of the wild-type genome is not minimized, but rather, may have evolved toward an optimal level that balances both stability and low-level karyotype variation for evolutionary adaptation. PMID:25823586

  14. Quantitative Research Methods in Chaos and Complexity: From Probability to Post Hoc Regression Analyses

    ERIC Educational Resources Information Center

    Gilstrap, Donald L.

    2013-01-01

    In addition to qualitative methods presented in chaos and complexity theories in educational research, this article addresses quantitative methods that may show potential for future research studies. Although much in the social and behavioral sciences literature has focused on computer simulations, this article explores current chaos and…

  15. [Clinical research XXIII. From clinical judgment to meta-analyses].

    PubMed

    Rivas-Ruiz, Rodolfo; Castelán-Martínez, Osvaldo D; Pérez-Rodríguez, Marcela; Palacios-Cruz, Lino; Noyola-Castillo, Maura E; Talavera, Juan O

    2014-01-01

    Systematic reviews (SR) are studies made in order to ask clinical questions based on original articles. Meta-analysis (MTA) is the mathematical analysis of SR. These analyses are divided in two groups, those which evaluate the measured results of quantitative variables (for example, the body mass index -BMI-) and those which evaluate qualitative variables (for example, if a patient is alive or dead, or if he is healing or not). Quantitative variables generally use the mean difference analysis and qualitative variables can be performed using several calculations: odds ratio (OR), relative risk (RR), absolute risk reduction (ARR) and hazard ratio (HR). These analyses are represented through forest plots which allow the evaluation of each individual study, as well as the heterogeneity between studies and the overall effect of the intervention. These analyses are mainly based on Student's t test and chi-squared. To take appropriate decisions based on the MTA, it is important to understand the characteristics of statistical methods in order to avoid misinterpretations.

  16. Accurate and efficient spin integration for particle accelerators

    DOE PAGES

    Abell, Dan T.; Meiser, Dominic; Ranjbar, Vahid H.; ...

    2015-02-01

    Accurate spin tracking is a valuable tool for understanding spin dynamics in particle accelerators and can help improve the performance of an accelerator. In this paper, we present a detailed discussion of the integrators in the spin tracking code GPUSPINTRACK. We have implemented orbital integrators based on drift-kick, bend-kick, and matrix-kick splits. On top of the orbital integrators, we have implemented various integrators for the spin motion. These integrators use quaternions and Romberg quadratures to accelerate both the computation and the convergence of spin rotations.We evaluate their performance and accuracy in quantitative detail for individual elements as well as formore » the entire RHIC lattice. We exploit the inherently data-parallel nature of spin tracking to accelerate our algorithms on graphics processing units.« less

  17. Impact of vaccine herd-protection effects in cost-effectiveness analyses of childhood vaccinations. A quantitative comparative analysis.

    PubMed

    Holubar, Marisa; Stavroulakis, Maria Christina; Maldonado, Yvonne; Ioannidis, John P A; Contopoulos-Ioannidis, Despina

    2017-01-01

    Inclusion of vaccine herd-protection effects in cost-effectiveness analyses (CEAs) can impact the CEAs-conclusions. However, empirical epidemiologic data on the size of herd-protection effects from original studies are limited. We performed a quantitative comparative analysis of the impact of herd-protection effects in CEAs for four childhood vaccinations (pneumococcal, meningococcal, rotavirus and influenza). We considered CEAs reporting incremental-cost-effectiveness-ratios (ICERs) (per quality-adjusted-life-years [QALY] gained; per life-years [LY] gained or per disability-adjusted-life-years [DALY] avoided), both with and without herd protection, while keeping all other model parameters stable. We calculated the size of the ICER-differences without vs with-herd-protection and estimated how often inclusion of herd-protection led to crossing of the cost-effectiveness threshold (of an assumed societal-willingness-to-pay) of $50,000 for more-developed countries or X3GDP/capita (WHO-threshold) for less-developed countries. We identified 35 CEA studies (20 pneumococcal, 4 meningococcal, 8 rotavirus and 3 influenza vaccines) with 99 ICER-analyses (55 per-QALY, 27 per-LY and 17 per-DALY). The median ICER-absolute differences per QALY, LY and DALY (without minus with herd-protection) were $15,620 (IQR: $877 to $48,376); $54,871 (IQR: $787 to $115,026) and $49 (IQR: $15 to $1,636) respectively. When the target-vaccination strategy was not cost-saving without herd-protection, inclusion of herd-protection always resulted in more favorable results. In CEAs that had ICERs above the cost-effectiveness threshold without herd-protection, inclusion of herd-protection led to crossing of that threshold in 45% of the cases. This impacted only CEAs for more developed countries, as all but one CEAs for less developed countries had ICERs below the WHO-cost-effectiveness threshold even without herd-protection. In several analyses, recommendation for the adoption of the target

  18. Impact of vaccine herd-protection effects in cost-effectiveness analyses of childhood vaccinations. A quantitative comparative analysis

    PubMed Central

    Maldonado, Yvonne; Ioannidis, John P. A.; Contopoulos-Ioannidis, Despina

    2017-01-01

    Background Inclusion of vaccine herd-protection effects in cost-effectiveness analyses (CEAs) can impact the CEAs-conclusions. However, empirical epidemiologic data on the size of herd-protection effects from original studies are limited. Methods We performed a quantitative comparative analysis of the impact of herd-protection effects in CEAs for four childhood vaccinations (pneumococcal, meningococcal, rotavirus and influenza). We considered CEAs reporting incremental-cost-effectiveness-ratios (ICERs) (per quality-adjusted-life-years [QALY] gained; per life-years [LY] gained or per disability-adjusted-life-years [DALY] avoided), both with and without herd protection, while keeping all other model parameters stable. We calculated the size of the ICER-differences without vs with-herd-protection and estimated how often inclusion of herd-protection led to crossing of the cost-effectiveness threshold (of an assumed societal-willingness-to-pay) of $50,000 for more-developed countries or X3GDP/capita (WHO-threshold) for less-developed countries. Results We identified 35 CEA studies (20 pneumococcal, 4 meningococcal, 8 rotavirus and 3 influenza vaccines) with 99 ICER-analyses (55 per-QALY, 27 per-LY and 17 per-DALY). The median ICER-absolute differences per QALY, LY and DALY (without minus with herd-protection) were $15,620 (IQR: $877 to $48,376); $54,871 (IQR: $787 to $115,026) and $49 (IQR: $15 to $1,636) respectively. When the target-vaccination strategy was not cost-saving without herd-protection, inclusion of herd-protection always resulted in more favorable results. In CEAs that had ICERs above the cost-effectiveness threshold without herd-protection, inclusion of herd-protection led to crossing of that threshold in 45% of the cases. This impacted only CEAs for more developed countries, as all but one CEAs for less developed countries had ICERs below the WHO-cost-effectiveness threshold even without herd-protection. In several analyses, recommendation for the

  19. Quantitative solid-state 13C nuclear magnetic resonance spectrometric analyses of wood xylen: effect of increasing carbohydrate content

    USGS Publications Warehouse

    Bates, A.L.; Hatcher, P.G.

    1992-01-01

    Isolated lignin with a low carbohydrate content was spiked with increasing amounts of alpha-cellulose, and then analysed by solid-state 13C nuclear magnetic resonance (NMR) using cross-polarization with magic angle spinning (CPMAS) and dipolar dephasing methods in order to assess the quantitative reliability of CPMAS measurement of carbohydrate content and to determine how increasingly intense resonances for carbohydrate carbons affect calculations of the degree of lignin's aromatic ring substitution and methoxyl carbon content. Comparisons were made of the carbohydrate content calculated by NMR with carbohydrate concentrations obtained by phenol-sulfuric acid assay and by the calculation from the known amounts of cellulose added. The NMR methods used in this study yield overestimates for carbohydrate carbons due to resonance area overlap from the aliphatic side chain carbons of lignin. When corrections are made for these overlapping resonance areas, the NMR results agree very well with results obtained by other methods. Neither the calculated methoxyl carbon content nor the degree of aromatic ring substitution in lignin, both calculated from dipolar dephasing spectra, change with cellulose content. Likewise, lignin methoxyl content does not correlate with cellulose abundance when measured by integration of CPMAS spectra. ?? 1992.

  20. Quantitative characterization of surface topography using spectral analysis

    NASA Astrophysics Data System (ADS)

    Jacobs, Tevis D. B.; Junge, Till; Pastewka, Lars

    2017-03-01

    Roughness determines many functional properties of surfaces, such as adhesion, friction, and (thermal and electrical) contact conductance. Recent analytical models and simulations enable quantitative prediction of these properties from knowledge of the power spectral density (PSD) of the surface topography. The utility of the PSD is that it contains statistical information that is unbiased by the particular scan size and pixel resolution chosen by the researcher. In this article, we first review the mathematical definition of the PSD, including the one- and two-dimensional cases, and common variations of each. We then discuss strategies for reconstructing an accurate PSD of a surface using topography measurements at different size scales. Finally, we discuss detecting and mitigating artifacts at the smallest scales, and computing upper/lower bounds on functional properties obtained from models. We accompany our discussion with virtual measurements on computer-generated surfaces. This discussion summarizes how to analyze topography measurements to reconstruct a reliable PSD. Analytical models demonstrate the potential for tuning functional properties by rationally tailoring surface topography—however, this potential can only be achieved through the accurate, quantitative reconstruction of the PSDs of real-world surfaces.

  1. Utility of high-resolution accurate MS to eliminate interferences in the bioanalysis of ribavirin and its phosphate metabolites.

    PubMed

    Wei, Cong; Grace, James E; Zvyaga, Tatyana A; Drexler, Dieter M

    2012-08-01

    The polar nucleoside drug ribavirin (RBV) combined with IFN-α is a front-line treatment for chronic hepatitis C virus infection. RBV acts as a prodrug and exerts its broad antiviral activity primarily through its active phosphorylated metabolite ribavirin 5´-triphosphate (RTP), and also possibly through ribavirin 5´-monophosphate (RMP). To study RBV transport, diffusion, metabolic clearance and its impact on drug-metabolizing enzymes, a LC-MS method is needed to simultaneously quantify RBV and its phosphorylated metabolites (RTP, ribavirin 5´-diphosphate and RMP). In a recombinant human UGT1A1 assay, the assay buffer components uridine and its phosphorylated derivatives are isobaric with RBV and its phosphorylated metabolites, leading to significant interference when analyzed by LC-MS with the nominal mass resolution mode. Presented here is a LC-MS method employing LC coupled with full-scan high-resolution accurate MS analysis for the simultaneous quantitative determination of RBV, RMP, ribavirin 5´-diphosphate and RTP by differentiating RBV and its phosphorylated metabolites from uridine and its phosphorylated derivatives by accurate mass, thus avoiding interference. The developed LC-high-resolution accurate MS method allows for quantitation of RBV and its phosphorylated metabolites, eliminating the interferences from uridine and its phosphorylated derivatives in recombinant human UGT1A1 assays.

  2. Quantitation of spatially-localized proteins in tissue samples using MALDI-MRM imaging.

    PubMed

    Clemis, Elizabeth J; Smith, Derek S; Camenzind, Alexander G; Danell, Ryan M; Parker, Carol E; Borchers, Christoph H

    2012-04-17

    MALDI imaging allows the creation of a "molecular image" of a tissue slice. This image is reconstructed from the ion abundances in spectra obtained while rastering the laser over the tissue. These images can then be correlated with tissue histology to detect potential biomarkers of, for example, aberrant cell types. MALDI, however, is known to have problems with ion suppression, making it difficult to correlate measured ion abundance with concentration. It would be advantageous to have a method which could provide more accurate protein concentration measurements, particularly for screening applications or for precise comparisons between samples. In this paper, we report the development of a novel MALDI imaging method for the localization and accurate quantitation of proteins in tissues. This method involves optimization of in situ tryptic digestion, followed by reproducible and uniform deposition of an isotopically labeled standard peptide from a target protein onto the tissue, using an aerosol-generating device. Data is acquired by MALDI multiple reaction monitoring (MRM) mass spectrometry (MS), and accurate peptide quantitation is determined from the ratio of MRM transitions for the endogenous unlabeled proteolytic peptides to the corresponding transitions from the applied isotopically labeled standard peptides. In a parallel experiment, the quantity of the labeled peptide applied to the tissue was determined using a standard curve generated from MALDI time-of-flight (TOF) MS data. This external calibration curve was then used to determine the quantity of endogenous peptide in a given area. All standard curves generate by this method had coefficients of determination greater than 0.97. These proof-of-concept experiments using MALDI MRM-based imaging show the feasibility for the precise and accurate quantitation of tissue protein concentrations over 2 orders of magnitude, while maintaining the spatial localization information for the proteins.

  3. Quantitative analyses of the behavior of exogenously added bacteria during an acidulocomposting process.

    PubMed

    Suematsu, Takatoshi; Yamashita, Satoshi; Hemmi, Hisashi; Yoshinari, Ayaka; Shimoyama, Takefumi; Nakayama, Toru; Nishino, Tokuzo

    2012-07-01

    The behavior of adventitious bacteria during an acidulocomposting process was quantitatively analyzed in garbage-free trials. The numbers of the added Bacillus subtilis and Pseudomonas putida cells diminished in a first-order manner with t(1/2) values of 0.45d and 0.79d, respectively, consistent with the observed stability of the acidulocomposting function. Copyright © 2012 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  4. Quantitative proteomic analyses of the microbial degradation of estrone under various background nitrogen and carbon conditions.

    PubMed

    Du, Zhe; Chen, Yinguang; Li, Xu

    2017-10-15

    Microbial degradation of estrogenic compounds can be affected by the nitrogen source and background carbon in the environment. However, the underlying mechanisms are not well understood. The objective of this study was to elucidate the molecular mechanisms of estrone (E1) biodegradation at the protein level under various background nitrogen (nitrate or ammonium) and carbon conditions (no background carbon, acetic acid, or humic acid as background carbon) by a newly isolated bacterial strain. The E1 degrading bacterial strain, Hydrogenophaga atypica ZD1, was isolated from river sediments and its proteome was characterized under various experimental conditions using quantitative proteomics. Results show that the E1 degradation rate was faster when ammonium was used as the nitrogen source than with nitrate. The degradation rate was also faster when either acetic acid or humic acid was present in the background. Proteomics analyses suggested that the E1 biodegradation products enter the tyrosine metabolism pathway. Compared to nitrate, ammonium likely promoted E1 degradation by increasing the activities of the branched-chain-amino-acid aminotransferase (IlvE) and enzymes involved in the glutamine synthetase-glutamine oxoglutarate aminotransferase (GS-GOGAT) pathway. The increased E1 degradation rate with acetic acid or humic acid in the background can also be attributed to the up-regulation of IlvE. Results from this study can help predict and explain E1 biodegradation kinetics under various environmental conditions. Copyright © 2017 Elsevier Ltd. All rights reserved.

  5. AssayR: A Simple Mass Spectrometry Software Tool for Targeted Metabolic and Stable Isotope Tracer Analyses.

    PubMed

    Wills, Jimi; Edwards-Hicks, Joy; Finch, Andrew J

    2017-09-19

    Metabolic analyses generally fall into two classes: unbiased metabolomic analyses and analyses that are targeted toward specific metabolites. Both techniques have been revolutionized by the advent of mass spectrometers with detectors that afford high mass accuracy and resolution, such as time-of-flights (TOFs) and Orbitraps. One particular area where this technology is key is in the field of metabolic flux analysis because the resolution of these spectrometers allows for discrimination between 13 C-containing isotopologues and those containing 15 N or other isotopes. While XCMS-based software is freely available for untargeted analysis of mass spectrometric data sets, it does not always identify metabolites of interest in a targeted assay. Furthermore, there is a paucity of vendor-independent software that deals with targeted analyses of metabolites and of isotopologues in particular. Here, we present AssayR, an R package that takes high resolution wide-scan liquid chromatography-mass spectrometry (LC-MS) data sets and tailors peak detection for each metabolite through a simple, iterative user interface. It automatically integrates peak areas for all isotopologues and outputs extracted ion chromatograms (EICs), absolute and relative stacked bar charts for all isotopologues, and a .csv data file. We demonstrate several examples where AssayR provides more accurate and robust quantitation than XCMS, and we propose that tailored peak detection should be the preferred approach for targeted assays. In summary, AssayR provides easy and robust targeted metabolite and stable isotope analyses on wide-scan data sets from high resolution mass spectrometers.

  6. AssayR: A Simple Mass Spectrometry Software Tool for Targeted Metabolic and Stable Isotope Tracer Analyses

    PubMed Central

    2017-01-01

    Metabolic analyses generally fall into two classes: unbiased metabolomic analyses and analyses that are targeted toward specific metabolites. Both techniques have been revolutionized by the advent of mass spectrometers with detectors that afford high mass accuracy and resolution, such as time-of-flights (TOFs) and Orbitraps. One particular area where this technology is key is in the field of metabolic flux analysis because the resolution of these spectrometers allows for discrimination between 13C-containing isotopologues and those containing 15N or other isotopes. While XCMS-based software is freely available for untargeted analysis of mass spectrometric data sets, it does not always identify metabolites of interest in a targeted assay. Furthermore, there is a paucity of vendor-independent software that deals with targeted analyses of metabolites and of isotopologues in particular. Here, we present AssayR, an R package that takes high resolution wide-scan liquid chromatography–mass spectrometry (LC-MS) data sets and tailors peak detection for each metabolite through a simple, iterative user interface. It automatically integrates peak areas for all isotopologues and outputs extracted ion chromatograms (EICs), absolute and relative stacked bar charts for all isotopologues, and a .csv data file. We demonstrate several examples where AssayR provides more accurate and robust quantitation than XCMS, and we propose that tailored peak detection should be the preferred approach for targeted assays. In summary, AssayR provides easy and robust targeted metabolite and stable isotope analyses on wide-scan data sets from high resolution mass spectrometers. PMID:28850215

  7. Pinhole Micro-SPECT/CT for Noninvasive Monitoring and Quantitation of Oncolytic Virus Dispersion and Percent Infection in Solid Tumors

    PubMed Central

    Penheiter, Alan R.; Griesmann, Guy E.; Federspiel, Mark J.; Dingli, David; Russell, Stephen J.; Carlson, Stephanie K.

    2011-01-01

    The purpose of our study was to validate the ability of pinhole micro-single-photon emission computed tomography/computed tomography (SPECT/CT) to 1) accurately resolve the intratumoral dispersion pattern and 2) quantify the infection percentage in solid tumors of an oncolytic measles virus encoding the human sodium iodide symporter (MV-NIS). NIS RNA level and dispersion pattern were determined in control and MV-NIS infected BxPC-3 pancreatic tumor cells and mouse xenografts using quantitative, real-time, reverse transcriptase, polymerase chain reaction, autoradiography, and immunohistochemistry (IHC). Mice with BxPC-3 xenografts were imaged with 123I or 99TcO4 micro-SPECT/CT. Tumor dimensions and radionuclide localization were determined with imaging software. Linear regression and correlation analyses were performed to determine the relationship between tumor infection percentage and radionuclide uptake (% injected dose per gram) above background and a highly significant correlation was observed (r2 = 0.947). A detection threshold of 1.5-fold above the control tumor uptake (background) yielded a sensitivity of 2.7% MV-NIS infected tumor cells. We reliably resolved multiple distinct intratumoral zones of infection from noninfected regions. Pinhole micro-SPECT/CT imaging using the NIS reporter demonstrated precise localization and quantitation of oncolytic MV-NIS infection and can replace more time-consuming and expensive analyses (eg, autoradiography and IHC) that require animal sacrifice. PMID:21753796

  8. Quantitative analysis of rib movement based on dynamic chest bone images: preliminary results

    NASA Astrophysics Data System (ADS)

    Tanaka, R.; Sanada, S.; Oda, M.; Mitsutaka, M.; Suzuki, K.; Sakuta, K.; Kawashima, H.

    2014-03-01

    Rib movement during respiration is one of the diagnostic criteria in pulmonary impairments. In general, the rib movement is assessed in fluoroscopy. However, the shadows of lung vessels and bronchi overlapping ribs prevent accurate quantitative analysis of rib movement. Recently, an image-processing technique for separating bones from soft tissue in static chest radiographs, called "bone suppression technique", has been developed. Our purpose in this study was to evaluate the usefulness of dynamic bone images created by the bone suppression technique in quantitative analysis of rib movement. Dynamic chest radiographs of 10 patients were obtained using a dynamic flat-panel detector (FPD). Bone suppression technique based on a massive-training artificial neural network (MTANN) was applied to the dynamic chest images to create bone images. Velocity vectors were measured in local areas on the dynamic bone images, which formed a map. The velocity maps obtained with bone and original images for scoliosis and normal cases were compared to assess the advantages of bone images. With dynamic bone images, we were able to quantify and distinguish movements of ribs from those of other lung structures accurately. Limited rib movements of scoliosis patients appeared as reduced rib velocity vectors. Vector maps in all normal cases exhibited left-right symmetric distributions, whereas those in abnormal cases showed nonuniform distributions. In conclusion, dynamic bone images were useful for accurate quantitative analysis of rib movements: Limited rib movements were indicated as a reduction of rib movement and left-right asymmetric distribution on vector maps. Thus, dynamic bone images can be a new diagnostic tool for quantitative analysis of rib movements without additional radiation dose.

  9. Quantitative Investigation of the Role of Intra-/Intercellular Dynamics in Bacterial Quorum Sensing.

    PubMed

    Leaman, Eric J; Geuther, Brian Q; Behkam, Bahareh

    2018-04-20

    Bacteria utilize diffusible signals to regulate population density-dependent coordinated gene expression in a process called quorum sensing (QS). While the intracellular regulatory mechanisms of QS are well-understood, the effect of spatiotemporal changes in the population configuration on the sensitivity and robustness of the QS response remains largely unexplored. Using a microfluidic device, we quantitatively characterized the emergent behavior of a population of swimming E. coli bacteria engineered with the lux QS system and a GFP reporter. We show that the QS activation time follows a power law with respect to bacterial population density, but this trend is disrupted significantly by microscale variations in population configuration and genetic circuit noise. We then developed a computational model that integrates population dynamics with genetic circuit dynamics to enable accurate (less than 7% error) quantitation of the bacterial QS activation time. Through modeling and experimental analyses, we show that changes in spatial configuration of swimming bacteria can drastically alter the QS activation time, by up to 22%. The integrative model developed herein also enables examination of the performance robustness of synthetic circuits with respect to growth rate, circuit sensitivity, and the population's initial size and spatial structure. Our framework facilitates quantitative tuning of microbial systems performance through rational engineering of synthetic ribosomal binding sites. We have demonstrated this through modulation of QS activation time over an order of magnitude. Altogether, we conclude that predictive engineering of QS-based bacterial systems requires not only the precise temporal modulation of gene expression (intracellular dynamics) but also accounting for the spatiotemporal changes in population configuration (intercellular dynamics).

  10. Industrial ecology: Quantitative methods for exploring a lower carbon future

    NASA Astrophysics Data System (ADS)

    Thomas, Valerie M.

    2015-03-01

    Quantitative methods for environmental and cost analyses of energy, industrial, and infrastructure systems are briefly introduced and surveyed, with the aim of encouraging broader utilization and development of quantitative methods in sustainable energy research. Material and energy flow analyses can provide an overall system overview. The methods of engineering economics and cost benefit analysis, such as net present values, are the most straightforward approach for evaluating investment options, with the levelized cost of energy being a widely used metric in electricity analyses. Environmental lifecycle assessment has been extensively developed, with both detailed process-based and comprehensive input-output approaches available. Optimization methods provide an opportunity to go beyond engineering economics to develop detailed least-cost or least-impact combinations of many different choices.

  11. Quantitation of specific binding ratio in 123I-FP-CIT SPECT: accurate processing strategy for cerebral ventricular enlargement with use of 3D-striatal digital brain phantom.

    PubMed

    Furuta, Akihiro; Onishi, Hideo; Amijima, Hizuru

    2018-06-01

    This study aimed to evaluate the effect of ventricular enlargement on the specific binding ratio (SBR) and to validate the cerebrospinal fluid (CSF)-Mask algorithm for quantitative SBR assessment of 123 I-FP-CIT single-photon emission computed tomography (SPECT) images with the use of a 3D-striatum digital brain (SDB) phantom. Ventricular enlargement was simulated by three-dimensional extensions in a 3D-SDB phantom comprising segments representing the striatum, ventricle, brain parenchyma, and skull bone. The Evans Index (EI) was measured in 3D-SDB phantom images of an enlarged ventricle. Projection data sets were generated from the 3D-SDB phantoms with blurring, scatter, and attenuation. Images were reconstructed using the ordered subset expectation maximization (OSEM) algorithm and corrected for attenuation, scatter, and resolution recovery. We bundled DaTView (Southampton method) with the CSF-Mask processing software for SBR. We assessed SBR with the use of various coefficients (f factor) of the CSF-Mask. Specific binding ratios of 1, 2, 3, 4, and 5 corresponded to SDB phantom simulations with true values. Measured SBRs > 50% that were underestimated with EI increased compared with the true SBR and this trend was outstanding at low SBR. The CSF-Mask improved 20% underestimates and brought the measured SBR closer to the true values at an f factor of 1.0 despite an increase in EI. We connected the linear regression function (y = - 3.53x + 1.95; r = 0.95) with the EI and f factor using root-mean-square error. Processing with CSF-Mask generates accurate quantitative SBR from dopamine transporter SPECT images of patients with ventricular enlargement.

  12. Quantitation of fixative-induced morphologic and antigenic variation in mouse and human breast cancers

    PubMed Central

    Cardiff, Robert D; Hubbard, Neil E; Engelberg, Jesse A; Munn, Robert J; Miller, Claramae H; Walls, Judith E; Chen, Jane Q; Velásquez-García, Héctor A; Galvez, Jose J; Bell, Katie J; Beckett, Laurel A; Li, Yue-Ju; Borowsky, Alexander D

    2013-01-01

    Quantitative Image Analysis (QIA) of digitized whole slide images for morphometric parameters and immunohistochemistry of breast cancer antigens was used to evaluate the technical reproducibility, biological variability, and intratumoral heterogeneity in three transplantable mouse mammary tumor models of human breast cancer. The relative preservation of structure and immunogenicity of the three mouse models and three human breast cancers was also compared when fixed with representatives of four distinct classes of fixatives. The three mouse mammary tumor cell models were an ER + /PR + model (SSM2), a Her2 + model (NDL), and a triple negative model (MET1). The four breast cancer antigens were ER, PR, Her2, and Ki67. The fixatives included examples of (1) strong cross-linkers, (2) weak cross-linkers, (3) coagulants, and (4) combination fixatives. Each parameter was quantitatively analyzed using modified Aperio Technologies ImageScope algorithms. Careful pre-analytical adjustments to the algorithms were required to provide accurate results. The QIA permitted rigorous statistical analysis of results and grading by rank order. The analyses suggested excellent technical reproducibility and confirmed biological heterogeneity within each tumor. The strong cross-linker fixatives, such as formalin, consistently ranked higher than weak cross-linker, coagulant and combination fixatives in both the morphometric and immunohistochemical parameters. PMID:23399853

  13. Measurements of the quantitative lateral analytical resolution at evaporated aluminium and silver layers with the JEOL JXA-8530F FEG-EPMA

    NASA Astrophysics Data System (ADS)

    Berger, D.; Nissen, J.

    2018-01-01

    The studies in this paper are part of systematic investigations of the lateral analytical resolution of the field emission electron microprobe JEOL JXA-8530F. Hereby, the quantitative lateral resolution, which is achieved in practise, is in the focus of interest. The approach is to determine the minimum thickness of a metallic layer for which an accurate quantitative element analysis in cross-section is still possible. Previous measurements were accomplished at sputtered gold (Z = 79) layers, where a lateral resolution in the range of 140 to 170 nm was achieved at suitable parameters of the microprobe. To study the Z-dependence of the lateral resolution, now aluminium (Z = 13) resp. silver (Z = 47) layers with different thicknesses were generated by evaporation and prepared in cross-section subsequently by use of a focussed Ga-ion beam (FIB). Each layer was analysed quantitatively with different electron energies. The thinnest layer which can be resolved specifies the best lateral resolution. These measured values were compared on the one hand with Monte Carlo simulations and on the other hand with predictions from formulas from the literature. The measurements fit well to the simulated and calculated values, except the ones at the lowest primary electron energies with an overvoltage below ˜ 2. The reason for this discrepancy is not clear yet and has to be clarified by further investigations. The results apply for any microanalyser - even with energy-dispersive X-ray spectrometry (EDS) detection - if the probe diameters, which might deviate from those of the JEOL JXA-8530F, at suitable analysing parameters are considered.

  14. Quantitative microlocalization of diffusible ions in normal and galactose cataractous rat lens by secondary ion mass spectrometry.

    PubMed

    Burns, M S; File, D M

    1986-11-01

    Secondary ion mass spectrometry (SIMS) is a surface analytical technique with high sensitivity for elemental detection and microlocalization capabilities within the micrometre range. Quantitative analysis of epoxy resins and gelatin have been reported (Burns-Bellhorn & File, 1979). We report here the first application of this technique to quantitative microlocalization in the context of a physiological problem--analyses of sodium, potassium and calcium in normal and galactose-induced cataract in rat lens. It is known that during the development of galactose-induced cataract the whole lens content of potassium is decreased, sodium is increased and, in late stages, calcium concentration increases. Whether these alterations in diffusible ions occur homogeneously or heterogeneously is not known. Standard curves were generated from epoxy resins containing known concentrations of sodium, potassium or calcium organometallic compounds using the Cameca IMS 300 Secondary Ion Mass Spectrometer. Normal and cataractous lenses were prepared by freezing in isopentane in a liquid nitrogen bath followed by freeze-drying at -30 degrees C. After dry embedding in epoxy resin, 10 microns thick sections of lens were pressure mounted on silicon wafers, overcoated with gold, and ion emission measured under the same instrumental conditions used to obtain the standard curves. Quantitative analysis of an area 27 microns in diameter, or a total analysed volume of 1.1 microns3, was performed by using a mechanical aperture in the ion optical system. Ion images provided qualitative microanalysis with a lateral resolution of 1 micron. Control rat lenses gave values for sodium and potassium content with a precision of +/- 17% or less. These values were compared to flame photometry and atomic absorption measurements of normal lenses and were accurate within 25%. Analysis of serum and blood also gave accurate and precise measurements of these elements. Normal rat lenses had a gradient of sodium, and

  15. Accurate forced-choice recognition without awareness of memory retrieval.

    PubMed

    Voss, Joel L; Baym, Carol L; Paller, Ken A

    2008-06-01

    Recognition confidence and the explicit awareness of memory retrieval commonly accompany accurate responding in recognition tests. Memory performance in recognition tests is widely assumed to measure explicit memory, but the generality of this assumption is questionable. Indeed, whether recognition in nonhumans is always supported by explicit memory is highly controversial. Here we identified circumstances wherein highly accurate recognition was unaccompanied by hallmark features of explicit memory. When memory for kaleidoscopes was tested using a two-alternative forced-choice recognition test with similar foils, recognition was enhanced by an attentional manipulation at encoding known to degrade explicit memory. Moreover, explicit recognition was most accurate when the awareness of retrieval was absent. These dissociations between accuracy and phenomenological features of explicit memory are consistent with the notion that correct responding resulted from experience-dependent enhancements of perceptual fluency with specific stimuli--the putative mechanism for perceptual priming effects in implicit memory tests. This mechanism may contribute to recognition performance in a variety of frequently-employed testing circumstances. Our results thus argue for a novel view of recognition, in that analyses of its neurocognitive foundations must take into account the potential for both (1) recognition mechanisms allied with implicit memory and (2) recognition mechanisms allied with explicit memory.

  16. Quantitative Characterization of the Filiform Mechanosensory Hair Array on the Cricket Cercus

    PubMed Central

    Miller, John P.; Krueger, Susan; Heys, Jeffrey J.; Gedeon, Tomas

    2011-01-01

    Background Crickets and other orthopteran insects sense air currents with a pair of abdominal appendages resembling antennae, called cerci. Each cercus in the common house cricket Acheta domesticus is approximately 1 cm long, and is covered with 500 to 750 filiform mechanosensory hairs. The distribution of the hairs on the cerci, as well as the global patterns of their movement vectors, have been characterized semi-quantitatively in studies over the last 40 years, and have been shown to be very stereotypical across different animals in this species. Although the cercal sensory system has been the focus of many studies in the areas of neuroethology, development, biomechanics, sensory function and neural coding, there has not yet been a quantitative study of the functional morphology of the receptor array of this important model system. Methodology/Principal Findings We present a quantitative characterization of the structural characteristics and functional morphology of the cercal filiform hair array. We demonstrate that the excitatory direction along each hair's movement plane can be identified by features of its socket that are visible at the light-microscopic level, and that the length of the hair associated with each socket can also be estimated accurately from a structural parameter of the socket. We characterize the length and directionality of all hairs on the basal half of a sample of three cerci, and present statistical analyses of the distributions. Conclusions/Significance The inter-animal variation of several global organizational features is low, consistent with constraints imposed by functional effectiveness and/or developmental processes. Contrary to previous reports, however, we show that the filiform hairs are not re-identifiable in the strict sense. PMID:22132155

  17. DNA DAMAGE QUANTITATION BY ALKALINE GEL ELECTROPHORESIS.

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

    SUTHERLAND,B.M.; BENNETT,P.V.; SUTHERLAND, J.C.

    2004-03-24

    Physical and chemical agents in the environment, those used in clinical applications, or encountered during recreational exposures to sunlight, induce damages in DNA. Understanding the biological impact of these agents requires quantitation of the levels of such damages in laboratory test systems as well as in field or clinical samples. Alkaline gel electrophoresis provides a sensitive (down to {approx} a few lesions/5Mb), rapid method of direct quantitation of a wide variety of DNA damages in nanogram quantities of non-radioactive DNAs from laboratory, field, or clinical specimens, including higher plants and animals. This method stems from velocity sedimentation studies of DNAmore » populations, and from the simple methods of agarose gel electrophoresis. Our laboratories have developed quantitative agarose gel methods, analytical descriptions of DNA migration during electrophoresis on agarose gels (1-6), and electronic imaging for accurate determinations of DNA mass (7-9). Although all these components improve sensitivity and throughput of large numbers of samples (7,8,10), a simple version using only standard molecular biology equipment allows routine analysis of DNA damages at moderate frequencies. We present here a description of the methods, as well as a brief description of the underlying principles, required for a simplified approach to quantitation of DNA damages by alkaline gel electrophoresis.« less

  18. Accurate FRET Measurements within Single Diffusing Biomolecules Using Alternating-Laser Excitation

    PubMed Central

    Lee, Nam Ki; Kapanidis, Achillefs N.; Wang, You; Michalet, Xavier; Mukhopadhyay, Jayanta; Ebright, Richard H.; Weiss, Shimon

    2005-01-01

    Fluorescence resonance energy transfer (FRET) between a donor (D) and an acceptor (A) at the single-molecule level currently provides qualitative information about distance, and quantitative information about kinetics of distance changes. Here, we used the sorting ability of confocal microscopy equipped with alternating-laser excitation (ALEX) to measure accurate FRET efficiencies and distances from single molecules, using corrections that account for cross-talk terms that contaminate the FRET-induced signal, and for differences in the detection efficiency and quantum yield of the probes. ALEX yields accurate FRET independent of instrumental factors, such as excitation intensity or detector alignment. Using DNA fragments, we showed that ALEX-based distances agree well with predictions from a cylindrical model of DNA; ALEX-based distances fit better to theory than distances obtained at the ensemble level. Distance measurements within transcription complexes agreed well with ensemble-FRET measurements, and with structural models based on ensemble-FRET and x-ray crystallography. ALEX can benefit structural analysis of biomolecules, especially when such molecules are inaccessible to conventional structural methods due to heterogeneity or transient nature. PMID:15653725

  19. Stroke onset time estimation from multispectral quantitative magnetic resonance imaging in a rat model of focal permanent cerebral ischemia.

    PubMed

    McGarry, Bryony L; Rogers, Harriet J; Knight, Michael J; Jokivarsi, Kimmo T; Sierra, Alejandra; Gröhn, Olli Hj; Kauppinen, Risto A

    2016-08-01

    Quantitative T2 relaxation magnetic resonance imaging allows estimation of stroke onset time. We aimed to examine the accuracy of quantitative T1 and quantitative T2 relaxation times alone and in combination to provide estimates of stroke onset time in a rat model of permanent focal cerebral ischemia and map the spatial distribution of elevated quantitative T1 and quantitative T2 to assess tissue status. Permanent middle cerebral artery occlusion was induced in Wistar rats. Animals were scanned at 9.4T for quantitative T1, quantitative T2, and Trace of Diffusion Tensor (Dav) up to 4 h post-middle cerebral artery occlusion. Time courses of differentials of quantitative T1 and quantitative T2 in ischemic and non-ischemic contralateral brain tissue (ΔT1, ΔT2) and volumes of tissue with elevated T1 and T2 relaxation times (f1, f2) were determined. TTC staining was used to highlight permanent ischemic damage. ΔT1, ΔT2, f1, f2, and the volume of tissue with both elevated quantitative T1 and quantitative T2 (V(Overlap)) increased with time post-middle cerebral artery occlusion allowing stroke onset time to be estimated. V(Overlap) provided the most accurate estimate with an uncertainty of ±25 min. At all times-points regions with elevated relaxation times were smaller than areas with Dav defined ischemia. Stroke onset time can be determined by quantitative T1 and quantitative T2 relaxation times and tissue volumes. Combining quantitative T1 and quantitative T2 provides the most accurate estimate and potentially identifies irreversibly damaged brain tissue. © 2016 World Stroke Organization.

  20. Quantitative 4D analyses of epithelial folding during Drosophila gastrulation.

    PubMed

    Khan, Zia; Wang, Yu-Chiun; Wieschaus, Eric F; Kaschube, Matthias

    2014-07-01

    Understanding the cellular and mechanical processes that underlie the shape changes of individual cells and their collective behaviors in a tissue during dynamic and complex morphogenetic events is currently one of the major frontiers in developmental biology. The advent of high-speed time-lapse microscopy and its use in monitoring the cellular events in fluorescently labeled developing organisms demonstrate tremendous promise in establishing detailed descriptions of these events and could potentially provide a foundation for subsequent hypothesis-driven research strategies. However, obtaining quantitative measurements of dynamic shapes and behaviors of cells and tissues in a rapidly developing metazoan embryo using time-lapse 3D microscopy remains technically challenging, with the main hurdle being the shortage of robust imaging processing and analysis tools. We have developed EDGE4D, a software tool for segmenting and tracking membrane-labeled cells using multi-photon microscopy data. Our results demonstrate that EDGE4D enables quantification of the dynamics of cell shape changes, cell interfaces and neighbor relations at single-cell resolution during a complex epithelial folding event in the early Drosophila embryo. We expect this tool to be broadly useful for the analysis of epithelial cell geometries and movements in a wide variety of developmental contexts. © 2014. Published by The Company of Biologists Ltd.

  1. Microfluidics-based digital quantitative PCR for single-cell small RNA quantification.

    PubMed

    Yu, Tian; Tang, Chong; Zhang, Ying; Zhang, Ruirui; Yan, Wei

    2017-09-01

    Quantitative analyses of small RNAs at the single-cell level have been challenging because of limited sensitivity and specificity of conventional real-time quantitative PCR methods. A digital quantitative PCR (dqPCR) method for miRNA quantification has been developed, but it requires the use of proprietary stem-loop primers and only applies to miRNA quantification. Here, we report a microfluidics-based dqPCR (mdqPCR) method, which takes advantage of the Fluidigm BioMark HD system for both template partition and the subsequent high-throughput dqPCR. Our mdqPCR method demonstrated excellent sensitivity and reproducibility suitable for quantitative analyses of not only miRNAs but also all other small RNA species at the single-cell level. Using this method, we discovered that each sperm has a unique miRNA profile. © The Authors 2017. Published by Oxford University Press on behalf of Society for the Study of Reproduction. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  2. Single-Cell Based Quantitative Assay of Chromosome Transmission Fidelity.

    PubMed

    Zhu, Jin; Heinecke, Dominic; Mulla, Wahid A; Bradford, William D; Rubinstein, Boris; Box, Andrew; Haug, Jeffrey S; Li, Rong

    2015-03-30

    Errors in mitosis are a primary cause of chromosome instability (CIN), generating aneuploid progeny cells. Whereas a variety of factors can influence CIN, under most conditions mitotic errors are rare events that have been difficult to measure accurately. Here we report a green fluorescent protein-based quantitative chromosome transmission fidelity (qCTF) assay in budding yeast that allows sensitive and quantitative detection of CIN and can be easily adapted to high-throughput analysis. Using the qCTF assay, we performed genome-wide quantitative profiling of genes that affect CIN in a dosage-dependent manner and identified genes that elevate CIN when either increased (icCIN) or decreased in copy number (dcCIN). Unexpectedly, qCTF screening also revealed genes whose change in copy number quantitatively suppress CIN, suggesting that the basal error rate of the wild-type genome is not minimized, but rather, may have evolved toward an optimal level that balances both stability and low-level karyotype variation for evolutionary adaptation. Copyright © 2015 Zhu et al.

  3. Advances in the Quantitative Characterization of the Shape of Ash-Sized Pyroclast Populations: Fractal Analyses Coupled to Micro- and Nano-Computed Tomography Techniques

    NASA Astrophysics Data System (ADS)

    Rausch, J.; Vonlanthen, P.; Grobety, B. H.

    2014-12-01

    The quantification of shape parameters in pyroclasts is fundamental to infer the dominant type of magma fragmentation (magmatic vs. phreatomagmatic), as well as the behavior of volcanic plumes and clouds in the atmosphere. In a case study aiming at reconstructing the fragmentation mechanisms triggering maar eruptions in two geologically and compositionally distinctive volcanic fields (West and East Eifel, Germany), the shapes of a large number of ash particle contours obtained from SEM images were analyzed by a dilation-based fractal method. Volcanic particle contours are pseudo-fractals showing mostly two distinct slopes in Richardson plots related to the fractal dimensions D1 (small-scale "textural" dimension) and D2 (large-scale "morphological" dimension). The validity of the data obtained from 2D sections was tested by analysing SEM micro-CT slices of one particle cut in different orientations and positions. Results for West Eifel maar particles yield large D1 values (> 1.023), resembling typical values of magmatic particles, which are characterized by a complex shape, especially at small scales. In contrast, the D1 values of ash particles from one East Eifel maar deposit are much smaller, coinciding with the fractal dimensions obtained from phreatomagmatic end-member particles. These quantitative morphological analyses suggest that the studied maar eruptions were triggered by two different fragmentation processes: phreatomagmatic in the East Eifel and magmatic in the West Eifel. The application of fractal analysis to quantitatively characterize the shape of pyroclasts and the linking of fractal dimensions to specific fragmentation processes has turned out to be a very promising tool for studying the fragmentation history of any volcanic eruption. The next step is to extend morphological analysis of volcanic particles to 3 dimensions. SEM micro-CT, already applied in this study, offers the required resolution, but is not suitable for the analysis of a large

  4. Congruent climate-related genecological responses from molecular markers and quantitative traits for western white pine (Pinus monticola)

    Treesearch

    Bryce A. Richardson; Gerald E. Rehfeldt; Mee-Sook Kim

    2009-01-01

    Analyses of molecular and quantitative genetic data demonstrate the existence of congruent climate-related patterns in western white pine (Pinus monticola). Two independent studies allowed comparisons of amplified fragment length polymorphism (AFLP) markers with quantitative variation in adaptive traits. Principal component analyses...

  5. Quantitative Susceptibility Mapping after Sports-Related Concussion.

    PubMed

    Koch, K M; Meier, T B; Karr, R; Nencka, A S; Muftuler, L T; McCrea, M

    2018-06-07

    Quantitative susceptibility mapping using MR imaging can assess changes in brain tissue structure and composition. This report presents preliminary results demonstrating changes in tissue magnetic susceptibility after sports-related concussion. Longitudinal quantitative susceptibility mapping metrics were produced from imaging data acquired from cohorts of concussed and control football athletes. One hundred thirty-six quantitative susceptibility mapping datasets were analyzed across 3 separate visits (24 hours after injury, 8 days postinjury, and 6 months postinjury). Longitudinal quantitative susceptibility mapping group analyses were performed on stability-thresholded brain tissue compartments and selected subregions. Clinical concussion metrics were also measured longitudinally in both cohorts and compared with the measured quantitative susceptibility mapping. Statistically significant increases in white matter susceptibility were identified in the concussed athlete group during the acute (24 hour) and subacute (day 8) period. These effects were most prominent at the 8-day visit but recovered and showed no significant difference from controls at the 6-month visit. The subcortical gray matter showed no statistically significant group differences. Observed susceptibility changes after concussion appeared to outlast self-reported clinical recovery metrics at a group level. At an individual subject level, susceptibility increases within the white matter showed statistically significant correlations with return-to-play durations. The results of this preliminary investigation suggest that sports-related concussion can induce physiologic changes to brain tissue that can be detected using MR imaging-based magnetic susceptibility estimates. In group analyses, the observed tissue changes appear to persist beyond those detected on clinical outcome assessments and were associated with return-to-play duration after sports-related concussion. © 2018 by American Journal of

  6. Quantitative Analysis of Signaling Networks across Differentially Embedded Tumors Highlights Interpatient Heterogeneity in Human Glioblastoma

    PubMed Central

    2015-01-01

    Glioblastoma multiforme (GBM) is the most aggressive malignant primary brain tumor, with a dismal mean survival even with the current standard of care. Although in vitro cell systems can provide mechanistic insight into the regulatory networks governing GBM cell proliferation and migration, clinical samples provide a more physiologically relevant view of oncogenic signaling networks. However, clinical samples are not widely available and may be embedded for histopathologic analysis. With the goal of accurately identifying activated signaling networks in GBM tumor samples, we investigated the impact of embedding in optimal cutting temperature (OCT) compound followed by flash freezing in LN2 vs immediate flash freezing (iFF) in LN2 on protein expression and phosphorylation-mediated signaling networks. Quantitative proteomic and phosphoproteomic analysis of 8 pairs of tumor specimens revealed minimal impact of the different sample processing strategies and highlighted the large interpatient heterogeneity present in these tumors. Correlation analyses of the differentially processed tumor sections identified activated signaling networks present in selected tumors and revealed the differential expression of transcription, translation, and degradation associated proteins. This study demonstrates the capability of quantitative mass spectrometry for identification of in vivo oncogenic signaling networks from human tumor specimens that were either OCT-embedded or immediately flash-frozen. PMID:24927040

  7. Quantitative PCR for Detection and Enumeration of Genetic Markers of Bovine Fecal Pollution

    EPA Science Inventory

    Accurate assessment of health risks associated with bovine (cattle) fecal pollution requires a reliable host-specific genetic marker and a rapid quantification method. We report the development of quantitative PCR assays for the detection of two recently described cow feces-spec...

  8. Quantitative Imaging with a Mobile Phone Microscope

    PubMed Central

    Skandarajah, Arunan; Reber, Clay D.; Switz, Neil A.; Fletcher, Daniel A.

