Digital Imaging

NASA Technical Reports Server (NTRS)

1986-01-01

Digital Imaging is the computer processed numerical representation of physical images. Enhancement of images results in easier interpretation. Quantitative digital image analysis by Perceptive Scientific Instruments, locates objects within an image and measures them to extract quantitative information. Applications are CAT scanners, radiography, microscopy in medicine as well as various industrial and manufacturing uses. The PSICOM 327 performs all digital image analysis functions. It is based on Jet Propulsion Laboratory technology, is accurate and cost efficient.

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.

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...

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.

Photo ion spectrometer

DOEpatents

Gruen, Dieter M.; Young, Charles E.; Pellin, Michael J.

1989-01-01

A method and apparatus for extracting for quantitative analysis ions of selected atomic components of a sample. A lens system is configured to provide a slowly diminishing field region for a volume containing the selected atomic components, enabling accurate energy analysis of ions generated in the slowly diminishing field region. The lens system also enables focusing on a sample of a charged particle beam, such as an ion beam, along a path length perpendicular to the sample and extraction of the charged particles along a path length also perpendicular to the sample. Improvement of signal to noise ratio is achieved by laser excitation of ions to selected autoionization states before carrying out quantitative analysis. Accurate energy analysis of energetic charged particles is assured by using a preselected resistive thick film configuration disposed on an insulator substrate for generating predetermined electric field boundary conditions to achieve for analysis the required electric field potential. The spectrometer also is applicable in the fields of SIMS, ISS and electron spectroscopy.

Photo ion spectrometer

DOEpatents

Gruen, D.M.; Young, C.E.; Pellin, M.J.

1989-08-08

A method and apparatus are described for extracting for quantitative analysis ions of selected atomic components of a sample. A lens system is configured to provide a slowly diminishing field region for a volume containing the selected atomic components, enabling accurate energy analysis of ions generated in the slowly diminishing field region. The lens system also enables focusing on a sample of a charged particle beam, such as an ion beam, along a path length perpendicular to the sample and extraction of the charged particles along a path length also perpendicular to the sample. Improvement of signal to noise ratio is achieved by laser excitation of ions to selected auto-ionization states before carrying out quantitative analysis. Accurate energy analysis of energetic charged particles is assured by using a preselected resistive thick film configuration disposed on an insulator substrate for generating predetermined electric field boundary conditions to achieve for analysis the required electric field potential. The spectrometer also is applicable in the fields of SIMS, ISS and electron spectroscopy. 8 figs.

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.

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.

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.

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

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

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.

Electron Probe Microanalysis | Materials Science | NREL

Science.gov Websites

surveys of the area of interest before performing a more accurate quantitative analysis with WDS. WDS - Four spectrometers with ten diffracting crystals. The use of a single-channel analyzer allows much

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

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.

Improving the geological interpretation of magnetic and gravity satellite anomalies

NASA Technical Reports Server (NTRS)

Hinze, William J.; Braile, Lawrence W.; Vonfrese, Ralph R. B.

1987-01-01

Quantitative analysis of the geologic component of observed satellite magnetic and gravity fields requires accurate isolation of the geologic component of the observations, theoretically sound and viable inversion techniques, and integration of collateral, constraining geologic and geophysical data. A number of significant contributions were made which make quantitative analysis more accurate. These include procedures for: screening and processing orbital data for lithospheric signals based on signal repeatability and wavelength analysis; producing accurate gridded anomaly values at constant elevations from the orbital data by three-dimensional least squares collocation; increasing the stability of equivalent point source inversion and criteria for the selection of the optimum damping parameter; enhancing inversion techniques through an iterative procedure based on the superposition theorem of potential fields; and modeling efficiently regional-scale lithospheric sources of satellite magnetic anomalies. In addition, these techniques were utilized to investigate regional anomaly sources of North and South America and India and to provide constraints to continental reconstruction. Since the inception of this research study, eleven papers were presented with associated published abstracts, three theses were completed, four papers were published or accepted for publication, and an additional manuscript was submitted for publication.

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.

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

Quantitative analysis of binary polymorphs mixtures of fusidic acid by diffuse reflectance FTIR spectroscopy, diffuse reflectance FT-NIR spectroscopy, Raman spectroscopy and multivariate calibration.