    2014-01-01

    Use of optical imaging for medical and scientific applications requires accurate quantification of features such as object size, color, and brightness. High pixel density cameras available on modern mobile phones have made photography simple and convenient for consumer applications; however, the camera hardware and software that enables this simplicity can present a barrier to accurate quantification of image data. This issue is exacerbated by automated settings, proprietary image processing algorithms, rapid phone evolution, and the diversity of manufacturers. If mobile phone cameras are to live up to their potential to increase access to healthcare in low-resource settings, limitations of mobile phone–based imaging must be fully understood and addressed with procedures that minimize their effects on image quantification. Here we focus on microscopic optical imaging using a custom mobile phone microscope that is compatible with phones from multiple manufacturers. We demonstrate that quantitative microscopy with micron-scale spatial resolution can be carried out with multiple phones and that image linearity, distortion, and color can be corrected as needed. Using all versions of the iPhone and a selection of Android phones released between 2007 and 2012, we show that phones with greater than 5 MP are capable of nearly diffraction-limited resolution over a broad range of magnifications, including those relevant for single cell imaging. We find that automatic focus, exposure, and color gain standard on mobile phones can degrade image resolution and reduce accuracy of color capture if uncorrected, and we devise procedures to avoid these barriers to quantitative imaging. By accommodating the differences between mobile phone cameras and the scientific cameras, mobile phone microscopes can be reliably used to increase access to quantitative imaging for a variety of medical and scientific applications. PMID:24824072

  9. Optimization of metabolite basis sets prior to quantitation in magnetic resonance spectroscopy: an approach based on quantum mechanics

    NASA Astrophysics Data System (ADS)

    Lazariev, A.; Allouche, A.-R.; Aubert-Frécon, M.; Fauvelle, F.; Piotto, M.; Elbayed, K.; Namer, I.-J.; van Ormondt, D.; Graveron-Demilly, D.

    2011-11-01

    High-resolution magic angle spinning (HRMAS) nuclear magnetic resonance (NMR) is playing an increasingly important role for diagnosis. This technique enables setting up metabolite profiles of ex vivo pathological and healthy tissue. The need to monitor diseases and pharmaceutical follow-up requires an automatic quantitation of HRMAS 1H signals. However, for several metabolites, the values of chemical shifts of proton groups may slightly differ according to the micro-environment in the tissue or cells, in particular to its pH. This hampers the accurate estimation of the metabolite concentrations mainly when using quantitation algorithms based on a metabolite basis set: the metabolite fingerprints are not correct anymore. In this work, we propose an accurate method coupling quantum mechanical simulations and quantitation algorithms to handle basis-set changes. The proposed algorithm automatically corrects mismatches between the signals of the simulated basis set and the signal under analysis by maximizing the normalized cross-correlation between the mentioned signals. Optimized chemical shift values of the metabolites are obtained. This method, QM-QUEST, provides more robust fitting while limiting user involvement and respects the correct fingerprints of metabolites. Its efficiency is demonstrated by accurately quantitating 33 signals from tissue samples of human brains with oligodendroglioma, obtained at 11.7 tesla. The corresponding chemical shift changes of several metabolites within the series are also analyzed.

  10. Facile and quantitative electrochemical detection of yeast cell apoptosis

    NASA Astrophysics Data System (ADS)

    Yue, Qiulin; Xiong, Shiquan; Cai, Dongqing; Wu, Zhengyan; Zhang, Xin

    2014-03-01

    An electrochemical method based on square wave anodic stripping voltammetry (SWASV) was developed to detect the apoptosis of yeast cells conveniently and quantitatively through the high affinity between Cu2+ and phosphatidylserine (PS) translocated from the inner to the outer plasma membrane of the apoptotic cells. The combination of negatively charged PS and Cu2+ could decrease the electrochemical response of Cu2+ on the electrode. The results showed that the apoptotic rates of cells could be detected quantitatively through the variations of peak currents of Cu2+ by SWASV, and agreed well with those obtained through traditional flow cytometry detection. This work thus may provide a novel, simple, immediate and accurate detection method for cell apoptosis.

  11. DEMOGRAPHY AND VIABILITY ANALYSES OF A DIAMONDBACK TERRAPIN POPULATION

    EPA Science Inventory

    The diamondback terrapin Malaclemys terrapin is a long-lived species with special management requirements, but quantitative analyses to support management are lacking. I analyzed mark-recapture data and constructed an age-classified matrix population model to determine the status...

  12. Combined metabonomic and quantitative real-time PCR analyses reveal systems metabolic changes in Jurkat T-cells treated with HIV-1 Tat protein.

    PubMed

    Liao, Wenting; Tan, Guangguo; Zhu, Zhenyu; Chen, Qiuli; Lou, Ziyang; Dong, Xin; Zhang, Wei; Pan, Wei; Chai, Yifeng

    2012-11-02

    HIV-1 Tat protein is released by infected cells and can affect bystander uninfected T cells and induce numerous biological responses which contribute to its pathogenesis. To elucidate the complex pathogenic mechanism, we conducted a comprehensive investigation on Tat protein-related extracellular and intracellular metabolic changes in Jurkat T-cells using combined gas chromatography-mass spectrometry (GC-MS), reversed-phase liquid chromatography-mass spectrometry (RPLC-MS) and a hydrophilic interaction liquid chromatography-mass spectrometry (HILIC-MS)-based metabonomics approach. Quantitative real-time PCR (qRT-PCR) analyses were further employed to measure expressions of several relevant enzymes together with perturbed metabolic pathways. Combined metabonomic and qRT-PCR analyses revealed that HIV-1 Tat caused significant and comprehensive metabolic changes, as represented by significant changes of 37 metabolites and 10 relevant enzymes in HIV-1 Tat-treated cells. Using MetaboAnalyst 2.0, it was found that 11 pathways (Impact-value >0.10) among the regulated pathways were acutely perturbed, including sphingolipid metabolism, glycine, serine and threonine metabolism, pyruvate metabolism, inositol phosphate metabolism, arginine and proline metabolism, citrate cycle, phenylalanine metabolism, tryptophan metabolism, pentose phosphate pathway, glycerophospholipid metabolism, glycolysis or gluconeogenesis. These results provide metabolic evidence of the complex pathogenic mechanism of HIV-1 Tat protein as a "viral toxin", and would help obligate Tat protein as "an important target" for therapeutic intervention and vaccine development.

  13. Correction for isotopic interferences between analyte and internal standard in quantitative mass spectrometry by a nonlinear calibration function.

    PubMed

    Rule, Geoffrey S; Clark, Zlatuse D; Yue, Bingfang; Rockwood, Alan L

    2013-04-16

    Stable isotope-labeled internal standards are of great utility in providing accurate quantitation in mass spectrometry (MS). An implicit assumption has been that there is no "cross talk" between signals of the internal standard and the target analyte. In some cases, however, naturally occurring isotopes of the analyte do contribute to the signal of the internal standard. This phenomenon becomes more pronounced for isotopically rich compounds, such as those containing sulfur, chlorine, or bromine, higher molecular weight compounds, and those at high analyte/internal standard concentration ratio. This can create nonlinear calibration behavior that may bias quantitative results. Here, we propose the use of a nonlinear but more accurate fitting of data for these situations that incorporates one or two constants determined experimentally for each analyte/internal standard combination and an adjustable calibration parameter. This fitting provides more accurate quantitation in MS-based assays where contributions from analyte to stable labeled internal standard signal exist. It can also correct for the reverse situation where an analyte is present in the internal standard as an impurity. The practical utility of this approach is described, and by using experimental data, the approach is compared to alternative fits.

  14. A comparison of manual and quantitative elbow strength testing.

    PubMed

    Shahgholi, Leili; Bengtson, Keith A; Bishop, Allen T; Shin, Alexander Y; Spinner, Robert J; Basford, Jeffrey R; Kaufman, Kenton R

    2012-10-01

    The aim of this study was to compare the clinical ratings of elbow strength obtained by skilled clinicians with objective strength measurement obtained through quantitative testing. A retrospective comparison of subject clinical records with quantitative strength testing results in a motion analysis laboratory was conducted. A total of 110 individuals between the ages of 8 and 65 yrs with traumatic brachial plexus injuries were identified. Patients underwent manual muscle strength testing as assessed on the 5-point British Medical Research Council Scale (5/5, normal; 0/5, absent) and quantitative elbow flexion and extension strength measurements. A total of 92 subjects had elbow flexion testing. Half of the subjects clinically assessed as having normal (5/5) elbow flexion strength on manual muscle testing exhibited less than 42% of their age-expected strength on quantitative testing. Eighty-four subjects had elbow extension strength testing. Similarly, half of those displaying normal elbow extension strength on manual muscle testing were found to have less than 62% of their age-expected values on quantitative testing. Significant differences between manual muscle testing and quantitative findings were not detected for the lesser (0-4) strength grades. Manual muscle testing, even when performed by experienced clinicians, may be more misleading than expected for subjects graded as having normal (5/5) strength. Manual muscle testing estimates for the lesser strength grades (1-4/5) seem reasonably accurate.

  15. Monitoring the Single-Cell Stress Response of the Diatom Thalassiosira pseudonana by Quantitative Real-Time Reverse Transcription-PCR

    PubMed Central

    Shi, Xu; Gao, Weimin; Chao, Shih-hui

    2013-01-01

    Directly monitoring the stress response of microbes to their environments could be one way to inspect the health of microorganisms themselves, as well as the environments in which the microorganisms live. The ultimate resolution for such an endeavor could be down to a single-cell level. In this study, using the diatom Thalassiosira pseudonana as a model species, we aimed to measure gene expression responses of this organism to various stresses at a single-cell level. We developed a single-cell quantitative real-time reverse transcription-PCR (RT-qPCR) protocol and applied it to determine the expression levels of multiple selected genes under nitrogen, phosphate, and iron depletion stress conditions. The results, for the first time, provided a quantitative measurement of gene expression at single-cell levels in T. pseudonana and demonstrated that significant gene expression heterogeneity was present within the cell population. In addition, different expression patterns between single-cell- and bulk-cell-based analyses were also observed for all genes assayed in this study, suggesting that cell response heterogeneity needs to be taken into consideration in order to obtain accurate information that indicates the environmental stress condition. PMID:23315741

  16. Monitoring the single-cell stress response of the diatom Thalassiosira pseudonana by quantitative real-time reverse transcription-PCR.

    PubMed

    Shi, Xu; Gao, Weimin; Chao, Shih-hui; Zhang, Weiwen; Meldrum, Deirdre R

    2013-03-01

    Directly monitoring the stress response of microbes to their environments could be one way to inspect the health of microorganisms themselves, as well as the environments in which the microorganisms live. The ultimate resolution for such an endeavor could be down to a single-cell level. In this study, using the diatom Thalassiosira pseudonana as a model species, we aimed to measure gene expression responses of this organism to various stresses at a single-cell level. We developed a single-cell quantitative real-time reverse transcription-PCR (RT-qPCR) protocol and applied it to determine the expression levels of multiple selected genes under nitrogen, phosphate, and iron depletion stress conditions. The results, for the first time, provided a quantitative measurement of gene expression at single-cell levels in T. pseudonana and demonstrated that significant gene expression heterogeneity was present within the cell population. In addition, different expression patterns between single-cell- and bulk-cell-based analyses were also observed for all genes assayed in this study, suggesting that cell response heterogeneity needs to be taken into consideration in order to obtain accurate information that indicates the environmental stress condition.

  17. Quantitative Oxygenation Venography from MRI Phase

    PubMed Central

    Fan, Audrey P.; Bilgic, Berkin; Gagnon, Louis; Witzel, Thomas; Bhat, Himanshu; Rosen, Bruce R.; Adalsteinsson, Elfar

    2014-01-01

    Purpose To demonstrate acquisition and processing methods for quantitative oxygenation venograms that map in vivo oxygen saturation (SvO2) along cerebral venous vasculature. Methods Regularized quantitative susceptibility mapping (QSM) is used to reconstruct susceptibility values and estimate SvO2 in veins. QSM with ℓ1 and ℓ2 regularization are compared in numerical simulations of vessel structures with known magnetic susceptibility. Dual-echo, flow-compensated phase images are collected in three healthy volunteers to create QSM images. Bright veins in the susceptibility maps are vectorized and used to form a three-dimensional vascular mesh, or venogram, along which to display SvO2 values from QSM. Results Quantitative oxygenation venograms that map SvO2 along brain vessels of arbitrary orientation and geometry are shown in vivo. SvO2 values in major cerebral veins lie within the normal physiological range reported by 15O positron emission tomography. SvO2 from QSM is consistent with previous MR susceptometry methods for vessel segments oriented parallel to the main magnetic field. In vessel simulations, ℓ1 regularization results in less than 10% SvO2 absolute error across all vessel tilt orientations and provides more accurate SvO2 estimation than ℓ2 regularization. Conclusion The proposed analysis of susceptibility images enables reliable mapping of quantitative SvO2 along venograms and may facilitate clinical use of venous oxygenation imaging. PMID:24006229

  18. QTest: Quantitative Testing of Theories of Binary Choice.

    PubMed

    Regenwetter, Michel; Davis-Stober, Clintin P; Lim, Shiau Hong; Guo, Ying; Popova, Anna; Zwilling, Chris; Cha, Yun-Shil; Messner, William

    2014-01-01

    The goal of this paper is to make modeling and quantitative testing accessible to behavioral decision researchers interested in substantive questions. We provide a novel, rigorous, yet very general, quantitative diagnostic framework for testing theories of binary choice. This permits the nontechnical scholar to proceed far beyond traditionally rather superficial methods of analysis, and it permits the quantitatively savvy scholar to triage theoretical proposals before investing effort into complex and specialized quantitative analyses. Our theoretical framework links static algebraic decision theory with observed variability in behavioral binary choice data. The paper is supplemented with a custom-designed public-domain statistical analysis package, the QTest software. We illustrate our approach with a quantitative analysis using published laboratory data, including tests of novel versions of "Random Cumulative Prospect Theory." A major asset of the approach is the potential to distinguish decision makers who have a fixed preference and commit errors in observed choices from decision makers who waver in their preferences.

  19. QTest: Quantitative Testing of Theories of Binary Choice

    PubMed Central

    Regenwetter, Michel; Davis-Stober, Clintin P.; Lim, Shiau Hong; Guo, Ying; Popova, Anna; Zwilling, Chris; Cha, Yun-Shil; Messner, William

    2014-01-01

    The goal of this paper is to make modeling and quantitative testing accessible to behavioral decision researchers interested in substantive questions. We provide a novel, rigorous, yet very general, quantitative diagnostic framework for testing theories of binary choice. This permits the nontechnical scholar to proceed far beyond traditionally rather superficial methods of analysis, and it permits the quantitatively savvy scholar to triage theoretical proposals before investing effort into complex and specialized quantitative analyses. Our theoretical framework links static algebraic decision theory with observed variability in behavioral binary choice data. The paper is supplemented with a custom-designed public-domain statistical analysis package, the QTest software. We illustrate our approach with a quantitative analysis using published laboratory data, including tests of novel versions of “Random Cumulative Prospect Theory.” A major asset of the approach is the potential to distinguish decision makers who have a fixed preference and commit errors in observed choices from decision makers who waver in their preferences. PMID:24999495

  20. Accurate collision-induced line-coupling parameters for the fundamental band of CO in He - Close coupling and coupled states scattering calculations

    NASA Technical Reports Server (NTRS)

    Green, Sheldon; Boissoles, J.; Boulet, C.

    1988-01-01

    The first accurate theoretical values for off-diagonal (i.e., line-coupling) pressure-broadening cross sections are presented. Calculations were done for CO perturbed by He at thermal collision energies using an accurate ab initio potential energy surface. Converged close coupling, i.e., numerically exact values, were obtained for coupling to the R(0) and R(2) lines. These were used to test the coupled states (CS) and infinite order sudden (IOS) approximate scattering methods. CS was found to be of quantitative accuracy (a few percent) and has been used to obtain coupling values for lines to R(10). IOS values are less accurate, but, owing to their simplicity, may nonetheless prove useful as has been recently demonstrated.

  1. Detection and quantitation of Kaposi's sarcoma-associated herpesvirus (KSHV) by a single competitive-quantitative polymerase chain reaction.

    PubMed

    Curreli, Francesca; Robles, Monica A; Friedman-Kien, Alvin E; Flore, Ornella

    2003-02-01

    Kaposi's sarcoma-associated herpesvirus is a novel herpesvirus linked to AIDS-related neoplasms. Currently it is difficult to evaluate the number of virions in viral preparation or in samples obtained from patients with Kaposi's sarcoma (KS), since no protocol for determining the plaque forming units of KSHV exists. We constructed a fragment of a different size than the target viral DNA to carry out a competitive-quantitative PCR. Both fragment and viral DNA were added to a single PCR reaction to compete for the same set of primers. By knowing the amount of the competitor added to the reaction, we could determine the number of viral DNA molecules. We used this assay successfully to detect and quantify KSHV genomes from KS skin biopsies and pleural effusion lymphoma, and from different viral preparations. To date, this is the most convenient and economic method that allows an accurate and fast viral detection/quantitation with a single PCR.

  2. An efficient and accurate 3D displacements tracking strategy for digital volume correlation

    NASA Astrophysics Data System (ADS)

    Pan, Bing; Wang, Bo; Wu, Dafang; Lubineau, Gilles

    2014-07-01

    Owing to its inherent computational complexity, practical implementation of digital volume correlation (DVC) for internal displacement and strain mapping faces important challenges in improving its computational efficiency. In this work, an efficient and accurate 3D displacement tracking strategy is proposed for fast DVC calculation. The efficiency advantage is achieved by using three improvements. First, to eliminate the need of updating Hessian matrix in each iteration, an efficient 3D inverse compositional Gauss-Newton (3D IC-GN) algorithm is introduced to replace existing forward additive algorithms for accurate sub-voxel displacement registration. Second, to ensure the 3D IC-GN algorithm that converges accurately and rapidly and avoid time-consuming integer-voxel displacement searching, a generalized reliability-guided displacement tracking strategy is designed to transfer accurate and complete initial guess of deformation for each calculation point from its computed neighbors. Third, to avoid the repeated computation of sub-voxel intensity interpolation coefficients, an interpolation coefficient lookup table is established for tricubic interpolation. The computational complexity of the proposed fast DVC and the existing typical DVC algorithms are first analyzed quantitatively according to necessary arithmetic operations. Then, numerical tests are performed to verify the performance of the fast DVC algorithm in terms of measurement accuracy and computational efficiency. The experimental results indicate that, compared with the existing DVC algorithm, the presented fast DVC algorithm produces similar precision and slightly higher accuracy at a substantially reduced computational cost.

  3. 5-Aminolevulinic acid-induced protoporphyrin IX fluorescence in meningioma: qualitative and quantitative measurements in vivo.

    PubMed

    Valdes, Pablo A; Bekelis, Kimon; Harris, Brent T; Wilson, Brian C; Leblond, Frederic; Kim, Anthony; Simmons, Nathan E; Erkmen, Kadir; Paulsen, Keith D; Roberts, David W

    2014-03-01

    The use of 5-aminolevulinic acid (ALA)-induced protoporphyrin IX (PpIX) fluorescence has shown promise as a surgical adjunct for maximizing the extent of surgical resection in gliomas. To date, the clinical utility of 5-ALA in meningiomas is not fully understood, with most descriptive studies using qualitative approaches to 5-ALA-PpIX. To assess the diagnostic performance of 5-ALA-PpIX fluorescence during surgical resection of meningioma. ALA was administered to 15 patients with meningioma undergoing PpIX fluorescence-guided surgery at our institution. At various points during the procedure, the surgeon performed qualitative, visual assessments of fluorescence by using the surgical microscope, followed by a quantitative fluorescence measurement by using an intraoperative probe. Specimens were collected at each point for subsequent neuropathological analysis. Clustered data analysis of variance was used to ascertain a difference between groups, and receiver operating characteristic analyses were performed to assess diagnostic capabilities. Red-pink fluorescence was observed in 80% (12/15) of patients, with visible fluorescence generally demonstrating a strong, homogenous character. Quantitative fluorescence measured diagnostically significant PpIX concentrations (cPpIx) in both visibly and nonvisibly fluorescent tissues, with significantly higher cPpIx in both visibly fluorescent (P < .001) and tumor tissue (P = .002). Receiver operating characteristic analyses also showed diagnostic accuracies up to 90% for differentiating tumor from normal dura. ALA-induced PpIX fluorescence guidance is a potential and promising adjunct in accurately detecting neoplastic tissue during meningioma resective surgery. These results suggest a broader reach for PpIX as a biomarker for meningiomas than was previously noted in the literature.

  4. 5-Aminolevulinic Acid-Induced Protoporphyrin IX Fluorescence in Meningioma: Qualitative and Quantitative Measurements In Vivo

    PubMed Central

    Valdes, Pablo A.; Bekelis, Kimon; Harris, Brent T.; Wilson, Brian C.; Leblond, Frederic; Kim, Anthony; Simmons, Nathan E.; Erkmen, Kadir; Paulsen, Keith D.; Roberts, David W.

    2014-01-01

    BACKGROUND The use of 5-aminolevulinic acid (ALA)-induced protoporphyrin IX (PpIX) fluorescence has shown promise as a surgical adjunct for maximizing the extent of surgical resection in gliomas. To date, the clinical utility of 5-ALA in meningiomas is not fully understood, with most descriptive studies using qualitative approaches to 5-ALA-PpIX. OBJECTIVE To assess the diagnostic performance of 5-ALA-PpIX fluorescence during surgical resection of meningioma. METHODS ALA was administered to 15 patients with meningioma undergoing PpIX fluorescence-guided surgery at our institution. At various points during the procedure, the surgeon performed qualitative, visual assessments of fluorescence by using the surgical microscope, followed by a quantitative fluorescence measurement by using an intra-operative probe. Specimens were collected at each point for subsequent neuropathological analysis. Clustered data analysis of variance was used to ascertain a difference between groups, and receiver operating characteristic analyses were performed to assess diagnostic capabilities. RESULTS Red-pink fluorescence was observed in 80% (12/15) of patients, with visible fluorescence generally demonstrating a strong, homogenous character. Quantitative fluorescence measured diagnostically significant PpIX concentrations (CPpIx) in both visibly and nonvisibly fluorescent tissues, with significantly higher CPpIx in both visibly fluorescent (P < .001) and tumor tissue (P = .002). Receiver operating characteristic analyses also showed diagnostic accuracies up to 90% for differentiating tumor from normal dura. CONCLUSION ALA-induced PpIX fluorescence guidance is a potential and promising adjunct in accurately detecting neoplastic tissue during meningioma resective surgery. These results suggest a broader reach for PpIX as a biomarker for meningiomas than was previously noted in the literature. PMID:23887194

  5. Magnetic Resonance Imaging of Intracranial Hypotension: Diagnostic Value of Combined Qualitative Signs and Quantitative Metrics.

    PubMed

    Aslan, Kerim; Gunbey, Hediye Pinar; Tomak, Leman; Ozmen, Zafer; Incesu, Lutfi

    The aim of this study was to investigate whether the use of combination quantitative metrics (mamillopontine distance [MPD], pontomesencephalic angle, and mesencephalon anterior-posterior/medial-lateral diameter ratios) with qualitative signs (dural enhancement, subdural collections/hematoma, venous engorgement, pituitary gland enlargements, and tonsillar herniations) provides a more accurate diagnosis of intracranial hypotension (IH). The quantitative metrics and qualitative signs of 34 patients and 34 control subjects were assessed by 2 independent observers. Receiver operating characteristic (ROC) curve was used to evaluate the diagnostic performance of quantitative metrics and qualitative signs, and for the diagnosis of IH, optimum cutoff values of quantitative metrics were found with ROC analysis. Combined ROC curve was measured for the quantitative metrics, and qualitative signs combinations in determining diagnostic accuracy and sensitivity, specificity, and positive and negative predictive values were found, and the best model combination was formed. Whereas MPD and pontomesencephalic angle were significantly lower in patients with IH when compared with the control group (P < 0.001), mesencephalon anterior-posterior/medial-lateral diameter ratio was significantly higher (P < 0.001). For qualitative signs, the highest individual distinctive power was dural enhancement with area under the ROC curve (AUC) of 0.838. For quantitative metrics, the highest individual distinctive power was MPD with AUC of 0.947. The best accuracy in the diagnosis of IH was obtained by combination of dural enhancement, venous engorgement, and MPD with an AUC of 1.00. This study showed that the combined use of dural enhancement, venous engorgement, and MPD had diagnostic accuracy of 100 % for the diagnosis of IH. Therefore, a more accurate IH diagnosis can be provided with combination of quantitative metrics with qualitative signs.

  6. Targeted Quantitation of Proteins by Mass Spectrometry

    PubMed Central

    2013-01-01

    Quantitative measurement of proteins is one of the most fundamental analytical tasks in a biochemistry laboratory, but widely used immunochemical methods often have limited specificity and high measurement variation. In this review, we discuss applications of multiple-reaction monitoring (MRM) mass spectrometry, which allows sensitive, precise quantitative analyses of peptides and the proteins from which they are derived. Systematic development of MRM assays is permitted by databases of peptide mass spectra and sequences, software tools for analysis design and data analysis, and rapid evolution of tandem mass spectrometer technology. Key advantages of MRM assays are the ability to target specific peptide sequences, including variants and modified forms, and the capacity for multiplexing that allows analysis of dozens to hundreds of peptides. Different quantitative standardization methods provide options that balance precision, sensitivity, and assay cost. Targeted protein quantitation by MRM and related mass spectrometry methods can advance biochemistry by transforming approaches to protein measurement. PMID:23517332

  7. Targeted quantitation of proteins by mass spectrometry.

    PubMed

    Liebler, Daniel C; Zimmerman, Lisa J

    2013-06-04

    Quantitative measurement of proteins is one of the most fundamental analytical tasks in a biochemistry laboratory, but widely used immunochemical methods often have limited specificity and high measurement variation. In this review, we discuss applications of multiple-reaction monitoring (MRM) mass spectrometry, which allows sensitive, precise quantitative analyses of peptides and the proteins from which they are derived. Systematic development of MRM assays is permitted by databases of peptide mass spectra and sequences, software tools for analysis design and data analysis, and rapid evolution of tandem mass spectrometer technology. Key advantages of MRM assays are the ability to target specific peptide sequences, including variants and modified forms, and the capacity for multiplexing that allows analysis of dozens to hundreds of peptides. Different quantitative standardization methods provide options that balance precision, sensitivity, and assay cost. Targeted protein quantitation by MRM and related mass spectrometry methods can advance biochemistry by transforming approaches to protein measurement.

  8. Improved accuracy in quantitative laser-induced breakdown spectroscopy using sub-models

    USGS Publications Warehouse

    Anderson, Ryan; Clegg, Samuel M.; Frydenvang, Jens; Wiens, Roger C.; McLennan, Scott M.; Morris, Richard V.; Ehlmann, Bethany L.; Dyar, M. Darby

    2017-01-01

    Accurate quantitative analysis of diverse geologic materials is one of the primary challenges faced by the Laser-Induced Breakdown Spectroscopy (LIBS)-based ChemCam instrument on the Mars Science Laboratory (MSL) rover. The SuperCam instrument on the Mars 2020 rover, as well as other LIBS instruments developed for geochemical analysis on Earth or other planets, will face the same challenge. Consequently, part of the ChemCam science team has focused on the development of improved multivariate analysis calibrations methods. Developing a single regression model capable of accurately determining the composition of very different target materials is difficult because the response of an element’s emission lines in LIBS spectra can vary with the concentration of other elements. We demonstrate a conceptually simple “sub-model” method for improving the accuracy of quantitative LIBS analysis of diverse target materials. The method is based on training several regression models on sets of targets with limited composition ranges and then “blending” these “sub-models” into a single final result. Tests of the sub-model method show improvement in test set root mean squared error of prediction (RMSEP) for almost all cases. The sub-model method, using partial least squares regression (PLS), is being used as part of the current ChemCam quantitative calibration, but the sub-model method is applicable to any multivariate regression method and may yield similar improvements.

  9. Detection and quantitation of chromosomal mosaicism in human blastocysts using copy number variation sequencing.

    PubMed

    Ruttanajit, Tida; Chanchamroen, Sujin; Cram, David S; Sawakwongpra, Kritchakorn; Suksalak, Wanwisa; Leng, Xue; Fan, Junmei; Wang, Li; Yao, Yuanqing; Quangkananurug, Wiwat

    2016-02-01

    Currently, our understanding of the nature and reproductive potential of blastocysts associated with trophectoderm (TE) lineage chromosomal mosaicism is limited. The objective of this study was to first validate copy number variation sequencing (CNV-Seq) for measuring the level of mosaicism and second, examine the nature and level of mosaicism in TE biopsies of patient's blastocysts. TE biopy samples were analysed by array comparative genomic hybridization (CGH) and CNV-Seq to discriminate between euploid, aneuploid and mosaic blastocysts. Using artificial models of TE mosaicism for five different chromosomes, CNV-Seq accurately and reproducibly quantitated mosaicism at levels of 50% and 20%. In a comparative 24-chromosome study of 49 blastocysts by array CGH and CNV-Seq, 43 blastocysts (87.8%) had a concordant diagnosis and 6 blastocysts (12.2%) were discordant. The discordance was attributed to low to medium levels of chromosomal mosaicism (30-70%) not detected by array CGH. In an expanded study of 399 blastocysts using CNV-Seq as the sole diagnostic method, the proportion of diploid-aneuploid mosaics (34, 8.5%) was significantly higher than aneuploid mosaics (18, 4.5%) (p < 0.02). Mosaicism is a significant chromosomal abnormality associated with the TE lineage of human blastocysts that can be reliably and accurately detected by CNV-Seq. © 2015 John Wiley & Sons, Ltd.

  10. Quantitative real-time PCR approaches for microbial community studies in wastewater treatment systems: applications and considerations.

    PubMed

    Kim, Jaai; Lim, Juntaek; Lee, Changsoo

    2013-12-01

    Quantitative real-time PCR (qPCR) has been widely used in recent environmental microbial ecology studies as a tool for detecting and quantifying microorganisms of interest, which aids in better understandings of the complexity of wastewater microbial communities. Although qPCR can be used to provide more specific and accurate quantification than other molecular techniques, it does have limitations that must be considered when applying it in practice. This article reviews the principle of qPCR quantification and its applications to microbial ecology studies in various wastewater treatment environments. Here we also address several limitations of qPCR-based approaches that can affect the validity of quantification data: template nucleic acid quality, nucleic acid extraction efficiency, specificity of group-specific primers and probes, amplification of nonviable DNA, gene copy number variation, and limited number of sequences in the database. Even with such limitations, qPCR is reportedly among the best methods for quantitatively investigating environmental microbial communities. The application of qPCR is and will continue to be increasingly common in studies of wastewater treatment systems. To obtain reliable analyses, however, the limitations that have often been overlooked must be carefully considered when interpreting the results. Copyright © 2013 Elsevier Inc. All rights reserved.

  11. Quantitative Analysis of Repertoire-Scale Immunoglobulin Properties in Vaccine-Induced B-Cell Responses

    DTIC Science & Technology

    2017-05-10

    repertoire-wide properties. Finally, through 75 the use of appropriate statistical analyses, the repertoire profiles can be quantitatively compared and 76...cell response to eVLP and 503 quantitatively compare GC B-cell repertoires from immunization conditions. We partitioned the 504 resulting clonotype... Quantitative analysis of repertoire-scale immunoglobulin properties in vaccine-induced B-cell responses Ilja V. Khavrutskii1, Sidhartha Chaudhury*1

  12. Quantitatively accurate activity measurements with a dedicated cardiac SPECT camera: Physical phantom experiments

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

    Pourmoghaddas, Amir, E-mail: apour@ottawaheart.ca; Wells, R. Glenn

    Purpose: Recently, there has been increased interest in dedicated cardiac single photon emission computed tomography (SPECT) scanners with pinhole collimation and improved detector technology due to their improved count sensitivity and resolution over traditional parallel-hole cameras. With traditional cameras, energy-based approaches are often used in the clinic for scatter compensation because they are fast and easily implemented. Some of the cardiac cameras use cadmium-zinc-telluride (CZT) detectors which can complicate the use of energy-based scatter correction (SC) due to the low-energy tail—an increased number of unscattered photons detected with reduced energy. Modified energy-based scatter correction methods can be implemented, but theirmore » level of accuracy is unclear. In this study, the authors validated by physical phantom experiments the quantitative accuracy and reproducibility of easily implemented correction techniques applied to {sup 99m}Tc myocardial imaging with a CZT-detector-based gamma camera with multiple heads, each with a single-pinhole collimator. Methods: Activity in the cardiac compartment of an Anthropomorphic Torso phantom (Data Spectrum Corporation) was measured through 15 {sup 99m}Tc-SPECT acquisitions. The ratio of activity concentrations in organ compartments resembled a clinical {sup 99m}Tc-sestamibi scan and was kept consistent across all experiments (1.2:1 heart to liver and 1.5:1 heart to lung). Two background activity levels were considered: no activity (cold) and an activity concentration 1/10th of the heart (hot). A plastic “lesion” was placed inside of the septal wall of the myocardial insert to simulate the presence of a region without tracer uptake and contrast in this lesion was calculated for all images. The true net activity in each compartment was measured with a dose calibrator (CRC-25R, Capintec, Inc.). A 10 min SPECT image was acquired using a dedicated cardiac camera with CZT detectors (Discovery NM530c

  13. Evaluation of coronary stenosis with the aid of quantitative image analysis in histological cross sections.

    PubMed

    Dulohery, Kate; Papavdi, Asteria; Michalodimitrakis, Manolis; Kranioti, Elena F

    2012-11-01

    Coronary artery atherosclerosis is a hugely prevalent condition in the Western World and is often encountered during autopsy. Atherosclerotic plaques can cause luminal stenosis: which, if over a significant level (75%), is said to contribute to cause of death. Estimation of stenosis can be macroscopically performed by the forensic pathologists at the time of autopsy or by microscopic examination. This study compares macroscopic estimation with quantitative microscopic image analysis with a particular focus on the assessment of significant stenosis (>75%). A total of 131 individuals were analysed. The sample consists of an atherosclerotic group (n=122) and a control group (n=9). The results of the two methods were significantly different from each other (p=0.001) and the macroscopic method gave a greater percentage stenosis by an average of 3.5%. Also, histological examination of coronary artery stenosis yielded a difference in significant stenosis in 11.5% of cases. The differences were attributed to either histological quantitative image analysis underestimation; gross examination overestimation; or, a combination of both. The underestimation may have come from tissue shrinkage during tissue processing for histological specimen. The overestimation from the macroscopic assessment can be attributed to the lumen shape, to the examiner observer error or to a possible bias to diagnose coronary disease when no other cause of death is apparent. The results indicate that the macroscopic estimation is open to more biases and that histological quantitative image analysis only gives a precise assessment of stenosis ex vivo. Once tissue shrinkage, if any, is accounted for then histological quantitative image analysis will yield a more accurate assessment of in vivo stenosis. It may then be considered a complementary tool for the examination of coronary stenosis. Copyright © 2012 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.

  14. Shedding quantitative fluorescence light on novel regulatory mechanisms in skeletal biomedicine and biodentistry.

    PubMed

    Lee, Ji-Won; Iimura, Tadahiro

    2017-02-01

    Digitalized fluorescence images contain numerical information such as color (wavelength), fluorescence intensity and spatial position. However, quantitative analyses of acquired data and their validation remained to be established. Our research group has applied quantitative fluorescence imaging on tissue sections and uncovered novel findings in skeletal biomedicine and biodentistry. This review paper includes a brief background of quantitative fluorescence imaging and discusses practical applications by introducing our previous research. Finally, the future perspectives of quantitative fluorescence imaging are discussed.

  15. Liquid chromatography-mass spectrometry-based quantitative proteomics.

    PubMed

    Linscheid, Michael W; Ahrends, Robert; Pieper, Stefan; Kühn, Andreas

    2009-01-01

    During the last decades, molecular sciences revolutionized biomedical research and gave rise to the biotechnology industry. During the next decades, the application of the quantitative sciences--informatics, physics, chemistry, and engineering--to biomedical research brings about the next revolution that will improve human healthcare and certainly create new technologies, since there is no doubt that small changes can have great effects. It is not a question of "yes" or "no," but of "how much," to make best use of the medical options we will have. In this context, the development of accurate analytical methods must be considered a cornerstone, since the understanding of biological processes will be impossible without information about the minute changes induced in cells by interactions of cell constituents with all sorts of endogenous and exogenous influences and disturbances. The first quantitative techniques, which were developed, allowed monitoring relative changes only, but they clearly showed the significance of the information obtained. The recent advent of techniques claiming to quantify proteins and peptides not only relative to each other, but also in an absolute fashion, promised another quantum leap, since knowing the absolute amount will allow comparing even unrelated species and the definition of parameters will permit to model biological systems much more accurate than before. To bring these promises to life, several approaches are under development at this point in time and this review is focused on those developments.

  16. Tomosynthesis can facilitate accurate measurement of joint space width under the condition of the oblique incidence of X-rays in patients with rheumatoid arthritis.

    PubMed

    Ono, Yohei; Kashihara, Rina; Yasojima, Nobutoshi; Kasahara, Hideki; Shimizu, Yuka; Tamura, Kenichi; Tsutsumi, Kaori; Sutherland, Kenneth; Koike, Takao; Kamishima, Tamotsu

    2016-06-01

    Accurate evaluation of joint space width (JSW) is important in the assessment of rheumatoid arthritis (RA). In clinical radiography of bilateral hands, the oblique incidence of X-rays is unavoidable, which may cause perceptional or measurement error of JSW. The objective of this study was to examine whether tomosynthesis, a recently developed modality, can facilitate a more accurate evaluation of JSW than radiography under the condition of oblique incidence of X-rays. We investigated quantitative errors derived from the oblique incidence of X-rays by imaging phantoms simulating various finger joint spaces using radiographs and tomosynthesis images. We then compared the qualitative results of the modified total Sharp score of a total of 320 joints from 20 patients with RA between these modalities. A quantitative error was prominent when the location of the phantom was shifted along the JSW direction. Modified total Sharp scores of tomosynthesis images were significantly higher than those of radiography, that is to say JSW was regarded as narrower in tomosynthesis than in radiography when finger joints were located where the oblique incidence of X-rays is expected in the JSW direction. Tomosynthesis can facilitate accurate evaluation of JSW in finger joints of patients with RA, even with oblique incidence of X-rays. Accurate evaluation of JSW is necessary for the management of patients with RA. Through phantom and clinical studies, we demonstrate that tomosynthesis may achieve more accurate evaluation of JSW.

  17. Quantitative measures for redox signaling.

    PubMed

    Pillay, Ché S; Eagling, Beatrice D; Driscoll, Scott R E; Rohwer, Johann M

    2016-07-01

    Redox signaling is now recognized as an important regulatory mechanism for a number of cellular processes including the antioxidant response, phosphokinase signal transduction and redox metabolism. While there has been considerable progress in identifying the cellular machinery involved in redox signaling, quantitative measures of redox signals have been lacking, limiting efforts aimed at understanding and comparing redox signaling under normoxic and pathogenic conditions. Here we have outlined some of the accepted principles for redox signaling, including the description of hydrogen peroxide as a signaling molecule and the role of kinetics in conferring specificity to these signaling events. Based on these principles, we then develop a working definition for redox signaling and review a number of quantitative methods that have been employed to describe signaling in other systems. Using computational modeling and published data, we show how time- and concentration- dependent analyses, in particular, could be used to quantitatively describe redox signaling and therefore provide important insights into the functional organization of redox networks. Finally, we consider some of the key challenges with implementing these methods. Copyright © 2016 Elsevier Inc. All rights reserved.

  18. Incorporation of unique molecular identifiers in TruSeq adapters improves the accuracy of quantitative sequencing.

    PubMed

    Hong, Jungeui; Gresham, David

    2017-11-01

    Quantitative analysis of next-generation sequencing (NGS) data requires discriminating duplicate reads generated by PCR from identical molecules that are of unique origin. Typically, PCR duplicates are identified as sequence reads that align to the same genomic coordinates using reference-based alignment. However, identical molecules can be independently generated during library preparation. Misidentification of these molecules as PCR duplicates can introduce unforeseen biases during analyses. Here, we developed a cost-effective sequencing adapter design by modifying Illumina TruSeq adapters to incorporate a unique molecular identifier (UMI) while maintaining the capacity to undertake multiplexed, single-index sequencing. Incorporation of UMIs into TruSeq adapters (TrUMIseq adapters) enables identification of bona fide PCR duplicates as identically mapped reads with identical UMIs. Using TrUMIseq adapters, we show that accurate removal of PCR duplicates results in improved accuracy of both allele frequency (AF) estimation in heterogeneous populations using DNA sequencing and gene expression quantification using RNA-Seq.

  19. Communication—Quantitative Voltammetric Analysis of High Concentration Actinides in Molten Salts

    DOE PAGES

    Hoyt, Nathaniel C.; Willit, James L.; Williamson, Mark A.

    2017-01-18

    Previous electroanalytical studies have shown that cyclic voltammetry can provide accurate quantitative measurements of actinide concentrations at low weight loadings in molten salts. However, above 2 wt%, the techniques were found to underpredict the concentrations of the reactant species. Here this work will demonstrate that much of the discrepancy is caused by uncompensated resistance and cylindrical diffusion. An improved electroanalytical approach has therefore been developed using the results of digital simulations to take these effects into account. This approach allows for accurate electroanalytical predictions across the full range of weight loadings expected to be encountered in operational nuclear fuel processingmore » equipment.« less

  20. Communication—Quantitative Voltammetric Analysis of High Concentration Actinides in Molten Salts

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

    Hoyt, Nathaniel C.; Willit, James L.; Williamson, Mark A.

    Previous electroanalytical studies have shown that cyclic voltammetry can provide accurate quantitative measurements of actinide concentrations at low weight loadings in molten salts. However, above 2 wt%, the techniques were found to underpredict the concentrations of the reactant species. Here this work will demonstrate that much of the discrepancy is caused by uncompensated resistance and cylindrical diffusion. An improved electroanalytical approach has therefore been developed using the results of digital simulations to take these effects into account. This approach allows for accurate electroanalytical predictions across the full range of weight loadings expected to be encountered in operational nuclear fuel processingmore » equipment.« less

  1. Design and analysis issues in quantitative proteomics studies.

    PubMed

    Karp, Natasha A; Lilley, Kathryn S

    2007-09-01

    Quantitative proteomics is the comparison of distinct proteomes which enables the identification of protein species which exhibit changes in expression or post-translational state in response to a given stimulus. Many different quantitative techniques are being utilized and generate large datasets. Independent of the technique used, these large datasets need robust data analysis to ensure valid conclusions are drawn from such studies. Approaches to address the problems that arise with large datasets are discussed to give insight into the types of statistical analyses of data appropriate for the various experimental strategies that can be employed by quantitative proteomic studies. This review also highlights the importance of employing a robust experimental design and highlights various issues surrounding the design of experiments. The concepts and examples discussed within will show how robust design and analysis will lead to confident results that will ensure quantitative proteomics delivers.

  2. Quantitative and Sensitive Detection of Chloramphenicol by Surface-Enhanced Raman Scattering

    PubMed Central

    Ding, Yufeng; Yin, Hongjun; Meng, Qingyun; Zhao, Yongmei; Liu, Luo; Wu, Zhenglong; Xu, Haijun

    2017-01-01

    We used surface-enhanced Raman scattering (SERS) for the quantitative and sensitive detection of chloramphenicol (CAP). Using 30 nm colloidal Au nanoparticles (NPs), a low detection limit for CAP of 10−8 M was obtained. The characteristic Raman peak of CAP centered at 1344 cm−1 was used for the rapid quantitative detection of CAP in three different types of CAP eye drops, and the accuracy of the measurement result was verified by high-performance liquid chromatography (HPLC). The experimental results reveal that the SERS technique based on colloidal Au NPs is accurate and sensitive, and can be used for the rapid detection of various antibiotics. PMID:29261161

  3. Assessing the reporting of categorised quantitative variables in observational epidemiological studies.

    PubMed

    Mabikwa, Onkabetse V; Greenwood, Darren C; Baxter, Paul D; Fleming, Sarah J

    2017-03-14

    One aspect to consider when reporting results of observational studies in epidemiology is how quantitative risk factors are analysed. The STROBE (Strengthening the Reporting of Observational Studies in Epidemiology) guidelines recommend that researchers describe how they handle quantitative variables when analysing data. For categorised quantitative variables, the authors are required to provide reasons and justifications informing their practice. We investigated and assessed the practices and reporting of categorised quantitative variables in epidemiology. The assessment was based on five medical journals that publish epidemiological research. Observational studies published between April and June 2015 and investigating the relationships between quantitative exposures (or risk factors) and the outcomes were considered for assessment. A standard form was used to collect the data, and the reporting patterns amongst eligible studies were quantified and described. Out of 61 articles assessed for eligibility, 23 observational studies were included in the assessment. Categorisation of quantitative exposures occurred in 61% of these studies and reasons informing the practice were rarely provided. Only one article explained the choice of categorisation in the analysis. Transformation of quantitative exposures into four or five groups was common and dominant amongst studies using equally spaced categories. Dichotomisation was not popular; the practice featured in one article. Overall, the majority (86%) of the studies preferred ordered or arbitrary group categories. Other criterions used to decide categorical boundaries were based on established guidelines such as consensus statements and WHO standards. Categorisation of continuous variables remains a dominant practice in epidemiological studies. The reasons informing the practice of categorisation within published work are limited and remain unknown in most articles. The existing STROBE guidelines could provide stronger

  4. An autoanalyzer test for the quantitation of platelet-associated IgG

    NASA Technical Reports Server (NTRS)

    Levitan, Nathan; Teno, Richard A.; Szymanski, Irma O.

    1986-01-01

    A new quantitative antiglobulin consumption (QAC) test for the measurement of platelet-associated IgG is described. In this test washed platelets are incubated with anti-IgG at a final dilution of 1:2 million. The unneutralized fraction of anti-IgG remaining in solution is then measured with an Autoanalyzer and soluble IgG is used for calibration. The dose-response curves depicting the percent neutralization of anti-IgG by platelets and by soluble IgG were compared in detail and found to be nearly identical, indicating that platelet-associated IgG can be accurately quantitated by this method. The mean IgG values were 2287 molecules/platelet for normal adults and 38,112 molecules/platelet for ITP patients. The Autoanalyzer QAC test is a sensitive and reproducible assay for the quantitation of platelet-associated IgG.

  5. Good practices for quantitative bias analysis.

    PubMed

    Lash, Timothy L; Fox, Matthew P; MacLehose, Richard F; Maldonado, George; McCandless, Lawrence C; Greenland, Sander

    2014-12-01

    Quantitative bias analysis serves several objectives in epidemiological research. First, it provides a quantitative estimate of the direction, magnitude and uncertainty arising from systematic errors. Second, the acts of identifying sources of systematic error, writing down models to quantify them, assigning values to the bias parameters and interpreting the results combat the human tendency towards overconfidence in research results, syntheses and critiques and the inferences that rest upon them. Finally, by suggesting aspects that dominate uncertainty in a particular research result or topic area, bias analysis can guide efficient allocation of sparse research resources. The fundamental methods of bias analyses have been known for decades, and there have been calls for more widespread use for nearly as long. There was a time when some believed that bias analyses were rarely undertaken because the methods were not widely known and because automated computing tools were not readily available to implement the methods. These shortcomings have been largely resolved. We must, therefore, contemplate other barriers to implementation. One possibility is that practitioners avoid the analyses because they lack confidence in the practice of bias analysis. The purpose of this paper is therefore to describe what we view as good practices for applying quantitative bias analysis to epidemiological data, directed towards those familiar with the methods. We focus on answering questions often posed to those of us who advocate incorporation of bias analysis methods into teaching and research. These include the following. When is bias analysis practical and productive? How does one select the biases that ought to be addressed? How does one select a method to model biases? How does one assign values to the parameters of a bias model? How does one present and interpret a bias analysis?. We hope that our guide to good practices for conducting and presenting bias analyses will encourage

  6. Fluorescence-based Western blotting for quantitation of protein biomarkers in clinical samples.

    PubMed

    Zellner, Maria; Babeluk, Rita; Diestinger, Michael; Pirchegger, Petra; Skeledzic, Senada; Oehler, Rudolf

    2008-09-01

    Since most high throughput techniques used in biomarker discovery are very time and cost intensive, highly specific and quantitative analytical alternative application methods are needed for the routine analysis. Conventional Western blotting allows detection of specific proteins to the level of single isotypes while its quantitative accuracy is rather limited. We report a novel and improved quantitative Western blotting method. The use of fluorescently labelled secondary antibodies strongly extends the dynamic range of the quantitation and improves the correlation with the protein amount (r=0.997). By an additional fluorescent staining of all proteins immediately after their transfer to the blot membrane, it is possible to visualise simultaneously the antibody binding and the total protein profile. This allows for an accurate correction for protein load. Applying this normalisation it could be demonstrated that fluorescence-based Western blotting is able to reproduce a quantitative analysis of two specific proteins in blood platelet samples from 44 subjects with different diseases as initially conducted by 2D-DIGE. These results show that the proposed fluorescence-based Western blotting is an adequate application technique for biomarker quantitation and suggest possibilities of employment that go far beyond.

  7. Performance Evaluation and Quantitative Accuracy of Multipinhole NanoSPECT/CT Scanner for Theranostic Lu-177 Imaging

    NASA Astrophysics Data System (ADS)

    Gupta, Arun; Kim, Kyeong Yun; Hwang, Donghwi; Lee, Min Sun; Lee, Dong Soo; Lee, Jae Sung

    2018-06-01

    SPECT plays important role in peptide receptor targeted radionuclide therapy using theranostic radionuclides such as Lu-177 for the treatment of various cancers. However, SPECT studies must be quantitatively accurate because the reliable assessment of tumor uptake and tumor-to-normal tissue ratios can only be performed using quantitatively accurate images. Hence, it is important to evaluate performance parameters and quantitative accuracy of preclinical SPECT systems for therapeutic radioisotopes before conducting pre- and post-therapy SPECT imaging or dosimetry studies. In this study, we evaluated system performance and quantitative accuracy of NanoSPECT/CT scanner for Lu-177 imaging using point source and uniform phantom studies. We measured recovery coefficient, uniformity, spatial resolution, system sensitivity and calibration factor for mouse whole body standard aperture. We also performed the experiments using Tc-99m to compare the results with that of Lu-177. We found that the recovery coefficient of more than 70% for Lu-177 at the optimum noise level when nine iterations were used. The spatial resolutions of Lu-177 with and without adding uniform background was comparable to that of Tc-99m in axial, radial and tangential directions. System sensitivity measured for Lu-177 was almost three times less than that of Tc-99m.

  8. Less label, more free: approaches in label-free quantitative mass spectrometry.

    PubMed

    Neilson, Karlie A; Ali, Naveid A; Muralidharan, Sridevi; Mirzaei, Mehdi; Mariani, Michael; Assadourian, Gariné; Lee, Albert; van Sluyter, Steven C; Haynes, Paul A

    2011-02-01

    In this review we examine techniques, software, and statistical analyses used in label-free quantitative proteomics studies for area under the curve and spectral counting approaches. Recent advances in the field are discussed in an order that reflects a logical workflow design. Examples of studies that follow this design are presented to highlight the requirement for statistical assessment and further experiments to validate results from label-free quantitation. Limitations of label-free approaches are considered, label-free approaches are compared with labelling techniques, and forward-looking applications for label-free quantitative data are presented. We conclude that label-free quantitative proteomics is a reliable, versatile, and cost-effective alternative to labelled quantitation. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. A novel statistical method for quantitative comparison of multiple ChIP-seq datasets.

    PubMed

    Chen, Li; Wang, Chi; Qin, Zhaohui S; Wu, Hao

    2015-06-15

    ChIP-seq is a powerful technology to measure the protein binding or histone modification strength in the whole genome scale. Although there are a number of methods available for single ChIP-seq data analysis (e.g. 'peak detection'), rigorous statistical method for quantitative comparison of multiple ChIP-seq datasets with the considerations of data from control experiment, signal to noise ratios, biological variations and multiple-factor experimental designs is under-developed. In this work, we develop a statistical method to perform quantitative comparison of multiple ChIP-seq datasets and detect genomic regions showing differential protein binding or histone modification. We first detect peaks from all datasets and then union them to form a single set of candidate regions. The read counts from IP experiment at the candidate regions are assumed to follow Poisson distribution. The underlying Poisson rates are modeled as an experiment-specific function of artifacts and biological signals. We then obtain the estimated biological signals and compare them through the hypothesis testing procedure in a linear model framework. Simulations and real data analyses demonstrate that the proposed method provides more accurate and robust results compared with existing ones. An R software package ChIPComp is freely available at http://web1.sph.emory.edu/users/hwu30/software/ChIPComp.html. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  10. QUANTITATION OF MENSTRUAL BLOOD LOSS: A RADIOACTIVE METHOD UTILIZING A COUNTING DOME

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

    Tauxe, W.N.

    A description has been given of a simple, accurate tech nique for the quantitation of menstrual blood loss, involving the determination of a three- dimensional isosensitivity curve and the fashioning of a lucite dome with cover to fit these specifications. Ten normal subjects lost no more than 50 ml each per menstrual period. (auth)

  11. Monitoring cell morphology during necrosis and apoptosis by quantitative phase imaging

    NASA Astrophysics Data System (ADS)

    Mugnano, Martina; Calabuig, Alejandro; Grilli, Simonetta; Miccio, Lisa; Ferraro, Pietro

    2015-05-01

    Cellular morphology changes and volume alterations play significant roles in many biological processes and they are mirrors of cell functions. In this paper, we propose the Digital Holographic microscope (DH) as a non-invasive imaging technique for a rapid and accurate extraction of morphological information related to cell death. In particular, we investigate the morphological variations that occur during necrosis and apoptosis. The study of necrosis is extremely important because it is often associated with unwarranted loss of cells in human pathologies such as ischemia, trauma, and some forms of neurodegeneration; therefore, a better elucidation in terms of cell morphological changes could pave the way for new treatments. Also, apoptosis is extremely important because it's involved in cancer, both in its formation and in medical treatments. Because the inability to initiate apoptosis enhances tumour formation, current cancer treatments target this pathway. Within this framework, we have developed a transmission off-axis DH apparatus integrated with a micro incubator for investigation of living cells in a temperature and CO2 controlled environment. We employ DH to analyse the necrosis cell death induced by laser light (wavelength 473 nm, light power 4 mW). We have chosen as cellular model NIH 3T3 mouse embryonic fibroblasts because their adhesive features such as morphological changes, and the time needed to adhere and spread have been well characterized in the literature. We have monitored cell volume changes and morphological alterations in real time in order to study the necrosis process accurately and quantitatively. Cell volume changes were evaluated from the measured phase changes of light transmitted through cells. Our digital holographic experiments showed that after exposure of cells to laser light for 90-120 min., they swell and then take on a balloon-like shape until the plasma membrane ruptures and finally the cell volume decreases. Furthermore, we

  12. A General Method for Targeted Quantitative Cross-Linking Mass Spectrometry.

    PubMed

    Chavez, Juan D; Eng, Jimmy K; Schweppe, Devin K; Cilia, Michelle; Rivera, Keith; Zhong, Xuefei; Wu, Xia; Allen, Terrence; Khurgel, Moshe; Kumar, Akhilesh; Lampropoulos, Athanasios; Larsson, Mårten; Maity, Shuvadeep; Morozov, Yaroslav; Pathmasiri, Wimal; Perez-Neut, Mathew; Pineyro-Ruiz, Coriness; Polina, Elizabeth; Post, Stephanie; Rider, Mark; Tokmina-Roszyk, Dorota; Tyson, Katherine; Vieira Parrine Sant'Ana, Debora; Bruce, James E

    2016-01-01

    Chemical cross-linking mass spectrometry (XL-MS) provides protein structural information by identifying covalently linked proximal amino acid residues on protein surfaces. The information gained by this technique is complementary to other structural biology methods such as x-ray crystallography, NMR and cryo-electron microscopy[1]. The extension of traditional quantitative proteomics methods with chemical cross-linking can provide information on the structural dynamics of protein structures and protein complexes. The identification and quantitation of cross-linked peptides remains challenging for the general community, requiring specialized expertise ultimately limiting more widespread adoption of the technique. We describe a general method for targeted quantitative mass spectrometric analysis of cross-linked peptide pairs. We report the adaptation of the widely used, open source software package Skyline, for the analysis of quantitative XL-MS data as a means for data analysis and sharing of methods. We demonstrate the utility and robustness of the method with a cross-laboratory study and present data that is supported by and validates previously published data on quantified cross-linked peptide pairs. This advance provides an easy to use resource so that any lab with access to a LC-MS system capable of performing targeted quantitative analysis can quickly and accurately measure dynamic changes in protein structure and protein interactions.

  13. A Methodology for Conducting Integrative Mixed Methods Research and Data Analyses

    PubMed Central

    Castro, Felipe González; Kellison, Joshua G.; Boyd, Stephen J.; Kopak, Albert

    2011-01-01

    Mixed methods research has gained visibility within the last few years, although limitations persist regarding the scientific caliber of certain mixed methods research designs and methods. The need exists for rigorous mixed methods designs that integrate various data analytic procedures for a seamless transfer of evidence across qualitative and quantitative modalities. Such designs can offer the strength of confirmatory results drawn from quantitative multivariate analyses, along with “deep structure” explanatory descriptions as drawn from qualitative analyses. This article presents evidence generated from over a decade of pilot research in developing an integrative mixed methods methodology. It presents a conceptual framework and methodological and data analytic procedures for conducting mixed methods research studies, and it also presents illustrative examples from the authors' ongoing integrative mixed methods research studies. PMID:22167325

  14. Magnetoresistive biosensors for quantitative proteomics

    NASA Astrophysics Data System (ADS)

    Zhou, Xiahan; Huang, Chih-Cheng; Hall, Drew A.

    2017-08-01

    Quantitative proteomics, as a developing method for study of proteins and identification of diseases, reveals more comprehensive and accurate information of an organism than traditional genomics. A variety of platforms, such as mass spectrometry, optical sensors, electrochemical sensors, magnetic sensors, etc., have been developed for detecting proteins quantitatively. The sandwich immunoassay is widely used as a labeled detection method due to its high specificity and flexibility allowing multiple different types of labels. While optical sensors use enzyme and fluorophore labels to detect proteins with high sensitivity, they often suffer from high background signal and challenges in miniaturization. Magnetic biosensors, including nuclear magnetic resonance sensors, oscillator-based sensors, Hall-effect sensors, and magnetoresistive sensors, use the specific binding events between magnetic nanoparticles (MNPs) and target proteins to measure the analyte concentration. Compared with other biosensing techniques, magnetic sensors take advantage of the intrinsic lack of magnetic signatures in biological samples to achieve high sensitivity and high specificity, and are compatible with semiconductor-based fabrication process to have low-cost and small-size for point-of-care (POC) applications. Although still in the development stage, magnetic biosensing is a promising technique for in-home testing and portable disease monitoring.

  15. Improved accuracy in quantitative laser-induced breakdown spectroscopy using sub-models

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

    Anderson, Ryan B.; Clegg, Samuel M.; Frydenvang, Jens

    We report that accurate quantitative analysis of diverse geologic materials is one of the primary challenges faced by the Laser-Induced Breakdown Spectroscopy (LIBS)-based ChemCam instrument on the Mars Science Laboratory (MSL) rover. The SuperCam instrument on the Mars 2020 rover, as well as other LIBS instruments developed for geochemical analysis on Earth or other planets, will face the same challenge. Consequently, part of the ChemCam science team has focused on the development of improved multivariate analysis calibrations methods. Developing a single regression model capable of accurately determining the composition of very different target materials is difficult because the response ofmore » an element’s emission lines in LIBS spectra can vary with the concentration of other elements. We demonstrate a conceptually simple “submodel” method for improving the accuracy of quantitative LIBS analysis of diverse target materials. The method is based on training several regression models on sets of targets with limited composition ranges and then “blending” these “sub-models” into a single final result. Tests of the sub-model method show improvement in test set root mean squared error of prediction (RMSEP) for almost all cases. Lastly, the sub-model method, using partial least squares regression (PLS), is being used as part of the current ChemCam quantitative calibration, but the sub-model method is applicable to any multivariate regression method and may yield similar improvements.« less

  16. Improved accuracy in quantitative laser-induced breakdown spectroscopy using sub-models

    DOE PAGES

    Anderson, Ryan B.; Clegg, Samuel M.; Frydenvang, Jens; ...

    2016-12-15

    We report that accurate quantitative analysis of diverse geologic materials is one of the primary challenges faced by the Laser-Induced Breakdown Spectroscopy (LIBS)-based ChemCam instrument on the Mars Science Laboratory (MSL) rover. The SuperCam instrument on the Mars 2020 rover, as well as other LIBS instruments developed for geochemical analysis on Earth or other planets, will face the same challenge. Consequently, part of the ChemCam science team has focused on the development of improved multivariate analysis calibrations methods. Developing a single regression model capable of accurately determining the composition of very different target materials is difficult because the response ofmore » an element’s emission lines in LIBS spectra can vary with the concentration of other elements. We demonstrate a conceptually simple “submodel” method for improving the accuracy of quantitative LIBS analysis of diverse target materials. The method is based on training several regression models on sets of targets with limited composition ranges and then “blending” these “sub-models” into a single final result. Tests of the sub-model method show improvement in test set root mean squared error of prediction (RMSEP) for almost all cases. Lastly, the sub-model method, using partial least squares regression (PLS), is being used as part of the current ChemCam quantitative calibration, but the sub-model method is applicable to any multivariate regression method and may yield similar improvements.« less

  17. Using Qualitative Metasummary to Synthesize Qualitative and Quantitative Descriptive Findings

    PubMed Central

    Sandelowski, Margarete; Barroso, Julie; Voils, Corrine I.

    2008-01-01

    The new imperative in the health disciplines to be more methodologically inclusive has generated a growing interest in mixed research synthesis, or the integration of qualitative and quantitative research findings. Qualitative metasummary is a quantitatively oriented aggregation of qualitative findings originally developed to accommodate the distinctive features of qualitative surveys. Yet these findings are similar in form and mode of production to the descriptive findings researchers often present in addition to the results of bivariate and multivariable analyses. Qualitative metasummary, which includes the extraction, grouping, and formatting of findings, and the calculation of frequency and intensity effect sizes, can be used to produce mixed research syntheses and to conduct a posteriori analyses of the relationship between reports and findings. PMID:17243111

  18. Quantitative prediction of drug side effects based on drug-related features.

    PubMed

    Niu, Yanqing; Zhang, Wen

    2017-09-01

    Unexpected side effects of drugs are great concern in the drug development, and the identification of side effects is an important task. Recently, machine learning methods are proposed to predict the presence or absence of interested side effects for drugs, but it is difficult to make the accurate prediction for all of them. In this paper, we transform side effect profiles of drugs as their quantitative scores, by summing up their side effects with weights. The quantitative scores may measure the dangers of drugs, and thus help to compare the risk of different drugs. Here, we attempt to predict quantitative scores of drugs, namely the quantitative prediction. Specifically, we explore a variety of drug-related features and evaluate their discriminative powers for the quantitative prediction. Then, we consider several feature combination strategies (direct combination, average scoring ensemble combination) to integrate three informative features: chemical substructures, targets, and treatment indications. Finally, the average scoring ensemble model which produces the better performances is used as the final quantitative prediction model. Since weights for side effects are empirical values, we randomly generate different weights in the simulation experiments. The experimental results show that the quantitative method is robust to different weights, and produces satisfying results. Although other state-of-the-art methods cannot make the quantitative prediction directly, the prediction results can be transformed as the quantitative scores. By indirect comparison, the proposed method produces much better results than benchmark methods in the quantitative prediction. In conclusion, the proposed method is promising for the quantitative prediction of side effects, which may work cooperatively with existing state-of-the-art methods to reveal dangers of drugs.

  19. Local structure in LaMnO3 and CaMnO3 perovskites: A quantitative structural refinement of Mn K -edge XANES data

    NASA Astrophysics Data System (ADS)

    Monesi, C.; Meneghini, C.; Bardelli, F.; Benfatto, M.; Mobilio, S.; Manju, U.; Sarma, D. D.

    2005-11-01

    Hole-doped perovskites such as La1-xCaxMnO3 present special magnetic and magnetotransport properties, and it is commonly accepted that the local atomic structure around Mn ions plays a crucial role in determining these peculiar features. Therefore experimental techniques directly probing the local atomic structure, like x-ray absorption spectroscopy (XAS), have been widely exploited to deeply understand the physics of these compounds. Quantitative XAS analysis usually concerns the extended region [extended x-ray absorption fine structure (EXAFS)] of the absorption spectra. The near-edge region [x-ray absorption near-edge spectroscopy (XANES)] of XAS spectra can provide detailed complementary information on the electronic structure and local atomic topology around the absorber. However, the complexity of the XANES analysis usually prevents a quantitative understanding of the data. This work exploits the recently developed MXAN code to achieve a quantitative structural refinement of the Mn K -edge XANES of LaMnO3 and CaMnO3 compounds; they are the end compounds of the doped manganite series LaxCa1-xMnO3 . The results derived from the EXAFS and XANES analyses are in good agreement, demonstrating that a quantitative picture of the local structure can be obtained from XANES in these crystalline compounds. Moreover, the quantitative XANES analysis provides topological information not directly achievable from EXAFS data analysis. This work demonstrates that combining the analysis of extended and near-edge regions of Mn K -edge XAS spectra could provide a complete and accurate description of Mn local atomic environment in these compounds.

  20. A quantitative description for efficient financial markets

    NASA Astrophysics Data System (ADS)

    Immonen, Eero

    2015-09-01

    In this article we develop a control system model for describing efficient financial markets. We define the efficiency of a financial market in quantitative terms by robust asymptotic price-value equality in this model. By invoking the Internal Model Principle of robust output regulation theory we then show that under No Bubble Conditions, in the proposed model, the market is efficient if and only if the following conditions hold true: (1) the traders, as a group, can identify any mispricing in asset value (even if no one single trader can do it accurately), and (2) the traders, as a group, incorporate an internal model of the value process (again, even if no one single trader knows it). This main result of the article, which deliberately avoids the requirement for investor rationality, demonstrates, in quantitative terms, that the more transparent the markets are, the more efficient they are. An extensive example is provided to illustrate the theoretical development.

  1. Mapping of quantitative trait loci controlling adaptive traits in coastal Douglas-fir

    Treesearch

    Nicholas C. Wheeler; Kathleen D. Jermstad; Konstantin V. Krutovsky; Sally N. Aitken; Glenn T. Howe; Jodie Krakowski; David B. Neale

    2005-01-01

    Quantitative trait locus (QTL) analyses are used by geneticists to characterize the genetic architecture of quantitative traits, provide a foundation for marker-aided-selection (MAS), and provide a framework for positional selection of candidate genes. The most useful QTL for breeding applications are those that have been verified in time, space, and/or genetic...

  2. Bayesian B-spline mapping for dynamic quantitative traits.

    PubMed

    Xing, Jun; Li, Jiahan; Yang, Runqing; Zhou, Xiaojing; Xu, Shizhong

    2012-04-01

    Owing to their ability and flexibility to describe individual gene expression at different time points, random regression (RR) analyses have become a popular procedure for the genetic analysis of dynamic traits whose phenotypes are collected over time. Specifically, when modelling the dynamic patterns of gene expressions in the RR framework, B-splines have been proved successful as an alternative to orthogonal polynomials. In the so-called Bayesian B-spline quantitative trait locus (QTL) mapping, B-splines are used to characterize the patterns of QTL effects and individual-specific time-dependent environmental errors over time, and the Bayesian shrinkage estimation method is employed to estimate model parameters. Extensive simulations demonstrate that (1) in terms of statistical power, Bayesian B-spline mapping outperforms the interval mapping based on the maximum likelihood; (2) for the simulated dataset with complicated growth curve simulated by B-splines, Legendre polynomial-based Bayesian mapping is not capable of identifying the designed QTLs accurately, even when higher-order Legendre polynomials are considered and (3) for the simulated dataset using Legendre polynomials, the Bayesian B-spline mapping can find the same QTLs as those identified by Legendre polynomial analysis. All simulation results support the necessity and flexibility of B-spline in Bayesian mapping of dynamic traits. The proposed method is also applied to a real dataset, where QTLs controlling the growth trajectory of stem diameters in Populus are located.

  3. Quantitative SIMS Imaging of Agar-Based Microbial Communities.

    PubMed

    Dunham, Sage J B; Ellis, Joseph F; Baig, Nameera F; Morales-Soto, Nydia; Cao, Tianyuan; Shrout, Joshua D; Bohn, Paul W; Sweedler, Jonathan V

    2018-05-01

    After several decades of widespread use for mapping elemental ions and small molecular fragments in surface science, secondary ion mass spectrometry (SIMS) has emerged as a powerful analytical tool for molecular imaging in biology. Biomolecular SIMS imaging has primarily been used as a qualitative technique; although the distribution of a single analyte can be accurately determined, it is difficult to map the absolute quantity of a compound or even to compare the relative abundance of one molecular species to that of another. We describe a method for quantitative SIMS imaging of small molecules in agar-based microbial communities. The microbes are cultivated on a thin film of agar, dried under nitrogen, and imaged directly with SIMS. By use of optical microscopy, we show that the area of the agar is reduced by 26 ± 2% (standard deviation) during dehydration, but the overall biofilm morphology and analyte distribution are largely retained. We detail a quantitative imaging methodology, in which the ion intensity of each analyte is (1) normalized to an external quadratic regression curve, (2) corrected for isomeric interference, and (3) filtered for sample-specific noise and lower and upper limits of quantitation. The end result is a two-dimensional surface density image for each analyte. The sample preparation and quantitation methods are validated by quantitatively imaging four alkyl-quinolone and alkyl-quinoline N-oxide signaling molecules (including Pseudomonas quinolone signal) in Pseudomonas aeruginosa colony biofilms. We show that the relative surface densities of the target biomolecules are substantially different from values inferred through direct intensity comparison and that the developed methodologies can be used to quantitatively compare as many ions as there are available standards.

  4. Broadband rotor noise analyses

    NASA Technical Reports Server (NTRS)

    George, A. R.; Chou, S. T.

    1984-01-01

    The various mechanisms which generate broadband noise on a range of rotors studied include load fluctuations due to inflow turbulence, due to turbulent boundary layers passing the blades' trailing edges, and due to tip vortex formation. Existing analyses are used and extensions to them are developed to make more accurate predictions of rotor noise spectra and to determine which mechanisms are important in which circumstances. Calculations based on the various prediction methods in existing experiments were compared. The present analyses are adequate to predict the spectra from a wide variety of experiments on fans, full scale and model scale helicopter rotors, wind turbines, and propellers to within about 5 to 10 dB. Better knowledge of the inflow turbulence improves the accuracy of the predictions. Results indicate that inflow turbulence noise depends strongly on ambient conditions and dominates at low frequencies. Trailing edge noise and tip vortex noise are important at higher frequencies if inflow turbulence is weak. Boundary layer trailing edge noise, important, for large sized rotors, increases slowly with angle of attack but not as rapidly as tip vortex noise.

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

    PubMed

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

    2010-06-28

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

  6. Challenge in Enhancing the Teaching and Learning of Variable Measurements in Quantitative Research

    ERIC Educational Resources Information Center

    Kee, Chang Peng; Osman, Kamisah; Ahmad, Fauziah

    2013-01-01

    Statistical analysis is one component that cannot be avoided in a quantitative research. Initial observations noted that students in higher education institution faced difficulty analysing quantitative data which were attributed to the confusions of various variable measurements. This paper aims to compare the outcomes of two approaches applied in…

  7. Performance Metrics for Liquid Chromatography-Tandem Mass Spectrometry Systems in Proteomics Analyses*

    PubMed Central

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

    2010-01-01

    A major unmet need in LC-MS/MS-based proteomics analyses is a set of tools for quantitative assessment of system performance and evaluation of technical variability. Here we describe 46 system performance metrics for monitoring chromatographic performance, electrospray source stability, MS1 and MS2 signals, dynamic sampling of ions for MS/MS, and peptide identification. Applied to data sets from replicate LC-MS/MS analyses, these metrics displayed consistent, reasonable responses to controlled perturbations. The metrics typically displayed variations less than 10% and thus can reveal even subtle differences in performance of system components. Analyses of data from interlaboratory studies conducted under a common standard operating procedure identified outlier data and provided clues to specific causes. Moreover, interlaboratory variation reflected by the metrics indicates which system components vary the most between laboratories. Application of these metrics enables rational, quantitative quality assessment for proteomics and other LC-MS/MS analytical applications. PMID:19837981

  8. Two schemes for quantitative photoacoustic tomography based on Monte Carlo simulation

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

    Liu, Yubin; Yuan, Zhen, E-mail: zhenyuan@umac.mo

    Purpose: The aim of this study was to develop novel methods for photoacoustically determining the optical absorption coefficient of biological tissues using Monte Carlo (MC) simulation. Methods: In this study, the authors propose two quantitative photoacoustic tomography (PAT) methods for mapping the optical absorption coefficient. The reconstruction methods combine conventional PAT with MC simulation in a novel way to determine the optical absorption coefficient of biological tissues or organs. Specifically, the authors’ two schemes were theoretically and experimentally examined using simulations, tissue-mimicking phantoms, ex vivo, and in vivo tests. In particular, the authors explored these methods using several objects withmore » different absorption contrasts embedded in turbid media and by using high-absorption media when the diffusion approximation was not effective at describing the photon transport. Results: The simulations and experimental tests showed that the reconstructions were quantitatively accurate in terms of the locations, sizes, and optical properties of the targets. The positions of the recovered targets were accessed by the property profiles, where the authors discovered that the off center error was less than 0.1 mm for the circular target. Meanwhile, the sizes and quantitative optical properties of the targets were quantified by estimating the full width half maximum of the optical absorption property. Interestingly, for the reconstructed sizes, the authors discovered that the errors ranged from 0 for relatively small-size targets to 26% for relatively large-size targets whereas for the recovered optical properties, the errors ranged from 0% to 12.5% for different cases. Conclusions: The authors found that their methods can quantitatively reconstruct absorbing objects of different sizes and optical contrasts even when the diffusion approximation is unable to accurately describe the photon propagation in biological tissues. In particular

  9. Underutilisation of routinely collected data in the HIV programme in Zambia: a review of quantitatively analysed peer-reviewed articles.

    PubMed

    Munthali, Tendai; Musonda, Patrick; Mee, Paul; Gumede, Sehlulekile; Schaap, Ab; Mwinga, Alwyn; Phiri, Caroline; Kapata, Nathan; Michelo, Charles; Todd, Jim

    2017-06-13

    The extent to which routinely collected HIV data from Zambia has been used in peer-reviewed published articles remains unexplored. This paper is an analysis of peer-reviewed articles that utilised routinely collected HIV data from Zambia within six programme areas from 2004 to 2014. Articles on HIV, published in English, listed in the Directory of open access journals, African Journals Online, Google scholar, and PubMed were reviewed. Only articles from peer-reviewed journals, that utilised routinely collected data and included quantitative data analysis methods were included. Multi-country studies involving Zambia and another country, where the specific results for Zambia were not reported, as well as clinical trials and intervention studies that did not take place under routine care conditions were excluded, although community trials which referred patients to the routine clinics were included. Independent extraction was conducted using a predesigned data collection form. Pooled analysis was not possible due to diversity in topics reviewed. A total of 69 articles were extracted for review. Of these, 7 were excluded. From the 62 articles reviewed, 39 focused on HIV treatment and retention in care, 15 addressed prevention of mother-to-child transmission, 4 assessed social behavioural change, and 4 reported on voluntary counselling and testing. In our search, no articles were found on condom programming or voluntary male medical circumcision. The most common outcome measures reported were CD4+ count, clinical failure or mortality. The population analysed was children in 13 articles, women in 16 articles, and both adult men and women in 33 articles. During the 10 year period of review, only 62 articles were published analysing routinely collected HIV data in Zambia. Serious consideration needs to be made to maximise the utility of routinely collected data, and to benefit from the funds and efforts to collect these data. This could be achieved with government support

  10. 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.

  11. Accurate estimation of sigma(exp 0) using AIRSAR data

    NASA Technical Reports Server (NTRS)

    Holecz, Francesco; Rignot, Eric

    1995-01-01

    During recent years signature analysis, classification, and modeling of Synthetic Aperture Radar (SAR) data as well as estimation of geophysical parameters from SAR data have received a great deal of interest. An important requirement for the quantitative use of SAR data is the accurate estimation of the backscattering coefficient sigma(exp 0). In terrain with relief variations radar signals are distorted due to the projection of the scene topography into the slant range-Doppler plane. The effect of these variations is to change the physical size of the scattering area, leading to errors in the radar backscatter values and incidence angle. For this reason the local incidence angle, derived from sensor position and Digital Elevation Model (DEM) data must always be considered. Especially in the airborne case, the antenna gain pattern can be an additional source of radiometric error, because the radar look angle is not known precisely as a result of the the aircraft motions and the local surface topography. Consequently, radiometric distortions due to the antenna gain pattern must also be corrected for each resolution cell, by taking into account aircraft displacements (position and attitude) and position of the backscatter element, defined by the DEM data. In this paper, a method to derive an accurate estimation of the backscattering coefficient using NASA/JPL AIRSAR data is presented. The results are evaluated in terms of geometric accuracy, radiometric variations of sigma(exp 0), and precision of the estimated forest biomass.

  12. UNiquant, a program for quantitative proteomics analysis using stable isotope labeling.

    PubMed

    Huang, Xin; Tolmachev, Aleksey V; Shen, Yulei; Liu, Miao; Huang, Lin; Zhang, Zhixin; Anderson, Gordon A; Smith, Richard D; Chan, Wing C; Hinrichs, Steven H; Fu, Kai; Ding, Shi-Jian

    2011-03-04

    Stable isotope labeling (SIL) methods coupled with nanoscale liquid chromatography and high resolution tandem mass spectrometry are increasingly useful for elucidation of the proteome-wide differences between multiple biological samples. Development of more effective programs for the sensitive identification of peptide pairs and accurate measurement of the relative peptide/protein abundance are essential for quantitative proteomic analysis. We developed and evaluated the performance of a new program, termed UNiquant, for analyzing quantitative proteomics data using stable isotope labeling. UNiquant was compared with two other programs, MaxQuant and Mascot Distiller, using SILAC-labeled complex proteome mixtures having either known or unknown heavy/light ratios. For the SILAC-labeled Jeko-1 cell proteome digests with known heavy/light ratios (H/L = 1:1, 1:5, and 1:10), UNiquant quantified a similar number of peptide pairs as MaxQuant for the H/L = 1:1 and 1:5 mixtures. In addition, UNiquant quantified significantly more peptides than MaxQuant and Mascot Distiller in the H/L = 1:10 mixtures. UNiquant accurately measured relative peptide/protein abundance without the need for postmeasurement normalization of peptide ratios, which is required by the other programs.

  13. UNiquant, a Program for Quantitative Proteomics Analysis Using Stable Isotope Labeling

    PubMed Central

    Huang, Xin; Tolmachev, Aleksey V.; Shen, Yulei; Liu, Miao; Huang, Lin; Zhang, Zhixin; Anderson, Gordon A.; Smith, Richard D.; Chan, Wing C.; Hinrichs, Steven H.; Fu, Kai; Ding, Shi-Jian

    2011-01-01

    Stable isotope labeling (SIL) methods coupled with nanoscale liquid chromatography and high resolution tandem mass spectrometry are increasingly useful for elucidation of the proteome-wide differences between multiple biological samples. Development of more effective programs for the sensitive identification of peptide pairs and accurate measurement of the relative peptide/protein abundance are essential for quantitative proteomic analysis. We developed and evaluated the performance of a new program, termed UNiquant, for analyzing quantitative proteomics data using stable isotope labeling. UNiquant was compared with two other programs, MaxQuant and Mascot Distiller, using SILAC-labeled complex proteome mixtures having either known or unknown heavy/light ratios. For the SILAC-labeled Jeko-1 cell proteome digests with known heavy/light ratios (H/L = 1:1, 1:5, and 1:10), UNiquant quantified a similar number of peptide pairs as MaxQuant for the H/L = 1:1 and 1:5 mixtures. In addition, UNiquant quantified significantly more peptides than MaxQuant and Mascot Distiller in the H/L = 1:10 mixtures. UNiquant accurately measured relative peptide/protein abundance without the need for post-measurement normalization of peptide ratios, which is required by the other programs. PMID:21158445

  14. Quantitative DNA Methylation Profiling in Cancer.

    PubMed

    Ammerpohl, Ole; Haake, Andrea; Kolarova, Julia; Siebert, Reiner

    2016-01-01

    Epigenetic mechanisms including DNA methylation are fundamental for the regulation of gene expression. Epigenetic alterations can lead to the development and the evolution of malignant tumors as well as the emergence of phenotypically different cancer cells or metastasis from one single tumor cell. Here we describe bisulfite pyrosequencing, a technology to perform quantitative DNA methylation analyses, to detect aberrant DNA methylation in malignant tumors.

  15. Image interpolation allows accurate quantitative bone morphometry in registered micro-computed tomography scans.

    PubMed

    Schulte, Friederike A; Lambers, Floor M; Mueller, Thomas L; Stauber, Martin; Müller, Ralph

    2014-04-01

    Time-lapsed in vivo micro-computed tomography is a powerful tool to analyse longitudinal changes in the bone micro-architecture. Registration can overcome problems associated with spatial misalignment between scans; however, it requires image interpolation which might affect the outcome of a subsequent bone morphometric analysis. The impact of the interpolation error itself, though, has not been quantified to date. Therefore, the purpose of this ex vivo study was to elaborate the effect of different interpolator schemes [nearest neighbour, tri-linear and B-spline (BSP)] on bone morphometric indices. None of the interpolator schemes led to significant differences between interpolated and non-interpolated images, with the lowest interpolation error found for BSPs (1.4%). Furthermore, depending on the interpolator, the processing order of registration, Gaussian filtration and binarisation played a role. Independent from the interpolator, the present findings suggest that the evaluation of bone morphometry should be done with images registered using greyscale information.

  16. Accurate quantification of microRNA via single strand displacement reaction on DNA origami motif.

    PubMed

    Zhu, Jie; Feng, Xiaolu; Lou, Jingyu; Li, Weidong; Li, Sheng; Zhu, Hongxin; Yang, Lun; Zhang, Aiping; He, Lin; Li, Can

    2013-01-01

    DNA origami is an emerging technology that assembles hundreds of staple strands and one single-strand DNA into certain nanopattern. It has been widely used in various fields including detection of biological molecules such as DNA, RNA and proteins. MicroRNAs (miRNAs) play important roles in post-transcriptional gene repression as well as many other biological processes such as cell growth and differentiation. Alterations of miRNAs' expression contribute to many human diseases. However, it is still a challenge to quantitatively detect miRNAs by origami technology. In this study, we developed a novel approach based on streptavidin and quantum dots binding complex (STV-QDs) labeled single strand displacement reaction on DNA origami to quantitatively detect the concentration of miRNAs. We illustrated a linear relationship between the concentration of an exemplary miRNA as miRNA-133 and the STV-QDs hybridization efficiency; the results demonstrated that it is an accurate nano-scale miRNA quantifier motif. In addition, both symmetrical rectangular motif and asymmetrical China-map motif were tested. With significant linearity in both motifs, our experiments suggested that DNA Origami motif with arbitrary shape can be utilized in this method. Since this DNA origami-based method we developed owns the unique advantages of simple, time-and-material-saving, potentially multi-targets testing in one motif and relatively accurate for certain impurity samples as counted directly by atomic force microscopy rather than fluorescence signal detection, it may be widely used in quantification of miRNAs.

  17. Accurate Quantification of microRNA via Single Strand Displacement Reaction on DNA Origami Motif

    PubMed Central

    Lou, Jingyu; Li, Weidong; Li, Sheng; Zhu, Hongxin; Yang, Lun; Zhang, Aiping; He, Lin; Li, Can

    2013-01-01

    DNA origami is an emerging technology that assembles hundreds of staple strands and one single-strand DNA into certain nanopattern. It has been widely used in various fields including detection of biological molecules such as DNA, RNA and proteins. MicroRNAs (miRNAs) play important roles in post-transcriptional gene repression as well as many other biological processes such as cell growth and differentiation. Alterations of miRNAs' expression contribute to many human diseases. However, it is still a challenge to quantitatively detect miRNAs by origami technology. In this study, we developed a novel approach based on streptavidin and quantum dots binding complex (STV-QDs) labeled single strand displacement reaction on DNA origami to quantitatively detect the concentration of miRNAs. We illustrated a linear relationship between the concentration of an exemplary miRNA as miRNA-133 and the STV-QDs hybridization efficiency; the results demonstrated that it is an accurate nano-scale miRNA quantifier motif. In addition, both symmetrical rectangular motif and asymmetrical China-map motif were tested. With significant linearity in both motifs, our experiments suggested that DNA Origami motif with arbitrary shape can be utilized in this method. Since this DNA origami-based method we developed owns the unique advantages of simple, time-and-material-saving, potentially multi-targets testing in one motif and relatively accurate for certain impurity samples as counted directly by atomic force microscopy rather than fluorescence signal detection, it may be widely used in quantification of miRNAs. PMID:23990889

  18. Accurate inclusion mass screening: a bridge from unbiased discovery to targeted assay development for biomarker verification.

    PubMed

    Jaffe, Jacob D; Keshishian, Hasmik; Chang, Betty; Addona, Theresa A; Gillette, Michael A; Carr, Steven A

    2008-10-01

    Verification of candidate biomarker proteins in blood is typically done using multiple reaction monitoring (MRM) of peptides by LC-MS/MS on triple quadrupole MS systems. MRM assay development for each protein requires significant time and cost, much of which is likely to be of little value if the candidate biomarker is below the detection limit in blood or a false positive in the original discovery data. Here we present a new technology, accurate inclusion mass screening (AIMS), designed to provide a bridge from unbiased discovery to MS-based targeted assay development. Masses on the software inclusion list are monitored in each scan on the Orbitrap MS system, and MS/MS spectra for sequence confirmation are acquired only when a peptide from the list is detected with both the correct accurate mass and charge state. The AIMS experiment confirms that a given peptide (and thus the protein from which it is derived) is present in the plasma. Throughput of the method is sufficient to qualify up to a hundred proteins/week. The sensitivity of AIMS is similar to MRM on a triple quadrupole MS system using optimized sample preparation methods (low tens of ng/ml in plasma), and MS/MS data from the AIMS experiments on the Orbitrap can be directly used to configure MRM assays. The method was shown to be at least 4-fold more efficient at detecting peptides of interest than undirected LC-MS/MS experiments using the same instrumentation, and relative quantitation information can be obtained by AIMS in case versus control experiments. Detection by AIMS ensures that a quantitative MRM-based assay can be configured for that protein. The method has the potential to qualify large number of biomarker candidates based on their detection in plasma prior to committing to the time- and resource-intensive steps of establishing a quantitative assay.

  19. Effects of sampling close relatives on some elementary population genetics analyses.

    PubMed

    Wang, Jinliang

    2018-01-01

    Many molecular ecology analyses assume the genotyped individuals are sampled at random from a population and thus are representative of the population. Realistically, however, a sample may contain excessive close relatives (ECR) because, for example, localized juveniles are drawn from fecund species. Our knowledge is limited about how ECR affect the routinely conducted elementary genetics analyses, and how ECR are best dealt with to yield unbiased and accurate parameter estimates. This study quantifies the effects of ECR on some popular population genetics analyses of marker data, including the estimation of allele frequencies, F-statistics, expected heterozygosity (H e ), effective and observed numbers of alleles, and the tests of Hardy-Weinberg equilibrium (HWE) and linkage equilibrium (LE). It also investigates several strategies for handling ECR to mitigate their impact and to yield accurate parameter estimates. My analytical work, assisted by simulations, shows that ECR have large and global effects on all of the above marker analyses. The naïve approach of simply ignoring ECR could yield low-precision and often biased parameter estimates, and could cause too many false rejections of HWE and LE. The bold approach, which simply identifies and removes ECR, and the cautious approach, which estimates target parameters (e.g., H e ) by accounting for ECR and using naïve allele frequency estimates, eliminate the bias and the false HWE and LE rejections, but could reduce estimation precision substantially. The likelihood approach, which accounts for ECR in estimating allele frequencies and thus target parameters relying on allele frequencies, usually yields unbiased and the most accurate parameter estimates. Which of the four approaches is the most effective and efficient may depend on the particular marker analysis to be conducted. The results are discussed in the context of using marker data for understanding population properties and marker properties. © 2017

  20. Fluctuation localization imaging-based fluorescence in situ hybridization (fliFISH) for accurate detection and counting of RNA copies in single cells

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

    Cui, Yi; Hu, Dehong; Markillie, Lye Meng

    Quantitative gene expression analysis in intact single cells can be achieved using single molecule- based fluorescence in situ hybridization (smFISH). This approach relies on fluorescence intensity to distinguish between true signals, emitted from an RNA copy hybridized with multiple FISH sub-probes, and background noise. Thus, the precision in smFISH is often compromised by partial or nonspecific binding of sub-probes and tissue autofluorescence, limiting its accuracy. Here we provide an accurate approach for setting quantitative thresholds between true and false signals, which relies on blinking frequencies of photoswitchable dyes. This fluctuation localization imaging-based FISH (fliFISH) uses blinking frequency patterns, emitted frommore » a transcript bound to multiple sub-probes, which are distinct from blinking patterns emitted from partial or nonspecifically bound sub-probes and autofluorescence. Using multicolor fliFISH, we identified radial gene expression patterns in mouse pancreatic islets for insulin, the transcription factor, NKX2-2, and their ratio (Nkx2-2/Ins2). These radial patterns, showing higher values in β cells at the islet core and lower values in peripheral cells, were lost in diabetic mouse islets. In summary, fliFISH provides an accurate, quantitative approach for detecting and counting true RNA copies and rejecting false signals by their distinct blinking frequency patterns, laying the foundation for reliable single-cell transcriptomics.« less

  1. Quantitative Live-Cell Confocal Imaging of 3D Spheroids in a High-Throughput Format.

    PubMed

    Leary, Elizabeth; Rhee, Claire; Wilks, Benjamin T; Morgan, Jeffrey R

    2018-06-01

    Accurately predicting the human response to new compounds is critical to a wide variety of industries. Standard screening pipelines (including both in vitro and in vivo models) often lack predictive power. Three-dimensional (3D) culture systems of human cells, a more physiologically relevant platform, could provide a high-throughput, automated means to test the efficacy and/or toxicity of novel substances. However, the challenge of obtaining high-magnification, confocal z stacks of 3D spheroids and understanding their respective quantitative limitations must be overcome first. To address this challenge, we developed a method to form spheroids of reproducible size at precise spatial locations across a 96-well plate. Spheroids of variable radii were labeled with four different fluorescent dyes and imaged with a high-throughput confocal microscope. 3D renderings of the spheroid had a complex bowl-like appearance. We systematically analyzed these confocal z stacks to determine the depth of imaging and the effect of spheroid size and dyes on quantitation. Furthermore, we have shown that this loss of fluorescence can be addressed through the use of ratio imaging. Overall, understanding both the limitations of confocal imaging and the tools to correct for these limits is critical for developing accurate quantitative assays using 3D spheroids.

  2. Quantitative Peptidomics with Five-plex Reductive Methylation labels

    NASA Astrophysics Data System (ADS)

    Tashima, Alexandre K.; Fricker, Lloyd D.

    2017-12-01

    Quantitative peptidomics and proteomics often use chemical tags to covalently modify peptides with reagents that differ in the number of stable isotopes, allowing for quantitation of the relative peptide levels in the original sample based on the peak height of each isotopic form. Different chemical reagents have been used as tags for quantitative peptidomics and proteomics, and all have strengths and weaknesses. One of the simplest approaches uses formaldehyde and sodium cyanoborohydride to methylate amines, converting primary and secondary amines into tertiary amines. Up to five different isotopic forms can be generated, depending on the isotopic forms of formaldehyde and cyanoborohydride reagents, allowing for five-plex quantitation. However, the mass difference between each of these forms is only 1 Da per methyl group incorporated into the peptide, and for many peptides there is substantial overlap from the natural abundance of 13C and other isotopes. In this study, we calculated the contribution from the natural isotopes for 26 native peptides and derived equations to correct the peak intensities. These equations were applied to data from a study using human embryonic kidney HEK293T cells in which five replicates were treated with 100 nM vinblastine for 3 h and compared with five replicates of cells treated with control medium. The correction equations brought the replicates to the expected 1:1 ratios and revealed significant decreases in levels of 21 peptides upon vinblastine treatment. These equations enable accurate quantitation of small changes in peptide levels using the reductive methylation labeling approach. [Figure not available: see fulltext.

  3. Quantitative Peptidomics with Five-plex Reductive Methylation labels

    NASA Astrophysics Data System (ADS)

    Tashima, Alexandre K.; Fricker, Lloyd D.

    2018-05-01

    Quantitative peptidomics and proteomics often use chemical tags to covalently modify peptides with reagents that differ in the number of stable isotopes, allowing for quantitation of the relative peptide levels in the original sample based on the peak height of each isotopic form. Different chemical reagents have been used as tags for quantitative peptidomics and proteomics, and all have strengths and weaknesses. One of the simplest approaches uses formaldehyde and sodium cyanoborohydride to methylate amines, converting primary and secondary amines into tertiary amines. Up to five different isotopic forms can be generated, depending on the isotopic forms of formaldehyde and cyanoborohydride reagents, allowing for five-plex quantitation. However, the mass difference between each of these forms is only 1 Da per methyl group incorporated into the peptide, and for many peptides there is substantial overlap from the natural abundance of 13C and other isotopes. In this study, we calculated the contribution from the natural isotopes for 26 native peptides and derived equations to correct the peak intensities. These equations were applied to data from a study using human embryonic kidney HEK293T cells in which five replicates were treated with 100 nM vinblastine for 3 h and compared with five replicates of cells treated with control medium. The correction equations brought the replicates to the expected 1:1 ratios and revealed significant decreases in levels of 21 peptides upon vinblastine treatment. These equations enable accurate quantitation of small changes in peptide levels using the reductive methylation labeling approach. [Figure not available: see fulltext.

  4. Beyond Math Skills: Measuring Quantitative Reasoning in Context

    ERIC Educational Resources Information Center

    Grawe, Nathan D.

    2011-01-01

    It might be argued that quantitative and qualitative analyses are merely two alternative reflections of an overarching critical thinking. For instance, just as instructors of numeracy warn their charges to consider the construction of variables, teachers of qualitative approaches caution students to define terms. Similarly, an advocate of…

  5. Efficient and accurate causal inference with hidden confounders from genome-transcriptome variation data

    PubMed Central

    2017-01-01

    Mapping gene expression as a quantitative trait using whole genome-sequencing and transcriptome analysis allows to discover the functional consequences of genetic variation. We developed a novel method and ultra-fast software Findr for higly accurate causal inference between gene expression traits using cis-regulatory DNA variations as causal anchors, which improves current methods by taking into consideration hidden confounders and weak regulations. Findr outperformed existing methods on the DREAM5 Systems Genetics challenge and on the prediction of microRNA and transcription factor targets in human lymphoblastoid cells, while being nearly a million times faster. Findr is publicly available at https://github.com/lingfeiwang/findr. PMID:28821014

  6. Re-evaluation of a novel approach for quantitative myocardial oedema detection by analysing tissue inhomogeneity in acute myocarditis using T2-mapping.