PubMed

Guo, Canyong; Luo, Xuefang; Zhou, Xiaohua; Shi, Beijia; Wang, Juanjuan; Zhao, Jinqi; Zhang, Xiaoxia

2017-06-05

Vibrational spectroscopic techniques such as infrared, near-infrared and Raman spectroscopy have become popular in detecting and quantifying polymorphism of pharmaceutics since they are fast and non-destructive. This study assessed the ability of three vibrational spectroscopy combined with multivariate analysis to quantify a low-content undesired polymorph within a binary polymorphic mixture. Partial least squares (PLS) regression and support vector machine (SVM) regression were employed to build quantitative models. Fusidic acid, a steroidal antibiotic, was used as the model compound. It was found that PLS regression performed slightly better than SVM regression in all the three spectroscopic techniques. Root mean square errors of prediction (RMSEP) were ranging from 0.48% to 1.17% for diffuse reflectance FTIR spectroscopy and 1.60-1.93% for diffuse reflectance FT-NIR spectroscopy and 1.62-2.31% for Raman spectroscopy. The results indicate that diffuse reflectance FTIR spectroscopy offers significant advantages in providing accurate measurement of polymorphic content in the fusidic acid binary mixtures, while Raman spectroscopy is the least accurate technique for quantitative analysis of polymorphs. Copyright © 2017 Elsevier B.V. All rights reserved.

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.

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

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

CPTAC Accelerates Precision Proteomics Biomedical Research | Office of Cancer Clinical Proteomics Research

Cancer.gov

The accurate quantitation of proteins or peptides using Mass Spectrometry (MS) is gaining prominence in the biomedical research community as an alternative method for analyte measurement. The Clinical Proteomic Tumor Analysis Consortium (CPTAC) investigators have been at the forefront in the promotion of reproducible MS techniques, through the development and application of standardized proteomic methods for protein quantitation on biologically relevant samples.

Factors That Contribute to Assay Variation in Quantitative Analysis of Sex Steroid Hormones Using Liquid and Gas Chromatography-Mass Spectrometry

ERIC Educational Resources Information Center

Xu, Xia; Veenstra, Timothy D.

2012-01-01

The list of physiological events in which sex steroids play a role continues to increase. To decipher the roles that sex steroids play in any condition requires high quality cohorts of samples and assays that provide highly accurate quantitative measures. Liquid and gas chromatography coupled with mass spectrometry (LC-MS and GC-MS) have…

Determination of T-2 and HT-2 toxins from maize by direct analysis in real time mass spectrometry

USDA-ARS?s Scientific Manuscript database

Direct analysis in real time (DART) ionization coupled to mass spectrometry (MS) was used for the rapid quantitative analysis of T-2 toxin, and the related HT-2 toxin, extracted from corn. Sample preparation procedures and instrument parameters were optimized to obtain sensitive and accurate determi...

Precise Estimation of Allele Frequencies of Single-Nucleotide Polymorphisms by a Quantitative SSCP Analysis of Pooled DNA

PubMed Central

Sasaki, Tomonari; Tahira, Tomoko; Suzuki, Akari; Higasa, Koichiro; Kukita, Yoji; Baba, Shingo; Hayashi, Kenshi

2001-01-01

We show that single-nucleotide polymorphisms (SNPs) of moderate to high heterozygosity (minor allele frequencies >10%) can be efficiently detected, and their allele frequencies accurately estimated, by pooling the DNA samples and applying a capillary-based SSCP analysis. In this method, alleles are separated into peaks, and their frequencies can be reliably and accurately quantified from their peak heights (SD <1.8%). We found that as many as 40% of publicly available SNPs that were analyzed by this method have widely differing allele frequency distributions among groups of different ethnicity (parents of Centre d'Etude Polymorphisme Humaine families vs. Japanese individuals). These results demonstrate the effectiveness of the present pooling method in the reevaluation of candidate SNPs that have been collected by examination of limited numbers of individuals. The method should also serve as a robust quantitative technique for studies in which a precise estimate of SNP allele frequencies is essential—for example, in linkage disequilibrium analysis. PMID:11083945

Quantitative capillary electrophoresis and its application in analysis of alkaloids in tea, coffee, coca cola, and theophylline tablets.

PubMed

Li, Mengjia; Zhou, Junyi; Gu, Xue; Wang, Yan; Huang, Xiaojing; Yan, Chao

2009-01-01

A quantitative CE (qCE) system with high precision has been developed, in which a 4-port nano-valve was isolated from the electric field and served as sample injector. The accurate amount of sample was introduced into the CE system with high reproducibility. Based on this system, consecutive injections and separations were performed without voltage interruption. Reproducibilities in terms of RSD lower than 0.8% for retention time and 1.7% for peak area were achieved. The effectiveness of the system was demonstrated by the quantitative analysis of caffeine, theobromine, and theophylline in real samples, such as tea leaf, roasted coffee, coca cola, and theophylline tablets.