    PubMed

    Baeßler, Bettina; Schaarschmidt, Frank; Treutlein, Melanie; Stehning, Christian; Schnackenburg, Bernhard; Michels, Guido; Maintz, David; Bunck, Alexander C

    2017-12-01

    To re-evaluate a recently suggested approach of quantifying myocardial oedema and increased tissue inhomogeneity in myocarditis by T2-mapping. Cardiac magnetic resonance data of 99 patients with myocarditis were retrospectively analysed. Thirthy healthy volunteers served as controls. T2-mapping data were acquired at 1.5 T using a gradient-spin-echo T2-mapping sequence. T2-maps were segmented according to the 16-segments AHA-model. Segmental T2-values, segmental pixel-standard deviation (SD) and the derived parameters maxT2, maxSD and madSD were analysed and compared to the established Lake Louise criteria (LLC). A re-estimation of logistic regression models revealed that all models containing an SD-parameter were superior to any model containing global myocardial T2. Using a combined cut-off of 1.8 ms for madSD + 68 ms for maxT2 resulted in a diagnostic sensitivity of 75% and specificity of 80% and showed a similar diagnostic performance compared to LLC in receiver-operating-curve analyses. Combining madSD, maxT2 and late gadolinium enhancement (LGE) in a model resulted in a superior diagnostic performance compared to LLC (sensitivity 93%, specificity 83%). The results show that the novel T2-mapping-derived parameters exhibit an additional diagnostic value over LGE with the inherent potential to overcome the current limitations of T2-mapping. • A novel quantitative approach to myocardial oedema imaging in myocarditis was re-evaluated. • The T2-mapping-derived parameters maxT2 and madSD were compared to traditional Lake-Louise criteria. • Using maxT2 and madSD with dedicated cut-offs performs similarly to Lake-Louise criteria. • Adding maxT2 and madSD to LGE results in further increased diagnostic performance. • This novel approach has the potential to overcome the limitations of T2-mapping.

  7. Review of Department of Defense Education Activity (DoDEA) Schools. Volume II: Quantitative Analysis of Educational Quality. IDA Paper.

    ERIC Educational Resources Information Center

    Anderson, Lowell Bruce; Bracken, Jerome; Bracken, Marilyn C.

    This volume compiles, and presents in integrated form, the Institute for Defense Analyses' (IDA) quantitative analysis of educational quality provided by the Department of Defense's dependent schools. It covers the quantitative aspects of volume 1 in greater detail and presents some analyses deemed too technical for that volume. The first task in…

  8. Will Quantitative Proteomics Redefine Some of the Key Concepts in Skeletal Muscle Physiology?

    PubMed

    Gizak, Agnieszka; Rakus, Dariusz

    2016-01-11

    Molecular and cellular biology methodology is traditionally based on the reasoning called "the mechanistic explanation". In practice, this means identifying and selecting correlations between biological processes which result from our manipulation of a biological system. In theory, a successful application of this approach requires precise knowledge about all parameters of a studied system. However, in practice, due to the systems' complexity, this requirement is rarely, if ever, accomplished. Typically, it is limited to a quantitative or semi-quantitative measurements of selected parameters (e.g., concentrations of some metabolites), and a qualitative or semi-quantitative description of expression/post-translational modifications changes within selected proteins. A quantitative proteomics approach gives a possibility of quantitative characterization of the entire proteome of a biological system, in the context of the titer of proteins as well as their post-translational modifications. This enables not only more accurate testing of novel hypotheses but also provides tools that can be used to verify some of the most fundamental dogmas of modern biology. In this short review, we discuss some of the consequences of using quantitative proteomics to verify several key concepts in skeletal muscle physiology.

  9. Unsteady aerodynamic analyses for turbomachinery aeroelastic predictions

    NASA Technical Reports Server (NTRS)

    Verdon, Joseph M.; Barnett, M.; Ayer, T. C.

    1994-01-01

    Applications for unsteady aerodynamics analysis in this report are: (1) aeroelastic: blade flutter and forced vibration; (2) aeroacoustic: noise generation; (3) vibration and noise control; and (4) effects of unsteadiness on performance. This requires that the numerical simulations and analytical modeling be accurate and efficient and contain realistic operating conditions and arbitrary modes of unsteady excitation. The assumptions of this application contend that: (1) turbulence and transition can be modeled with the Reynolds averaged and using Navier-Stokes equations; (2) 'attached' flow with high Reynolds number will require thin-layer Navier-Stokes equations, or inviscid/viscid interaction analyses; (3) small-amplitude unsteady excitations will need nonlinear steady and linearized unsteady analyses; and (4) Re to infinity will concern inviscid flow. Several computer programs (LINFLO, CLT, UNSVIS, AND SFLOW-IVI) are utilized for these analyses. Results and computerized grid examples are shown. This report was given during NASA LeRC Workshop on Forced Response in Turbomachinery in August of 1993.

  10. Qualitative and Quantitative Drug residue analyses: Florfenicol in white-tailed deer (Odocoileus virginianus) and supermarket meat by liquid chromatography tandem-mass spectrometry.

    PubMed

    Anderson, Shanoy C; Subbiah, Seenivasan; Gentles, Angella; Austin, Galen; Stonum, Paul; Brooks, Tiffanie A; Brooks, Chance; Smith, Ernest E

    2016-10-15

    A method for confirmation and detection of Florfenicol amine residues in white-tailed deer tissues was developed and validated in our laboratory. Tissue samples were extracted with ethyl acetate and cleaned up on sorbent (Chem-elut) cartridges. Liguid chromatography (LC) separation was achieved on a Zorbax Eclipse plus C18 column with gradient elution using a mobile phase composed of ammonium acetate in water and methanol at a flow rate of 300μL/min. Qualitative and quantitative analyses were carried out using liquid chromatography - heated electrospray ionization(HESI) and atmospheric pressure chemical ionization (APCI)-tandem mass spectrometry in the multiple reaction monitoring (MRM) interface. The limits of detection (LODs) for HESI and APCI probe were 1.8ng/g and 1.4ng/g respectively. Limits of quantitation (LOQs) for HESI and APCI probe were 5.8ng/g and 3.4ng/g respectively. Mean recovery values ranged from 79% to 111% for APCI and 30% to 60% for HESI. The validated method was used to determine white-tailed deer florfenicol tissue residue concentration 10-days after exposure. Florfenicol tissue residues concentration ranged from 0.4 to 0.6μg/g for liver and 0.02-0.05μg/g for muscle and a trace in blood samples. The concentration found in the tested edible tissues were lower than the maximum residual limit (MRL) values established by the federal drug administration (FDA) for bovine tissues. In summary, the resulting optimization procedures using the sensitivity of HESI and APCI probes in the determination of florfenicol in white-tailed deer tissue are the most compelling conclusions in this study, to the extent that we have applied this method in the evaluation of supermarket samples drug residue levels as a proof of principle. Copyright © 2016. Published by Elsevier B.V.

  11. Structural and quantitative expression analyses of HERV gene family in human tissues.

    PubMed

    Ahn, Kung; Kim, Heui-Soo

    2009-08-31

    Human endogenous retroviruses (HERVs) have been implicated in the pathogenesis of several human diseases as multi-copy members in the human genome. Their gene expression profiling could provide us with important insights into the pathogenic relationship between HERVs and cancer. In this study, we have evaluated the genomic structure and quantitatively determined the expression patterns in the env gene of a variety of HERV family members located on six specific loci by the RetroTector 10 program, as well as real-time RT-PCR amplification. The env gene transcripts evidenced significant differences in the human tumor/normal adjacent tissues (colon, liver, uterus, lung and testis). As compared to the adjacent normal tissues, high levels of expression were noted in testis tumor tissues for HERV-K, in liver and lung tumor tissues for HERV-R, in liver, lung, and testis tumor tissues for HERV-H, and in colon and liver tumor tissues for HERV-P. These data warrant further studies with larger groups of patients to develop biomarkers for specific human cancers.

  12. CIU and Main Event Analyses of the Structured Discourse of Older and Younger Adults

    ERIC Educational Resources Information Center

    Capilouto, Gilson; Wright, Heather Harris; Wagovich, Stacy A.

    2005-01-01

    Correct information unit (CIU) and main event analyses are quantitative measures for analyzing discourse of individuals with aphasia. Comparative data from healthy younger (YG) and older (OD) adults and an investigation of the influence of stimuli type would considerably extend the usefulness of such analyses. The objectives were (a) to compare…

  13. Quantitative analysis of drugs in hair by UHPLC high resolution mass spectrometry.

    PubMed

    Kronstrand, Robert; Forsman, Malin; Roman, Markus

    2018-02-01

    Liquid chromatographic methods coupled to high resolution mass spectrometry are increasingly used to identify compounds in various matrices including hair but there are few recommendations regarding the parameters and their criteria to identify a compound. In this study we present a method for the identification and quantification of a range of drugs and discuss the parameters used to identify a compound with high resolution mass spectrometry. Drugs were extracted from hair by incubation in a buffer:solvent mixture at 37°C during 18h. Analysis was performed on a chromatographic system comprised of an Agilent 6550 QTOF coupled to a 1290 Infinity UHPLC system. High resolution accurate mass data were acquired in the All Ions mode and exported into Mass Hunter Quantitative software for quantitation and identification using qualifier fragment ions. Validation included selectivity, matrix effects, calibration range, within day and between day precision and accuracy. The analytes were 7-amino-flunitrazepam, 7-amino-clonazepam, 7-amino-nitrazepam, acetylmorphine, alimemazine, alprazolam, amphetamine, benzoylecgonine, buprenorphine, diazepam, ethylmorphine, fentanyl, hydroxyzine, ketobemidone, codeine, cocaine, MDMA, methadone, methamphetamine, morphine, oxycodone, promethazine, propiomazine, propoxyphene, tramadol, zaleplone, zolpidem, and zopiclone. As proof of concept, hair from 29 authentic post mortem cases were analysed. The calibration range was established between 0.05ng/mg to 5.0ng/mg for all analytes except fentanyl (0.02-2.0), buprenorphine (0.04-2.0), and ketobemidone (0.05-4.0) as well as for alimemazine, amphetamine, cocaine, methadone, and promethazine (0.10-5.0). For all analytes, the accuracy of the fortified pooled hair matrix was 84-108% at the low level and 89-106% at the high level. The within series precisions were between 1.4 and 6.7% and the between series precisions were between 1.4 and 10.1%. From the 29 autopsy cases, 121 positive findings were

  14. Quantitative Resistance to Plant Pathogens in Pyramiding Strategies for Durable Crop Protection.

    PubMed

    Pilet-Nayel, Marie-Laure; Moury, Benoît; Caffier, Valérie; Montarry, Josselin; Kerlan, Marie-Claire; Fournet, Sylvain; Durel, Charles-Eric; Delourme, Régine

    2017-01-01

    Quantitative resistance has gained interest in plant breeding for pathogen control in low-input cropping systems. Although quantitative resistance frequently has only a partial effect and is difficult to select, it is considered more durable than major resistance (R) genes. With the exponential development of molecular markers over the past 20 years, resistance QTL have been more accurately detected and better integrated into breeding strategies for resistant varieties with increased potential for durability. This review summarizes current knowledge on the genetic inheritance, molecular basis, and durability of quantitative resistance. Based on this knowledge, we discuss how strategies that combine major R genes and QTL in crops can maintain the effectiveness of plant resistance to pathogens. Combining resistance QTL with complementary modes of action appears to be an interesting strategy for breeding effective and potentially durable resistance. Combining quantitative resistance with major R genes has proven to be a valuable approach for extending the effectiveness of major genes. In the plant genomics era, improved tools and methods are becoming available to better integrate quantitative resistance into breeding strategies. Nevertheless, optimal combinations of resistance loci will still have to be identified to preserve resistance effectiveness over time for durable crop protection.

  15. Comparison of salivary collection and processing methods for quantitative HHV-8 detection.

    PubMed

    Speicher, D J; Johnson, N W

    2014-10-01

    Saliva is a proved diagnostic fluid for the qualitative detection of infectious agents, but the accuracy of viral load determinations is unknown. Stabilising fluids impede nucleic acid degradation, compared with collection onto ice and then freezing, and we have shown that the DNA Genotek P-021 prototype kit (P-021) can produce high-quality DNA after 14 months of storage at room temperature. Here we evaluate the quantitative capability of 10 collection/processing methods. Unstimulated whole mouth fluid was spiked with a mixture of HHV-8 cloned constructs, 10-fold serial dilutions were produced, and samples were extracted and then examined with quantitative PCR (qPCR). Calibration curves were compared by linear regression and qPCR dynamics. All methods extracted with commercial spin columns produced linear calibration curves with large dynamic range and gave accurate viral loads. Ethanol precipitation of the P-021 does not produce a linear standard curve, and virus is lost in the cell pellet. DNA extractions from the P-021 using commercial spin columns produced linear standard curves with wide dynamic range and excellent limit of detection. When extracted with spin columns, the P-021 enables accurate viral loads down to 23 copies μl(-1) DNA. The quantitative and long-term storage capability of this system makes it ideal for study of salivary DNA viruses in resource-poor settings. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  16. Quantitative analysis of benzodiazepines in vitreous humor by high-performance liquid chromatography

    PubMed Central

    Bazmi, Elham; Behnoush, Behnam; Akhgari, Maryam; Bahmanabadi, Leila

    2016-01-01

    Objective: Benzodiazepines are frequently screened drugs in emergency toxicology, drugs of abuse testing, and in forensic cases. As the variations of benzodiazepines concentrations in biological samples during bleeding, postmortem changes, and redistribution could be biasing forensic medicine examinations, hence selecting a suitable sample and a validated accurate method is essential for the quantitative analysis of these main drug categories. The aim of this study was to develop a valid method for the determination of four benzodiazepines (flurazepam, lorazepam, alprazolam, and diazepam) in vitreous humor using liquid–liquid extraction and high-performance liquid chromatography. Methods: Sample preparation was carried out using liquid–liquid extraction with n-hexane: ethyl acetate and subsequent detection by high-performance liquid chromatography method coupled to diode array detector. This method was applied to quantify benzodiazepines in 21 authentic vitreous humor samples. Linear curve for each drug was obtained within the range of 30–3000 ng/mL with coefficient of correlation higher than 0.99. Results: The limit of detection and quantitation were 30 and 100 ng/mL respectively for four drugs. The method showed an appropriate intra- and inter-day precision (coefficient of variation < 10%). Benzodiazepines recoveries were estimated to be over 80%. The method showed high selectivity; no additional peak due to interfering substances in samples was observed. Conclusion: The present method was selective, sensitive, accurate, and precise for the quantitative analysis of benzodiazepines in vitreous humor samples in forensic toxicology laboratory. PMID:27635251

  17. Quantitative Analyse von Korallengemeinschaften des Sanganeb-Atolls (mittleres Rotes Meer). I. Die Besiedlungsstruktur hydrodynamisch unterschiedlich exponierter Außen- und Innenriffe

    NASA Astrophysics Data System (ADS)

    Mergner, H.; Schuhmacher, H.

    1985-12-01

    The Sanganeb-Atoll off Port Sudan is an elongate annular reef which rests on a probably raised block in the fracture zone along the Red Sea-graben. Its gross morphology was most likely formed by subaerial erosion during low sealevel conditions. Features of its topography and hydrography are described. The prevailing wind waves are from NE, Hence, the outer and inner reef slopes are exposed to different hydrodynamic conditions. The sessile benthos was analysed using the quadrat method. Four test quadrats (5×5 m each) were selected on the outer and inner slopes at a depth of 10 m along a SSW-NNE transect across the atoll. Cnidaria were by far the most dominating group; coralline algae, Porifera, Bryozoa and Ascidia, however, counted for just under 3 % living cover. Light and temperature intensities did not differ significantly at the sites studied; water movement, however, decreased in the following order: TQ IV (outer NE side of the reef ring) was exposed to strong swell and surf; TQ II (inner side of the SW-ring) was met by a strong longreef current; TQ I was situated on the outer lee of the SW-atoll ring and TQ III in the inner lee of the NE-side. This hydrodynamic gradient correlates with the composition of the coral communities from predominantly branching Scleractinia (staghorn-like and other Acropora species and Pocillopora) in TQ IV, through a Lobophyllia, Porites and Xenia-dominated community in TQ II, and a mixed community with an increasing percentage of xeniid and alcyoniid soft corals in TQ I, to a community in TQ III which is dominated by the soft corals Sinularia and Dendronephthya. The cnidarian cover ranged between 42.4 and 56.6 % whereby the two exposed test quadrats had a higher living coverage than the protected ones. In total, 2649 colonies comprising 124 species of stony, soft and hydrocorals were recorded by an elaborate method of accurate in-situ mapping. The 90 scleractinian species found include 3 species new to the Red Sea and 11 hitherto

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

    PubMed Central

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

    2010-01-01

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

  19. Analysing magnetism using scanning SQUID microscopy.

    PubMed

    Reith, P; Renshaw Wang, X; Hilgenkamp, H

    2017-12-01

    Scanning superconducting quantum interference device microscopy (SSM) is a scanning probe technique that images local magnetic flux, which allows for mapping of magnetic fields with high field and spatial accuracy. Many studies involving SSM have been published in the last few decades, using SSM to make qualitative statements about magnetism. However, quantitative analysis using SSM has received less attention. In this work, we discuss several aspects of interpreting SSM images and methods to improve quantitative analysis. First, we analyse the spatial resolution and how it depends on several factors. Second, we discuss the analysis of SSM scans and the information obtained from the SSM data. Using simulations, we show how signals evolve as a function of changing scan height, SQUID loop size, magnetization strength, and orientation. We also investigated 2-dimensional autocorrelation analysis to extract information about the size, shape, and symmetry of magnetic features. Finally, we provide an outlook on possible future applications and improvements.

  20. Analysing magnetism using scanning SQUID microscopy

    NASA Astrophysics Data System (ADS)

    Reith, P.; Renshaw Wang, X.; Hilgenkamp, H.

    2017-12-01

    Scanning superconducting quantum interference device microscopy (SSM) is a scanning probe technique that images local magnetic flux, which allows for mapping of magnetic fields with high field and spatial accuracy. Many studies involving SSM have been published in the last few decades, using SSM to make qualitative statements about magnetism. However, quantitative analysis using SSM has received less attention. In this work, we discuss several aspects of interpreting SSM images and methods to improve quantitative analysis. First, we analyse the spatial resolution and how it depends on several factors. Second, we discuss the analysis of SSM scans and the information obtained from the SSM data. Using simulations, we show how signals evolve as a function of changing scan height, SQUID loop size, magnetization strength, and orientation. We also investigated 2-dimensional autocorrelation analysis to extract information about the size, shape, and symmetry of magnetic features. Finally, we provide an outlook on possible future applications and improvements.

  1. NNLOPS accurate associated HW production

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

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

  2. Grey literature in meta-analyses.

    PubMed

    Conn, Vicki S; Valentine, Jeffrey C; Cooper, Harris M; Rantz, Marilyn J

    2003-01-01

    In meta-analysis, researchers combine the results of individual studies to arrive at cumulative conclusions. Meta-analysts sometimes include "grey literature" in their evidential base, which includes unpublished studies and studies published outside widely available journals. Because grey literature is a source of data that might not employ peer review, critics have questioned the validity of its data and the results of meta-analyses that include it. To examine evidence regarding whether grey literature should be included in meta-analyses and strategies to manage grey literature in quantitative synthesis. This article reviews evidence on whether the results of studies published in peer-reviewed journals are representative of results from broader samplings of research on a topic as a rationale for inclusion of grey literature. Strategies to enhance access to grey literature are addressed. The most consistent and robust difference between published and grey literature is that published research is more likely to contain results that are statistically significant. Effect size estimates of published research are about one-third larger than those of unpublished studies. Unfunded and small sample studies are less likely to be published. Yet, importantly, methodological rigor does not differ between published and grey literature. Meta-analyses that exclude grey literature likely (a) over-represent studies with statistically significant findings, (b) inflate effect size estimates, and (c) provide less precise effect size estimates than meta-analyses including grey literature. Meta-analyses should include grey literature to fully reflect the existing evidential base and should assess the impact of methodological variations through moderator analysis.

  3. Quantitative Large-Scale Three-Dimensional Imaging of Human Kidney Biopsies: A Bridge to Precision Medicine in Kidney Disease.

    PubMed

    Winfree, Seth; Dagher, Pierre C; Dunn, Kenneth W; Eadon, Michael T; Ferkowicz, Michael; Barwinska, Daria; Kelly, Katherine J; Sutton, Timothy A; El-Achkar, Tarek M

    2018-06-05

    Kidney biopsy remains the gold standard for uncovering the pathogenesis of acute and chronic kidney diseases. However, the ability to perform high resolution, quantitative, molecular and cellular interrogation of this precious tissue is still at a developing stage compared to other fields such as oncology. Here, we discuss recent advances in performing large-scale, three-dimensional (3D), multi-fluorescence imaging of kidney biopsies and quantitative analysis referred to as 3D tissue cytometry. This approach allows the accurate measurement of specific cell types and their spatial distribution in a thick section spanning the entire length of the biopsy. By uncovering specific disease signatures, including rare occurrences, and linking them to the biology in situ, this approach will enhance our understanding of disease pathogenesis. Furthermore, by providing accurate quantitation of cellular events, 3D cytometry may improve the accuracy of prognosticating the clinical course and response to therapy. Therefore, large-scale 3D imaging and cytometry of kidney biopsy is poised to become a bridge towards personalized medicine for patients with kidney disease. © 2018 S. Karger AG, Basel.

  4. Sample normalization methods in quantitative metabolomics.

    PubMed

    Wu, Yiman; Li, Liang

    2016-01-22

    To reveal metabolomic changes caused by a biological event in quantitative metabolomics, it is critical to use an analytical tool that can perform accurate and precise quantification to examine the true concentration differences of individual metabolites found in different samples. A number of steps are involved in metabolomic analysis including pre-analytical work (e.g., sample collection and storage), analytical work (e.g., sample analysis) and data analysis (e.g., feature extraction and quantification). Each one of them can influence the quantitative results significantly and thus should be performed with great care. Among them, the total sample amount or concentration of metabolites can be significantly different from one sample to another. Thus, it is critical to reduce or eliminate the effect of total sample amount variation on quantification of individual metabolites. In this review, we describe the importance of sample normalization in the analytical workflow with a focus on mass spectrometry (MS)-based platforms, discuss a number of methods recently reported in the literature and comment on their applicability in real world metabolomics applications. Sample normalization has been sometimes ignored in metabolomics, partially due to the lack of a convenient means of performing sample normalization. We show that several methods are now available and sample normalization should be performed in quantitative metabolomics where the analyzed samples have significant variations in total sample amounts. Copyright © 2015 Elsevier B.V. All rights reserved.

  5. Quantitative measurements of electromechanical response with a combined optical beam and interferometric atomic force microscope

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

    Labuda, Aleksander; Proksch, Roger

    An ongoing challenge in atomic force microscope (AFM) experiments is the quantitative measurement of cantilever motion. The vast majority of AFMs use the optical beam deflection (OBD) method to infer the deflection of the cantilever. The OBD method is easy to implement, has impressive noise performance, and tends to be mechanically robust. However, it represents an indirect measurement of the cantilever displacement, since it is fundamentally an angular rather than a displacement measurement. Here, we demonstrate a metrological AFM that combines an OBD sensor with a laser Doppler vibrometer (LDV) to enable accurate measurements of the cantilever velocity and displacement.more » The OBD/LDV AFM allows a host of quantitative measurements to be performed, including in-situ measurements of cantilever oscillation modes in piezoresponse force microscopy. As an example application, we demonstrate how this instrument can be used for accurate quantification of piezoelectric sensitivity—a longstanding goal in the electromechanical community.« less

  6. Diagnostic performance of semi-quantitative and quantitative stress CMR perfusion analysis: a meta-analysis.

    PubMed

    van Dijk, R; van Assen, M; Vliegenthart, R; de Bock, G H; van der Harst, P; Oudkerk, M

    2017-11-27

    Stress cardiovascular magnetic resonance (CMR) perfusion imaging is a promising modality for the evaluation of coronary artery disease (CAD) due to high spatial resolution and absence of radiation. Semi-quantitative and quantitative analysis of CMR perfusion are based on signal-intensity curves produced during the first-pass of gadolinium contrast. Multiple semi-quantitative and quantitative parameters have been introduced. Diagnostic performance of these parameters varies extensively among studies and standardized protocols are lacking. This study aims to determine the diagnostic accuracy of semi- quantitative and quantitative CMR perfusion parameters, compared to multiple reference standards. Pubmed, WebOfScience, and Embase were systematically searched using predefined criteria (3272 articles). A check for duplicates was performed (1967 articles). Eligibility and relevance of the articles was determined by two reviewers using pre-defined criteria. The primary data extraction was performed independently by two researchers with the use of a predefined template. Differences in extracted data were resolved by discussion between the two researchers. The quality of the included studies was assessed using the 'Quality Assessment of Diagnostic Accuracy Studies Tool' (QUADAS-2). True positives, false positives, true negatives, and false negatives were subtracted/calculated from the articles. The principal summary measures used to assess diagnostic accuracy were sensitivity, specificity, andarea under the receiver operating curve (AUC). Data was pooled according to analysis territory, reference standard and perfusion parameter. Twenty-two articles were eligible based on the predefined study eligibility criteria. The pooled diagnostic accuracy for segment-, territory- and patient-based analyses showed good diagnostic performance with sensitivity of 0.88, 0.82, and 0.83, specificity of 0.72, 0.83, and 0.76 and AUC of 0.90, 0.84, and 0.87, respectively. In per territory

  7. Note on the chromatographic analyses of marine polyunsaturated fatty acids

    USGS Publications Warehouse

    Schultz, D.M.; Quinn, J.G.

    1977-01-01

    Gas-liquid chromatography was used to study the effects of saponification/methylation and thin-layer chromatographic isolation on the analyses of polyunsaturated fatty acids. Using selected procedures, the qualitative and quantitative distribution of these acids in marine organisms can be determined with a high degree of accuracy. ?? 1977 Springer-Verlag.

  8. Quantitative EPMA of Nano-Phase Iron-Silicides in Apollo 16 Lunar Regolith

    NASA Astrophysics Data System (ADS)

    Gopon, P.; Fournelle, J.; Valley, J. W.; Pinard, P. T.; Sobol, P.; Horn, W.; Spicuzza, M.; Llovet, X.; Richter, S.

    2013-12-01

    Until recently, quantitative EPMA of phases under a few microns in size has been extremely difficult. In order to achieve analytical volumes to analyze sub-micron features, accelerating voltages between 5 and 8 keV need to be used. At these voltages the normally used K X-ray transitions (of higher Z elements) are no longer excited, and we must rely of outer shell transitions (L and M). These outer shell transitions are difficult to use for quantitative EPMA because they are strongly affected by different bonding environments, the error associated with their mass attenuation coefficients (MAC), and their proximity to absorption edges. These problems are especially prevalent for the transition metals, because of the unfilled M5 electron shell where the Lα transition originates. Previous studies have tried to overcome these limitations by using standards that almost exactly matched their unknowns. This, however, is cumbersome and requires accurate knowledge of the composition of your sample beforehand, as well as an exorbitant number of well characterized standards. Using a 5 keV electron beam and utilizing non-standard X-ray transitions (Ll) for the transition metals, we are able to conduct accurate quantitative analyses of phases down to ~300nm. The Ll transition in the transition metals behaves more like a core-state transition, and unlike the Lα/β lines, is unaffected by bonding effects and does not lie near an absorption edge. This allows for quantitative analysis using standards do not have to exactly match the unknown. In our case pure metal standards were used for all elements except phosphorus. We present here data on iron-silicides in two Apollo 16 regolith grains. These plagioclase grains (A6-7 and A6-8) were collected between North and South Ray Craters, in the lunar highlands, and thus are associated with one or more large impact events. We report the presence of carbon, nickel, and phosphorus (in order of abundance) in these iron-silicide phases

  9. Accurate Arabic Script Language/Dialect Classification

    DTIC Science & Technology

    2014-01-01

    Army Research Laboratory Accurate Arabic Script Language/Dialect Classification by Stephen C. Tratz ARL-TR-6761 January 2014 Approved for public...1197 ARL-TR-6761 January 2014 Accurate Arabic Script Language/Dialect Classification Stephen C. Tratz Computational and Information Sciences...Include area code) Standard Form 298 (Rev. 8/98) Prescribed by ANSI Std. Z39.18 January 2014 Final Accurate Arabic Script Language/Dialect Classification

  10. Accurate object tracking system by integrating texture and depth cues

    NASA Astrophysics Data System (ADS)

    Chen, Ju-Chin; Lin, Yu-Hang

    2016-03-01

    A robust object tracking system that is invariant to object appearance variations and background clutter is proposed. Multiple instance learning with a boosting algorithm is applied to select discriminant texture information between the object and background data. Additionally, depth information, which is important to distinguish the object from a complicated background, is integrated. We propose two depth-based models that can compensate texture information to cope with both appearance variants and background clutter. Moreover, in order to reduce the risk of drifting problem increased for the textureless depth templates, an update mechanism is proposed to select more precise tracking results to avoid incorrect model updates. In the experiments, the robustness of the proposed system is evaluated and quantitative results are provided for performance analysis. Experimental results show that the proposed system can provide the best success rate and has more accurate tracking results than other well-known algorithms.

  11. Self-Expression on Social Media: Do Tweets Present Accurate and Positive Portraits of Impulsivity, Self-Esteem, and Attachment Style?

    PubMed

    Orehek, Edward; Human, Lauren J

    2017-01-01

    Self-expression values are at an all-time high, and people are increasingly relying upon social media platforms to express themselves positively and accurately. We examined whether self-expression on the social media platform Twitter elicits positive and accurate social perceptions. Eleven perceivers rated 128 individuals (targets; total dyadic impressions = 1,408) on their impulsivity, self-esteem, and attachment style, based solely on the information provided in targets' 10 most recent tweets. Targets were on average perceived normatively and with distinctive self-other agreement, indicating both positive and accurate social perceptions. There were also individual differences in how positively and accurately targets were perceived, which exploratory analyses indicated may be partially driven by differential word usage, such as the use of positive emotion words and self- versus other-focus. This study demonstrates that self-expression on social media can elicit both positive and accurate perceptions and begins to shed light on how to curate such perceptions.

  12. Phase calibration target for quantitative phase imaging with ptychography.

    PubMed

    Godden, T M; Muñiz-Piniella, A; Claverley, J D; Yacoot, A; Humphry, M J

    2016-04-04

    Quantitative phase imaging (QPI) utilizes refractive index and thickness variations that lead to optical phase shifts. This gives contrast to images of transparent objects. In quantitative biology, phase images are used to accurately segment cells and calculate properties such as dry mass, volume and proliferation rate. The fidelity of the measured phase shifts is of critical importance in this field. However to date, there has been no standardized method for characterizing the performance of phase imaging systems. Consequently, there is an increasing need for protocols to test the performance of phase imaging systems using well-defined phase calibration and resolution targets. In this work, we present a candidate for a standardized phase resolution target, and measurement protocol for the determination of the transfer of spatial frequencies, and sensitivity of a phase imaging system. The target has been carefully designed to contain well-defined depth variations over a broadband range of spatial frequencies. In order to demonstrate the utility of the target, we measure quantitative phase images on a ptychographic microscope, and compare the measured optical phase shifts with Atomic Force Microscopy (AFM) topography maps and surface profile measurements from coherence scanning interferometry. The results show that ptychography has fully quantitative nanometer sensitivity in optical path differences over a broadband range of spatial frequencies for feature sizes ranging from micrometers to hundreds of micrometers.

  13. End-to-end deep neural network for optical inversion in quantitative photoacoustic imaging.

    PubMed

    Cai, Chuangjian; Deng, Kexin; Ma, Cheng; Luo, Jianwen

    2018-06-15

    An end-to-end deep neural network, ResU-net, is developed for quantitative photoacoustic imaging. A residual learning framework is used to facilitate optimization and to gain better accuracy from considerably increased network depth. The contracting and expanding paths enable ResU-net to extract comprehensive context information from multispectral initial pressure images and, subsequently, to infer a quantitative image of chromophore concentration or oxygen saturation (sO 2 ). According to our numerical experiments, the estimations of sO 2 and indocyanine green concentration are accurate and robust against variations in both optical property and object geometry. An extremely short reconstruction time of 22 ms is achieved.

  14. Quantitative Analyse der Korallenbesiedlung eines Vorriffareals bei Aqaba (Rotes Meer)

    NASA Astrophysics Data System (ADS)

    Mergner, H.; Schuhmacher, H.

    1981-09-01

    Previous descriptions of the ecology and zonation of Aqaba reefs (Mergner & Schuhmacher, 1974) are supplemented by this quantitative study of a test quadrat (5×5 m in size), randomly chosen in some 10 m depth in the middle fore reef of a coastal fringing reef. Of the total surface of 25 m2 Cnidaria represent 42.31%, sponges 0.17%, calcareous algae 0.20%, dead coral rock and pebble 30.27% and sand and coral debris 26.15%. The cnidarian cover is roughly equally contributed by 50.86% Scleractinia and 48.61% Alcyonaria, mainly Xeniidae (35.81%). For each species the percentage of the total cover (measured as vertical projection), colony number, average and maximal colony size are given. A total number of 104 cnidarian species was recorded, among which the 78 scleractinian species represent 34 of the 55 coral genera known from the Red Sea. The well balanced regime of moderate light and current conditions which are tolerated both by shallow and deep water species may account for the high species number. Disturbances such as occasional sedimentation, grazing of sea urchins (Diadema setosum) and overgrowth of stony corals by xeniids result in continuous fluctuations of the coral community, in small colony size and in high colony number. Abiotic factors and biotic interactions maintain a diversity (H=3.67) which ranks among the greatest ever found in reef communities. The data obtained from the fore reef square are compared with those of a similar test square in the lagoon of the same reef and with results from transect zonations on the opposite coast of the Gulf of Aqaba. These comparisons indicate that the fore reef harbours the richest coral fauna in the reef. The inventory of coral species at the northern end of the Gulf of Aqaba, one of the northernmost outposts of the coral reef belt, is only little reduced when compared with that of the central Red Sea; this great species diversity is in contrast to the worldwide decrease of species number towards the periphery of

  15. Accurately controlled sequential self-folding structures by polystyrene film

    NASA Astrophysics Data System (ADS)

    Deng, Dongping; Yang, Yang; Chen, Yong; Lan, Xing; Tice, Jesse

    2017-08-01

    Four-dimensional (4D) printing overcomes the traditional fabrication limitations by designing heterogeneous materials to enable the printed structures evolve over time (the fourth dimension) under external stimuli. Here, we present a simple 4D printing of self-folding structures that can be sequentially and accurately folded. When heated above their glass transition temperature pre-strained polystyrene films shrink along the XY plane. In our process silver ink traces printed on the film are used to provide heat stimuli by conducting current to trigger the self-folding behavior. The parameters affecting the folding process are studied and discussed. Sequential folding and accurately controlled folding angles are achieved by using printed ink traces and angle lock design. Theoretical analyses are done to guide the design of the folding processes. Programmable structures such as a lock and a three-dimensional antenna are achieved to test the feasibility and potential applications of this method. These self-folding structures change their shapes after fabrication under controlled stimuli (electric current) and have potential applications in the fields of electronics, consumer devices, and robotics. Our design and fabrication method provides an easy way by using silver ink printed on polystyrene films to 4D print self-folding structures for electrically induced sequential folding with angular control.

  16. Fluctuation localization imaging-based fluorescence in situ hybridization (fliFISH) for accurate detection and counting of RNA copies in single cells

    DOE PAGES

    Cui, Yi; Hu, Dehong; Markillie, Lye Meng; ...

    2017-10-04

    Here, quantitative gene expression analysis in intact single cells can be achieved using single molecule-based fluorescence in situ hybridization (smFISH). This approach relies on fluorescence intensity to distinguish between true signals, emitted from an RNA copy hybridized with multiple oligonucleotide probes, and background noise. Thus, the precision in smFISH is often compromised by partial or nonspecific probe binding and tissue autofluorescence, especially when only a small number of probes can be fitted to the target transcript. Here we provide an accurate approach for setting quantitative thresholds between true and false signals, which relies on on-off duty cycles of photoswitchable dyes.more » This fluctuation localization imaging-based FISH (fliFISH) uses on-time fractions (measured over a series of exposures) collected from transcripts bound to as low as 8 probes, which are distinct from on-time fractions collected from nonspecifically bound probes or autofluorescence. Using multicolor fliFISH, we identified radial gene expression patterns in mouse pancreatic islets for insulin, the transcription factor, NKX2-2 and their ratio ( Nkx2- 2/Ins2). These radial patterns, showing higher values in β cells at the islet core and lower values in peripheral cells, were lost in diabetic mouse islets. In summary, fliFISH provides an accurate, quantitative approach for detecting and counting true RNA copies and rejecting false signals by their distinct on-time fractions, laying the foundation for reliable single-cell transcriptomics.« less

  17. Fluctuation localization imaging-based fluorescence in situ hybridization (fliFISH) for accurate detection and counting of RNA copies in single cells

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

    Cui, Yi; Hu, Dehong; Markillie, Lye Meng

    Here, quantitative gene expression analysis in intact single cells can be achieved using single molecule-based fluorescence in situ hybridization (smFISH). This approach relies on fluorescence intensity to distinguish between true signals, emitted from an RNA copy hybridized with multiple oligonucleotide probes, and background noise. Thus, the precision in smFISH is often compromised by partial or nonspecific probe binding and tissue autofluorescence, especially when only a small number of probes can be fitted to the target transcript. Here we provide an accurate approach for setting quantitative thresholds between true and false signals, which relies on on-off duty cycles of photoswitchable dyes.more » This fluctuation localization imaging-based FISH (fliFISH) uses on-time fractions (measured over a series of exposures) collected from transcripts bound to as low as 8 probes, which are distinct from on-time fractions collected from nonspecifically bound probes or autofluorescence. Using multicolor fliFISH, we identified radial gene expression patterns in mouse pancreatic islets for insulin, the transcription factor, NKX2-2 and their ratio ( Nkx2- 2/Ins2). These radial patterns, showing higher values in β cells at the islet core and lower values in peripheral cells, were lost in diabetic mouse islets. In summary, fliFISH provides an accurate, quantitative approach for detecting and counting true RNA copies and rejecting false signals by their distinct on-time fractions, laying the foundation for reliable single-cell transcriptomics.« less

  18. Vibrational algorithms for quantitative crystallographic analyses of hydroxyapatite-based biomaterials: I, theoretical foundations.

    PubMed

    Pezzotti, Giuseppe; Zhu, Wenliang; Boffelli, Marco; Adachi, Tetsuya; Ichioka, Hiroaki; Yamamoto, Toshiro; Marunaka, Yoshinori; Kanamura, Narisato

    2015-05-01

    The Raman spectroscopic method has quantitatively been applied to the analysis of local crystallographic orientation in both single-crystal hydroxyapatite and human teeth. Raman selection rules for all the vibrational modes of the hexagonal structure were expanded into explicit functions of Euler angles in space and six Raman tensor elements (RTE). A theoretical treatment has also been put forward according to the orientation distribution function (ODF) formalism, which allows one to resolve the statistical orientation patterns of the nm-sized hydroxyapatite crystallite comprised in the Raman microprobe. Close-form solutions could be obtained for the Euler angles and their statistical distributions resolved with respect to the direction of the average texture axis. Polarized Raman spectra from single-crystalline hydroxyapatite and textured polycrystalline (teeth enamel) samples were compared, and a validation of the proposed Raman method could be obtained through confirming the agreement between RTE values obtained from different samples.

  19. Large-Scale and Deep Quantitative Proteome Profiling Using Isobaric Labeling Coupled with Two-Dimensional LC-MS/MS

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

    Gritsenko, Marina A.; Xu, Zhe; Liu, Tao

    Comprehensive, quantitative information on abundances of proteins and their post-translational modifications (PTMs) can potentially provide novel biological insights into diseases pathogenesis and therapeutic intervention. Herein, we introduce a quantitative strategy utilizing isobaric stable isotope-labelling techniques combined with two-dimensional liquid chromatography-tandem mass spectrometry (2D-LC-MS/MS) for large-scale, deep quantitative proteome profiling of biological samples or clinical specimens such as tumor tissues. The workflow includes isobaric labeling of tryptic peptides for multiplexed and accurate quantitative analysis, basic reversed-phase LC fractionation and concatenation for reduced sample complexity, and nano-LC coupled to high resolution and high mass accuracy MS analysis for high confidence identification andmore » quantification of proteins. This proteomic analysis strategy has been successfully applied for in-depth quantitative proteomic analysis of tumor samples, and can also be used for integrated proteome and PTM characterization, as well as comprehensive quantitative proteomic analysis across samples from large clinical cohorts.« less

  20. Large-Scale and Deep Quantitative Proteome Profiling Using Isobaric Labeling Coupled with Two-Dimensional LC-MS/MS.

    PubMed

    Gritsenko, Marina A; Xu, Zhe; Liu, Tao; Smith, Richard D

    2016-01-01

    Comprehensive, quantitative information on abundances of proteins and their posttranslational modifications (PTMs) can potentially provide novel biological insights into diseases pathogenesis and therapeutic intervention. Herein, we introduce a quantitative strategy utilizing isobaric stable isotope-labeling techniques combined with two-dimensional liquid chromatography-tandem mass spectrometry (2D-LC-MS/MS) for large-scale, deep quantitative proteome profiling of biological samples or clinical specimens such as tumor tissues. The workflow includes isobaric labeling of tryptic peptides for multiplexed and accurate quantitative analysis, basic reversed-phase LC fractionation and concatenation for reduced sample complexity, and nano-LC coupled to high resolution and high mass accuracy MS analysis for high confidence identification and quantification of proteins. This proteomic analysis strategy has been successfully applied for in-depth quantitative proteomic analysis of tumor samples and can also be used for integrated proteome and PTM characterization, as well as comprehensive quantitative proteomic analysis across samples from large clinical cohorts.

  1. Appraising Quantitative Research in Health Education: Guidelines for Public Health Educators

    PubMed Central

    Hayes, Sandra C.; Scharalda, Jeanfreau G.; Stetson, Barbara; Jones-Jack, Nkenge H.; Valliere, Matthew; Kirchain, William R.; Fagen, Michael; LeBlanc, Cris

    2010-01-01

    Many practicing health educators do not feel they possess the skills necessary to critically appraise quantitative research. This publication is designed to help provide practicing health educators with basic tools helpful to facilitate a better understanding of quantitative research. This article describes the major components—title, introduction, methods, analyses, results and discussion sections—of quantitative research. Readers will be introduced to information on the various types of study designs and seven key questions health educators can use to facilitate the appraisal process. Upon reading, health educators will be in a better position to determine whether research studies are well designed and executed. PMID:20400654

  2. RECENT ADVANCES IN QUANTITATIVE NEUROPROTEOMICS

    PubMed Central

    Craft, George E; Chen, Anshu; Nairn, Angus C

    2014-01-01

    The field of proteomics is undergoing rapid development in a number of different areas including improvements in mass spectrometric platforms, peptide identification algorithms and bioinformatics. In particular, new and/or improved approaches have established robust methods that not only allow for in-depth and accurate peptide and protein identification and modification, but also allow for sensitive measurement of relative or absolute quantitation. These methods are beginning to be applied to the area of neuroproteomics, but the central nervous system poses many specific challenges in terms of quantitative proteomics, given the large number of different neuronal cell types that are intermixed and that exhibit distinct patterns of gene and protein expression. This review highlights the recent advances that have been made in quantitative neuroproteomics, with a focus on work published over the last five years that applies emerging methods to normal brain function as well as to various neuropsychiatric disorders including schizophrenia and drug addiction as well as of neurodegenerative diseases including Parkinson’s disease and Alzheimer’s disease. While older methods such as two-dimensional polyacrylamide electrophoresis continued to be used, a variety of more in-depth MS-based approaches including both label (ICAT, iTRAQ, TMT, SILAC, SILAM), label-free (label-free, MRM, SWATH) and absolute quantification methods, are rapidly being applied to neurobiological investigations of normal and diseased brain tissue as well as of cerebrospinal fluid (CSF). While the biological implications of many of these studies remain to be clearly established, that there is a clear need for standardization of experimental design and data analysis, and that the analysis of protein changes in specific neuronal cell types in the central nervous system remains a serious challenge, it appears that the quality and depth of the more recent quantitative proteomics studies is beginning to

  3. Recent advances in quantitative neuroproteomics.

    PubMed

    Craft, George E; Chen, Anshu; Nairn, Angus C

    2013-06-15

    The field of proteomics is undergoing rapid development in a number of different areas including improvements in mass spectrometric platforms, peptide identification algorithms and bioinformatics. In particular, new and/or improved approaches have established robust methods that not only allow for in-depth and accurate peptide and protein identification and modification, but also allow for sensitive measurement of relative or absolute quantitation. These methods are beginning to be applied to the area of neuroproteomics, but the central nervous system poses many specific challenges in terms of quantitative proteomics, given the large number of different neuronal cell types that are intermixed and that exhibit distinct patterns of gene and protein expression. This review highlights the recent advances that have been made in quantitative neuroproteomics, with a focus on work published over the last five years that applies emerging methods to normal brain function as well as to various neuropsychiatric disorders including schizophrenia and drug addiction as well as of neurodegenerative diseases including Parkinson's disease and Alzheimer's disease. While older methods such as two-dimensional polyacrylamide electrophoresis continued to be used, a variety of more in-depth MS-based approaches including both label (ICAT, iTRAQ, TMT, SILAC, SILAM), label-free (label-free, MRM, SWATH) and absolute quantification methods, are rapidly being applied to neurobiological investigations of normal and diseased brain tissue as well as of cerebrospinal fluid (CSF). While the biological implications of many of these studies remain to be clearly established, that there is a clear need for standardization of experimental design and data analysis, and that the analysis of protein changes in specific neuronal cell types in the central nervous system remains a serious challenge, it appears that the quality and depth of the more recent quantitative proteomics studies is beginning to shed

  4. Generalized PSF modeling for optimized quantitation in PET imaging.

    PubMed

    Ashrafinia, Saeed; Mohy-Ud-Din, Hassan; Karakatsanis, Nicolas A; Jha, Abhinav K; Casey, Michael E; Kadrmas, Dan J; Rahmim, Arman

    2017-06-21

    Point-spread function (PSF) modeling offers the ability to account for resolution degrading phenomena within the PET image generation framework. PSF modeling improves resolution and enhances contrast, but at the same time significantly alters image noise properties and induces edge overshoot effect. Thus, studying the effect of PSF modeling on quantitation task performance can be very important. Frameworks explored in the past involved a dichotomy of PSF versus no-PSF modeling. By contrast, the present work focuses on quantitative performance evaluation of standard uptake value (SUV) PET images, while incorporating a wide spectrum of PSF models, including those that under- and over-estimate the true PSF, for the potential of enhanced quantitation of SUVs. The developed framework first analytically models the true PSF, considering a range of resolution degradation phenomena (including photon non-collinearity, inter-crystal penetration and scattering) as present in data acquisitions with modern commercial PET systems. In the context of oncologic liver FDG PET imaging, we generated 200 noisy datasets per image-set (with clinically realistic noise levels) using an XCAT anthropomorphic phantom with liver tumours of varying sizes. These were subsequently reconstructed using the OS-EM algorithm with varying PSF modelled kernels. We focused on quantitation of both SUV mean and SUV max , including assessment of contrast recovery coefficients, as well as noise-bias characteristics (including both image roughness and coefficient of-variability), for different tumours/iterations/PSF kernels. It was observed that overestimated PSF yielded more accurate contrast recovery for a range of tumours, and typically improved quantitative performance. For a clinically reasonable number of iterations, edge enhancement due to PSF modeling (especially due to over-estimated PSF) was in fact seen to lower SUV mean bias in small tumours. Overall, the results indicate that exactly matched PSF

  5. Adipose tissue MRI for quantitative measurement of central obesity.

    PubMed

    Poonawalla, Aziz H; Sjoberg, Brett P; Rehm, Jennifer L; Hernando, Diego; Hines, Catherine D; Irarrazaval, Pablo; Reeder, Scott B

    2013-03-01

    To validate adipose tissue magnetic resonance imaging (atMRI) for rapid, quantitative volumetry of visceral adipose tissue (VAT) and total adipose tissue (TAT). Data were acquired on normal adults and clinically overweight girls with Institutional Review Board (IRB) approval/parental consent using sagittal 6-echo 3D-spoiled gradient-echo (SPGR) (26-sec single-breath-hold) at 3T. Fat-fraction images were reconstructed with quantitative corrections, permitting measurement of a physiologically based fat-fraction threshold in normals to identify adipose tissue, for automated measurement of TAT, and semiautomated measurement of VAT. TAT accuracy was validated using oil phantoms and in vivo TAT/VAT measurements validated with manual segmentation. Group comparisons were performed between normals and overweight girls using TAT, VAT, VAT-TAT-ratio (VTR), body-mass-index (BMI), waist circumference, and waist-hip-ratio (WHR). Oil phantom measurements were highly accurate (<3% error). The measured adipose fat-fraction threshold was 96% ± 2%. VAT and TAT correlated strongly with manual segmentation (normals r(2) ≥ 0.96, overweight girls r(2) ≥ 0.99). VAT segmentation required 30 ± 11 minutes/subject (14 ± 5 sec/slice) using atMRI, versus 216 ± 73 minutes/subject (99 ± 31 sec/slice) manually. Group discrimination was significant using WHR (P < 0.001) and VTR (P = 0.004). The atMRI technique permits rapid, accurate measurements of TAT, VAT, and VTR. Copyright © 2012 Wiley Periodicals, Inc.

  6. Approaches for the accurate definition of geological time boundaries

    NASA Astrophysics Data System (ADS)

    Schaltegger, Urs; Baresel, Björn; Ovtcharova, Maria; Goudemand, Nicolas; Bucher, Hugo

    2015-04-01

    Which strategies lead to the most precise and accurate date of a given geological boundary? Geological units are usually defined by the occurrence of characteristic taxa and hence boundaries between these geological units correspond to dramatic faunal and/or floral turnovers and they are primarily defined using first or last occurrences of index species, or ideally by the separation interval between two consecutive, characteristic associations of fossil taxa. These boundaries need to be defined in a way that enables their worldwide recognition and correlation across different stratigraphic successions, using tools as different as bio-, magneto-, and chemo-stratigraphy, and astrochronology. Sedimentary sequences can be dated in numerical terms by applying high-precision chemical-abrasion, isotope-dilution, thermal-ionization mass spectrometry (CA-ID-TIMS) U-Pb age determination to zircon (ZrSiO4) in intercalated volcanic ashes. But, though volcanic activity is common in geological history, ashes are not necessarily close to the boundary we would like to date precisely and accurately. In addition, U-Pb zircon data sets may be very complex and difficult to interpret in terms of the age of ash deposition. To overcome these difficulties we use a multi-proxy approach we applied to the precise and accurate dating of the Permo-Triassic and Early-Middle Triassic boundaries in South China. a) Dense sampling of ashes across the critical time interval and a sufficiently large number of analysed zircons per ash sample can guarantee the recognition of all system complexities. Geochronological datasets from U-Pb dating of volcanic zircon may indeed combine effects of i) post-crystallization Pb loss from percolation of hydrothermal fluids (even using chemical abrasion), with ii) age dispersion from prolonged residence of earlier crystallized zircon in the magmatic system. As a result, U-Pb dates of individual zircons are both apparently younger and older than the depositional age

  7. Descriptive and Experimental Analyses of Potential Precursors to Problem Behavior

    PubMed Central

    Borrero, Carrie S.W; Borrero, John C

    2008-01-01

    We conducted descriptive observations of severe problem behavior for 2 individuals with autism to identify precursors to problem behavior. Several comparative probability analyses were conducted in addition to lag-sequential analyses using the descriptive data. Results of the descriptive analyses showed that the probability of the potential precursor was greater given problem behavior compared to the unconditional probability of the potential precursor. Results of the lag-sequential analyses showed a marked increase in the probability of a potential precursor in the 1-s intervals immediately preceding an instance of problem behavior, and that the probability of problem behavior was highest in the 1-s intervals immediately following an instance of the precursor. We then conducted separate functional analyses of problem behavior and the precursor to identify respective operant functions. Results of the functional analyses showed that both problem behavior and the precursor served the same operant functions. These results replicate prior experimental analyses on the relation between problem behavior and precursors and extend prior research by illustrating a quantitative method to identify precursors to more severe problem behavior. PMID:18468281

  8. Influence of Pre-Analytical Factors on Thymus- and Activation-Regulated Chemokine Quantitation in Plasma

    PubMed Central

    Zhao, Xuemei; Delgado, Liliana; Weiner, Russell; Laterza, Omar F.

    2015-01-01

    Thymus- and activation-regulated chemokine (TARC) in serum/plasma associates with the disease activity of atopic dermatitis (AD), and is a promising tool for assessing the response to the treatment of the disease. TARC also exists within platelets, with elevated levels detectable in AD patients. We examined the effects of pre-analytical factors on the quantitation of TARC in human EDTA plasma. TARC levels in platelet-free plasma were significantly lower than those in platelet-containing plasma. After freeze-thaw, TARC levels increased in platelet-containing plasma, but remained unchanged in platelet-free plasma, suggesting TARC was released from the platelets during the freeze-thaw process. In contrast, TARC levels were stable in serum independent of freeze-thaw. These findings underscore the importance of pre-analytical factors to TARC quantitation. Plasma TARC levels should be measured in platelet-free plasma for accurate quantitation. Pre-analytical factors influence the quantitation, interpretation, and implementation of circulating TARC as a biomarker for the development of AD therapeutics. PMID:28936246

  9. 38 CFR 4.46 - Accurate measurement.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... RATING DISABILITIES Disability Ratings The Musculoskeletal System § 4.46 Accurate measurement. Accurate... indispensable in examinations conducted within the Department of Veterans Affairs. Muscle atrophy must also be...

  10. 38 CFR 4.46 - Accurate measurement.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... RATING DISABILITIES Disability Ratings The Musculoskeletal System § 4.46 Accurate measurement. Accurate... indispensable in examinations conducted within the Department of Veterans Affairs. Muscle atrophy must also be...

  11. 38 CFR 4.46 - Accurate measurement.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... RATING DISABILITIES Disability Ratings The Musculoskeletal System § 4.46 Accurate measurement. Accurate... indispensable in examinations conducted within the Department of Veterans Affairs. Muscle atrophy must also be...

  12. 38 CFR 4.46 - Accurate measurement.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... RATING DISABILITIES Disability Ratings The Musculoskeletal System § 4.46 Accurate measurement. Accurate... indispensable in examinations conducted within the Department of Veterans Affairs. Muscle atrophy must also be...

  13. 38 CFR 4.46 - Accurate measurement.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... RATING DISABILITIES Disability Ratings The Musculoskeletal System § 4.46 Accurate measurement. Accurate... indispensable in examinations conducted within the Department of Veterans Affairs. Muscle atrophy must also be...

  14. Feedback about More Accurate versus Less Accurate Trials: Differential Effects on Self-Confidence and Activation

    ERIC Educational Resources Information Center

    Badami, Rokhsareh; VaezMousavi, Mohammad; Wulf, Gabriele; Namazizadeh, Mahdi

    2012-01-01

    One purpose of the present study was to examine whether self-confidence or anxiety would be differentially affected by feedback from more accurate rather than less accurate trials. The second purpose was to determine whether arousal variations (activation) would predict performance. On Day 1, participants performed a golf putting task under one of…

  15. Accurate perception of negative emotions predicts functional capacity in schizophrenia.

    PubMed

    Abram, Samantha V; Karpouzian, Tatiana M; Reilly, James L; Derntl, Birgit; Habel, Ute; Smith, Matthew J

    2014-04-30

    Several studies suggest facial affect perception (FAP) deficits in schizophrenia are linked to poorer social functioning. However, whether reduced functioning is associated with inaccurate perception of specific emotional valence or a global FAP impairment remains unclear. The present study examined whether impairment in the perception of specific emotional valences (positive, negative) and neutrality were uniquely associated with social functioning, using a multimodal social functioning battery. A sample of 59 individuals with schizophrenia and 41 controls completed a computerized FAP task, and measures of functional capacity, social competence, and social attainment. Participants also underwent neuropsychological testing and symptom assessment. Regression analyses revealed that only accurately perceiving negative emotions explained significant variance (7.9%) in functional capacity after accounting for neurocognitive function and symptoms. Partial correlations indicated that accurately perceiving anger, in particular, was positively correlated with functional capacity. FAP for positive, negative, or neutral emotions were not related to social competence or social attainment. Our findings were consistent with prior literature suggesting negative emotions are related to functional capacity in schizophrenia. Furthermore, the observed relationship between perceiving anger and performance of everyday living skills is novel and warrants further exploration. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  16. Geodetic analysis of disputed accurate qibla direction

    NASA Astrophysics Data System (ADS)

    Saksono, Tono; Fulazzaky, Mohamad Ali; Sari, Zamah

    2018-04-01

    Muslims perform the prayers facing towards the correct qibla direction would be the only one of the practical issues in linking theoretical studies with practice. The concept of facing towards the Kaaba in Mecca during the prayers has long been the source of controversy among the muslim communities to not only in poor and developing countries but also in developed countries. The aims of this study were to analyse the geodetic azimuths of qibla calculated using three different models of the Earth. The use of ellipsoidal model of the Earth could be the best method for determining the accurate direction of Kaaba from anywhere on the Earth's surface. A muslim cannot direct himself towards the qibla correctly if he cannot see the Kaaba due to setting out process and certain motions during the prayer this can significantly shift the qibla direction from the actual position of the Kaaba. The requirement of muslim prayed facing towards the Kaaba is more as spiritual prerequisite rather than physical evidence.

  17. Accurate Quantitation and Analysis of Nitrofuran Metabolites, Chloramphenicol, and Florfenicol in Seafood by Ultrahigh-Performance Liquid Chromatography-Tandem Mass Spectrometry: Method Validation and Regulatory Samples.

    PubMed

    Aldeek, Fadi; Hsieh, Kevin C; Ugochukwu, Obiadada N; Gerard, Ghislain; Hammack, Walter

    2018-05-23

    We developed and validated a method for the extraction, identification, and quantitation of four nitrofuran metabolites, 3-amino-2-oxazolidinone (AOZ), 3-amino-5-morpholinomethyl-2-oxazolidinone (AMOZ), semicarbazide (SC), and 1-aminohydantoin (AHD), as well as chloramphenicol and florfenicol in a variety of seafood commodities. Samples were extracted by liquid-liquid extraction techniques, analyzed by ultrahigh-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS), and quantitated using commercially sourced, derivatized nitrofuran metabolites, with their isotopically labeled internal standards in-solvent. We obtained recoveries of 90-100% at various fortification levels. The limit of detection (LOD) was set at 0.25 ng/g for AMOZ and AOZ, 1 ng/g for AHD and SC, and 0.1 ng/g for the phenicols. Various extraction methods, standard stability, derivatization efficiency, and improvements to conventional quantitation techniques were also investigated. We successfully applied this method to the identification and quantitation of nitrofuran metabolites and phenicols in 102 imported seafood products. Our results revealed that four of the samples contained residues from banned veterinary drugs.

  18. Inverse methods for 3D quantitative optical coherence elasticity imaging (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Dong, Li; Wijesinghe, Philip; Hugenberg, Nicholas; Sampson, David D.; Munro, Peter R. T.; Kennedy, Brendan F.; Oberai, Assad A.

    2017-02-01

    In elastography, quantitative elastograms are desirable as they are system and operator independent. Such quantification also facilitates more accurate diagnosis, longitudinal studies and studies performed across multiple sites. In optical elastography (compression, surface-wave or shear-wave), quantitative elastograms are typically obtained by assuming some form of homogeneity. This simplifies data processing at the expense of smearing sharp transitions in elastic properties, and/or introducing artifacts in these regions. Recently, we proposed an inverse problem-based approach to compression OCE that does not assume homogeneity, and overcomes the drawbacks described above. In this approach, the difference between the measured and predicted displacement field is minimized by seeking the optimal distribution of elastic parameters. The predicted displacements and recovered elastic parameters together satisfy the constraint of the equations of equilibrium. This approach, which has been applied in two spatial dimensions assuming plane strain, has yielded accurate material property distributions. Here, we describe the extension of the inverse problem approach to three dimensions. In addition to the advantage of visualizing elastic properties in three dimensions, this extension eliminates the plane strain assumption and is therefore closer to the true physical state. It does, however, incur greater computational costs. We address this challenge through a modified adjoint problem, spatially adaptive grid resolution, and three-dimensional decomposition techniques. Through these techniques the inverse problem is solved on a typical desktop machine within a wall clock time of 20 hours. We present the details of the method and quantitative elasticity images of phantoms and tissue samples.

  19. Identification of Novel Tumor-Associated Cell Surface Sialoglycoproteins in Human Glioblastoma Tumors Using Quantitative Proteomics

    PubMed Central

    Autelitano, François; Loyaux, Denis; Roudières, Sébastien; Déon, Catherine; Guette, Frédérique; Fabre, Philippe; Ping, Qinggong; Wang, Su; Auvergne, Romane; Badarinarayana, Vasudeo; Smith, Michael; Guillemot, Jean-Claude; Goldman, Steven A.; Natesan, Sridaran; Ferrara, Pascual; August, Paul

    2014-01-01

    Glioblastoma multiform (GBM) remains clinical indication with significant “unmet medical need”. Innovative new therapy to eliminate residual tumor cells and prevent tumor recurrences is critically needed for this deadly disease. A major challenge of GBM research has been the identification of novel molecular therapeutic targets and accurate diagnostic/prognostic biomarkers. Many of the current clinical therapeutic targets of immunotoxins and ligand-directed toxins for high-grade glioma (HGG) cells are surface sialylated glycoproteins. Therefore, methods that systematically and quantitatively analyze cell surface sialoglycoproteins in human clinical tumor samples would be useful for the identification of potential diagnostic markers and therapeutic targets for malignant gliomas. In this study, we used the bioorthogonal chemical reporter strategy (BOCR) in combination with label-free quantitative mass spectrometry (LFQ-MS) to characterize and accurately quantify the individual cell surface sialoproteome in human GBM tissues, in fetal, adult human astrocytes, and in human neural progenitor cells (NPCs). We identified and quantified a total of 843 proteins, including 801 glycoproteins. Among the 843 proteins, 606 (72%) are known cell surface or secreted glycoproteins, including 156 CD-antigens, all major classes of cell surface receptor proteins, transporters, and adhesion proteins. Our findings identified several known as well as new cell surface antigens whose expression is predominantly restricted to human GBM tumors as confirmed by microarray transcription profiling, quantitative RT-PCR and immunohistochemical staining. This report presents the comprehensive identification of new biomarkers and therapeutic targets for the treatment of malignant gliomas using quantitative sialoglycoproteomics with clinically relevant, patient derived primary glioma cells. PMID:25360666

  20. Identification of novel tumor-associated cell surface sialoglycoproteins in human glioblastoma tumors using quantitative proteomics.

    PubMed

    Autelitano, François; Loyaux, Denis; Roudières, Sébastien; Déon, Catherine; Guette, Frédérique; Fabre, Philippe; Ping, Qinggong; Wang, Su; Auvergne, Romane; Badarinarayana, Vasudeo; Smith, Michael; Guillemot, Jean-Claude; Goldman, Steven A; Natesan, Sridaran; Ferrara, Pascual; August, Paul

    2014-01-01

    Glioblastoma multiform (GBM) remains clinical indication with significant "unmet medical need". Innovative new therapy to eliminate residual tumor cells and prevent tumor recurrences is critically needed for this deadly disease. A major challenge of GBM research has been the identification of novel molecular therapeutic targets and accurate diagnostic/prognostic biomarkers. Many of the current clinical therapeutic targets of immunotoxins and ligand-directed toxins for high-grade glioma (HGG) cells are surface sialylated glycoproteins. Therefore, methods that systematically and quantitatively analyze cell surface sialoglycoproteins in human clinical tumor samples would be useful for the identification of potential diagnostic markers and therapeutic targets for malignant gliomas. In this study, we used the bioorthogonal chemical reporter strategy (BOCR) in combination with label-free quantitative mass spectrometry (LFQ-MS) to characterize and accurately quantify the individual cell surface sialoproteome in human GBM tissues, in fetal, adult human astrocytes, and in human neural progenitor cells (NPCs). We identified and quantified a total of 843 proteins, including 801 glycoproteins. Among the 843 proteins, 606 (72%) are known cell surface or secreted glycoproteins, including 156 CD-antigens, all major classes of cell surface receptor proteins, transporters, and adhesion proteins. Our findings identified several known as well as new cell surface antigens whose expression is predominantly restricted to human GBM tumors as confirmed by microarray transcription profiling, quantitative RT-PCR and immunohistochemical staining. This report presents the comprehensive identification of new biomarkers and therapeutic targets for the treatment of malignant gliomas using quantitative sialoglycoproteomics with clinically relevant, patient derived primary glioma cells.

  1. Analyses and descriptions of geochemical samples from the Rich Mountain Roadless Area, Fannin and Gilmer counties, Georgia

    USGS Publications Warehouse

    Sears, C.M.; Foose, M.P.; Day, G.W.; Ericksen, M.S.

    1983-01-01

    Semi-quantitative spectrographic analyses for 31 elements on rock, soil, fine-grained stream sediment, bulk stream sediment, and panned stream sediment samples collected in the Rich Mountain Roadless Area, Fannin and Gilmer Counties, Georgia, are reported here. Atomic absorption analyses for gold and fluorometric analyses for uranium are also reported. Brief descriptions of all rock samples analyzed are included.

  2. Magnetic fingerprints of rolling cells for quantitative flow cytometry in whole blood

    NASA Astrophysics Data System (ADS)

    Reisbeck, Mathias; Helou, Michael Johannes; Richter, Lukas; Kappes, Barbara; Friedrich, Oliver; Hayden, Oliver

    2016-09-01

    Over the past 50 years, flow cytometry has had a profound impact on preclinical and clinical applications requiring single cell function information for counting, sub-typing and quantification of epitope expression. At the same time, the workflow complexity and high costs of such optical systems still limit flow cytometry applications to specialized laboratories. Here, we present a quantitative magnetic flow cytometer that incorporates in situ magnetophoretic cell focusing for highly accurate and reproducible rolling of the cellular targets over giant magnetoresistance sensing elements. Time-of-flight analysis is used to unveil quantitative single cell information contained in its magnetic fingerprint. Furthermore, we used erythrocytes as a biological model to validate our methodology with respect to precise analysis of the hydrodynamic cell diameter, quantification of binding capacity of immunomagnetic labels, and discrimination of cell morphology. The extracted time-of-flight information should enable point-of-care quantitative flow cytometry in whole blood for clinical applications, such as immunology and primary hemostasis.

  3. Quantitation of valve regurgitation severity by three-dimensional vena contracta area is superior to flow convergence method of quantitation on transesophageal echocardiography.

    PubMed

    Abudiab, Muaz M; Chao, Chieh-Ju; Liu, Shuang; Naqvi, Tasneem Z

    2017-07-01

    Quantitation of regurgitation severity using the proximal isovelocity acceleration (PISA) method to calculate effective regurgitant orifice (ERO) area has limitations. Measurement of three-dimensional (3D) vena contracta area (VCA) accurately grades mitral regurgitation (MR) severity on transthoracic echocardiography (TTE). We evaluated 3D VCA quantitation of regurgitant jet severity using 3D transesophageal echocardiography (TEE) in 110 native mitral, aortic, and tricuspid valves and six prosthetic valves in patients with at least mild valvular regurgitation. The ASE-recommended integrative method comprising semiquantitative and quantitative assessment of valvular regurgitation was used as a reference method, including ERO area by 2D PISA for assigning severity of regurgitation grade. Mean age was 62.2±14.4 years; 3D VCA quantitation was feasible in 91% regurgitant valves compared to 78% by the PISA method. When both methods were feasible and in the presence of a single regurgitant jet, 3D VCA and 2D PISA were similar in differentiating assigned severity (ANOVAP<.001). In valves with multiple jets, however, 3D VCA had a better correlation to assigned severity (ANOVAP<.0001). The agreement of 2D PISA and 3D VCA with the integrative method was 47% and 58% for moderate and 65% and 88% for severe regurgitation, respectively. Measurement of 3D VCA by TEE is superior to the 2D PISA method in determination of regurgitation severity in multiple native and prosthetic valves. © 2017, Wiley Periodicals, Inc.

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

    NASA Technical Reports Server (NTRS)

    Petersen, Gene R.

    1988-01-01

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

  5. Continuous Measurements of Eyeball Area and Their Spectrum Analyses -- Toward the Quantification of Rest Rhythm of Horses by Image Processing

    DTIC Science & Technology

    2001-10-25

    analyses of electroencephalogram at half- closed eye and fully closed eye. This study aimed at quantitative estimating rest rhythm of horses by the...analyses of eyeball movement. The mask attached with a miniature CCD camera was newly developed. The continuous images of the horse eye for about 24...eyeball area were calculated. As for the results, the fluctuating status of eyeball area was analyzed quantitatively, and the rest rhythm of horses was

  6. Strategies for cloud-top phase determination: differentiation between thin cirrus clouds and snow in manual (ground truth) analyses

    NASA Astrophysics Data System (ADS)

    Hutchison, Keith D.; Etherton, Brian J.; Topping, Phillip C.

    1996-12-01

    Quantitative assessments on the performance of automated cloud analysis algorithms require the creation of highly accurate, manual cloud, no cloud (CNC) images from multispectral meteorological satellite data. In general, the methodology to create ground truth analyses for the evaluation of cloud detection algorithms is relatively straightforward. However, when focus shifts toward quantifying the performance of automated cloud classification algorithms, the task of creating ground truth images becomes much more complicated since these CNC analyses must differentiate between water and ice cloud tops while ensuring that inaccuracies in automated cloud detection are not propagated into the results of the cloud classification algorithm. The process of creating these ground truth CNC analyses may become particularly difficult when little or no spectral signature is evident between a cloud and its background, as appears to be the case when thin cirrus is present over snow-covered surfaces. In this paper, procedures are described that enhance the researcher's ability to manually interpret and differentiate between thin cirrus clouds and snow-covered surfaces in daytime AVHRR imagery. The methodology uses data in up to six AVHRR spectral bands, including an additional band derived from the daytime 3.7 micron channel, which has proven invaluable for the manual discrimination between thin cirrus clouds and snow. It is concluded that while the 1.6 micron channel remains essential to differentiate between thin ice clouds and snow. However, this capability that may be lost if the 3.7 micron data switches to a nighttime-only transmission with the launch of future NOAA satellites.

  7. Quantitative inference of population response properties across eccentricity from motion-induced maps in macaque V1

    PubMed Central

    Chen, Ming; Wu, Si; Lu, Haidong D.; Roe, Anna W.

    2013-01-01

    Interpreting population responses in the primary visual cortex (V1) remains a challenge especially with the advent of techniques measuring activations of large cortical areas simultaneously with high precision. For successful interpretation, a quantitatively precise model prediction is of great importance. In this study, we investigate how accurate a spatiotemporal filter (STF) model predicts average response profiles to coherently drifting random dot motion obtained by optical imaging of intrinsic signals in V1 of anesthetized macaques. We establish that orientation difference maps, obtained by subtracting orthogonal axis-of-motion, invert with increasing drift speeds, consistent with the motion streak effect. Consistent with perception, the speed at which the map inverts (the critical speed) depends on cortical eccentricity and systematically increases from foveal to parafoveal. We report that critical speeds and response maps to drifting motion are excellently reproduced by the STF model. Our study thus suggests that the STF model is quantitatively accurate enough to be used as a first model of choice for interpreting responses obtained with intrinsic imaging methods in V1. We show further that this good quantitative correspondence opens the possibility to infer otherwise not easily accessible population receptive field properties from responses to complex stimuli, such as drifting random dot motions. PMID:23197457

  8. Quantitative microbiome profiling links gut community variation to microbial load.

    PubMed

    Vandeputte, Doris; Kathagen, Gunter; D'hoe, Kevin; Vieira-Silva, Sara; Valles-Colomer, Mireia; Sabino, João; Wang, Jun; Tito, Raul Y; De Commer, Lindsey; Darzi, Youssef; Vermeire, Séverine; Falony, Gwen; Raes, Jeroen

    2017-11-23

    Current sequencing-based analyses of faecal microbiota quantify microbial taxa and metabolic pathways as fractions of the sample sequence library generated by each analysis. Although these relative approaches permit detection of disease-associated microbiome variation, they are limited in their ability to reveal the interplay between microbiota and host health. Comparative analyses of relative microbiome data cannot provide information about the extent or directionality of changes in taxa abundance or metabolic potential. If microbial load varies substantially between samples, relative profiling will hamper attempts to link microbiome features to quantitative data such as physiological parameters or metabolite concentrations. Saliently, relative approaches ignore the possibility that altered overall microbiota abundance itself could be a key identifier of a disease-associated ecosystem configuration. To enable genuine characterization of host-microbiota interactions, microbiome research must exchange ratios for counts. Here we build a workflow for the quantitative microbiome profiling of faecal material, through parallelization of amplicon sequencing and flow cytometric enumeration of microbial cells. We observe up to tenfold differences in the microbial loads of healthy individuals and relate this variation to enterotype differentiation. We show how microbial abundances underpin both microbiota variation between individuals and covariation with host phenotype. Quantitative profiling bypasses compositionality effects in the reconstruction of gut microbiota interaction networks and reveals that the taxonomic trade-off between Bacteroides and Prevotella is an artefact of relative microbiome analyses. Finally, we identify microbial load as a key driver of observed microbiota alterations in a cohort of patients with Crohn's disease, here associated with a low-cell-count Bacteroides enterotype (as defined through relative profiling).

  9. High resolution rare-earth elements analyses of natural apatite and its application in geo-sciences: Combined micro-PIXE, quantitative CL spectroscopy and electron spin resonance analyses

    NASA Astrophysics Data System (ADS)

    Habermann, D.; Götte, T.; Meijer, J.; Stephan, A.; Richter, D. K.; Niklas, J. R.

    2000-03-01

    The rare-earth element (REE) distribution in natural apatite is analysed by micro-PIXE, cathodoluminescence (CL) microscopy and spectroscopy and electron spin resonance (ESR) spectroscopy. The micro-PIXE analyses of an apatite crystal from Cerro de Mercado (Mexico) and the summary of 20 analyses of six francolite (conodonts of Triassic age) samples indicate that most of the REEs are enriched in apatite and francolite comparative to average shale standard (NASC). The analyses of fossil francolite revealing the REE-distribution not to be in balance with the REE-distribution of seawater and fish bone debris. Strong inhomogenous lateral REE-distribution in fossil conodont material is shown by CL-mapping and most probably not being a vital effect. Therefore, the resulting REE-signal from fossil francolite is the sum of vital and post-mortem incorporation. The necessary charge compensation for the substitution of divalent Ca by trivalent REE being done by different kind of electron defects and defect ions.

  10. Qualitative and quantitative studies of chemical composition of sandarac resin by GC-MS.

    PubMed

    Kononenko, I; de Viguerie, L; Rochut, S; Walter, Ph

    2017-01-01

    The chemical composition of sandarac resin was investigated qualitatively and quantitatively by gas chromatography-mass spectrometry (GC-MS). Six compounds with labdane and pimarane skeletons were identified in the resin. The obtained mass spectra were interpreted and the mass spectrometric behaviour of these diterpenoids under EI conditions was described. Quantitative analysis by the method of internal standard revealed that identified diterpenoids represent only 10-30% of the analysed sample. The sandarac resin from different suppliers was analysed (from Kremer, Okhra, Color Rare, La Marchande de Couleurs, L'Atelier Montessori, Hevea). The analysis of different lumps of resins showed that the chemical composition differs from one lump to another, varying mainly in the relative distributions of the components.

  11. Analyses on Regional Cultivated Land Changebased on Quantitative Method

    NASA Astrophysics Data System (ADS)

    Cao, Yingui; Yuan, Chun; Zhou, Wei; Wang, Jing

    Three Gorges Project is the great project in the world, which accelerates economic development in the reservoir area of Three Gorges Project. In the process of development in the reservoir area of Three Gorges Project, cultivated land has become the important resources, a lot of cultivated land has been occupied and become the constructing land. In the same time, a lot of cultivated land has been flooded because of the rising of the water level. This paper uses the cultivated land areas and social economic indicators of reservoir area of Three Gorges in 1990-2004, takes the statistic analyses and example research in order to analyze the process of cultivated land, get the driving forces of cultivated land change, find the new methods to stimulate and forecast the cultivated land areas in the future, and serve for the cultivated land protection and successive development in reservoir area of Three Gorges. The results indicate as follow, firstly, in the past 15 years, the cultivated land areas has decreased 200142 hm2, the decreasing quantity per year is 13343 hm2. The whole reservoir area is divided into three different areas, they are upper reaches area, belly area and lower reaches area. The trends of cultivated land change in different reservoir areas are similar to the whole reservoir area. Secondly, the curve of cultivated land areas and per capita GDP takes on the reverse U, and the steps between the change rate of cultivated land and the change rate of GDP are different in some years, which indicates that change of cultivated land and change of GDP are decoupling, besides that, change of cultivated land is connection with the development of urbanization and the policy of returning forestry greatly. Lastly, the precision of multi-regression is lower than the BP neural network in the stimulation of cultivated land, then takes use of the BP neural network to forecast the cultivated land areas in 2005, 2010 and 2015, and the forecasting results are reasonable.

  12. Quantitative Analyses of Core Promoters Enable Precise Engineering of Regulated Gene Expression in Mammalian Cells.

    PubMed

    Ede, Christopher; Chen, Ximin; Lin, Meng-Yin; Chen, Yvonne Y

    2016-05-20

    Inducible transcription systems play a crucial role in a wide array of synthetic biology circuits. However, the majority of inducible promoters are constructed from a limited set of tried-and-true promoter parts, which are susceptible to common shortcomings such as high basal expression levels (i.e., leakiness). To expand the toolbox for regulated mammalian gene expression and facilitate the construction of mammalian genetic circuits with precise functionality, we quantitatively characterized a panel of eight core promoters, including sequences with mammalian, viral, and synthetic origins. We demonstrate that this selection of core promoters can provide a wide range of basal gene expression levels and achieve a gradient of fold-inductions spanning 2 orders of magnitude. Furthermore, commonly used parts such as minimal CMV and minimal SV40 promoters were shown to achieve robust gene expression upon induction, but also suffer from high levels of leakiness. In contrast, a synthetic promoter, YB_TATA, was shown to combine low basal expression with high transcription rate in the induced state to achieve significantly higher fold-induction ratios compared to all other promoters tested. These behaviors remain consistent when the promoters are coupled to different genetic outputs and different response elements, as well as across different host-cell types and DNA copy numbers. We apply this quantitative understanding of core promoter properties to the successful engineering of human T cells that respond to antigen stimulation via chimeric antigen receptor signaling specifically under hypoxic environments. Results presented in this study can facilitate the design and calibration of future mammalian synthetic biology systems capable of precisely programmed functionality.

  13. Accurate measurement of transgene copy number in crop plants using droplet digital PCR.

    PubMed

    Collier, Ray; Dasgupta, Kasturi; Xing, Yan-Ping; Hernandez, Bryan Tarape; Shao, Min; Rohozinski, Dominica; Kovak, Emma; Lin, Jeanie; de Oliveira, Maria Luiza P; Stover, Ed; McCue, Kent F; Harmon, Frank G; Blechl, Ann; Thomson, James G; Thilmony, Roger

    2017-06-01

    Genetic transformation is a powerful means for the improvement of crop plants, but requires labor- and resource-intensive methods. An efficient method for identifying single-copy transgene insertion events from a population of independent transgenic lines is desirable. Currently, transgene copy number is estimated by either Southern blot hybridization analyses or quantitative polymerase chain reaction (qPCR) experiments. Southern hybridization is a convincing and reliable method, but it also is expensive, time-consuming and often requires a large amount of genomic DNA and radioactively labeled probes. Alternatively, qPCR requires less DNA and is potentially simpler to perform, but its results can lack the accuracy and precision needed to confidently distinguish between one- and two-copy events in transgenic plants with large genomes. To address this need, we developed a droplet digital PCR-based method for transgene copy number measurement in an array of crops: rice, citrus, potato, maize, tomato and wheat. The method utilizes specific primers to amplify target transgenes, and endogenous reference genes in a single duplexed reaction containing thousands of droplets. Endpoint amplicon production in the droplets is detected and quantified using sequence-specific fluorescently labeled probes. The results demonstrate that this approach can generate confident copy number measurements in independent transgenic lines in these crop species. This method and the compendium of probes and primers will be a useful resource for the plant research community, enabling the simple and accurate determination of transgene copy number in these six important crop species. Published 2017. This article is a U.S. Government work and is in the public domain in the USA.

  14. Accurate reliability analysis method for quantum-dot cellular automata circuits

    NASA Astrophysics Data System (ADS)

    Cui, Huanqing; Cai, Li; Wang, Sen; Liu, Xiaoqiang; Yang, Xiaokuo

    2015-10-01

    Probabilistic transfer matrix (PTM) is a widely used model in the reliability research of circuits. However, PTM model cannot reflect the impact of input signals on reliability, so it does not completely conform to the mechanism of the novel field-coupled nanoelectronic device which is called quantum-dot cellular automata (QCA). It is difficult to get accurate results when PTM model is used to analyze the reliability of QCA circuits. To solve this problem, we present the fault tree models of QCA fundamental devices according to different input signals. After that, the binary decision diagram (BDD) is used to quantitatively investigate the reliability of two QCA XOR gates depending on the presented models. By employing the fault tree models, the impact of input signals on reliability can be identified clearly and the crucial components of a circuit can be found out precisely based on the importance values (IVs) of components. So this method is contributive to the construction of reliable QCA circuits.

  15. Using multiple PCR and CE with chemiluminescence detection for simultaneous qualitative and quantitative analysis of genetically modified organism.

    PubMed

    Guo, Longhua; Qiu, Bin; Chi, Yuwu; Chen, Guonan

    2008-09-01

    In this paper, an ultrasensitive CE-CL detection system coupled with a novel double-on-column coaxial flow detection interface was developed for the detection of PCR products. A reliable procedure based on this system had been demonstrated for qualitative and quantitative analysis of genetically modified organism-the detection of Roundup Ready Soy (RRS) samples was presented as an example. The promoter, terminator, function and two reference genes of RRS were amplified with multiplex PCR simultaneously. After that, the multiplex PCR products were labeled with acridinium ester at the 5'-terminal through an amino modification and then analyzed by the proposed CE-CL system. Reproducibility of analysis times and peak heights for the CE-CL analysis were determined to be better than 0.91 and 3.07% (RSD, n=15), respectively, for three consecutive days. It was shown that this method could accurately and qualitatively detect RRS standards and the simulative samples. The evaluation in terms of quantitative analysis of RRS provided by this new method was confirmed by comparing our assay results with those of the standard real-time quantitative PCR (RT-QPCR) using SYBR Green I dyes. The results showed a good coherence between the two methods. This approach demonstrated the possibility for accurate qualitative and quantitative detection of GM plants in a single run.

  16. Machine learning of accurate energy-conserving molecular force fields.

    PubMed

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

    2017-05-01

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

  17. Machine learning of accurate energy-conserving molecular force fields

    PubMed Central

    Chmiela, Stefan; Tkatchenko, Alexandre; Sauceda, Huziel E.; Poltavsky, Igor; Schütt, Kristof T.; Müller, Klaus-Robert

    2017-01-01

    Using conservation of energy—a fundamental property of closed classical and quantum mechanical systems—we develop an efficient gradient-domain machine learning (GDML) approach to construct accurate molecular force fields using a restricted number of samples from ab initio molecular dynamics (AIMD) trajectories. The GDML implementation is able to reproduce global potential energy surfaces of intermediate-sized molecules with an accuracy of 0.3 kcal mol−1 for energies and 1 kcal mol−1 Å̊−1 for atomic forces using only 1000 conformational geometries for training. We demonstrate this accuracy for AIMD trajectories of molecules, including benzene, toluene, naphthalene, ethanol, uracil, and aspirin. The challenge of constructing conservative force fields is accomplished in our work by learning in a Hilbert space of vector-valued functions that obey the law of energy conservation. The GDML approach enables quantitative molecular dynamics simulations for molecules at a fraction of cost of explicit AIMD calculations, thereby allowing the construction of efficient force fields with the accuracy and transferability of high-level ab initio methods. PMID:28508076

  18. 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

  19. Accurate sparse-projection image reconstruction via nonlocal TV regularization.

    PubMed

    Zhang, Yi; Zhang, Weihua; Zhou, Jiliu

    2014-01-01

    Sparse-projection image reconstruction is a useful approach to lower the radiation dose; however, the incompleteness of projection data will cause degeneration of imaging quality. As a typical compressive sensing method, total variation has obtained great attention on this problem. Suffering from the theoretical imperfection, total variation will produce blocky effect on smooth regions and blur edges. To overcome this problem, in this paper, we introduce the nonlocal total variation into sparse-projection image reconstruction and formulate the minimization problem with new nonlocal total variation norm. The qualitative and quantitative analyses of numerical as well as clinical results demonstrate the validity of the proposed method. Comparing to other existing methods, our method more efficiently suppresses artifacts caused by low-rank reconstruction and reserves structure information better.

  20. Improved centroid moment tensor analyses in the NIED AQUA (Accurate and QUick Analysis system for source parameters)

    NASA Astrophysics Data System (ADS)

    Kimura, H.; Asano, Y.; Matsumoto, T.

    2012-12-01

    The rapid determination of hypocentral parameters and their transmission to the public are valuable components of disaster mitigation. We have operated an automatic system for this purpose—termed the Accurate and QUick Analysis system for source parameters (AQUA)—since 2005 (Matsumura et al., 2006). In this system, the initial hypocenter, the moment tensor (MT), and the centroid moment tensor (CMT) solutions are automatically determined and posted on the NIED Hi-net Web site (www.hinet.bosai.go.jp). This paper describes improvements made to the AQUA to overcome limitations that became apparent after the 2011 Tohoku Earthquake (05:46:17, March 11, 2011 in UTC). The improvements included the processing of NIED F-net velocity-type strong motion records, because NIED F-net broadband seismographs are saturated for great earthquakes such as the 2011 Tohoku Earthquake. These velocity-type strong motion seismographs provide unsaturated records not only for the 2011 Tohoku Earthquake, but also for recording stations located close to the epicenters of M>7 earthquakes. We used 0.005-0.020 Hz records for M>7.5 earthquakes, in contrast to the 0.01-0.05 Hz records employed in the original system. The initial hypocenters determined based on arrival times picked by using seismograms recorded by NIED Hi-net stations can have large errors in terms of magnitude and hypocenter location, especially for great earthquakes or earthquakes located far from the onland Hi-net network. The size of the 2011 Tohoku Earthquake was initially underestimated in the AQUA to be around M5 at the initial stage of rupture. Numerous aftershocks occurred at the outer rise east of the Japan trench, where a great earthquake is anticipated to occur. Hence, we modified the system to repeat the MT analyses assuming a larger size, for all earthquakes for which the magnitude was initially underestimated. We also broadened the search range of centroid depth for earthquakes located far from the onland Hi

  1. Residual Strength Analyses of Riveted Lap-Splice Joints

    NASA Technical Reports Server (NTRS)

    Seshadri, B. R.; Newman, J. C., Jr.

    2000-01-01

    The objective of this paper was to analyze the crack-linkup behavior in riveted-stiffened lap-splice joint panels with small multiple-site damage (MSD) cracks at several adjacent rivet holes. Analyses are based on the STAGS (STructural Analysis of General Shells) code with the critical crack-tip-opening angle (CTOA) fracture criterion. To account for high constraint around a crack front, the "plane strain core" option in STAGS was used. The importance of modeling rivet flexibility with fastener elements that accurately model load transfer across the joint is discussed. Fastener holes are not modeled but rivet connectivity is accounted for by attaching rivets to the sheet on one side of the cracks that simulated both the rivet diameter and MSD cracks. Residual strength analyses made on 2024-T3 alloy (1.6-mm thick) riveted-lap-splice joints with a lead crack and various size MSD cracks were compared with test data from Boeing Airplane Company. Analyses were conducted for both restrained and unrestrained buckling conditions. Comparison of results from these analyses and results from lap-splice-joint test panels, which were partially restrained against buckling indicate that the test results were bounded by the failure loads predicted by the analyses with restrained and unrestrained conditions.

  2. Correcting false positive medium-chain acyl-CoA dehydrogenase deficiency results from newborn screening; synthesis, purification, and standardization of branched-chain C8 acylcarnitines for use in their selective and accurate absolute quantitation by UHPLC-MS/MS.

    PubMed

    Minkler, Paul E; Stoll, Maria S K; Ingalls, Stephen T; Hoppel, Charles L

    2017-04-01

    While selectively quantifying acylcarnitines in thousands of patient samples using UHPLC-MS/MS, we have occasionally observed unidentified branched-chain C8 acylcarnitines. Such observations are not possible using tandem MS methods, which generate pseudo-quantitative acylcarnitine "profiles". Since these "profiles" select for mass alone, they cannot distinguish authentic signal from isobaric and isomeric interferences. For example, some of the samples containing branched-chain C8 acylcarnitines were, in fact, expanded newborn screening false positive "profiles" for medium-chain acyl-CoA dehydrogenase deficiency (MCADD). Using our fast, highly selective, and quantitatively accurate UHPLC-MS/MS acylcarnitine determination method, we corrected the false positive tandem MS results and reported the sample results as normal for octanoylcarnitine (the marker for MCADD). From instances such as these, we decided to further investigate the presence of branched-chain C8 acylcarnitines in patient samples. To accomplish this, we synthesized and chromatographically characterized several branched-chain C8 acylcarnitines (in addition to valproylcarnitine): 2-methylheptanoylcarnitine, 6-methylheptanoylcarnitine, 2,2-dimethylhexanoylcarnitine, 3,3-dimethylhexanoylcarnitine, 3,5-dimethylhexanoylcarnitine, 2-ethylhexanoylcarnitine, and 2,4,4-trimethylpentanoylcarnitine. We then compared their behavior with branched-chain C8 acylcarnitines observed in patient samples and demonstrated our ability to chromographically resolve, and thus distinguish, octanoylcarnitine from branched-chain C8 acylcarnitines, correcting false positive MCADD results from expanded newborn screening. Copyright © 2017 Elsevier Inc. All rights reserved.

  3. Experimental Null Method to Guide the Development of Technical Procedures and to Control False-Positive Discovery in Quantitative Proteomics.

    PubMed

    Shen, Xiaomeng; Hu, Qiang; Li, Jun; Wang, Jianmin; Qu, Jun

    2015-10-02

    Comprehensive and accurate evaluation of data quality and false-positive biomarker discovery is critical to direct the method development/optimization for quantitative proteomics, which nonetheless remains challenging largely due to the high complexity and unique features of proteomic data. Here we describe an experimental null (EN) method to address this need. Because the method experimentally measures the null distribution (either technical or biological replicates) using the same proteomic samples, the same procedures and the same batch as the case-vs-contol experiment, it correctly reflects the collective effects of technical variability (e.g., variation/bias in sample preparation, LC-MS analysis, and data processing) and project-specific features (e.g., characteristics of the proteome and biological variation) on the performances of quantitative analysis. To show a proof of concept, we employed the EN method to assess the quantitative accuracy and precision and the ability to quantify subtle ratio changes between groups using different experimental and data-processing approaches and in various cellular and tissue proteomes. It was found that choices of quantitative features, sample size, experimental design, data-processing strategies, and quality of chromatographic separation can profoundly affect quantitative precision and accuracy of label-free quantification. The EN method was also demonstrated as a practical tool to determine the optimal experimental parameters and rational ratio cutoff for reliable protein quantification in specific proteomic experiments, for example, to identify the necessary number of technical/biological replicates per group that affords sufficient power for discovery. Furthermore, we assessed the ability of EN method to estimate levels of false-positives in the discovery of altered proteins, using two concocted sample sets mimicking proteomic profiling using technical and biological replicates, respectively, where the true

  4. Comparative study of quantitative phase imaging techniques for refractometry of optical fibers

    NASA Astrophysics Data System (ADS)

    de Dorlodot, Bertrand; Bélanger, Erik; Bérubé, Jean-Philippe; Vallée, Réal; Marquet, Pierre

    2018-02-01

    The refractive index difference profile of optical fibers is the key design parameter because it determines, among other properties, the insertion losses and propagating modes. Therefore, an accurate refractive index profiling method is of paramount importance to their development and optimization. Quantitative phase imaging (QPI) is one of the available tools to retrieve structural characteristics of optical fibers, including the refractive index difference profile. Having the advantage of being non-destructive, several different QPI methods have been developed over the last decades. Here, we present a comparative study of three different available QPI techniques, namely the transport-of-intensity equation, quadriwave lateral shearing interferometry and digital holographic microscopy. To assess the accuracy and precision of those QPI techniques, quantitative phase images of the core of a well-characterized optical fiber have been retrieved for each of them and a robust image processing procedure has been applied in order to retrieve their refractive index difference profiles. As a result, even if the raw images for all the three QPI methods were suffering from different shortcomings, our robust automated image-processing pipeline successfully corrected these. After this treatment, all three QPI techniques yielded accurate, reliable and mutually consistent refractive index difference profiles in agreement with the accuracy and precision of the refracted near-field benchmark measurement.

  5. Comparison of semi-quantitative and quantitative dynamic contrast-enhanced MRI evaluations of vertebral marrow perfusion in a rat osteoporosis model.

    PubMed

    Zhu, Jingqi; Xiong, Zuogang; Zhang, Jiulong; Qiu, Yuyou; Hua, Ting; Tang, Guangyu

    2017-11-14

    in the OVX group from week 3. The MVD values of the OVX group decreased significantly compared with those of the control group only at week 12 (p=0.023). A weak positive correlation of E max and a strong positive correlation of K trans with MVD were found. Compared with semi-quantitative DCE-MRI, the quantitative DCE-MRI parameter K trans is a more sensitive and accurate index for detecting early reduced perfusion in osteoporotic bone.

  6. Optimization of homonuclear 2D NMR for fast quantitative analysis: application to tropine-nortropine mixtures.

    PubMed

    Giraudeau, Patrick; Guignard, Nadia; Hillion, Emilie; Baguet, Evelyne; Akoka, Serge

    2007-03-12

    Quantitative analysis by (1)H NMR is often hampered by heavily overlapping signals that may occur for complex mixtures, especially those containing similar compounds. Bidimensional homonuclear NMR spectroscopy can overcome this difficulty. A thorough review of acquisition and post-processing parameters was carried out to obtain accurate and precise, quantitative 2D J-resolved and DQF-COSY spectra in a much reduced time, thus limiting the spectrometer instabilities in the course of time. The number of t(1) increments was reduced as much as possible, and standard deviation was improved by optimization of spectral width, number of transients, phase cycling and apodization function. Localized polynomial baseline corrections were applied to the relevant chemical shift areas. Our method was applied to tropine-nortropine mixtures. Quantitative J-resolved spectra were obtained in less than 3 min and quantitative DQF-COSY spectra in 12 min, with an accuracy of 3% for J-spectroscopy and 2% for DQF-COSY, and a standard deviation smaller than 1%.

  7. Spatial problem-solving in a wheel-shaped maze: quantitative and qualitative analyses of the behavioural changes following damage to the hippocampus in the rat.

    PubMed

    Buhot, M C; Chapuis, N; Scardigli, P; Herrmann, T

    1991-07-01

    The behaviour of sham-operated rats and rats with damage to the dorsal hippocampus was compared in a complex spatial problem-solving task using a 'hub-spoke-rim' wheel type maze. Compared to the classical Olton 8-arm radial maze and Morris water maze, this apparatus presents the animal with a series of possible alternative routes both direct and indirect to the goal (food). The task included 3 main stages: exploration, feeding and testing, as do the classic problem-solving tasks. During exploration, hippocampal rats were found to be more active than sham rats. Nevertheless, they displayed habituation and a relatively efficient circumnavigation, though, in both cases, different from those of sham rats. During test trials, hippocampal rats were characterized as being less accurate, making more errors than sham rats. Nevertheless, both groups increased their accuracy of first choices over trials. The qualitative analyses of test trial performance indicated that hippocampal rats were less accurate in terms of the initial error's deviation from the goal, and less efficient in terms of corrective behaviour than sham rats which used either the periphery or the spokes to attain economically the goal. Surprisingly, hippocampal rats were not limited to a taxon type orientation but learned to use the periphery, a tendency which developed over time. Seemingly, for sham rats, the problem-solving process took the form of updating information during transit. For hippocampal rats, the use of periphery reflected both an ability to discriminate its usefulness in reaching the goal via a taxis type behaviour, and some sparing of ability to generalize the closeness and the location of the goal. These results, especially the strategic correction patterns, are discussed in the light of Sutherland and Rudy's 'configurational association theory'.

  8. Quantitative radiomics studies for tissue characterization: a review of technology and methodological procedures.

    PubMed

    Larue, Ruben T H M; Defraene, Gilles; De Ruysscher, Dirk; Lambin, Philippe; van Elmpt, Wouter

    2017-02-01

    Quantitative analysis of tumour characteristics based on medical imaging is an emerging field of research. In recent years, quantitative imaging features derived from CT, positron emission tomography and MR scans were shown to be of added value in the prediction of outcome parameters in oncology, in what is called the radiomics field. However, results might be difficult to compare owing to a lack of standardized methodologies to conduct quantitative image analyses. In this review, we aim to present an overview of the current challenges, technical routines and protocols that are involved in quantitative imaging studies. The first issue that should be overcome is the dependency of several features on the scan acquisition and image reconstruction parameters. Adopting consistent methods in the subsequent target segmentation step is evenly crucial. To further establish robust quantitative image analyses, standardization or at least calibration of imaging features based on different feature extraction settings is required, especially for texture- and filter-based features. Several open-source and commercial software packages to perform feature extraction are currently available, all with slightly different functionalities, which makes benchmarking quite challenging. The number of imaging features calculated is typically larger than the number of patients studied, which emphasizes the importance of proper feature selection and prediction model-building routines to prevent overfitting. Even though many of these challenges still need to be addressed before quantitative imaging can be brought into daily clinical practice, radiomics is expected to be a critical component for the integration of image-derived information to personalize treatment in the future.

  9. Natural bacterial communities serve as quantitative geochemical biosensors.

    PubMed

    Smith, Mark B; Rocha, Andrea M; Smillie, Chris S; Olesen, Scott W; Paradis, Charles; Wu, Liyou; Campbell, James H; Fortney, Julian L; Mehlhorn, Tonia L; Lowe, Kenneth A; Earles, Jennifer E; Phillips, Jana; Techtmann, Steve M; Joyner, Dominique C; Elias, Dwayne A; Bailey, Kathryn L; Hurt, Richard A; Preheim, Sarah P; Sanders, Matthew C; Yang, Joy; Mueller, Marcella A; Brooks, Scott; Watson, David B; Zhang, Ping; He, Zhili; Dubinsky, Eric A; Adams, Paul D; Arkin, Adam P; Fields, Matthew W; Zhou, Jizhong; Alm, Eric J; Hazen, Terry C

    2015-05-12

    Biological sensors can be engineered to measure a wide range of environmental conditions. Here we show that statistical analysis of DNA from natural microbial communities can be used to accurately identify environmental contaminants, including uranium and nitrate at a nuclear waste site. In addition to contamination, sequence data from the 16S rRNA gene alone can quantitatively predict a rich catalogue of 26 geochemical features collected from 93 wells with highly differing geochemistry characteristics. We extend this approach to identify sites contaminated with hydrocarbons from the Deepwater Horizon oil spill, finding that altered bacterial communities encode a memory of prior contamination, even after the contaminants themselves have been fully degraded. We show that the bacterial strains that are most useful for detecting oil and uranium are known to interact with these substrates, indicating that this statistical approach uncovers ecologically meaningful interactions consistent with previous experimental observations. Future efforts should focus on evaluating the geographical generalizability of these associations. Taken as a whole, these results indicate that ubiquitous, natural bacterial communities can be used as in situ environmental sensors that respond to and capture perturbations caused by human impacts. These in situ biosensors rely on environmental selection rather than directed engineering, and so this approach could be rapidly deployed and scaled as sequencing technology continues to become faster, simpler, and less expensive. Here we show that DNA from natural bacterial communities can be used as a quantitative biosensor to accurately distinguish unpolluted sites from those contaminated with uranium, nitrate, or oil. These results indicate that bacterial communities can be used as environmental sensors that respond to and capture perturbations caused by human impacts. Copyright © 2015 Smith et al.

  10. Natural bacterial communities serve as quantitative geochemical biosensors

    DOE PAGES

    Smith, Mark B.; Rocha, Andrea M.; Smillie, Chris S.; ...

    2015-05-12

    Biological sensors can be engineered to measure a wide range of environmental conditions. Here we show that statistical analysis of DNA from natural microbial communities can be used to accurately identify environmental contaminants, including uranium and nitrate at a nuclear waste site. In addition to contamination, sequence data from the 16S rRNA gene alone can quantitatively predict a rich catalogue of 26 geochemical features collected from 93 wells with highly differing geochemistry characteristics. We extend this approach to identify sites contaminated with hydrocarbons from the Deepwater Horizon oil spill, finding that altered bacterial communities encode a memory of prior contamination,more » even after the contaminants themselves have been fully degraded. We show that the bacterial strains that are most useful for detecting oil and uranium are known to interact with these substrates, indicating that this statistical approach uncovers ecologically meaningful interactions consistent with previous experimental observations. Future efforts should focus on evaluating the geographical generalizability of these associations. Taken as a whole, these results indicate that ubiquitous, natural bacterial communities can be used as in situ environmental sensors that respond to and capture perturbations caused by human impacts. These in situ biosensors rely on environmental selection rather than directed engineering, and so this approach could be rapidly deployed and scaled as sequencing technology continues to become faster, simpler, and less expensive. Here we show that DNA from natural bacterial communities can be used as a quantitative biosensor to accurately distinguish unpolluted sites from those contaminated with uranium, nitrate, or oil. These results indicate that bacterial communities can be used as environmental sensors that respond to and capture perturbations caused by human impacts.« less

  11. Accurate quantification of fluorescent targets within turbid media based on a decoupled fluorescence Monte Carlo model.

    PubMed

    Deng, Yong; Luo, Zhaoyang; Jiang, Xu; Xie, Wenhao; Luo, Qingming

    2015-07-01

    We propose a method based on a decoupled fluorescence Monte Carlo model for constructing fluorescence Jacobians to enable accurate quantification of fluorescence targets within turbid media. The effectiveness of the proposed method is validated using two cylindrical phantoms enclosing fluorescent targets within homogeneous and heterogeneous background media. The results demonstrate that our method can recover relative concentrations of the fluorescent targets with higher accuracy than the perturbation fluorescence Monte Carlo method. This suggests that our method is suitable for quantitative fluorescence diffuse optical tomography, especially for in vivo imaging of fluorophore targets for diagnosis of different diseases and abnormalities.

  12. Folding Properties of Two-Dimensional Deployable Membrane Using FEM Analyses

    NASA Astrophysics Data System (ADS)

    Satou, Yasutaka; Furuya, Hiroshi

    Folding FEM analyses are presented to examine folding properties of a two-dimensional deployable membrane for a precise deployment simulation. A fold model of the membrane is proposed by dividing the wrapping fold process into two regions which are the folded state and the transient process. The cross-section of the folded state is assumed to be a repeating structure, and analytical procedures of the repeating structure are constructed. To investigate the mechanical properties of the crease in detail, the bending stiffness is considered in the FEM analyses. As the results of the FEM analyses, the configuration of the membrane and the contact force by the adjacent membrane are obtained quantitatively for an arbitrary layer pitch. Possible occurrence of the plastic deformation is estimated using the Mises stress in the crease. The FEM results are compared with one-dimensional approximation analyses to evaluate these results.

  13. Global Quantitative Modeling of Chromatin Factor Interactions

    PubMed Central

    Zhou, Jian; Troyanskaya, Olga G.

    2014-01-01

    Chromatin is the driver of gene regulation, yet understanding the molecular interactions underlying chromatin factor combinatorial patterns (or the “chromatin codes”) remains a fundamental challenge in chromatin biology. Here we developed a global modeling framework that leverages chromatin profiling data to produce a systems-level view of the macromolecular complex of chromatin. Our model ultilizes maximum entropy modeling with regularization-based structure learning to statistically dissect dependencies between chromatin factors and produce an accurate probability distribution of chromatin code. Our unsupervised quantitative model, trained on genome-wide chromatin profiles of 73 histone marks and chromatin proteins from modENCODE, enabled making various data-driven inferences about chromatin profiles and interactions. We provided a highly accurate predictor of chromatin factor pairwise interactions validated by known experimental evidence, and for the first time enabled higher-order interaction prediction. Our predictions can thus help guide future experimental studies. The model can also serve as an inference engine for predicting unknown chromatin profiles — we demonstrated that with this approach we can leverage data from well-characterized cell types to help understand less-studied cell type or conditions. PMID:24675896

  14. Separation and quantitation of polyethylene glycols 400 and 3350 from human urine by high-performance liquid chromatography.

    PubMed

    Ryan, C M; Yarmush, M L; Tompkins, R G

    1992-04-01

    Polyethylene glycol 3350 (PEG 3350) is useful as an orally administered probe to measure in vivo intestinal permeability to macromolecules. Previous methods to detect polyethylene glycol (PEG) excreted in the urine have been hampered by inherent inaccuracies associated with liquid-liquid extraction and turbidimetric analysis. For accurate quantitation by previous methods, radioactive labels were required. This paper describes a method to separate and quantitate PEG 3350 and PEG 400 in human urine that is independent of radioactive labels and is accurate in clinical practice. The method uses sized regenerated cellulose membranes and mixed ion-exchange resin for sample preparation and high-performance liquid chromatography with refractive index detection for analysis. The 24-h excretion for normal individuals after an oral dose of 40 g of PEG 3350 and 5 g of PEG 400 was 0.12 +/- 0.04% of the original dose of PEG 3350 and 26.3 +/- 5.1% of the original dose of PEG 400.

  15. Quantitative X-ray diffraction and fluorescence analysis of paint pigment systems : final report.

    DOT National Transportation Integrated Search

    1978-01-01

    This study attempted to correlate measured X-ray intensities with concentrations of each member of paint pigment systems, thereby establishing calibration curves for the quantitative analyses of such systems.

  16. Quantitative in vivo Analyses Reveal Calcium-dependent Phosphorylation Sites and Identifies a Novel Component of the Toxoplasma Invasion Motor Complex

    PubMed Central

    Nebl, Thomas; Prieto, Judith Helena; Kapp, Eugene; Smith, Brian J.; Williams, Melanie J.; Yates, John R.; Cowman, Alan F.; Tonkin, Christopher J.

    2011-01-01

    Apicomplexan parasites depend on the invasion of host cells for survival and proliferation. Calcium-dependent signaling pathways appear to be essential for micronemal release and gliding motility, yet the target of activated kinases remains largely unknown. We have characterized calcium-dependent phosphorylation events during Toxoplasma host cell invasion. Stimulation of live tachyzoites with Ca2+-mobilizing drugs leads to phosphorylation of numerous parasite proteins, as shown by differential 2-DE display of 32[P]-labeled protein extracts. Multi-dimensional Protein Identification Technology (MudPIT) identified ∼546 phosphorylation sites on over 300 Toxoplasma proteins, including 10 sites on the actomyosin invasion motor. Using a Stable Isotope of Amino Acids in Culture (SILAC)-based quantitative LC-MS/MS analyses we monitored changes in the abundance and phosphorylation of the invasion motor complex and defined Ca2+-dependent phosphorylation patterns on three of its components - GAP45, MLC1 and MyoA. Furthermore, calcium-dependent phosphorylation of six residues across GAP45, MLC1 and MyoA is correlated with invasion motor activity. By analyzing proteins that appear to associate more strongly with the invasion motor upon calcium stimulation we have also identified a novel 15-kDa Calmodulin-like protein that likely represents the MyoA Essential Light Chain of the Toxoplasma invasion motor. This suggests that invasion motor activity could be regulated not only by phosphorylation but also by the direct binding of calcium ions to this new component. PMID:21980283

  17. Refining the quantitative pathway of the Pathways to Mathematics model.

    PubMed

    Sowinski, Carla; LeFevre, Jo-Anne; Skwarchuk, Sheri-Lynn; Kamawar, Deepthi; Bisanz, Jeffrey; Smith-Chant, Brenda

    2015-03-01

    In the current study, we adopted the Pathways to Mathematics model of LeFevre et al. (2010). In this model, there are three cognitive domains--labeled as the quantitative, linguistic, and working memory pathways--that make unique contributions to children's mathematical development. We attempted to refine the quantitative pathway by combining children's (N=141 in Grades 2 and 3) subitizing, counting, and symbolic magnitude comparison skills using principal components analysis. The quantitative pathway was examined in relation to dependent numerical measures (backward counting, arithmetic fluency, calculation, and number system knowledge) and a dependent reading measure, while simultaneously accounting for linguistic and working memory skills. Analyses controlled for processing speed, parental education, and gender. We hypothesized that the quantitative, linguistic, and working memory pathways would account for unique variance in the numerical outcomes; this was the case for backward counting and arithmetic fluency. However, only the quantitative and linguistic pathways (not working memory) accounted for unique variance in calculation and number system knowledge. Not surprisingly, only the linguistic pathway accounted for unique variance in the reading measure. These findings suggest that the relative contributions of quantitative, linguistic, and working memory skills vary depending on the specific cognitive task. Copyright © 2014 Elsevier Inc. All rights reserved.

  18. Finite element analyses of two dimensional, anisotropic heat transfer in wood

    Treesearch

    John F. Hunt; Hongmei Gu

    2004-01-01

    The anisotropy of wood creates a complex problem for solving heat and mass transfer problems that require analyses be based on fundamental material properties of the wood structure. Inputting basic orthogonal properties of the wood material alone are not sufficient for accurate modeling because wood is a combination of porous fiber cells that are aligned and mis-...

  19. Identification of internal control genes for quantitative expression analysis by real-time PCR in bovine peripheral lymphocytes.

    PubMed

    Spalenza, Veronica; Girolami, Flavia; Bevilacqua, Claudia; Riondato, Fulvio; Rasero, Roberto; Nebbia, Carlo; Sacchi, Paola; Martin, Patrice

    2011-09-01

    Gene expression studies in blood cells, particularly lymphocytes, are useful for monitoring potential exposure to toxicants or environmental pollutants in humans and livestock species. Quantitative PCR is the method of choice for obtaining accurate quantification of mRNA transcripts although variations in the amount of starting material, enzymatic efficiency, and the presence of inhibitors can lead to evaluation errors. As a result, normalization of data is of crucial importance. The most common approach is the use of endogenous reference genes as an internal control, whose expression should ideally not vary among individuals and under different experimental conditions. The accurate selection of reference genes is therefore an important step in interpreting quantitative PCR studies. Since no systematic investigation in bovine lymphocytes has been performed, the aim of the present study was to assess the expression stability of seven candidate reference genes in circulating lymphocytes collected from 15 dairy cows. Following the characterization by flow cytometric analysis of the cell populations obtained from blood through a density gradient procedure, three popular softwares were used to evaluate the gene expression data. The results showed that two genes are sufficient for normalization of quantitative PCR studies in cattle lymphocytes and that YWAHZ, S24 and PPIA are the most stable genes. Copyright © 2010 Elsevier Ltd. All rights reserved.

  20. Reporting completeness and transparency of meta-analyses of depression screening tool accuracy: A comparison of meta-analyses published before and after the PRISMA statement.

    PubMed

    Rice, Danielle B; Kloda, Lorie A; Shrier, Ian; Thombs, Brett D

    2016-08-01

    Meta-analyses that are conducted rigorously and reported completely and transparently can provide accurate evidence to inform the best possible healthcare decisions. Guideline makers have raised concerns about the utility of existing evidence on the diagnostic accuracy of depression screening tools. The objective of our study was to evaluate the transparency and completeness of reporting in meta-analyses of the diagnostic accuracy of depression screening tools using the PRISMA tool adapted for diagnostic test accuracy meta-analyses. We searched MEDLINE and PsycINFO from January 1, 2005 through March 13, 2016 for recent meta-analyses in any language on the diagnostic accuracy of depression screening tools. Two reviewers independently assessed the transparency in reporting using the PRISMA tool with appropriate adaptations made for studies of diagnostic test accuracy. We identified 21 eligible meta-analyses. Twelve of 21 meta-analyses complied with at least 50% of adapted PRISMA items. Of 30 adapted PRISMA items, 11 were fulfilled by ≥80% of included meta-analyses, 3 by 50-79% of meta-analyses, 7 by 25-45% of meta-analyses, and 9 by <25%. On average, post-PRISMA meta-analyses complied with 17 of 30 items compared to 13 of 30 items pre-PRISMA. Deficiencies in the transparency of reporting in meta-analyses of the diagnostic test accuracy of depression screening tools of meta-analyses were identified. Authors, reviewers, and editors should adhere to the PRISMA statement to improve the reporting of meta-analyses of the diagnostic accuracy of depression screening tools. Copyright © 2016 Elsevier Inc. All rights reserved.

  1. Determination of subthalamic nucleus location by quantitative analysis of despiked background neural activity from microelectrode recordings obtained during deep brain stimulation surgery.

    PubMed

    Danish, Shabbar F; Baltuch, Gordon H; Jaggi, Jurg L; Wong, Stephen

    2008-04-01

    Microelectrode recording during deep brain stimulation surgery is a useful adjunct for subthalamic nucleus (STN) localization. We hypothesize that information in the nonspike background activity can help identify STN boundaries. We present results from a novel quantitative analysis that accomplishes this goal. Thirteen consecutive microelectrode recordings were retrospectively analyzed. Spikes were removed from the recordings with an automated algorithm. The remaining "despiked" signals were converted via root mean square amplitude and curve length calculations into "feature profile" time series. Subthalamic nucleus boundaries determined by inspection, based on sustained deviations from baseline for each feature profile, were compared against those determined intraoperatively by the clinical neurophysiologist. Feature profile activity within STN exhibited a sustained rise in 10 of 13 tracks (77%). The sensitivity of STN entry was 60% and 90% for curve length and root mean square amplitude, respectively, when agreement within 0.5 mm of the neurophysiologist's prediction was used. Sensitivities were 70% and 100% for 1 mm accuracy. Exit point sensitivities were 80% and 90% for both features within 0.5 mm and 1.0 mm, respectively. Reproducible activity patterns in deep brain stimulation microelectrode recordings can allow accurate identification of STN boundaries. Quantitative analyses of this type may provide useful adjunctive information for electrode placement in deep brain stimulation surgery.

  2. A Novel ImageJ Macro for Automated Cell Death Quantitation in the Retina

    PubMed Central

    Maidana, Daniel E.; Tsoka, Pavlina; Tian, Bo; Dib, Bernard; Matsumoto, Hidetaka; Kataoka, Keiko; Lin, Haijiang; Miller, Joan W.; Vavvas, Demetrios G.

    2015-01-01

    Purpose TUNEL assay is widely used to evaluate cell death. Quantification of TUNEL-positive (TUNEL+) cells in tissue sections is usually performed manually, ideally by two masked observers. This process is time consuming, prone to measurement errors, and not entirely reproducible. In this paper, we describe an automated quantification approach to address these difficulties. Methods We developed an ImageJ macro to quantitate cell death by TUNEL assay in retinal cross-section images. The script was coded using IJ1 programming language. To validate this tool, we selected a dataset of TUNEL assay digital images, calculated layer area and cell count manually (done by two observers), and compared measurements between observers and macro results. Results The automated macro segmented outer nuclear layer (ONL) and inner nuclear layer (INL) successfully. Automated TUNEL+ cell counts were in-between counts of inexperienced and experienced observers. The intraobserver coefficient of variation (COV) ranged from 13.09% to 25.20%. The COV between both observers was 51.11 ± 25.83% for the ONL and 56.07 ± 24.03% for the INL. Comparing observers' results with macro results, COV was 23.37 ± 15.97% for the ONL and 23.44 ± 18.56% for the INL. Conclusions We developed and validated an ImageJ macro that can be used as an accurate and precise quantitative tool for retina researchers to achieve repeatable, unbiased, fast, and accurate cell death quantitation. We believe that this standardized measurement tool could be advantageous to compare results across different research groups, as it is freely available as open source. PMID:26469755

  3. Quantitative Decision Support Requires Quantitative User Guidance

    NASA Astrophysics Data System (ADS)

    Smith, L. A.

    2009-12-01

    Is it conceivable that models run on 2007 computer hardware could provide robust and credible probabilistic information for decision support and user guidance at the ZIP code level for sub-daily meteorological events in 2060? In 2090? Retrospectively, how informative would output from today’s models have proven in 2003? or the 1930’s? Consultancies in the United Kingdom, including the Met Office, are offering services to “future-proof” their customers from climate change. How is a US or European based user or policy maker to determine the extent to which exciting new Bayesian methods are relevant here? or when a commercial supplier is vastly overselling the insights of today’s climate science? How are policy makers and academic economists to make the closely related decisions facing them? How can we communicate deep uncertainty in the future at small length-scales without undermining the firm foundation established by climate science regarding global trends? Three distinct aspects of the communication of the uses of climate model output targeting users and policy makers, as well as other specialist adaptation scientists, are discussed. First, a brief scientific evaluation of the length and time scales at which climate model output is likely to become uninformative is provided, including a note on the applicability the latest Bayesian methodology to current state-of-the-art general circulation models output. Second, a critical evaluation of the language often employed in communication of climate model output, a language which accurately states that models are “better”, have “improved” and now “include” and “simulate” relevant meteorological processed, without clearly identifying where the current information is thought to be uninformative and misleads, both for the current climate and as a function of the state of the (each) climate simulation. And thirdly, a general approach for evaluating the relevance of quantitative climate model output

  4. Genetic interactions contribute less than additive effects to quantitative trait variation in yeast

    PubMed Central

    Bloom, Joshua S.; Kotenko, Iulia; Sadhu, Meru J.; Treusch, Sebastian; Albert, Frank W.; Kruglyak, Leonid

    2015-01-01

    Genetic mapping studies of quantitative traits typically focus on detecting loci that contribute additively to trait variation. Genetic interactions are often proposed as a contributing factor to trait variation, but the relative contribution of interactions to trait variation is a subject of debate. Here we use a very large cross between two yeast strains to accurately estimate the fraction of phenotypic variance due to pairwise QTL–QTL interactions for 20 quantitative traits. We find that this fraction is 9% on average, substantially less than the contribution of additive QTL (43%). Statistically significant QTL–QTL pairs typically have small individual effect sizes, but collectively explain 40% of the pairwise interaction variance. We show that pairwise interaction variance is largely explained by pairs of loci at least one of which has a significant additive effect. These results refine our understanding of the genetic architecture of quantitative traits and help guide future mapping studies. PMID:26537231

  5. Bohr effect of avian hemoglobins: Quantitative analyses based on the Wyman equation.

    PubMed

    Okonjo, Kehinde O

    2016-12-07

    The Bohr effect data for bar-headed goose, greylag goose and pheasant hemoglobins can be fitted with the Wyman equation for the Bohr effect, but under one proviso: that the pK a of His146β does not change following the T→R quaternary transition. This assumption is based on the x-ray structure of bar-headed goose hemoglobin, which shows that the salt-bridge formed between His146β and Asp94β in human deoxyhemoglobin is not formed in goose deoxyhemoglobin. When the Bohr data for chicken hemoglobin were fitted by making the same assumption, the pK a of the NH 3 + terminal group of Val1α decreased from 7.76 to 6.48 following the T→R transition. When the data were fitted without making any assumption, the pK a of the NH 3 + terminal group increased from 7.57 to 7.77 following the T→R transition. We demonstrate that avian hemoglobin Bohr data are readily fitted with the Wyman equation because avian hemoglobins lack His77β. From curve-fitting to Bohr data we estimate the pK a s of the NH 3 + terminal group of Val1α in the R and T states to be 6.33±0.1 and 7.22±0.1, respectively. We provide evidence indicating that these pK a s are more accurate than estimates from kinetic studies. Copyright © 2016 Elsevier Ltd. All rights reserved.

  6. Analysis of ribosomal RNA stability in dead cells of wine yeast by quantitative PCR.

    PubMed

    Sunyer-Figueres, Merce; Wang, Chunxiao; Mas, Albert

    2018-04-02

    During wine production, some yeasts enter a Viable But Not Culturable (VBNC) state, which may influence the quality and stability of the final wine through remnant metabolic activity or by resuscitation. Culture-independent techniques are used for obtaining an accurate estimation of the number of live cells, and quantitative PCR could be the most accurate technique. As a marker of cell viability, rRNA was evaluated by analyzing its stability in dead cells. The species-specific stability of rRNA was tested in Saccharomyces cerevisiae, as well as in three species of non-Saccharomyces yeast (Hanseniaspora uvarum, Torulaspora delbrueckii and Starmerella bacillaris). High temperature and antimicrobial dimethyl dicarbonate (DMDC) treatments were efficient in lysing the yeast cells. rRNA gene and rRNA (as cDNA) were analyzed over 48 h after cell lysis by quantitative PCR. The results confirmed the stability of rRNA for 48 h after the cell lysis treatments. To sum up, rRNA may not be a good marker of cell viability in the wine yeasts that were tested. Copyright © 2018 Elsevier B.V. All rights reserved.

  7. The APOSTEL recommendations for reporting quantitative optical coherence tomography studies.

    PubMed

    Cruz-Herranz, Andrés; Balk, Lisanne J; Oberwahrenbrock, Timm; Saidha, Shiv; Martinez-Lapiscina, Elena H; Lagreze, Wolf A; Schuman, Joel S; Villoslada, Pablo; Calabresi, Peter; Balcer, Laura; Petzold, Axel; Green, Ari J; Paul, Friedemann; Brandt, Alexander U; Albrecht, Philipp

    2016-06-14

    To develop consensus recommendations for reporting of quantitative optical coherence tomography (OCT) study results. A panel of experienced OCT researchers (including 11 neurologists, 2 ophthalmologists, and 2 neuroscientists) discussed requirements for performing and reporting quantitative analyses of retinal morphology and developed a list of initial recommendations based on experience and previous studies. The list of recommendations was subsequently revised during several meetings of the coordinating group. We provide a 9-point checklist encompassing aspects deemed relevant when reporting quantitative OCT studies. The areas covered are study protocol, acquisition device, acquisition settings, scanning protocol, funduscopic imaging, postacquisition data selection, postacquisition data analysis, recommended nomenclature, and statistical analysis. The Advised Protocol for OCT Study Terminology and Elements recommendations include core items to standardize and improve quality of reporting in quantitative OCT studies. The recommendations will make reporting of quantitative OCT studies more consistent and in line with existing standards for reporting research in other biomedical areas. The recommendations originated from expert consensus and thus represent Class IV evidence. They will need to be regularly adjusted according to new insights and practices. © 2016 American Academy of Neurology.

  8. Affinity Proteomics for Fast, Sensitive, Quantitative Analysis of Proteins in Plasma.

    PubMed

    O'Grady, John P; Meyer, Kevin W; Poe, Derrick N

    2017-01-01

    The improving efficacy of many biological therapeutics and identification of low-level biomarkers are driving the analytical proteomics community to deal with extremely high levels of sample complexity relative to their analytes. Many protein quantitation and biomarker validation procedures utilize an immunoaffinity enrichment step to purify the sample and maximize the sensitivity of the corresponding liquid chromatography tandem mass spectrometry measurements. In order to generate surrogate peptides with better mass spectrometric properties, protein enrichment is followed by a proteolytic cleavage step. This is often a time-consuming multistep process. Presented here is a workflow which enables rapid protein enrichment and proteolytic cleavage to be performed in a single, easy-to-use reactor. Using this strategy Klotho, a low-abundance biomarker found in plasma, can be accurately quantitated using a protocol that takes under 5 h from start to finish.

  9. Issues to Consider When Measuring and Applying Socioeconomic Position Quantitatively in Immigrant Health Research

    PubMed Central

    Nielsen, Signe Smith; Hempler, Nana Folmann; Krasnik, Allan

    2013-01-01

    The relationship between migration and health is complex, yet, immigrant-related inequalities in health are largely influenced by socioeconomic position. Drawing upon previous findings, this paper discusses issues to consider when measuring and applying socioeconomic position in quantitative immigrant health research. When measuring socioeconomic position, it is important to be aware of four aspects: (1) there is a lack of clarity about how socioeconomic position should be measured; (2) different types of socioeconomic position may be relevant to immigrants compared with the native-born population; (3) choices of measures of socioeconomic position in quantitative analyses often rely on data availability; and (4) different measures of socioeconomic position have different effects in population groups. Therefore, caution should be used in the collection, presentation, analyses, and interpretation of data and researchers need to display their proposed conceptual models and data limitations as well as apply different approaches for analyses. PMID:24287857

  10. Experimental Influences in the Accurate Measurement of Cartilage Thickness in MRI.

    PubMed

    Wang, Nian; Badar, Farid; Xia, Yang

    2018-01-01

    Objective To study the experimental influences to the measurement of cartilage thickness by magnetic resonance imaging (MRI). Design The complete thicknesses of healthy and trypsin-degraded cartilage were measured at high-resolution MRI under different conditions, using two intensity-based imaging sequences (ultra-short echo [UTE] and multislice-multiecho [MSME]) and 3 quantitative relaxation imaging sequences (T 1 , T 2 , and T 1 ρ). Other variables included different orientations in the magnet, 2 soaking solutions (saline and phosphate buffered saline [PBS]), and external loading. Results With cartilage soaked in saline, UTE and T 1 methods yielded complete and consistent measurement of cartilage thickness, while the thickness measurement by T 2 , T 1 ρ, and MSME methods were orientation dependent. The effect of external loading on cartilage thickness is also sequence and orientation dependent. All variations in cartilage thickness in MRI could be eliminated with the use of a 100 mM PBS or imaged by UTE sequence. Conclusions The appearance of articular cartilage and the measurement accuracy of cartilage thickness in MRI can be influenced by a number of experimental factors in ex vivo MRI, from the use of various pulse sequences and soaking solutions to the health of the tissue. T 2 -based imaging sequence, both proton-intensity sequence and quantitative relaxation sequence, similarly produced the largest variations. With adequate resolution, the accurate measurement of whole cartilage tissue in clinical MRI could be utilized to detect differences between healthy and osteoarthritic cartilage after compression.

  11. Accurate Critical Stress Intensity Factor Griffith Crack Theory Measurements by Numerical Techniques

    PubMed Central

    Petersen, Richard C.

    2014-01-01

    Critical stress intensity factor (KIc) has been an approximation for fracture toughness using only load-cell measurements. However, artificial man-made cracks several orders of magnitude longer and wider than natural flaws have required a correction factor term (Y) that can be up to about 3 times the recorded experimental value [1-3]. In fact, over 30 years ago a National Academy of Sciences advisory board stated that empirical KIc testing was of serious concern and further requested that an accurate bulk fracture toughness method be found [4]. Now that fracture toughness can be calculated accurately by numerical integration from the load/deflection curve as resilience, work of fracture (WOF) and strain energy release (SIc) [5, 6], KIc appears to be unnecessary. However, the large body of previous KIc experimental test results found in the literature offer the opportunity for continued meta analysis with other more practical and accurate fracture toughness results using energy methods and numerical integration. Therefore, KIc is derived from the classical Griffith Crack Theory [6] to include SIc as a more accurate term for strain energy release rate (𝒢Ic), along with crack surface energy (γ), crack length (a), modulus (E), applied stress (σ), Y, crack-tip plastic zone defect region (rp) and yield strength (σys) that can all be determined from load and deflection data. Polymer matrix discontinuous quartz fiber-reinforced composites to accentuate toughness differences were prepared for flexural mechanical testing comprising of 3 mm fibers at different volume percentages from 0-54.0 vol% and at 28.2 vol% with different fiber lengths from 0.0-6.0 mm. Results provided a new correction factor and regression analyses between several numerical integration fracture toughness test methods to support KIc results. Further, bulk KIc accurate experimental values are compared with empirical test results found in literature. Also, several fracture toughness mechanisms

  12. 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.

  13. Sexing chick mRNA: A protocol based on quantitative real-time polymerase chain reaction.

    PubMed

    Wan, Z; Lu, Y; Rui, L; Yu, X; Li, Z

    2017-03-01

    The accurate identification of sex in birds is important for research on avian sex determination and differentiation. Polymerase chain reaction (PCR)-based methods have been widely applied for the molecular sexing of birds. However, these methods have used genomic DNA. Here, we present the first sexing protocol for chick mRNA based on real-time quantitative PCR. We demonstrate that this method can accurately determine sex using mRNA from chick gonads and other tissues, such as heart, liver, spleen, lung, and muscle. The strategy of this protocol also may be suitable for other species in which sex is determined by the inheritance of sex chromosomes (ZZ male and ZW female). © 2016 Poultry Science Association Inc.

  14. Tissue microarrays and quantitative tissue-based image analysis as a tool for oncology biomarker and diagnostic development.

    PubMed

    Dolled-Filhart, Marisa P; Gustavson, Mark D

    2012-11-01

    Translational oncology has been improved by using tissue microarrays (TMAs), which facilitate biomarker analysis of large cohorts on a single slide. This has allowed for rapid analysis and validation of potential biomarkers for prognostic and predictive value, as well as for evaluation of biomarker prevalence. Coupled with quantitative analysis of immunohistochemical (IHC) staining, objective and standardized biomarker data from tumor samples can further advance companion diagnostic approaches for the identification of drug-responsive or resistant patient subpopulations. This review covers the advantages, disadvantages and applications of TMAs for biomarker research. Research literature and reviews of TMAs and quantitative image analysis methodology have been surveyed for this review (with an AQUA® analysis focus). Applications such as multi-marker diagnostic development and pathway-based biomarker subpopulation analyses are described. Tissue microarrays are a useful tool for biomarker analyses including prevalence surveys, disease progression assessment and addressing potential prognostic or predictive value. By combining quantitative image analysis with TMAs, analyses will be more objective and reproducible, allowing for more robust IHC-based diagnostic test development. Quantitative multi-biomarker IHC diagnostic tests that can predict drug response will allow for greater success of clinical trials for targeted therapies and provide more personalized clinical decision making.

  15. Quantitative determination of dimethylaminoethanol in cosmetic formulations by nuclear magnetic resonance spectroscopy.

    PubMed

    Batista, Ivani Aparecida Soares de Andrade; Gonçalves, Maria Inês de Almeida; Singh, Anil Kumar; Hackmann, Erika Rosa Maria Kedor; Santoro, Maria Inês Rocha Miritello

    2008-01-01

    A nuclear magnetic resonance (NMR) spectroscopic method was validated for the quantitative determination of dimethylaminoethanol (DMAE) in cosmetic formulations. The linearity in the range from 0.5000 to 1.5000 g (DMAE salt/mass maleic acid) presents a correlation coefficient > 0.99 for all DMAE salts. The repeatability (intraday), expressed as relative standard deviation, ranged from 1.08 to 1.44% for samples and 1.31 to 1.88% for raw materials. The detection limit and quantitation limit were 0.0017 and 0.0051 g for DMAE, 0.0018 and 0.0054 g for DMAE bitartrate, and 0.0023 and 0.0071 g for DMAE acetamidobenzoate, respectively. The proposed method is simple, precise, and accurate and can be used in the quality control of raw materials and cosmetic gels containing these compounds as active substances.

  16. Quantitative operando visualization of the energy band depth profile in solar cells.

    PubMed

    Chen, Qi; Mao, Lin; Li, Yaowen; Kong, Tao; Wu, Na; Ma, Changqi; Bai, Sai; Jin, Yizheng; Wu, Dan; Lu, Wei; Wang, Bing; Chen, Liwei

    2015-07-13

    The energy band alignment in solar cell devices is critically important because it largely governs elementary photovoltaic processes, such as the generation, separation, transport, recombination and collection of charge carriers. Despite the expenditure of considerable effort, the measurement of energy band depth profiles across multiple layers has been extremely challenging, especially for operando devices. Here we present direct visualization of the surface potential depth profile over the cross-sections of operando organic photovoltaic devices using scanning Kelvin probe microscopy. The convolution effect due to finite tip size and cantilever beam crosstalk has previously prohibited quantitative interpretation of scanning Kelvin probe microscopy-measured surface potential depth profiles. We develop a bias voltage-compensation method to address this critical problem and obtain quantitatively accurate measurements of the open-circuit voltage, built-in potential and electrode potential difference.

  17. Quantitative biology: where modern biology meets physical sciences.

    PubMed

    Shekhar, Shashank; Zhu, Lian; Mazutis, Linas; Sgro, Allyson E; Fai, Thomas G; Podolski, Marija

    2014-11-05

    Quantitative methods and approaches have been playing an increasingly important role in cell biology in recent years. They involve making accurate measurements to test a predefined hypothesis in order to compare experimental data with predictions generated by theoretical models, an approach that has benefited physicists for decades. Building quantitative models in experimental biology not only has led to discoveries of counterintuitive phenomena but has also opened up novel research directions. To make the biological sciences more quantitative, we believe a two-pronged approach needs to be taken. First, graduate training needs to be revamped to ensure biology students are adequately trained in physical and mathematical sciences and vice versa. Second, students of both the biological and the physical sciences need to be provided adequate opportunities for hands-on engagement with the methods and approaches necessary to be able to work at the intersection of the biological and physical sciences. We present the annual Physiology Course organized at the Marine Biological Laboratory (Woods Hole, MA) as a case study for a hands-on training program that gives young scientists the opportunity not only to acquire the tools of quantitative biology but also to develop the necessary thought processes that will enable them to bridge the gap between these disciplines. © 2014 Shekhar, Zhu, Mazutis, Sgro, Fai, and Podolski. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

  18. Optimized slice-selective 1H NMR experiments combined with highly accurate quantitative 13C NMR using an internal reference method.

    PubMed

    Jézéquel, Tangi; Silvestre, Virginie; Dinis, Katy; Giraudeau, Patrick; Akoka, Serge

    2018-04-01

    Isotope ratio monitoring by 13 C NMR spectrometry (irm- 13 C NMR) provides the complete 13 C intramolecular position-specific composition at natural abundance. It represents a powerful tool to track the (bio)chemical pathway which has led to the synthesis of targeted molecules, since it allows Position-specific Isotope Analysis (PSIA). Due to the very small composition range (which represents the range of variation of the isotopic composition of a given nuclei) of 13 C natural abundance values (50‰), irm- 13 C NMR requires a 1‰ accuracy and thus highly quantitative analysis by 13 C NMR. Until now, the conventional strategy to determine the position-specific abundance x i relies on the combination of irm-MS (isotopic ratio monitoring Mass Spectrometry) and 13 C quantitative NMR. However this approach presents a serious drawback since it relies on two different techniques and requires to measure separately the signal of all the carbons of the analyzed compound, which is not always possible. To circumvent this constraint, we recently proposed a new methodology to perform 13 C isotopic analysis using an internal reference method and relying on NMR only. The method combines a highly quantitative 1 H NMR pulse sequence (named DWET) with a 13 C isotopic NMR measurement. However, the recently published DWET sequence is unsuited for samples with short T 1 , which forms a serious limitation for irm- 13 C NMR experiments where a relaxing agent is added. In this context, we suggest two variants of the DWET called Multi-WET and Profiled-WET, developed and optimized to reach the same accuracy of 1‰ with a better immunity towards T 1 variations. Their performance is evaluated on the determination of the 13 C isotopic profile of vanillin. Both pulse sequences show a 1‰ accuracy with an increased robustness to pulse miscalibrations compared to the initial DWET method. This constitutes a major advance in the context of irm- 13 C NMR since it is now possible to perform

  19. Optimized slice-selective 1H NMR experiments combined with highly accurate quantitative 13C NMR using an internal reference method

    NASA Astrophysics Data System (ADS)

    Jézéquel, Tangi; Silvestre, Virginie; Dinis, Katy; Giraudeau, Patrick; Akoka, Serge

    2018-04-01

    Isotope ratio monitoring by 13C NMR spectrometry (irm-13C NMR) provides the complete 13C intramolecular position-specific composition at natural abundance. It represents a powerful tool to track the (bio)chemical pathway which has led to the synthesis of targeted molecules, since it allows Position-specific Isotope Analysis (PSIA). Due to the very small composition range (which represents the range of variation of the isotopic composition of a given nuclei) of 13C natural abundance values (50‰), irm-13C NMR requires a 1‰ accuracy and thus highly quantitative analysis by 13C NMR. Until now, the conventional strategy to determine the position-specific abundance xi relies on the combination of irm-MS (isotopic ratio monitoring Mass Spectrometry) and 13C quantitative NMR. However this approach presents a serious drawback since it relies on two different techniques and requires to measure separately the signal of all the carbons of the analyzed compound, which is not always possible. To circumvent this constraint, we recently proposed a new methodology to perform 13C isotopic analysis using an internal reference method and relying on NMR only. The method combines a highly quantitative 1H NMR pulse sequence (named DWET) with a 13C isotopic NMR measurement. However, the recently published DWET sequence is unsuited for samples with short T1, which forms a serious limitation for irm-13C NMR experiments where a relaxing agent is added. In this context, we suggest two variants of the DWET called Multi-WET and Profiled-WET, developed and optimized to reach the same accuracy of 1‰ with a better immunity towards T1 variations. Their performance is evaluated on the determination of the 13C isotopic profile of vanillin. Both pulse sequences show a 1‰ accuracy with an increased robustness to pulse miscalibrations compared to the initial DWET method. This constitutes a major advance in the context of irm-13C NMR since it is now possible to perform isotopic analysis with high

  20. Quantitative phase-digital holographic microscopy: a new imaging modality to identify original cellular biomarkers of diseases

    NASA Astrophysics Data System (ADS)

    Marquet, P.; Rothenfusser, K.; Rappaz, B.; Depeursinge, C.; Jourdain, P.; Magistretti, P. J.

    2016-03-01

    Quantitative phase microscopy (QPM) has recently emerged as a powerful label-free technique in the field of living cell imaging allowing to non-invasively measure with a nanometric axial sensitivity cell structure and dynamics. Since the phase retardation of a light wave when transmitted through the observed cells, namely the quantitative phase signal (QPS), is sensitive to both cellular thickness and intracellular refractive index related to the cellular content, its accurate analysis allows to derive various cell parameters and monitor specific cell processes, which are very likely to identify new cell biomarkers. Specifically, quantitative phase-digital holographic microscopy (QP-DHM), thanks to its numerical flexibility facilitating parallelization and automation processes, represents an appealing imaging modality to both identify original cellular biomarkers of diseases as well to explore the underlying pathophysiological processes.

  1. More comprehensive forensic genetic marker analyses for accurate human remains identification using massively parallel DNA sequencing.

    PubMed

    Ambers, Angie D; Churchill, Jennifer D; King, Jonathan L; Stoljarova, Monika; Gill-King, Harrell; Assidi, Mourad; Abu-Elmagd, Muhammad; Buhmeida, Abdelbaset; Al-Qahtani, Mohammed; Budowle, Bruce

    2016-10-17

    Although the primary objective of forensic DNA analyses of unidentified human remains is positive identification, cases involving historical or archaeological skeletal remains often lack reference samples for comparison. Massively parallel sequencing (MPS) offers an opportunity to provide biometric data in such cases, and these cases provide valuable data on the feasibility of applying MPS for characterization of modern forensic casework samples. In this study, MPS was used to characterize 140-year-old human skeletal remains discovered at a historical site in Deadwood, South Dakota, United States. The remains were in an unmarked grave and there were no records or other metadata available regarding the identity of the individual. Due to the high throughput of MPS, a variety of biometric markers could be typed using a single sample. Using MPS and suitable forensic genetic markers, more relevant information could be obtained from a limited quantity and quality sample. Results were obtained for 25/26 Y-STRs, 34/34 Y SNPs, 166/166 ancestry-informative SNPs, 24/24 phenotype-informative SNPs, 102/102 human identity SNPs, 27/29 autosomal STRs (plus amelogenin), and 4/8 X-STRs (as well as ten regions of mtDNA). The Y-chromosome (Y-STR, Y-SNP) and mtDNA profiles of the unidentified skeletal remains are consistent with the R1b and H1 haplogroups, respectively. Both of these haplogroups are the most common haplogroups in Western Europe. Ancestry-informative SNP analysis also supported European ancestry. The genetic results are consistent with anthropological findings that the remains belong to a male of European ancestry (Caucasian). Phenotype-informative SNP data provided strong support that the individual had light red hair and brown eyes. This study is among the first to genetically characterize historical human remains with forensic genetic marker kits specifically designed for MPS. The outcome demonstrates that substantially more genetic information can be obtained from

  2. Toward best practices in data processing and analysis for intact biotherapeutics by MS in quantitative bioanalysis.

    PubMed

    Kellie, John F; Kehler, Jonathan R; Karlinsey, Molly Z; Summerfield, Scott G

    2017-12-01

    Typically, quantitation of biotherapeutics from biological matrices by LC-MS is based on a surrogate peptide approach to determine molecule concentration. Recent efforts have focused on quantitation of the intact protein molecules or larger mass subunits of monoclonal antibodies. To date, there has been limited guidance for large or intact protein mass quantitation for quantitative bioanalysis. Intact- and subunit-level analyses of biotherapeutics from biological matrices are performed at 12-25 kDa mass range with quantitation data presented. Linearity, bias and other metrics are presented along with recommendations made on the viability of existing quantitation approaches. This communication is intended to start a discussion around intact protein data analysis and processing, recognizing that other published contributions will be required.

  3. Obtaining Accurate Probabilities Using Classifier Calibration

    ERIC Educational Resources Information Center

    Pakdaman Naeini, Mahdi

    2016-01-01

    Learning probabilistic classification and prediction models that generate accurate probabilities is essential in many prediction and decision-making tasks in machine learning and data mining. One way to achieve this goal is to post-process the output of classification models to obtain more accurate probabilities. These post-processing methods are…

  4. Diagnostic Performance and Utility of Quantitative EEG Analyses in Delirium: Confirmatory Results From a Large Retrospective Case-Control Study.

    PubMed

    Fleischmann, Robert; Tränkner, Steffi; Bathe-Peters, Rouven; Rönnefarth, Maria; Schmidt, Sein; Schreiber, Stephan J; Brandt, Stephan A

    2018-03-01

    The lack of objective disease markers is a major cause of misdiagnosis and nonstandardized approaches in delirium. Recent studies conducted in well-selected patients and confined study environments suggest that quantitative electroencephalography (qEEG) can provide such markers. We hypothesize that qEEG helps remedy diagnostic uncertainty not only in well-defined study cohorts but also in a heterogeneous hospital population. In this retrospective case-control study, EEG power spectra of delirious patients and age-/gender-matched controls (n = 31 and n = 345, respectively) were fitted in a linear model to test their performance as binary classifiers. We subsequently evaluated the diagnostic performance of the best classifiers in control samples with normal EEGs (n = 534) and real-world samples including pathologic findings (n = 4294). Test reliability was estimated through split-half analyses. We found that the combination of spectral power at F3-P4 at 2 Hz (area under the curve [AUC] = .994) and C3-O1 at 19 Hz (AUC = .993) provided a sensitivity of 100% and a specificity of 99% to identify delirious patients among normal controls. These classifiers also yielded a false positive rate as low as 5% and increased the pretest probability of being delirious by 57% in an unselected real-world sample. Split-half reliabilities were .98 and .99, respectively. This retrospective study yielded preliminary evidence that qEEG provides excellent diagnostic performance to identify delirious patients even outside confined study environments. It furthermore revealed reduced beta power as a novel specific finding in delirium and that a normal EEG excludes delirium. Prospective studies including parameters of pretest probability and delirium severity are required to elaborate on these promising findings.

  5. Approaching system equilibrium with accurate or not accurate feedback information in a two-route system

    NASA Astrophysics Data System (ADS)

    Zhao, Xiao-mei; Xie, Dong-fan; Li, Qi

    2015-02-01

    With the development of intelligent transport system, advanced information feedback strategies have been developed to reduce traffic congestion and enhance the capacity. However, previous strategies provide accurate information to travelers and our simulation results show that accurate information brings negative effects, especially in delay case. Because travelers prefer to the best condition route with accurate information, and delayed information cannot reflect current traffic condition but past. Then travelers make wrong routing decisions, causing the decrease of the capacity and the increase of oscillations and the system deviating from the equilibrium. To avoid the negative effect, bounded rationality is taken into account by introducing a boundedly rational threshold BR. When difference between two routes is less than the BR, routes have equal probability to be chosen. The bounded rationality is helpful to improve the efficiency in terms of capacity, oscillation and the gap deviating from the system equilibrium.

  6. Accurate, Sensitive, and Precise Multiplexed Proteomics Using the Complement Reporter Ion Cluster

    DOE PAGES

    Sonnett, Matthew; Yeung, Eyan; Wuhr, Martin

    2018-03-09

    We present that quantitative analysis of proteomes across multiple time points, organelles, and perturbations is essential for understanding both fundamental biology and disease states. The development of isobaric tags (e.g. TMT) have enabled the simultaneous measurement of peptide abundances across several different conditions. These multiplexed approaches are promising in principle because of advantages in throughput and measurement quality. However, in practice existing multiplexing approaches suffer from key limitations. In its simple implementation (TMT-MS2), measurements are distorted by chemical noise leading to poor measurement accuracy. The current state-of-the-art (TMT-MS3) addresses this, but requires specialized quadrupole-iontrap-Orbitrap instrumentation. The complement reporter ion approachmore » (TMTc) produces high accuracy measurements and is compatible with many more instruments, like quadrupole-Orbitraps. However, the required deconvolution of the TMTc cluster leads to poor measurement precision. Here, we introduce TMTc+, which adds the modeling of the MS2-isolation step into the deconvolution algorithm. The resulting measurements are comparable in precision to TMT-MS3/MS2. The improved duty cycle, and lower filtering requirements make TMTc+ more sensitive than TMT-MS3 and comparable with TMT-MS2. At the same time, unlike TMT-MS2, TMTc+ is exquisitely able to distinguish signal from chemical noise even outperforming TMT-MS3. Lastly, we compare TMTc+ to quantitative label-free proteomics of total HeLa lysate and find that TMTc+ quantifies 7.8k versus 3.9k proteins in a 5-plex sample. At the same time the median coefficient of variation improves from 13% to 4%. Furthermore, TMTc+ advances quantitative proteomics by enabling accurate, sensitive, and precise multiplexed experiments on more commonly used instruments.« less

  7. Accurate, Sensitive, and Precise Multiplexed Proteomics Using the Complement Reporter Ion Cluster

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

    Sonnett, Matthew; Yeung, Eyan; Wuhr, Martin

    We present that quantitative analysis of proteomes across multiple time points, organelles, and perturbations is essential for understanding both fundamental biology and disease states. The development of isobaric tags (e.g. TMT) have enabled the simultaneous measurement of peptide abundances across several different conditions. These multiplexed approaches are promising in principle because of advantages in throughput and measurement quality. However, in practice existing multiplexing approaches suffer from key limitations. In its simple implementation (TMT-MS2), measurements are distorted by chemical noise leading to poor measurement accuracy. The current state-of-the-art (TMT-MS3) addresses this, but requires specialized quadrupole-iontrap-Orbitrap instrumentation. The complement reporter ion approachmore » (TMTc) produces high accuracy measurements and is compatible with many more instruments, like quadrupole-Orbitraps. However, the required deconvolution of the TMTc cluster leads to poor measurement precision. Here, we introduce TMTc+, which adds the modeling of the MS2-isolation step into the deconvolution algorithm. The resulting measurements are comparable in precision to TMT-MS3/MS2. The improved duty cycle, and lower filtering requirements make TMTc+ more sensitive than TMT-MS3 and comparable with TMT-MS2. At the same time, unlike TMT-MS2, TMTc+ is exquisitely able to distinguish signal from chemical noise even outperforming TMT-MS3. Lastly, we compare TMTc+ to quantitative label-free proteomics of total HeLa lysate and find that TMTc+ quantifies 7.8k versus 3.9k proteins in a 5-plex sample. At the same time the median coefficient of variation improves from 13% to 4%. Furthermore, TMTc+ advances quantitative proteomics by enabling accurate, sensitive, and precise multiplexed experiments on more commonly used instruments.« less

  8. 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

  9. Design of primers and probes for quantitative real-time PCR methods.

    PubMed

    Rodríguez, Alicia; Rodríguez, Mar; Córdoba, Juan J; Andrade, María J

    2015-01-01

    Design of primers and probes is one of the most crucial factors affecting the success and quality of quantitative real-time PCR (qPCR) analyses, since an accurate and reliable quantification depends on using efficient primers and probes. Design of primers and probes should meet several criteria to find potential primers and probes for specific qPCR assays. The formation of primer-dimers and other non-specific products should be avoided or reduced. This factor is especially important when designing primers for SYBR(®) Green protocols but also in designing probes to ensure specificity of the developed qPCR protocol. To design primers and probes for qPCR, multiple software programs and websites are available being numerous of them free. These tools often consider the default requirements for primers and probes, although new research advances in primer and probe design should be progressively added to different algorithm programs. After a proper design, a precise validation of the primers and probes is necessary. Specific consideration should be taken into account when designing primers and probes for multiplex qPCR and reverse transcription qPCR (RT-qPCR). This chapter provides guidelines for the design of suitable primers and probes and their subsequent validation through the development of singlex qPCR, multiplex qPCR, and RT-qPCR protocols.

  10. Quantitation of hepatitis B virus DNA in plasma using a sensitive cost-effective "in-house" real-time PCR assay.

    PubMed

    Daniel, Hubert Darius J; Fletcher, John G; Chandy, George M; Abraham, Priya

    2009-01-01

    Sensitive nucleic acid testing for the detection and accurate quantitation of hepatitis B virus (HBV) is necessary to reduce transmission through blood and blood products and for monitoring patients on antiviral therapy. The aim of this study is to standardize an "in-house" real-time HBV polymerase chain reaction (PCR) for accurate quantitation and screening of HBV. The "in-house" real-time assay was compared with a commercial assay using 30 chronically infected individuals and 70 blood donors who are negative for hepatitis B surface antigen, hepatitis C virus (HCV) antibody and human immunodeficiency virus (HIV) antibody. Further, 30 HBV-genotyped samples were tested to evaluate the "in-house" assay's capacity to detect genotypes prevalent among individuals attending this tertiary care hospital. The lower limit of detection of this "in-house" HBV real-time PCR was assessed against the WHO international standard and found to be 50 IU/mL. The interassay and intra-assay coefficient of variation (CV) of this "in-house" assay ranged from 1.4% to 9.4% and 0.0% to 2.3%, respectively. Virus loads as estimated with this "in-house" HBV real-time assay correlated well with the commercial artus HBV RG PCR assay ( r = 0.95, P < 0.0001). This assay can be used for the detection and accurate quantitation of HBV viral loads in plasma samples. This assay can be employed for the screening of blood donations and can potentially be adapted to a multiplex format for simultaneous detection of HBV, HIV and HCV to reduce the cost of testing in blood banks.

  11. Age determination by teeth examination: a comparison between different morphologic and quantitative analyses.

    PubMed

    Amariti, M L; Restori, M; De Ferrari, F; Paganelli, C; Faglia, R; Legnani, G

    1999-06-01

    Age determination by teeth examination is one of the main means of determining personal identification. Current studies have suggested different techniques for determining the age of a subject by means of the analysis of microscopic and macroscopic structural modifications of the tooth with ageing. The histological approach is useful among the various methodologies utilized for this purpose. It is still unclear as to what is the best technique, as almost all the authors suggest the use of the approach they themselves have tested. In the present study, age determination by means of microscopic techniques has been based on the quantitative analysis of three parameters, all well recognized in specialized literature: 1. dentinal tubules density/sclerosis 2. tooth translucency 3. analysis of the cementum thickness. After a description of the three methodologies (with automatic image processing of the dentinal sclerosis utilizing an appropriate computer program developed by the authors) the results obtained on cases using the three different approaches are presented, and the merits and failings of each technique are identified with the intention of identifying the one offering the least degree of error in age determination.

  12. Missing heritability in the tails of quantitative traits? A simulation study on the impact of slightly altered true genetic models.

    PubMed

    Pütter, Carolin; Pechlivanis, Sonali; Nöthen, Markus M; Jöckel, Karl-Heinz; Wichmann, Heinz-Erich; Scherag, André

    2011-01-01

    Genome-wide association studies have identified robust associations between single nucleotide polymorphisms and complex traits. As the proportion of phenotypic variance explained is still limited for most of the traits, larger and larger meta-analyses are being conducted to detect additional associations. Here we investigate the impact of the study design and the underlying assumption about the true genetic effect in a bimodal mixture situation on the power to detect associations. We performed simulations of quantitative phenotypes analysed by standard linear regression and dichotomized case-control data sets from the extremes of the quantitative trait analysed by standard logistic regression. Using linear regression, markers with an effect in the extremes of the traits were almost undetectable, whereas analysing extremes by case-control design had superior power even for much smaller sample sizes. Two real data examples are provided to support our theoretical findings and to explore our mixture and parameter assumption. Our findings support the idea to re-analyse the available meta-analysis data sets to detect new loci in the extremes. Moreover, our investigation offers an explanation for discrepant findings when analysing quantitative traits in the general population and in the extremes. Copyright © 2011 S. Karger AG, Basel.

  13. An Accurate ab initio Quartic Force Field and Vibrational Frequencies for CH4 and Isotopomers

    NASA Technical Reports Server (NTRS)

    Lee, Timothy J.; Martin, Jan M. L.; Taylor, Peter R.

    1995-01-01

    A very accurate ab initio quartic force field for CH4 and its isotopomers is presented. The quartic force field was determined with the singles and doubles coupled-cluster procedure that includes a quasiperturbative estimate of the effects of connected triple excitations, CCSD(T), using the correlation consistent polarized valence triple zeta, cc-pVTZ, basis set. Improved quadratic force constants were evaluated with the correlation consistent polarized valence quadruple zeta, cc-pVQZ, basis set. Fundamental vibrational frequencies are determined using second-order perturbation theory anharmonic analyses. All fundamentals of CH4 and isotopomers for which accurate experimental values exist and for which there is not a large Fermi resonance, are predicted to within +/- 6 cm(exp -1). It is thus concluded that our predictions for the harmonic frequencies and the anharmonic constants are the most accurate estimates available. It is also shown that using cubic and quartic force constants determined with the correlation consistent polarized double zeta, cc-pVDZ, basis set in conjunction with the cc-pVQZ quadratic force constants and equilibrium geometry leads to accurate predictions for the fundamental vibrational frequencies of methane, suggesting that this approach may be a viable alternative for larger molecules. Using CCSD(T), core correlation is found to reduce the CH4 r(e), by 0.0015 A. Our best estimate for r, is 1.0862 +/- 0.0005 A.

  14. Signal-Detection Analyses of Conditional Discrimination and Delayed Matching-to-Sample Performance

    ERIC Educational Resources Information Center

    Alsop, Brent

    2004-01-01

    Quantitative analyses of stimulus control and reinforcer control in conditional discriminations and delayed matching-to-sample procedures often encounter a problem; it is not clear how to analyze data when subjects have not made errors. The present article examines two common methods for overcoming this problem. Monte Carlo simulations of…

  15. QUANTITATIVE TEMPLATE FOR SUBTYPING PRIMARY PROGRESSIVE APHASIA

    PubMed Central

    Mesulam, Marsel; Wieneke, Christina; Rogalski, Emily; Cobia, Derin; Thompson, Cynthia; Weintraub, Sandra

    2009-01-01

    Objective To provide a quantitative algorithm for classifying primary progressive aphasia (PPA) into agrammatic (PPA-G), semantic (PPA-S) and logopenic (PPA-L) variants, each of which is known to have a different probability of association with Alzheimer’s disease (AD) versus frontotemporal lobar degeneration (FTLD). Design Prospectively and consecutively enrolled 16 PPA patients tested with neuropsychological instruments and magnetic resonance imaging (MRI). Setting University medical center. Participants PPA patients recruited nationally in the USA as part of a longitudinal study. Results A two-dimensional template, reflecting performance on tests of syntax (Northwestern Anagram Test) and lexical semantics (Peabody Picture Vocabulary Test), classified all 16 patients in concordance with a clinical diagnosis that had been made prior to the administration of the quantitative tests. All three subtypes had distinctly asymmetrical atrophy of the left perisylvian language network. Each subtype also had distinctive peak atrophy sites. Only PPA-G had peak atrophy in the IFG (Broca’s area), only PPA-S had peak atrophy in the anterior temporal lobe, and only PPA-L had peak atrophy in area 37. Conclusions Once an accurate root diagnosis of PPA is made, subtyping can be quantitatively guided using a two-dimensional template based on orthogonal tasks of grammatical competence and word comprehension. Although the choice of tasks and precise cut-off levels may evolve in time, this set of 16 patients demonstrates the feasibility of using a simple algorithm for clinico-anatomical classification in PPA. Prospective studies will show whether this suptyping can improve the clinical prediction of underlying neuropathology. PMID:20008661

  16. Accurate formula for dissipative interaction in frequency modulation atomic force microscopy

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

    Suzuki, Kazuhiro; Matsushige, Kazumi; Yamada, Hirofumi

    2014-12-08

    Much interest has recently focused on the viscosity of nano-confined liquids. Frequency modulation atomic force microscopy (FM-AFM) is a powerful technique that can detect variations in the conservative and dissipative forces between a nanometer-scale tip and a sample surface. We now present an accurate formula to convert the dissipation power of the cantilever measured during the experiment to damping of the tip-sample system. We demonstrated the conversion of the dissipation power versus tip-sample separation curve measured using a colloidal probe cantilever on a mica surface in water to the damping curve, which showed a good agreement with the theoretical curve.more » Moreover, we obtained the damping curve from the dissipation power curve measured on the hydration layers on the mica surface using a nanometer-scale tip, demonstrating that the formula allows us to quantitatively measure the viscosity of a nano-confined liquid using FM-AFM.« less

  17. High-Resolution Enabled 12-Plex DiLeu Isobaric Tags for Quantitative Proteomics

    PubMed Central

    2015-01-01

    Multiplex isobaric tags (e.g., tandem mass tags (TMT) and isobaric tags for relative and absolute quantification (iTRAQ)) are a valuable tool for high-throughput mass spectrometry based quantitative proteomics. We have developed our own multiplex isobaric tags, DiLeu, that feature quantitative performance on par with commercial offerings but can be readily synthesized in-house as a cost-effective alternative. In this work, we achieve a 3-fold increase in the multiplexing capacity of the DiLeu reagent without increasing structural complexity by exploiting mass defects that arise from selective incorporation of 13C, 15N, and 2H stable isotopes in the reporter group. The inclusion of eight new reporter isotopologues that differ in mass from the existing four reporters by intervals of 6 mDa yields a 12-plex isobaric set that preserves the synthetic simplicity and quantitative performance of the original implementation. We show that the new reporter variants can be baseline-resolved in high-resolution higher-energy C-trap dissociation (HCD) spectra, and we demonstrate accurate 12-plex quantitation of a DiLeu-labeled Saccharomyces cerevisiae lysate digest via high-resolution nano liquid chromatography–tandem mass spectrometry (nanoLC–MS2) analysis on an Orbitrap Elite mass spectrometer. PMID:25405479

  18. Multi-laboratory comparison of quantitative PCR assays for detection and quantification of Fusarium virguliforme from soybean roots and soil

    USDA-ARS?s Scientific Manuscript database

    Accurate identification and quantification of Fusarium virguliforme, the cause of sudden death syndrome (SDS) in soybean, within root tissue and soil are important tasks. Several quantitative PCR (qPCR) assays have been developed but there are no reports comparing their use in sensitive and specific...

  19. Quantitative genetics

    USDA-ARS?s Scientific Manuscript database

    The majority of economically important traits targeted for cotton improvement are quantitatively inherited. In this chapter, the current state of cotton quantitative genetics is described and separated into four components. These components include: 1) traditional quantitative inheritance analysis, ...

  20. Quantitative characterization of the regressive ecological succession by fractal analysis of plant spatial patterns

    USGS Publications Warehouse

    Alados, C.L.; Pueyo, Y.; Giner, M.L.; Navarro, T.; Escos, J.; Barroso, F.; Cabezudo, B.; Emlen, J.M.

    2003-01-01

    We studied the effect of grazing on the degree of regression of successional vegetation dynamic in a semi-arid Mediterranean matorral. We quantified the spatial distribution patterns of the vegetation by fractal analyses, using the fractal information dimension and spatial autocorrelation measured by detrended fluctuation analyses (DFA). It is the first time that fractal analysis of plant spatial patterns has been used to characterize the regressive ecological succession. Plant spatial patterns were compared over a long-term grazing gradient (low, medium and heavy grazing pressure) and on ungrazed sites for two different plant communities: A middle dense matorral of Chamaerops and Periploca at Sabinar-Romeral and a middle dense matorral of Chamaerops, Rhamnus and Ulex at Requena-Montano. The two communities differed also in the microclimatic characteristics (sea oriented at the Sabinar-Romeral site and inland oriented at the Requena-Montano site). The information fractal dimension increased as we moved from a middle dense matorral to discontinuous and scattered matorral and, finally to the late regressive succession, at Stipa steppe stage. At this stage a drastic change in the fractal dimension revealed a change in the vegetation structure, accurately indicating end successional vegetation stages. Long-term correlation analysis (DFA) revealed that an increase in grazing pressure leads to unpredictability (randomness) in species distributions, a reduction in diversity, and an increase in cover of the regressive successional species, e.g. Stipa tenacissima L. These comparisons provide a quantitative characterization of the successional dynamic of plant spatial patterns in response to grazing perturbation gradient. ?? 2002 Elsevier Science B.V. All rights reserved.

  1. The selected reaction monitoring/multiple reaction monitoring-based mass spectrometry approach for the accurate quantitation of proteins: clinical applications in the cardiovascular diseases.

    PubMed

    Gianazza, Erica; Tremoli, Elena; Banfi, Cristina

    2014-12-01

    Selected reaction monitoring, also known as multiple reaction monitoring, is a powerful targeted mass spectrometry approach for a confident quantitation of proteins/peptides in complex biological samples. In recent years, its optimization and application have become pivotal and of great interest in clinical research to derive useful outcomes for patient care. Thus, selected reaction monitoring/multiple reaction monitoring is now used as a highly sensitive and selective method for the evaluation of protein abundances and biomarker verification with potential applications in medical screening. This review describes technical aspects for the development of a robust multiplex assay and discussing its recent applications in cardiovascular proteomics: verification of promising disease candidates to select only the highest quality peptides/proteins for a preclinical validation, as well as quantitation of protein isoforms and post-translational modifications.

  2. Radiomics biomarkers for accurate tumor progression prediction of oropharyngeal cancer

    NASA Astrophysics Data System (ADS)

    Hadjiiski, Lubomir; Chan, Heang-Ping; Cha, Kenny H.; Srinivasan, Ashok; Wei, Jun; Zhou, Chuan; Prince, Mark; Papagerakis, Silvana

    2017-03-01

    Accurate tumor progression prediction for oropharyngeal cancers is crucial for identifying patients who would best be treated with optimized treatment and therefore minimize the risk of under- or over-treatment. An objective decision support system that can merge the available radiomics, histopathologic and molecular biomarkers in a predictive model based on statistical outcomes of previous cases and machine learning may assist clinicians in making more accurate assessment of oropharyngeal tumor progression. In this study, we evaluated the feasibility of developing individual and combined predictive models based on quantitative image analysis from radiomics, histopathology and molecular biomarkers for oropharyngeal tumor progression prediction. With IRB approval, 31, 84, and 127 patients with head and neck CT (CT-HN), tumor tissue microarrays (TMAs) and molecular biomarker expressions, respectively, were collected. For 8 of the patients all 3 types of biomarkers were available and they were sequestered in a test set. The CT-HN lesions were automatically segmented using our level sets based method. Morphological, texture and molecular based features were extracted from CT-HN and TMA images, and selected features were merged by a neural network. The classification accuracy was quantified using the area under the ROC curve (AUC). Test AUCs of 0.87, 0.74, and 0.71 were obtained with the individual predictive models based on radiomics, histopathologic, and molecular features, respectively. Combining the radiomics and molecular models increased the test AUC to 0.90. Combining all 3 models increased the test AUC further to 0.94. This preliminary study demonstrates that the individual domains of biomarkers are useful and the integrated multi-domain approach is most promising for tumor progression prediction.

  3. Exploring a new quantitative image marker to assess benefit of chemotherapy to ovarian cancer patients

    NASA Astrophysics Data System (ADS)

    Mirniaharikandehei, Seyedehnafiseh; Patil, Omkar; Aghaei, Faranak; Wang, Yunzhi; Zheng, Bin

    2017-03-01

    Accurately assessing the potential benefit of chemotherapy to cancer patients is an important prerequisite to developing precision medicine in cancer treatment. The previous study has shown that total psoas area (TPA) measured on preoperative cross-section CT image might be a good image marker to predict long-term outcome of pancreatic cancer patients after surgery. However, accurate and automated segmentation of TPA from the CT image is difficult due to the fuzzy boundary or connection of TPA to other muscle areas. In this study, we developed a new interactive computer-aided detection (ICAD) scheme aiming to segment TPA from the abdominal CT images more accurately and assess the feasibility of using this new quantitative image marker to predict the benefit of ovarian cancer patients receiving Bevacizumab-based chemotherapy. ICAD scheme was applied to identify a CT image slice of interest, which is located at the level of L3 (vertebral spines). The cross-sections of the right and left TPA are segmented using a set of adaptively adjusted boundary conditions. TPA is then quantitatively measured. In addition, recent studies have investigated that muscle radiation attenuation which reflects fat deposition in the tissue might be a good image feature for predicting the survival rate of cancer patients. The scheme and TPA measurement task were applied to a large national clinical trial database involving 1,247 ovarian cancer patients. By comparing with manual segmentation results, we found that ICAD scheme could yield higher accuracy and consistency for this task. Using a new ICAD scheme can provide clinical researchers a useful tool to more efficiently and accurately extract TPA as well as muscle radiation attenuation as new image makers, and allow them to investigate the discriminatory power of it to predict progression-free survival and/or overall survival of the cancer patients before and after taking chemotherapy.

  4. Quantitative trait loci analyses and RNA-seq identify genes affecting stress response in rainbow trout

    USDA-ARS?s Scientific Manuscript database

    Genomic analyses have the potential to impact aquaculture production traits by identifying markers as proxies for traits which are expensive or difficult to measure and characterizing genetic variation and biochemical mechanisms underlying phenotypic variation. One such trait is the response of rai...

  5. Comparative analysis of quantitative methodologies for Vibrionaceae biofilms.

    PubMed

    Chavez-Dozal, Alba A; Nourabadi, Neda; Erken, Martina; McDougald, Diane; Nishiguchi, Michele K

    2016-11-01

    Multiple symbiotic and free-living Vibrio spp. grow as a form of microbial community known as a biofilm. In the laboratory, methods to quantify Vibrio biofilm mass include crystal violet staining, direct colony-forming unit (CFU) counting, dry biofilm cell mass measurement, and observation of development of wrinkled colonies. Another approach for bacterial biofilms also involves the use of tetrazolium (XTT) assays (used widely in studies of fungi) that are an appropriate measure of metabolic activity and vitality of cells within the biofilm matrix. This study systematically tested five techniques, among which the XTT assay and wrinkled colony measurement provided the most reproducible, accurate, and efficient methods for the quantitative estimation of Vibrionaceae biofilms.

  6. A two-factor error model for quantitative steganalysis

    NASA Astrophysics Data System (ADS)

    Böhme, Rainer; Ker, Andrew D.

    2006-02-01

    Quantitative steganalysis refers to the exercise not only of detecting the presence of hidden stego messages in carrier objects, but also of estimating the secret message length. This problem is well studied, with many detectors proposed but only a sparse analysis of errors in the estimators. A deep understanding of the error model, however, is a fundamental requirement for the assessment and comparison of different detection methods. This paper presents a rationale for a two-factor model for sources of error in quantitative steganalysis, and shows evidence from a dedicated large-scale nested experimental set-up with a total of more than 200 million attacks. Apart from general findings about the distribution functions found in both classes of errors, their respective weight is determined, and implications for statistical hypothesis tests in benchmarking scenarios or regression analyses are demonstrated. The results are based on a rigorous comparison of five different detection methods under many different external conditions, such as size of the carrier, previous JPEG compression, and colour channel selection. We include analyses demonstrating the effects of local variance and cover saturation on the different sources of error, as well as presenting the case for a relative bias model for between-image error.

  7. Demonstration of a viable quantitative theory for interplanetary type II radio bursts

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

    Schmidt, J. M., E-mail: jschmidt@physics.usyd.edu.au; Cairns, Iver H.

    Between 29 November and 1 December 2013 the two widely separated spacecraft STEREO A and B observed a long lasting, intermittent, type II radio burst for the extended frequency range ≈ 4 MHz to 30 kHz, including an intensification when the shock wave of the associated coronal mass ejection (CME) reached STEREO A. We demonstrate for the first time our ability to quantitatively and accurately simulate the fundamental (F) and harmonic (H) emission of type II bursts from the higher corona (near 11 solar radii) to 1 AU. Our modeling requires the combination of data-driven three-dimensional magnetohydrodynamic simulations for the CME andmore » plasma background, carried out with the BATS-R-US code, with an analytic quantitative kinetic model for both F and H radio emission, including the electron reflection at the shock, growth of Langmuir waves and radio waves, and the radiations propagation to an arbitrary observer. The intensities and frequencies of the observed radio emissions vary hugely by factors ≈ 10{sup 6} and ≈ 10{sup 3}, respectively; the theoretical predictions are impressively accurate, being typically in error by less than a factor of 10 and 20 %, for both STEREO A and B. We also obtain accurate predictions for the timing and characteristics of the shock and local radio onsets at STEREO A, the lack of such onsets at STEREO B, and the z-component of the magnetic field at STEREO A ahead of the shock, and in the sheath. Very strong support is provided by these multiple agreements for the theory, the efficacy of the BATS-R-US code, and the vision of using type IIs and associated data-theory iterations to predict whether a CME will impact Earth’s magnetosphere and drive space weather events.« less

  8. Demonstration of a viable quantitative theory for interplanetary type II radio bursts

    NASA Astrophysics Data System (ADS)

    Schmidt, J. M.; Cairns, Iver H.

    2016-03-01

    Between 29 November and 1 December 2013 the two widely separated spacecraft STEREO A and B observed a long lasting, intermittent, type II radio burst for the extended frequency range ≈ 4 MHz to 30 kHz, including an intensification when the shock wave of the associated coronal mass ejection (CME) reached STEREO A. We demonstrate for the first time our ability to quantitatively and accurately simulate the fundamental (F) and harmonic (H) emission of type II bursts from the higher corona (near 11 solar radii) to 1 AU. Our modeling requires the combination of data-driven three-dimensional magnetohydrodynamic simulations for the CME and plasma background, carried out with the BATS-R-US code, with an analytic quantitative kinetic model for both F and H radio emission, including the electron reflection at the shock, growth of Langmuir waves and radio waves, and the radiations propagation to an arbitrary observer. The intensities and frequencies of the observed radio emissions vary hugely by factors ≈ 106 and ≈ 103, respectively; the theoretical predictions are impressively accurate, being typically in error by less than a factor of 10 and 20 %, for both STEREO A and B. We also obtain accurate predictions for the timing and characteristics of the shock and local radio onsets at STEREO A, the lack of such onsets at STEREO B, and the z-component of the magnetic field at STEREO A ahead of the shock, and in the sheath. Very strong support is provided by these multiple agreements for the theory, the efficacy of the BATS-R-US code, and the vision of using type IIs and associated data-theory iterations to predict whether a CME will impact Earth's magnetosphere and drive space weather events.

  9. Effects of grain species and cultivar, thermal processing, and enzymatic hydrolysis on gluten quantitation.

    PubMed

    Pahlavan, Autusa; Sharma, Girdhari M; Pereira, Marion; Williams, Kristina M

    2016-10-01

    Gluten from wheat, rye, and barley can trigger IgE-mediated allergy or Celiac disease in sensitive individuals. Gluten-free labeled foods are available as a safe alternative. Immunoassays such as the enzyme-linked immunosorbent assay (ELISA) are commonly used to quantify gluten in foods. However, various non-assay related factors can affect gluten quantitation. The effect of gluten-containing grain cultivars, thermal processing, and enzymatic hydrolysis on gluten quantitation by various ELISA kits was evaluated. The ELISA kits exhibited variations in gluten quantitation depending on the gluten-containing grain and their cultivars. Acceptable gluten recoveries were obtained in 200mg/kg wheat, rye, and barley-spiked corn flour thermally processed at various conditions. However, depending on the enzyme, gluten grain source, and ELISA kit used, measured gluten content was significantly reduced in corn flour spiked with 200mg/kg hydrolyzed wheat, rye, and barley flour. Thus, the gluten grain source and processing conditions should be considered for accurate gluten analysis. Published by Elsevier Ltd.

  10. A review of bioinformatic methods for forensic DNA analyses.

    PubMed

    Liu, Yao-Yuan; Harbison, SallyAnn

    2018-03-01

    Short tandem repeats, single nucleotide polymorphisms, and whole mitochondrial analyses are three classes of markers which will play an important role in the future of forensic DNA typing. The arrival of massively parallel sequencing platforms in forensic science reveals new information such as insights into the complexity and variability of the markers that were previously unseen, along with amounts of data too immense for analyses by manual means. Along with the sequencing chemistries employed, bioinformatic methods are required to process and interpret this new and extensive data. As more is learnt about the use of these new technologies for forensic applications, development and standardization of efficient, favourable tools for each stage of data processing is being carried out, and faster, more accurate methods that improve on the original approaches have been developed. As forensic laboratories search for the optimal pipeline of tools, sequencer manufacturers have incorporated pipelines into sequencer software to make analyses convenient. This review explores the current state of bioinformatic methods and tools used for the analyses of forensic markers sequenced on the massively parallel sequencing (MPS) platforms currently most widely used. Copyright © 2017 Elsevier B.V. All rights reserved.

  11. Some strategies for quantitative scanning Auger electron microscopy

    NASA Technical Reports Server (NTRS)

    Browning, R.; Peacock, D. C.; Prutton, M.

    1985-01-01

    The general applicability of power law forms of the background in electron spectra is pointed out and exploited for background removal from under Auger peaks. This form of B(E) is found to be extremely sensitive to instrumental alignment and to fault-free construction - an observation which can be used to set up analyser configurations in an accurate way. Also, differences between N(E) and B(E) can be used to derive a spectrometer transmission function T(E). The questions of information density in an energy-analysing spatially-resolving instrument are addressed after reliable instrumental characterization has been established. Strategies involving ratio histograms, showing the population distribution of the ratio of a pair of Auger peak heights, composition scatter diagrams and windowed imaging are discussed and illustrated.

  12. A High-Density Genetic Map with Array-Based Markers Facilitates Structural and Quantitative Trait Locus Analyses of the Common Wheat Genome

    PubMed Central

    Iehisa, Julio Cesar Masaru; Ohno, Ryoko; Kimura, Tatsuro; Enoki, Hiroyuki; Nishimura, Satoru; Okamoto, Yuki; Nasuda, Shuhei; Takumi, Shigeo

    2014-01-01

    The large genome and allohexaploidy of common wheat have complicated construction of a high-density genetic map. Although improvements in the throughput of next-generation sequencing (NGS) technologies have made it possible to obtain a large amount of genotyping data for an entire mapping population by direct sequencing, including hexaploid wheat, a significant number of missing data points are often apparent due to the low coverage of sequencing. In the present study, a microarray-based polymorphism detection system was developed using NGS data obtained from complexity-reduced genomic DNA of two common wheat cultivars, Chinese Spring (CS) and Mironovskaya 808. After design and selection of polymorphic probes, 13,056 new markers were added to the linkage map of a recombinant inbred mapping population between CS and Mironovskaya 808. On average, 2.49 missing data points per marker were observed in the 201 recombinant inbred lines, with a maximum of 42. Around 40% of the new markers were derived from genic regions and 11% from repetitive regions. The low number of retroelements indicated that the new polymorphic markers were mainly derived from the less repetitive region of the wheat genome. Around 25% of the mapped sequences were useful for alignment with the physical map of barley. Quantitative trait locus (QTL) analyses of 14 agronomically important traits related to flowering, spikes, and seeds demonstrated that the new high-density map showed improved QTL detection, resolution, and accuracy over the original simple sequence repeat map. PMID:24972598

  13. Comparison of clinical semi-quantitative assessment of muscle fat infiltration with quantitative assessment using chemical shift-based water/fat separation in MR studies of the calf of post-menopausal women.

    PubMed

    Alizai, Hamza; Nardo, Lorenzo; Karampinos, Dimitrios C; Joseph, Gabby B; Yap, Samuel P; Baum, Thomas; Krug, Roland; Majumdar, Sharmila; Link, Thomas M

    2012-07-01

    The goal of this study was to compare the semi-quantitative Goutallier classification for fat infiltration with quantitative fat-fraction derived from a magnetic resonance imaging (MRI) chemical shift-based water/fat separation technique. Sixty-two women (age 61 ± 6 years), 27 of whom had diabetes, underwent MRI of the calf using a T1-weighted fast spin-echo sequence and a six-echo spoiled gradient-echo sequence at 3 T. Water/fat images and fat fraction maps were reconstructed using the IDEAL algorithm with T2* correction and a multi-peak model for the fat spectrum. Two radiologists scored fat infiltration on the T1-weighted images using the Goutallier classification in six muscle compartments. Spearman correlations between the Goutallier grades and the fat fraction were calculated; in addition, intra-observer and inter-observer agreement were calculated. A significant correlation between the clinical grading and the fat fraction values was found for all muscle compartments (P < 0.0001, R values ranging from 0.79 to 0.88). Goutallier grades 0-4 had a fat fraction ranging from 3.5 to 19%. Intra-observer and inter-observer agreement values of 0.83 and 0.81 were calculated for the semi-quantitative grading. Semi-quantitative grading of intramuscular fat and quantitative fat fraction were significantly correlated and both techniques had excellent reproducibility. However, the clinical grading was found to overestimate muscle fat. Fat infiltration of muscle commonly occurs in many metabolic and neuromuscular diseases. • Image-based semi-quantitative classifications for assessing fat infiltration are not well validated. • Quantitative MRI techniques provide an accurate assessment of muscle fat.

  14. 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.

  15. Enhanced Photoacoustic Gas Analyser Response Time and Impact on Accuracy at Fast Ventilation Rates during Multiple Breath Washout

    PubMed Central

    Horsley, Alex; Macleod, Kenneth; Gupta, Ruchi; Goddard, Nick; Bell, Nicholas

    2014-01-01

    Background The Innocor device contains a highly sensitive photoacoustic gas analyser that has been used to perform multiple breath washout (MBW) measurements using very low concentrations of the tracer gas SF6. Use in smaller subjects has been restricted by the requirement for a gas analyser response time of <100 ms, in order to ensure accurate estimation of lung volumes at rapid ventilation rates. Methods A series of previously reported and novel enhancements were made to the gas analyser to produce a clinically practical system with a reduced response time. An enhanced lung model system, capable of delivering highly accurate ventilation rates and volumes, was used to assess in vitro accuracy of functional residual capacity (FRC) volume calculation and the effects of flow and gas signal alignment on this. Results 10–90% rise time was reduced from 154 to 88 ms. In an adult/child lung model, accuracy of volume calculation was −0.9 to 2.9% for all measurements, including those with ventilation rate of 30/min and FRC of 0.5 L; for the un-enhanced system, accuracy deteriorated at higher ventilation rates and smaller FRC. In a separate smaller lung model (ventilation rate 60/min, FRC 250 ml, tidal volume 100 ml), mean accuracy of FRC measurement for the enhanced system was minus 0.95% (range −3.8 to 2.0%). Error sensitivity to flow and gas signal alignment was increased by ventilation rate, smaller FRC and slower analyser response time. Conclusion The Innocor analyser can be enhanced to reliably generate highly accurate FRC measurements down at volumes as low as those simulating infant lung settings. Signal alignment is a critical factor. With these enhancements, the Innocor analyser exceeds key technical component recommendations for MBW apparatus. PMID:24892522

  16. Quantitative operando visualization of the energy band depth profile in solar cells

    PubMed Central

    Chen, Qi; Mao, Lin; Li, Yaowen; Kong, Tao; Wu, Na; Ma, Changqi; Bai, Sai; Jin, Yizheng; Wu, Dan; Lu, Wei; Wang, Bing; Chen, Liwei

    2015-01-01

    The energy band alignment in solar cell devices is critically important because it largely governs elementary photovoltaic processes, such as the generation, separation, transport, recombination and collection of charge carriers. Despite the expenditure of considerable effort, the measurement of energy band depth profiles across multiple layers has been extremely challenging, especially for operando devices. Here we present direct visualization of the surface potential depth profile over the cross-sections of operando organic photovoltaic devices using scanning Kelvin probe microscopy. The convolution effect due to finite tip size and cantilever beam crosstalk has previously prohibited quantitative interpretation of scanning Kelvin probe microscopy-measured surface potential depth profiles. We develop a bias voltage-compensation method to address this critical problem and obtain quantitatively accurate measurements of the open-circuit voltage, built-in potential and electrode potential difference. PMID:26166580

  17. Quantitative tomographic measurements of opaque multiphase flows

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

    GEORGE,DARIN L.; TORCZYNSKI,JOHN R.; SHOLLENBERGER,KIM ANN

    2000-03-01

    An electrical-impedance tomography (EIT) system has been developed for quantitative measurements of radial phase distribution profiles in two-phase and three-phase vertical column flows. The EIT system is described along with the computer algorithm used for reconstructing phase volume fraction profiles. EIT measurements were validated by comparison with a gamma-densitometry tomography (GDT) system. The EIT system was used to accurately measure average solid volume fractions up to 0.05 in solid-liquid flows, and radial gas volume fraction profiles in gas-liquid flows with gas volume fractions up to 0.15. In both flows, average phase volume fractions and radial volume fraction profiles from GDTmore » and EIT were in good agreement. A minor modification to the formula used to relate conductivity data to phase volume fractions was found to improve agreement between the methods. GDT and EIT were then applied together to simultaneously measure the solid, liquid, and gas radial distributions within several vertical three-phase flows. For average solid volume fractions up to 0.30, the gas distribution for each gas flow rate was approximately independent of the amount of solids in the column. Measurements made with this EIT system demonstrate that EIT may be used successfully for noninvasive, quantitative measurements of dispersed multiphase flows.« less

  18. Glycan reductive isotope labeling for quantitative glycomics.

    PubMed

    Xia, Baoyun; Feasley, Christa L; Sachdev, Goverdhan P; Smith, David F; Cummings, Richard D

    2009-04-15

    Many diseases and disorders are characterized by quantitative and/or qualitative changes in complex carbohydrates. Mass spectrometry methods show promise in monitoring and detecting these important biological changes. Here we report a new glycomics method, termed glycan reductive isotope labeling (GRIL), where free glycans are derivatized by reductive amination with the differentially coded stable isotope tags [(12)C(6)]aniline and [(13)C(6)]aniline. These dual-labeled aniline-tagged glycans can be recovered by reverse-phase chromatography and can be quantified based on ultraviolet (UV) absorbance and relative ion abundances. Unlike previously reported isotopically coded reagents for glycans, GRIL does not contain deuterium, which can be chromatographically resolved. Our method shows no chromatographic resolution of differentially labeled glycans. Mixtures of differentially tagged glycans can be directly compared and quantified using mass spectrometric techniques. We demonstrate the use of GRIL to determine relative differences in glycan amount and composition. We analyze free glycans and glycans enzymatically or chemically released from a variety of standard glycoproteins, as well as human and mouse serum glycoproteins, using this method. This technique allows linear relative quantitation of glycans over a 10-fold concentration range and can accurately quantify sub-picomole levels of released glycans, providing a needed advancement in the field of glycomics.

  19. Quantitative confirmation of diffusion-limited oxidation theories

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

    Gillen, K.T.; Clough, R.L.

    1990-01-01

    Diffusion-limited (heterogeneous) oxidation effects are often important for studies of polymer degradation. Such effects are common in polymers subjected to ionizing radiation at relatively high dose rate. To better understand the underlying oxidation processes and to aid in the planning of accelerated aging studies, it would be desirable to be able to monitor and quantitatively understand these effects. In this paper, we briefly review a theoretical diffusion approach which derives model profiles for oxygen surrounded sheets of material by combining oxygen permeation rates with kinetically based oxygen consumption expressions. The theory leads to a simple governing expression involving the oxygenmore » consumption and permeation rates together with two model parameters {alpha} and {beta}. To test the theory, gamma-initiated oxidation of a sheet of commercially formulated EPDM rubber was performed under conditions which led to diffusion-limited oxidation. Profile shapes from the theoretical treatments are shown to accurately fit experimentally derived oxidation profiles. In addition, direct measurements on the same EPDM material of the oxygen consumption and permeation rates, together with values of {alpha} and {beta} derived from the fitting procedure, allow us to quantitatively confirm for the first time the governing theoretical relationship. 17 refs., 3 figs.« less

  20. Quantitative analysis on electrooculography (EOG) for neurodegenerative disease

    NASA Astrophysics Data System (ADS)

    Liu, Chang-Chia; Chaovalitwongse, W. Art; Pardalos, Panos M.; Seref, Onur; Xanthopoulos, Petros; Sackellares, J. C.; Skidmore, Frank M.

    2007-11-01

    Many studies have documented abnormal horizontal and vertical eye movements in human neurodegenerative disease as well as during altered states of consciousness (including drowsiness and intoxication) in healthy adults. Eye movement measurement may play an important role measuring the progress of neurodegenerative diseases and state of alertness in healthy individuals. There are several techniques for measuring eye movement, Infrared detection technique (IR). Video-oculography (VOG), Scleral eye coil and EOG. Among those available recording techniques, EOG is a major source for monitoring the abnormal eye movement. In this real-time quantitative analysis study, the methods which can capture the characteristic of the eye movement were proposed to accurately categorize the state of neurodegenerative subjects. The EOG recordings were taken while 5 tested subjects were watching a short (>120 s) animation clip. In response to the animated clip the participants executed a number of eye movements, including vertical smooth pursued (SVP), horizontal smooth pursued (HVP) and random saccades (RS). Detection of abnormalities in ocular movement may improve our diagnosis and understanding a neurodegenerative disease and altered states of consciousness. A standard real-time quantitative analysis will improve detection and provide a better understanding of pathology in these disorders.

  1. Brain electromagnetic activity and lightning: potentially congruent scale-invariant quantitative properties

    PubMed Central

    Persinger, Michael A.

    2012-01-01

    The space-time characteristics of the axonal action potential are remarkably similar to the scaled equivalents of lightning. The energy and current densities from these transients within their respective volumes or cross-sectional areas are the same order of magnitude. Length–velocity ratios and temporal durations are nearly identical. There are similar chemical consequences such as the production of nitric oxide. Careful, quantitative examination of the characteristics of lightning may reveal analogous features of the action potential that could lead to a more accurate understanding of these powerful correlates of neurocognitive processes. PMID:22615688

  2. Quantitative and fingerprint analyses of Chinese sweet tea plant (Rubus Suavissimus S. Lee)

    PubMed Central

    Chou, Guixin; Xu, Shun-Jun; Liu, Dong; Koh, Gar Yee; Zhang, Jian; Liu, Zhijun

    2009-01-01

    Quality of botanical food is increasingly assessed by the content of multiple bioactive compounds. In this study we report, for the first time, an HPLC fingerprinting method for the quality evaluation of Rubus suavissimus leaves possessing multiple bioactivities. Five constituents, gallic acid, rutin, ellagic acid, rubusoside, and steviol monoside were quantified and used in developing qualitative chromatographic fingerprints. The limits of detection and quantification ranged from 0.29 μg/mL to 37.86 μg/mL. The relative standard deviations (RSDs) of intra- and inter-day precisions were no more than 3.14% and 3.01%, respectively. The average recoveries were between 93.1% and 97.5%. The developed method was validated in analyzing fourteen leaf samples with satisfactory results. The contents of the five marker compounds accounted for an average of about 6% w/w with a variability of 16% among the fourteen samples collected from a single site and year. Gallic acid was the least whereas steviol monoside the most variable compounds among the fourteen leaf samples. The characteristic compound rubusoside that is responsible for the sweet taste accounted for 5% of leaf weight. The validated method can now be used to quantitatively and qualitatively assess the quality of Rubus suavissimus leaves as traditional beverage or potential medicines. PMID:19138116

  3. Quantitation of circulating tumor cells in blood samples from ovarian and prostate cancer patients using tumor-specific fluorescent ligands.

    PubMed

    He, Wei; Kularatne, Sumith A; Kalli, Kimberly R; Prendergast, Franklyn G; Amato, Robert J; Klee, George G; Hartmann, Lynn C; Low, Philip S

    2008-10-15

    Quantitation of circulating tumor cells (CTCs) can provide information on the stage of a malignancy, onset of disease progression and response to therapy. In an effort to more accurately quantitate CTCs, we have synthesized fluorescent conjugates of 2 high-affinity tumor-specific ligands (folate-AlexaFluor 488 and DUPA-FITC) that bind tumor cells >20-fold more efficiently than fluorescent antibodies. Here we determine whether these tumor-specific dyes can be exploited for quantitation of CTCs in peripheral blood samples from cancer patients. A CTC-enriched fraction was isolated from the peripheral blood of ovarian and prostate cancer patients by an optimized density gradient centrifugation protocol and labeled with the aforementioned fluorescent ligands. CTCs were then quantitated by flow cytometry. CTCs were detected in 18 of 20 ovarian cancer patients (mean 222 CTCs/ml; median 15 CTCs/ml; maximum 3,118 CTCs/ml), whereas CTC numbers in 16 gender-matched normal volunteers were negligible (mean 0.4 CTCs/ml; median 0.3 CTCs/ml; maximum 1.5 CTCs/ml; p < 0.001, chi(2)). CTCs were also detected in 10 of 13 prostate cancer patients (mean 26 CTCs/ml, median 14 CTCs/ml, maximum 94 CTCs/ml) but not in 18 gender-matched healthy donors (mean 0.8 CTCs/ml, median 1, maximum 3 CTC/ml; p < 0.0026, chi(2)). Tumor-specific fluorescent antibodies were much less efficient in quantitating CTCs because of their lower CTC labeling efficiency. Use of tumor-specific fluorescent ligands to label CTCs in peripheral blood can provide a simple, accurate and sensitive method for determining the number of cancer cells circulating in the bloodstream.

  4. Method for a quantitative investigation of the frozen flow hypothesis

    PubMed

    Schock; Spillar

    2000-09-01

    We present a technique to test the frozen flow hypothesis quantitatively, using data from wave-front sensors such as those found in adaptive optics systems. Detailed treatments of the theoretical background of the method and of the error analysis are presented. Analyzing data from the 1.5-m and 3.5-m telescopes at the Starfire Optical Range, we find that the frozen flow hypothesis is an accurate description of the temporal development of atmospheric turbulence on time scales of the order of 1-10 ms but that significant deviations from the frozen flow behavior are present for longer time scales.

  5. Capsular Outcomes After Pediatric Cataract Surgery Without Intraocular Lens Implantation: Qualitative Classification and Quantitative Measurement.

    PubMed

    Tan, Xuhua; Lin, Haotian; Lin, Zhuoling; Chen, Jingjing; Tang, Xiangchen; Luo, Lixia; Chen, Weirong; Liu, Yizhi

    2016-03-01

    The objective of this study was to investigate capsular outcomes 12 months after pediatric cataract surgery without intraocular lens implantation via qualitative classification and quantitative measurement.This study is a cross-sectional study that was approved by the institutional review board of Zhongshan Ophthalmic Center of Sun Yat-sen University in Guangzhou, China.Digital coaxial retro-illumination photographs of 329 aphakic pediatric eyes were obtained 12 months after pediatric cataract surgery without intraocular lens implantation. Capsule digital coaxial retro-illumination photographs were divided as follows: anterior capsule opening area (ACOA), posterior capsule opening area (PCOA), and posterior capsule opening opacity (PCOO). Capsular outcomes were qualitatively classified into 3 types based on the PCOO: Type I-capsule with mild opacification but no invasion into the capsule opening; Type II-capsule with moderate opacification accompanied by contraction of the ACOA and invasion to the occluding part of the PCOA; and Type III-capsule with severe opacification accompanied by total occlusion of the PCOA. Software was developed to quantitatively measure the ACOA, PCOA, and PCOO using standardized DCRPs. The relationships between the accurate intraoperative anterior and posterior capsulorhexis sizes and the qualitative capsular types were statistically analyzed.The DCRPs of 315 aphakic eyes (95.8%) of 191 children were included. Capsular outcomes were classified into 3 types: Type I-120 eyes (38.1%); Type II-157 eyes (49.8%); Type III-38 eyes (12.1%). The scores of the capsular outcomes were negatively correlated with intraoperative anterior capsulorhexis size (R = -0.572, P < 0.001), but no significant correlation with intraoperative posterior capsulorhexis size (R = -0.16, P = 0.122) was observed. The ACOA significantly decreased from Type I to Type II to Type III, the PCOA increased in size from Type I to Type II, and the PCOO increased

  6. Quantitation of the phosphoproteome using the library-assisted extracted ion chromatogram (LAXIC) strategy.

    PubMed

    Arrington, Justine V; Xue, Liang; Tao, W Andy

    2014-01-01

    Phosphorylation is a key posttranslational modification that regulates many signaling pathways, but quantifying changes in phosphorylation between samples can be challenging due to its low stoichiometry within cells. We have introduced a mass spectrometry-based label-free quantitation strategy termed LAXIC for the analysis of the phosphoproteome. This method uses a spiked-in synthetic peptide library designed to elute across the entire chromatogram for local normalization of phosphopeptides within complex samples. Normalization of phosphopeptides by library peptides that co-elute within a small time frame accounts for fluctuating ion suppression effects, allowing more accurate quantitation even when LC-MS performance varies. Here we explain the premise of LAXIC, the design of a suitable peptide library, and how the LAXIC algorithm can be implemented with software developed in-house.

  7. A unified material decomposition framework for quantitative dual- and triple-energy CT imaging.

    PubMed

    Zhao, Wei; Vernekohl, Don; Han, Fei; Han, Bin; Peng, Hao; Yang, Yong; Xing, Lei; Min, James K

    2018-04-21

    Many clinical applications depend critically on the accurate differentiation and classification of different types of materials in patient anatomy. This work introduces a unified framework for accurate nonlinear material decomposition and applies it, for the first time, in the concept of triple-energy CT (TECT) for enhanced material differentiation and classification as well as dual-energy CT (DECT). We express polychromatic projection into a linear combination of line integrals of material-selective images. The material decomposition is then turned into a problem of minimizing the least-squares difference between measured and estimated CT projections. The optimization problem is solved iteratively by updating the line integrals. The proposed technique is evaluated by using several numerical phantom measurements under different scanning protocols. The triple-energy data acquisition is implemented at the scales of micro-CT and clinical CT imaging with commercial "TwinBeam" dual-source DECT configuration and a fast kV switching DECT configuration. Material decomposition and quantitative comparison with a photon counting detector and with the presence of a bow-tie filter are also performed. The proposed method provides quantitative material- and energy-selective images examining realistic configurations for both DECT and TECT measurements. Compared to the polychromatic kV CT images, virtual monochromatic images show superior image quality. For the mouse phantom, quantitative measurements show that the differences between gadodiamide and iodine concentrations obtained using TECT and idealized photon counting CT (PCCT) are smaller than 8 and 1 mg/mL, respectively. TECT outperforms DECT for multicontrast CT imaging and is robust with respect to spectrum estimation. For the thorax phantom, the differences between the concentrations of the contrast map and the corresponding true reference values are smaller than 7 mg/mL for all of the realistic configurations. A unified

  8. Functional analyses of the digestive ß-Glucosidase of Formosan Subterranean Termites (Coptotermes formosanus)

    USDA-ARS?s Scientific Manuscript database

    The research was to elucidate the function of the ß-glucosidase of Formosan subterranean termites in vitro and in vivo. Quantitative RT-PCR analyses indicated that the gene transcript was relatively more abundant in the foraging worker caste than in other castes and salivary glands were the major ex...

  9. Quantitative 1H NMR: Development and Potential of an Analytical Method – an Update

    PubMed Central

    Pauli, Guido F.; Gödecke, Tanja; Jaki, Birgit U.; Lankin, David C.

    2012-01-01

    Covering the literature from mid-2004 until the end of 2011, this review continues a previous literature overview on quantitative 1H NMR (qHNMR) methodology and its applications in the analysis of natural products (NPs). Among the foremost advantages of qHNMR is its accurate function with external calibration, the lack of any requirement for identical reference materials, a high precision and accuracy when properly validated, and an ability to quantitate multiple analytes simultaneously. As a result of the inclusion of over 170 new references, this updated review summarizes a wealth of detailed experiential evidence and newly developed methodology that supports qHNMR as a valuable and unbiased analytical tool for natural product and other areas of research. PMID:22482996

  10. The relationship between international trade and non-nutritional health outcomes: A systematic review of quantitative studies.

    PubMed

    Burns, Darren K; Jones, Andrew P; Suhrcke, Marc

    2016-03-01

    Markets throughout the world have been reducing barriers to international trade and investment in recent years. The resulting increases in levels of international trade and investment have subsequently generated research interest into the potential population health impact. We present a systematic review of quantitative studies investigating the relationship between international trade, foreign direct investment and non-nutritional health outcomes. Articles were systematically collected from the SCOPUS, PubMed, EconLit and Web of Science databases. Due to the heterogeneous nature of the evidence considered, the 16 included articles were subdivided into individual level data analyses, selected country analyses and international panel analyses. Articles were then quality assessed using a tool developed as part of the project. Nine of the studies were assessed to be high quality, six as medium quality, and one as low quality. The evidence from the quantitative literature suggests that overall, there appears to be a beneficial association between international trade and population health. There was also evidence of the importance of foreign direct investment, yet a lack of research considering the direction of causality. Taken together, quantitative research into the relationship between trade and non-nutritional health indicates trade to be beneficial, yet this body of research is still in its infancy. Future quantitative studies based on this foundation will provide a stronger basis on which to inform relevant national and international institutions about the health consequences of trade policies. Copyright © 2016 Elsevier Ltd. All rights reserved.

  11. Accurate seismic phase identification and arrival time picking of glacial icequakes

    NASA Astrophysics Data System (ADS)

    Jones, G. A.; Doyle, S. H.; Dow, C.; Kulessa, B.; Hubbard, A.

    2010-12-01

    A catastrophic lake drainage event was monitored continuously using an array of 6, 4.5 Hz 3 component geophones in the Russell Glacier catchment, Western Greenland. Many thousands of events and arrival time phases (e.g., P- or S-wave) were recorded, often with events occurring simultaneously but at different locations. In addition, different styles of seismic events were identified from 'classical' tectonic earthquakes to tremors usually observed in volcanic regions. The presence of such a diverse and large dataset provides insight into the complex system of lake drainage. One of the most fundamental steps in seismology is the accurate identification of a seismic event and its associated arrival times. However, the collection of such a large and complex dataset makes the manual identification of a seismic event and picking of the arrival time phases time consuming with variable results. To overcome the issues of consistency and manpower, a number of different methods have been developed including short-term and long-term averages, spectrograms, wavelets, polarisation analyses, higher order statistics and auto-regressive techniques. Here we propose an automated procedure which establishes the phase type and accurately determines the arrival times. The procedure combines a number of different automated methods to achieve this, and is applied to the recently acquired lake drainage data. Accurate identification of events and their arrival time phases are the first steps in gaining a greater understanding of the extent of the deformation and the mechanism of such drainage events. A good knowledge of the propagation pathway of lake drainage meltwater through a glacier will have significant consequences for interpretation of glacial and ice sheet dynamics.

  12. Carbon analyses of IDP's sectioned in sulfur and supported on beryllium films

    NASA Technical Reports Server (NTRS)

    Bradley, J. P.; Keller, L.; Thomas, K. L.; Vanderwood, T. B.; Brownlee, D. E.

    1993-01-01

    Carbon is the only major element in interplanetary dust whose abundance, distribution and chemical state are not well understood. Information about carbon could clarify the relationship between the various classes of IDP's, conventional meteorites, and sources (e.g., comets vs. asteroids). To date, the most reliable estimates of C abundance in Interplanetary Dust Particles (IDP's) have been obtained by analyzing particles on thick-flat Be substrates using thin-window energy-dispersive spectroscopy in the SEM. These estimates of C abundance are valid only if C is homogeneously distributed, because detected C x-rays originate from the outer 0.1 micrometers of the particle. An alternative and potentially more accurate method of measuring C abundances is to analyze multiple thin sections (each less than 0.1 less than 0.1 micrometers thick) of IDP's. These efforts however, have been stymied because of a lack of a suitable non-carbonaceous embedding medium and the availability of C-free conductive substrates. We have embedded and thin-sectioned IDP's in glassy sulfur, and transferred the thin sections to Be support films approximately 25 nm thick. The sections were then analyzed in a 200 KeV analytical TEM. S sublimes rapidly under vacuum in the TEM, leaving non-embedded sections supported on Be. Apart from quantitative C (and O) analyses, S sectioning dramatically expands the range of analytical measurements that can be performed on a single IDP.

  13. Simultaneous quantitative determination of paracetamol and tramadol in tablet formulation using UV spectrophotometry and chemometric methods

    NASA Astrophysics Data System (ADS)

    Glavanović, Siniša; Glavanović, Marija; Tomišić, Vladislav

    2016-03-01

    The UV spectrophotometric methods for simultaneous quantitative determination of paracetamol and tramadol in paracetamol-tramadol tablets were developed. The spectrophotometric data obtained were processed by means of partial least squares (PLS) and genetic algorithm coupled with PLS (GA-PLS) methods in order to determine the content of active substances in the tablets. The results gained by chemometric processing of the spectroscopic data were statistically compared with those obtained by means of validated ultra-high performance liquid chromatographic (UHPLC) method. The accuracy and precision of data obtained by the developed chemometric models were verified by analysing the synthetic mixture of drugs, and by calculating recovery as well as relative standard error (RSE). A statistically good agreement was found between the amounts of paracetamol determined using PLS and GA-PLS algorithms, and that obtained by UHPLC analysis, whereas for tramadol GA-PLS results were proven to be more reliable compared to those of PLS. The simplest and the most accurate and precise models were constructed by using the PLS method for paracetamol (mean recovery 99.5%, RSE 0.89%) and the GA-PLS method for tramadol (mean recovery 99.4%, RSE 1.69%).

  14. The Eudaimonic and Hedonic Components of Happiness: Qualitative and Quantitative Findings

    ERIC Educational Resources Information Center

    Fave, Antonella Delle; Brdar, Ingrid; Freire, Teresa; Vella-Brodrick, Dianne; Wissing, Marie P.

    2011-01-01

    This paper illustrates a new project developed by a cross-country team of researchers, with the aim of studying the hedonic and eudaimonic components of happiness through a mixed method approach combining both qualitative and quantitative analyses. Data were collected from 666 participants in Australia, Croatia, Germany, Italy, Portugal, Spain,…

  15. Evaluation of empirical rule of linearly correlated peptide selection (ERLPS) for proteotypic peptide-based quantitative proteomics.

    PubMed

    Liu, Kehui; Zhang, Jiyang; Fu, Bin; Xie, Hongwei; Wang, Yingchun; Qian, Xiaohong

    2014-07-01

    Precise protein quantification is essential in comparative proteomics. Currently, quantification bias is inevitable when using proteotypic peptide-based quantitative proteomics strategy for the differences in peptides measurability. To improve quantification accuracy, we proposed an "empirical rule for linearly correlated peptide selection (ERLPS)" in quantitative proteomics in our previous work. However, a systematic evaluation on general application of ERLPS in quantitative proteomics under diverse experimental conditions needs to be conducted. In this study, the practice workflow of ERLPS was explicitly illustrated; different experimental variables, such as, different MS systems, sample complexities, sample preparations, elution gradients, matrix effects, loading amounts, and other factors were comprehensively investigated to evaluate the applicability, reproducibility, and transferability of ERPLS. The results demonstrated that ERLPS was highly reproducible and transferable within appropriate loading amounts and linearly correlated response peptides should be selected for each specific experiment. ERLPS was used to proteome samples from yeast to mouse and human, and in quantitative methods from label-free to O18/O16-labeled and SILAC analysis, and enabled accurate measurements for all proteotypic peptide-based quantitative proteomics over a large dynamic range. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Characterization of 3-Dimensional PET Systems for Accurate Quantification of Myocardial Blood Flow.

    PubMed

    Renaud, Jennifer M; Yip, Kathy; Guimond, Jean; Trottier, Mikaël; Pibarot, Philippe; Turcotte, Eric; Maguire, Conor; Lalonde, Lucille; Gulenchyn, Karen; Farncombe, Troy; Wisenberg, Gerald; Moody, Jonathan; Lee, Benjamin; Port, Steven C; Turkington, Timothy G; Beanlands, Rob S; deKemp, Robert A

    2017-01-01

    Three-dimensional (3D) mode imaging is the current standard for PET/CT systems. Dynamic imaging for quantification of myocardial blood flow with short-lived tracers, such as 82 Rb-chloride, requires accuracy to be maintained over a wide range of isotope activities and scanner counting rates. We proposed new performance standard measurements to characterize the dynamic range of PET systems for accurate quantitative imaging. 82 Rb or 13 N-ammonia (1,100-3,000 MBq) was injected into the heart wall insert of an anthropomorphic torso phantom. A decaying isotope scan was obtained over 5 half-lives on 9 different 3D PET/CT systems and 1 3D/2-dimensional PET-only system. Dynamic images (28 × 15 s) were reconstructed using iterative algorithms with all corrections enabled. Dynamic range was defined as the maximum activity in the myocardial wall with less than 10% bias, from which corresponding dead-time, counting rates, and/or injected activity limits were established for each scanner. Scatter correction residual bias was estimated as the maximum cavity blood-to-myocardium activity ratio. Image quality was assessed via the coefficient of variation measuring nonuniformity of the left ventricular myocardium activity distribution. Maximum recommended injected activity/body weight, peak dead-time correction factor, counting rates, and residual scatter bias for accurate cardiac myocardial blood flow imaging were 3-14 MBq/kg, 1.5-4.0, 22-64 Mcps singles and 4-14 Mcps prompt coincidence counting rates, and 2%-10% on the investigated scanners. Nonuniformity of the myocardial activity distribution varied from 3% to 16%. Accurate dynamic imaging is possible on the 10 3D PET systems if the maximum injected MBq/kg values are respected to limit peak dead-time losses during the bolus first-pass transit. © 2017 by the Society of Nuclear Medicine and Molecular Imaging.

  17. Quantitative Surface Chirality Detection with Sum Frequency Generation Vibrational Spectroscopy: Twin Polarization Angle Approach

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

    Wei, Feng; Xu, Yanyan; Guo, Yuan

    2009-12-27

    Here we report a novel twin polarization angle (TPA) approach in the quantitative chirality detection with the surface sum-frequency generation vibrational spectroscopy (SFG-VS). Generally, the achiral contribution dominates the surface SFG-VS signal, and the pure chiral signal is usually two or three orders of magnitude smaller. Therefore, it has been difficult to make quantitative detection and analysis of the chiral contributions to the surface SFG- VS signal. In the TPA method, by varying together the polarization angles of the incoming visible light and the sum frequency signal at fixed s or p polarization of the incoming infrared beam, the polarizationmore » dependent SFG signal can give not only direct signature of the chiral contribution in the total SFG-VS signal, but also the accurate measurement of the chiral and achiral components in the surface SFG signal. The general description of the TPA method is presented and the experiment test of the TPA approach is also presented for the SFG-VS from the S- and R-limonene chiral liquid surfaces. The most accurate degree of chiral excess values thus obtained for the 2878 cm⁻¹ spectral peak of the S- and R-limonene liquid surfaces are (23.7±0.4)% and ({25.4±1.3)%, respectively.« less

  18. A comparative study of quantitative microsegregation analyses performed during the solidification of the Ni-base superalloy CMSX-10

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

    Seo, Seong-Moon, E-mail: castme@kims.re.kr; Jeong, Hi-Won; Ahn, Young-Keun

    Quantitative microsegregation analyses were systematically carried out during the solidification of the Ni-base superalloy CMSX-10 to clarify the methodological effect on the quantification of microsegregation and to fully understand the solidification microstructure. Three experimental techniques, namely, mushy zone quenching (MZQ), planar directional solidification followed by quenching (PDSQ), and random sampling (RS), were implemented for the analysis of microsegregation tendency and the magnitude of solute elements by electron probe microanalysis. The microprobe data and the calculation results of the diffusion field ahead of the solid/liquid (S/L) interface of PDSQ samples revealed that the liquid composition at the S/L interface is significantlymore » influenced by quenching. By applying the PDSQ technique, it was also found that the partition coefficients of all solute elements do not change appreciably during the solidification of primary γ. All three techniques could reasonably predict the segregation behavior of most solute elements. Nevertheless, the RS approach has a tendency to overestimate the magnitude of segregation for most solute elements when compared to the MZQ and PDSQ techniques. Moreover, the segregation direction of Cr and Mo predicted by the RS approach was found to be opposite from the results obtained by the MZQ and PDSQ techniques. This conflicting segregation behavior of Cr and Mo was discussed intensively. It was shown that the formation of Cr-rich areas near the γ/γ′ eutectic in various Ni-base superalloys, including the CMSX-10 alloy, could be successfully explained by the results of microprobe analysis performed on a sample quenched during the planar directional solidification of γ/γ′ eutectic. - Highlights: • Methodological effect on the quantification of microsegregation was clarified. • The liquid composition at the S/L interface was influenced by quenching. • The segregation direction of Cr varied depending on

  19. Quantitative determination of low-Z elements in single atmospheric particles on boron substrates by automated scanning electron microscopy-energy-dispersive X-ray spectrometry.

    PubMed

    Choël, Marie; Deboudt, Karine; Osán, János; Flament, Pascal; Van Grieken, René

    2005-09-01

    Atmospheric aerosols consist of a complex heterogeneous mixture of particles. Single-particle analysis techniques are known to provide unique information on the size-resolved chemical composition of aerosols. A scanning electron microscope (SEM) combined with a thin-window energy-dispersive X-ray (EDX) detector enables the morphological and elemental analysis of single particles down to 0.1 microm with a detection limit of 1-10 wt %, low-Z elements included. To obtain data statistically representative of the air masses sampled, a computer-controlled procedure can be implemented in order to run hundreds of single-particle analyses (typically 1000-2000) automatically in a relatively short period of time (generally 4-8 h, depending on the setup and on the particle loading). However, automated particle analysis by SEM-EDX raises two practical challenges: the accuracy of the particle recognition and the reliability of the quantitative analysis, especially for micrometer-sized particles with low atomic number contents. Since low-Z analysis is hampered by the use of traditional polycarbonate membranes, an alternate choice of substrate is a prerequisite. In this work, boron is being studied as a promising material for particle microanalysis. As EDX is generally said to probe a volume of approximately 1 microm3, geometry effects arise from the finite size of microparticles. These particle geometry effects must be corrected by means of a robust concentration calculation procedure. Conventional quantitative methods developed for bulk samples generate elemental concentrations considerably in error when applied to microparticles. A new methodology for particle microanalysis, combining the use of boron as the substrate material and a reverse Monte Carlo quantitative program, was tested on standard particles ranging from 0.25 to 10 microm. We demonstrate that the quantitative determination of low-Z elements in microparticles is achievable and that highly accurate results can be

  20. Streamlined system for purifying and quantifying a diverse library of compounds and the effect of compound concentration measurements on the accurate interpretation of biological assay results.

    PubMed

    Popa-Burke, Ioana G; Issakova, Olga; Arroway, James D; Bernasconi, Paul; Chen, Min; Coudurier, Louis; Galasinski, Scott; Jadhav, Ajit P; Janzen, William P; Lagasca, Dennis; Liu, Darren; Lewis, Roderic S; Mohney, Robert P; Sepetov, Nikolai; Sparkman, Darren A; Hodge, C Nicholas

    2004-12-15

    As part of an overall systems approach to generating highly accurate screening data across large numbers of compounds and biological targets, we have developed and implemented streamlined methods for purifying and quantitating compounds at various stages of the screening process, coupled with automated "traditional" storage methods (DMSO, -20 degrees C). Specifically, all of the compounds in our druglike library are purified by LC/MS/UV and are then controlled for identity and concentration in their respective DMSO stock solutions by chemiluminescent nitrogen detection (CLND)/evaporative light scattering detection (ELSD) and MS/UV. In addition, the compound-buffer solutions used in the various biological assays are quantitated by LC/UV/CLND to determine the concentration of compound actually present during screening. Our results show that LC/UV/CLND/ELSD/MS is a widely applicable method that can be used to purify, quantitate, and identify most small organic molecules from compound libraries. The LC/UV/CLND technique is a simple and sensitive method that can be easily and cost-effectively employed to rapidly determine the concentrations of even small amounts of any N-containing compound in aqueous solution. We present data to establish error limits for concentration determination that are well within the overall variability of the screening process. This study demonstrates that there is a significant difference between the predicted amount of soluble compound from stock DMSO solutions following dilution into assay buffer and the actual amount present in assay buffer solutions, even at the low concentrations employed for the assays. We also demonstrate that knowledge of the concentrations of compounds to which the biological target is exposed is critical for accurate potency determinations. Accurate potency values are in turn particularly important for drug discovery, for understanding structure-activity relationships, and for building useful empirical models of

  1. A method for three-dimensional quantitative observation of the microstructure of biological samples

    NASA Astrophysics Data System (ADS)

    Wang, Pengfei; Chen, Dieyan; Ma, Wanyun; Wu, Hongxin; Ji, Liang; Sun, Jialin; Lv, Danyu; Zhang, Lu; Li, Ying; Tian, Ning; Zheng, Jinggao; Zhao, Fengying

    2009-07-01

    Contemporary biology has developed into the era of cell biology and molecular biology, and people try to study the mechanism of all kinds of biological phenomena at the microcosmic level now. Accurate description of the microstructure of biological samples is exigent need from many biomedical experiments. This paper introduces a method for 3-dimensional quantitative observation on the microstructure of vital biological samples based on two photon laser scanning microscopy (TPLSM). TPLSM is a novel kind of fluorescence microscopy, which has excellence in its low optical damage, high resolution, deep penetration depth and suitability for 3-dimensional (3D) imaging. Fluorescent stained samples were observed by TPLSM, and afterward the original shapes of them were obtained through 3D image reconstruction. The spatial distribution of all objects in samples as well as their volumes could be derived by image segmentation and mathematic calculation. Thus the 3-dimensionally and quantitatively depicted microstructure of the samples was finally derived. We applied this method to quantitative analysis of the spatial distribution of chromosomes in meiotic mouse oocytes at metaphase, and wonderful results came out last.

  2. Quantitative Thermochemical Measurements in High-Pressure Gaseous Combustion

    NASA Technical Reports Server (NTRS)

    Kojima, Jun J.; Fischer, David G.

    2012-01-01

    We present our strategic experiment and thermochemical analyses on combustion flow using a subframe burst gating (SBG) Raman spectroscopy. This unconventional laser diagnostic technique has promising ability to enhance accuracy of the quantitative scalar measurements in a point-wise single-shot fashion. In the presentation, we briefly describe an experimental methodology that generates transferable calibration standard for the routine implementation of the diagnostics in hydrocarbon flames. The diagnostic technology was applied to simultaneous measurements of temperature and chemical species in a swirl-stabilized turbulent flame with gaseous methane fuel at elevated pressure (17 atm). Statistical analyses of the space-/time-resolved thermochemical data provide insights into the nature of the mixing process and it impact on the subsequent combustion process in the model combustor.

  3. A no-gold-standard technique for objective assessment of quantitative nuclear-medicine imaging methods

    PubMed Central

    Jha, Abhinav K; Caffo, Brian; Frey, Eric C

    2016-01-01

    The objective optimization and evaluation of nuclear-medicine quantitative imaging methods using patient data is highly desirable but often hindered by the lack of a gold standard. Previously, a regression-without-truth (RWT) approach has been proposed for evaluating quantitative imaging methods in the absence of a gold standard, but this approach implicitly assumes that bounds on the distribution of true values are known. Several quantitative imaging methods in nuclear-medicine imaging measure parameters where these bounds are not known, such as the activity concentration in an organ or the volume of a tumor. We extended upon the RWT approach to develop a no-gold-standard (NGS) technique for objectively evaluating such quantitative nuclear-medicine imaging methods with patient data in the absence of any ground truth. Using the parameters estimated with the NGS technique, a figure of merit, the noise-to-slope ratio (NSR), can be computed, which can rank the methods on the basis of precision. An issue with NGS evaluation techniques is the requirement of a large number of patient studies. To reduce this requirement, the proposed method explored the use of multiple quantitative measurements from the same patient, such as the activity concentration values from different organs in the same patient. The proposed technique was evaluated using rigorous numerical experiments and using data from realistic simulation studies. The numerical experiments demonstrated that the NSR was estimated accurately using the proposed NGS technique when the bounds on the distribution of true values were not precisely known, thus serving as a very reliable metric for ranking the methods on the basis of precision. In the realistic simulation study, the NGS technique was used to rank reconstruction methods for quantitative single-photon emission computed tomography (SPECT) based on their performance on the task of estimating the mean activity concentration within a known volume of interest

  4. A no-gold-standard technique for objective assessment of quantitative nuclear-medicine imaging methods.

    PubMed

    Jha, Abhinav K; Caffo, Brian; Frey, Eric C

    2016-04-07

    The objective optimization and evaluation of nuclear-medicine quantitative imaging methods using patient data is highly desirable but often hindered by the lack of a gold standard. Previously, a regression-without-truth (RWT) approach has been proposed for evaluating quantitative imaging methods in the absence of a gold standard, but this approach implicitly assumes that bounds on the distribution of true values are known. Several quantitative imaging methods in nuclear-medicine imaging measure parameters where these bounds are not known, such as the activity concentration in an organ or the volume of a tumor. We extended upon the RWT approach to develop a no-gold-standard (NGS) technique for objectively evaluating such quantitative nuclear-medicine imaging methods with patient data in the absence of any ground truth. Using the parameters estimated with the NGS technique, a figure of merit, the noise-to-slope ratio (NSR), can be computed, which can rank the methods on the basis of precision. An issue with NGS evaluation techniques is the requirement of a large number of patient studies. To reduce this requirement, the proposed method explored the use of multiple quantitative measurements from the same patient, such as the activity concentration values from different organs in the same patient. The proposed technique was evaluated using rigorous numerical experiments and using data from realistic simulation studies. The numerical experiments demonstrated that the NSR was estimated accurately using the proposed NGS technique when the bounds on the distribution of true values were not precisely known, thus serving as a very reliable metric for ranking the methods on the basis of precision. In the realistic simulation study, the NGS technique was used to rank reconstruction methods for quantitative single-photon emission computed tomography (SPECT) based on their performance on the task of estimating the mean activity concentration within a known volume of interest

  5. Diagnosis of breast cancer biopsies using quantitative phase imaging

    NASA Astrophysics Data System (ADS)

    Majeed, Hassaan; Kandel, Mikhail E.; Han, Kevin; Luo, Zelun; Macias, Virgilia; Tangella, Krishnarao; Balla, Andre; Popescu, Gabriel

    2015-03-01

    The standard practice in the histopathology of breast cancers is to examine a hematoxylin and eosin (H&E) stained tissue biopsy under a microscope. The pathologist looks at certain morphological features, visible under the stain, to diagnose whether a tumor is benign or malignant. This determination is made based on qualitative inspection making it subject to investigator bias. Furthermore, since this method requires a microscopic examination by the pathologist it suffers from low throughput. A quantitative, label-free and high throughput method for detection of these morphological features from images of tissue biopsies is, hence, highly desirable as it would assist the pathologist in making a quicker and more accurate diagnosis of cancers. We present here preliminary results showing the potential of using quantitative phase imaging for breast cancer screening and help with differential diagnosis. We generated optical path length maps of unstained breast tissue biopsies using Spatial Light Interference Microscopy (SLIM). As a first step towards diagnosis based on quantitative phase imaging, we carried out a qualitative evaluation of the imaging resolution and contrast of our label-free phase images. These images were shown to two pathologists who marked the tumors present in tissue as either benign or malignant. This diagnosis was then compared against the diagnosis of the two pathologists on H&E stained tissue images and the number of agreements were counted. In our experiment, the agreement between SLIM and H&E based diagnosis was measured to be 88%. Our preliminary results demonstrate the potential and promise of SLIM for a push in the future towards quantitative, label-free and high throughput diagnosis.

  6. 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...

  7. Nondestructive application of laser-induced fluorescence spectroscopy for quantitative analyses of phenolic compounds in strawberry fruits (Fragaria x ananassa).

    PubMed

    Wulf, J S; Rühmann, S; Rego, I; Puhl, I; Treutter, D; Zude, M

    2008-05-14

    Laser-induced fluorescence spectroscopy (LIFS) was nondestructively applied on strawberries (EX = 337 nm, EM = 400-820 nm) to test the feasibility of quantitatively determining native phenolic compounds in strawberries. Eighteen phenolic compounds were identified in fruit skin by UV and MS spectroscopy and quantitatively determined by use of rp-HPLC for separation and diode-array or chemical reaction detection. Partial least-squares calibration models were built for single phenolic compounds by means of nondestructively recorded fluorescence spectra in the blue-green wavelength range using different data preprocessing methods. The direct orthogonal signal correction resulted in r (2) = 0.99 and rmsep < 8% for p-coumaroyl-glucose, and r (2) = 0.99 and rmsep < 24% for cinnamoyl-glucose. In comparison, the correction of the fluorescence spectral data with simultaneously recorded reflectance spectra did not further improve the calibration models. Results show the potential of LIFS for a rapid and nondestructive assessment of contents of p-coumaroyl-glucose and cinnamoyl-glucose in strawberry fruits.

  8. Untargeted Metabolic Quantitative Trait Loci Analyses Reveal a Relationship between Primary Metabolism and Potato Tuber Quality1[W][OA

    PubMed Central

    Carreno-Quintero, Natalia; Acharjee, Animesh; Maliepaard, Chris; Bachem, Christian W.B.; Mumm, Roland; Bouwmeester, Harro; Visser, Richard G.F.; Keurentjes, Joost J.B.

    2012-01-01

    Recent advances in -omics technologies such as transcriptomics, metabolomics, and proteomics along with genotypic profiling have permitted dissection of the genetics of complex traits represented by molecular phenotypes in nonmodel species. To identify the genetic factors underlying variation in primary metabolism in potato (Solanum tuberosum), we have profiled primary metabolite content in a diploid potato mapping population, derived from crosses between S. tuberosum and wild relatives, using gas chromatography-time of flight-mass spectrometry. In total, 139 polar metabolites were detected, of which we identified metabolite quantitative trait loci for approximately 72% of the detected compounds. In order to obtain an insight into the relationships between metabolic traits and classical phenotypic traits, we also analyzed statistical associations between them. The combined analysis of genetic information through quantitative trait locus coincidence and the application of statistical learning methods provide information on putative indicators associated with the alterations in metabolic networks that affect complex phenotypic traits. PMID:22223596

  9. Quantitative and qualitative 5-aminolevulinic acid–induced protoporphyrin IX fluorescence in skull base meningiomas

    PubMed Central

    Bekelis, Kimon; Valdés, Pablo A.; Erkmen, Kadir; Leblond, Frederic; Kim, Anthony; Wilson, Brian C.; Harris, Brent T.; Paulsen, Keith D.; Roberts, David W.

    2011-01-01

    Object Complete resection of skull base meningiomas provides patients with the best chance for a cure; however, surgery is frequently difficult given the proximity of lesions to vital structures, such as cranial nerves, major vessels, and venous sinuses. Accurate discrimination between tumor and normal tissue is crucial for optimal tumor resection. Qualitative assessment of protoporphyrin IX (PpIX) fluorescence following the exogenous administration of 5-aminolevulinic acid (ALA) has demonstrated utility in malignant glioma resection but limited use in meningiomas. Here the authors demonstrate the use of ALA-induced PpIX fluorescence guidance in resecting a skull base meningioma and elaborate on the advantages and disadvantages provided by both quantitative and qualitative fluorescence methodologies in skull base meningioma resection. Methods A 52-year-old patient with a sphenoid wing WHO Grade I meningioma underwent tumor resection as part of an institutional review board–approved prospective study of fluorescence-guided resection. A surgical microscope modified for fluorescence imaging was used for the qualitative assessment of visible fluorescence, and an intraoperative probe for in situ fluorescence detection was utilized for quantitative measurements of PpIX. The authors assessed the detection capabilities of both the qualitative and quantitative fluorescence approaches. Results The patient harboring a sphenoid wing meningioma with intraorbital extension underwent radical resection of the tumor with both visibly and nonvisibly fluorescent regions. The patient underwent a complete resection without any complications. Some areas of the tumor demonstrated visible fluorescence. The quantitative probe detected neoplastic tissue better than the qualitative modified surgical microscope. The intraoperative probe was particularly useful in areas that did not reveal visible fluorescence, and tissue from these areas was confirmed as tumor following histopathological

  10. Quantitative template for subtyping primary progressive aphasia.

    PubMed

    Mesulam, Marsel; Wieneke, Christina; Rogalski, Emily; Cobia, Derin; Thompson, Cynthia; Weintraub, Sandra

    2009-12-01

    The syndrome of primary progressive aphasia (PPA) is diagnosed when a gradual failure of word usage or comprehension emerges as the principal feature of a neurodegenerative disease. To provide a quantitative algorithm for classifying PPA into agrammatic (PPA-G), semantic (PPA-S), and logopenic (PPA-L) variants, each of which is known to have a different probability of association with Alzheimer disease vs frontotemporal lobar degeneration. Prospective study. University medical center. Sixteen consecutively enrolled patients with PPA who underwent neuropsychological testing and magnetic resonance imaging recruited nationally in the United States as part of a longitudinal study. A 2-dimensional template that reflects performance on tests of syntax (Northwestern Anagram Test) and lexical semantics (Peabody Picture Vocabulary Test-Fourth Edition) classified all 16 patients in concordance with a clinical diagnosis that had been made before the administration of quantitative tests. All 3 PPA subtypes had distinctly asymmetrical atrophy of the left perisylvian language network. Each subtype also had distinctive peak atrophy sites: PPA-G in the inferior frontal gyrus (Broca area), PPA-S in the anterior temporal lobe, and PPA-L in Brodmann area 37. Once an accurate root diagnosis of PPA is made, subtyping can be quantitatively guided using a 2-dimensional template based on orthogonal tasks of grammatical competence and word comprehension. Although the choice of tasks and the precise cutoff levels may need to be adjusted to fit linguistic and educational backgrounds, these 16 patients demonstrate the feasibility of using a simple algorithm for clinicoanatomical classification in PPA. Prospective studies will show whether this subtyping can improve clinical prediction of the underlying neuropathologic condition.

  11. LC–MS/MS Quantitation of Esophagus Disease Blood Serum Glycoproteins by Enrichment with Hydrazide Chemistry and Lectin Affinity Chromatography

    PubMed Central

    2015-01-01

    Changes in glycosylation have been shown to have a profound correlation with development/malignancy in many cancer types. Currently, two major enrichment techniques have been widely applied in glycoproteomics, namely, lectin affinity chromatography (LAC)-based and hydrazide chemistry (HC)-based enrichments. Here we report the LC–MS/MS quantitative analyses of human blood serum glycoproteins and glycopeptides associated with esophageal diseases by LAC- and HC-based enrichment. The separate and complementary qualitative and quantitative data analyses of protein glycosylation were performed using both enrichment techniques. Chemometric and statistical evaluations, PCA plots, or ANOVA test, respectively, were employed to determine and confirm candidate cancer-associated glycoprotein/glycopeptide biomarkers. Out of 139, 59 common glycoproteins (42% overlap) were observed in both enrichment techniques. This overlap is very similar to previously published studies. The quantitation and evaluation of significantly changed glycoproteins/glycopeptides are complementary between LAC and HC enrichments. LC–ESI–MS/MS analyses indicated that 7 glycoproteins enriched by LAC and 11 glycoproteins enriched by HC showed significantly different abundances between disease-free and disease cohorts. Multiple reaction monitoring quantitation resulted in 13 glycopeptides by LAC enrichment and 10 glycosylation sites by HC enrichment to be statistically different among disease cohorts. PMID:25134008

  12. Quantitative Effects of P Elements on Hybrid Dysgenesis in Drosophila Melanogaster

    PubMed Central

    Rasmusson, K. E.; Simmons, M. J.; Raymond, J. D.; McLarnon, C. F.

    1990-01-01

    Genetic analyses involving chromosomes from seven inbred lines derived from a single M' strain were used to study the quantitative relationships between the incidence and severity of P-M hybrid dysgenesis and the number of genomic P elements. In four separate analyses, the mutability of sn(w), a P element-insertion mutation of the X-linked singed locus, was found to be inversely related to the number of autosomal P elements. Since sn(w) mutability is caused by the action of the P transposase, this finding supports the hypothesis that genomic P elements titrate the transposase present within a cell. Other analyses demonstrated that autosomal transmission ratios were distorted by P element action. In these analyses, the amount of distortion against an autosome increased more or less linearly with the number of P elements carried by the autosome. Additional analyses showed that the magnitude of this distortion was reduced when a second P element-containing autosome was present in the genome. This reduction could adequately be explained by transposase titration; there was no evidence that it was due to repressor molecules binding to P elements and inhibiting their movement. The influence of genomic P elements on the incidence of gonadal dysgenesis was also investigated. Although no simple relationship between the number of P elements and the incidence of the trait could be discerned, it was clear that even a small number of elements could increase the incidence markedly. The failure to find a quantitative relationship between P element number and the incidence of gonadal dysgenesis probably reflects the complex etiology of this trait. PMID:2155853

  13. Size-exclusive Nanosensor for Quantitative Analysis of Fullerene C60: A Concept Paper

    EPA Science Inventory

    This paper presents the first development of a mass-sensitive nanosensor for the isolation and quantitative analyses of engineered fullerene (C60) nanoparticles, while excluding mixtures of structurally similar fullerenes. Amino-modified beta cyclodextrin (β-CD-NH

  14. Light scattering application for quantitative estimation of apoptosis

    NASA Astrophysics Data System (ADS)

    Bilyy, Rostyslav O.; Stoika, Rostyslav S.; Getman, Vasyl B.; Bilyi, Olexander I.

    2004-05-01

    Estimation of cell proliferation and apoptosis are in focus of instrumental methods used in modern biomedical sciences. Present study concerns monitoring of functional state of cells, specifically the development of their programmed death or apoptosis. The available methods for such purpose are either very expensive, or require time-consuming operations. Their specificity and sensitivity are frequently not sufficient for making conclusions which could be used in diagnostics or treatment monitoring. We propose a novel method for apoptosis measurement based on quantitative determination of cellular functional state taking into account their physical characteristics. This method uses the patented device -- laser microparticle analyser PRM-6 -- for analyzing light scattering by the microparticles, including cells. The method gives an opportunity for quick, quantitative, simple (without complicated preliminary cell processing) and relatively cheap measurement of apoptosis in cellular population. The elaborated method was used for studying apoptosis expression in murine leukemia cells of L1210 line and human lymphoblastic leukemia cells of K562 line. The results obtained by the proposed method permitted measuring cell number in tested sample, detecting and quantitative characterization of functional state of cells, particularly measuring the ratio of the apoptotic cells in suspension.

  15. The Quantitative Reasoning for College Science (QuaRCS) Assessment: Emerging Themes from 5 Years of Data

    NASA Astrophysics Data System (ADS)

    Follette, Katherine; Dokter, Erin; Buxner, Sanlyn

    2018-01-01

    The Quantitative Reasoning for College Science (QuaRCS) Assessment is a validated assessment instrument that was designed to measure changes in students' quantitative reasoning skills, attitudes toward mathematics, and ability to accurately assess their own quantitative abilities. It has been administered to more than 5,000 students at a variety of institutions at the start and end of a semester of general education college science instruction. I will begin by briefly summarizing our published work surrounding validation of the instrument and identification of underlying attitudinal factors (composite variables identified via factor analysis) that predict 50% of the variation in students' scores on the assessment. I will then discuss more recent unpublished work, including: (1) Development and validation of an abbreviated version of the assessment (The QuaRCS Light), which results in marked improvements in students' ability to maintain a high effort level throughout the assessment and has broad implications for quantitative reasoning assessments in general, and (2) Our efforts to revise the attitudinal portion of the assessment to better assess math anxiety level, another key factor in student performance on numerical assessments.

  16. Renal geology (quantitative renal stone analysis) by 'Fourier transform infrared spectroscopy'.

    PubMed

    Singh, Iqbal

    2008-01-01

    To prospectively determine the precise stone composition (quantitative analysis) by using infrared spectroscopy in patients with urinary stone disease presenting to our clinic. To determine an ideal method for stone analysis suitable for use in a clinical setting. After routine and a detailed metabolic workup of all patients of urolithiasis, stone samples of 50 patients of urolithiasis satisfying the entry criteria were subjected to the Fourier transform infrared spectroscopic analysis after adequate sample homogenization at a single testing center. Calcium oxalate monohydrate and dihydrate stone mixture was most commonly encountered in 35 (71%) followed by calcium phosphate, carbonate apatite, magnesium ammonium hexahydrate and xanthine stones. Fourier transform infrared spectroscopy allows an accurate, reliable quantitative method of stone analysis. It also helps in maintaining a computerized large reference library. Knowledge of precise stone composition may allow the institution of appropriate prophylactic therapy despite the absence of any detectable metabolic abnormalities. This may prevent and or delay stone recurrence.

  17. Profitable capitation requires accurate costing.

    PubMed

    West, D A; Hicks, L L; Balas, E A; West, T D

    1996-01-01

    In the name of costing accuracy, nurses are asked to track inventory use on per treatment basis when more significant costs, such as general overhead and nursing salaries, are usually allocated to patients or treatments on an average cost basis. Accurate treatment costing and financial viability require analysis of all resources actually consumed in treatment delivery, including nursing services and inventory. More precise costing information enables more profitable decisions as is demonstrated by comparing the ratio-of-cost-to-treatment method (aggregate costing) with alternative activity-based costing methods (ABC). Nurses must participate in this costing process to assure that capitation bids are based upon accurate costs rather than simple averages.

  18. Quantitative Metabolome Analysis Based on Chromatographic Peak Reconstruction in Chemical Isotope Labeling Liquid Chromatography Mass Spectrometry.

    PubMed

    Huan, Tao; Li, Liang

    2015-07-21

    Generating precise and accurate quantitative information on metabolomic changes in comparative samples is important for metabolomics research where technical variations in the metabolomic data should be minimized in order to reveal biological changes. We report a method and software program, IsoMS-Quant, for extracting quantitative information from a metabolomic data set generated by chemical isotope labeling (CIL) liquid chromatography mass spectrometry (LC-MS). Unlike previous work of relying on mass spectral peak ratio of the highest intensity peak pair to measure relative quantity difference of a differentially labeled metabolite, this new program reconstructs the chromatographic peaks of the light- and heavy-labeled metabolite pair and then calculates the ratio of their peak areas to represent the relative concentration difference in two comparative samples. Using chromatographic peaks to perform relative quantification is shown to be more precise and accurate. IsoMS-Quant is integrated with IsoMS for picking peak pairs and Zero-fill for retrieving missing peak pairs in the initial peak pairs table generated by IsoMS to form a complete tool for processing CIL LC-MS data. This program can be freely downloaded from the www.MyCompoundID.org web site for noncommercial use.

  19. Methods to achieve accurate projection of regional and global raster databases

    USGS Publications Warehouse

    Usery, E. Lynn; Seong, Jeong Chang; Steinwand, Dan

    2002-01-01

    Modeling regional and global activities of climatic and human-induced change requires accurate geographic data from which we can develop mathematical and statistical tabulations of attributes and properties of the environment. Many of these models depend on data formatted as raster cells or matrices of pixel values. Recently, it has been demonstrated that regional and global raster datasets are subject to significant error from mathematical projection and that these errors are of such magnitude that model results may be jeopardized (Steinwand, et al., 1995; Yang, et al., 1996; Usery and Seong, 2001; Seong and Usery, 2001). There is a need to develop methods of projection that maintain the accuracy of these datasets to support regional and global analyses and modeling

  20. Absolute quantitation of isoforms of post-translationally modified proteins in transgenic organism.

    PubMed

    Li, Yaojun; Shu, Yiwei; Peng, Changchao; Zhu, Lin; Guo, Guangyu; Li, Ning

    2012-08-01

    Post-translational modification isoforms of a protein are known to play versatile biological functions in diverse cellular processes. To measure the molar amount of each post-translational modification isoform (P(isf)) of a target protein present in the total protein extract using mass spectrometry, a quantitative proteomic protocol, absolute quantitation of isoforms of post-translationally modified proteins (AQUIP), was developed. A recombinant ERF110 gene overexpression transgenic Arabidopsis plant was used as the model organism for demonstration of the proof of concept. Both Ser-62-independent (14)N-coded synthetic peptide standards and (15)N-coded ERF110 protein standard isolated from the heavy nitrogen-labeled transgenic plants were employed simultaneously to determine the concentration of all isoforms (T(isf)) of ERF110 in the whole plant cell lysate, whereas a pair of Ser-62-dependent synthetic peptide standards were used to quantitate the Ser-62 phosphosite occupancy (R(aqu)). The P(isf) was finally determined by integrating the two empirically measured variables using the following equation: P(isf) = T(isf) · R(aqu). The absolute amount of Ser-62-phosphorylated isoform of ERF110 determined using AQUIP was substantiated with a stable isotope labeling in Arabidopsis-based relative and accurate quantitative proteomic approach. The biological role of the Ser-62-phosphorylated isoform was demonstrated in transgenic plants.