Finding the bottom and using it

PubMed Central

Sandoval, Ruben M.; Wang, Exing; Molitoris, Bruce A.

2014-01-01

Maximizing 2-photon parameters used in acquiring images for quantitative intravital microscopy, especially when high sensitivity is required, remains an open area of investigation. Here we present data on correctly setting the black level of the photomultiplier tube amplifier by adjusting the offset to allow for accurate quantitation of low intensity processes. When the black level is set too high some low intensity pixel values become zero and a nonlinear degradation in sensitivity occurs rendering otherwise quantifiable low intensity values virtually undetectable. Initial studies using a series of increasing offsets for a sequence of concentrations of fluorescent albumin in vitro revealed a loss of sensitivity for higher offsets at lower albumin concentrations. A similar decrease in sensitivity, and therefore the ability to correctly determine the glomerular permeability coefficient of albumin, occurred in vivo at higher offset. Finding the offset that yields accurate and linear data are essential for quantitative analysis when high sensitivity is required. PMID:25313346

New microfluidic-based sampling procedure for overcoming the hematocrit problem associated with dried blood spot analysis.

PubMed

Leuthold, Luc Alexis; Heudi, Olivier; Déglon, Julien; Raccuglia, Marc; Augsburger, Marc; Picard, Franck; Kretz, Olivier; Thomas, Aurélien

2015-02-17

Hematocrit (Hct) is one of the most critical issues associated with the bioanalytical methods used for dried blood spot (DBS) sample analysis. Because Hct determines the viscosity of blood, it may affect the spreading of blood onto the filter paper. Hence, accurate quantitative data can only be obtained if the size of the paper filter extracted contains a fixed blood volume. We describe for the first time a microfluidic-based sampling procedure to enable accurate blood volume collection on commercially available DBS cards. The system allows the collection of a controlled volume of blood (e.g., 5 or 10 μL) within several seconds. Reproducibility of the sampling volume was examined in vivo on capillary blood by quantifying caffeine and paraxanthine on 5 different extracted DBS spots at two different time points and in vitro with a test compound, Mavoglurant, on 10 different spots at two Hct levels. Entire spots were extracted. In addition, the accuracy and precision (n = 3) data for the Mavoglurant quantitation in blood with Hct levels between 26% and 62% were evaluated. The interspot precision data were below 9.0%, which was equivalent to that of a manually spotted volume with a pipet. No Hct effect was observed in the quantitative results obtained for Hct levels from 26% to 62%. These data indicate that our microfluidic-based sampling procedure is accurate and precise and that the analysis of Mavoglurant is not affected by the Hct values. This provides a simple procedure for DBS sampling with a fixed volume of capillary blood, which could eliminate the recurrent Hct issue linked to DBS sample analysis.

Recent advances on multidimensional liquid chromatography-mass spectrometry for proteomics: from qualitative to quantitative analysis--a review.

PubMed

Wu, Qi; Yuan, Huiming; Zhang, Lihua; Zhang, Yukui

2012-06-20

With the acceleration of proteome research, increasing attention has been paid to multidimensional liquid chromatography-mass spectrometry (MDLC-MS) due to its high peak capacity and separation efficiency. Recently, many efforts have been put to improve MDLC-based strategies including "top-down" and "bottom-up" to enable highly sensitive qualitative and quantitative analysis of proteins, as well as accelerate the whole analytical procedure. Integrated platforms with combination of sample pretreatment, multidimensional separations and identification were also developed to achieve high throughput and sensitive detection of proteomes, facilitating highly accurate and reproducible quantification. This review summarized the recent advances of such techniques and their applications in qualitative and quantitative analysis of proteomes. Copyright © 2012 Elsevier B.V. All rights reserved.

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-positives/negatives are known and span a wide concentration range. It was observed that the EN method correctly reflects the null distribution in a proteomic system and accurately measures false altered proteins discovery rate (FADR). In summary, the EN method provides a straightforward, practical, and accurate alternative to statistics-based approaches for the development and evaluation of proteomic experiments and can be universally adapted to various types of quantitative techniques.

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.

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.

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

A rapid quantitative analysis of bile acids, lysophosphatidylcholines and polyunsaturated fatty acids in biofluids based on ultraperformance liquid chromatography coupled with triple quadrupole tandem massspectrometry.

PubMed

Peng, Zhangxiao; Zhang, Qian; Mao, Ziming; Wang, Jie; Liu, Chunying; Lin, Xuejing; Li, Xin; Ji, Weidan; Fan, Jianhui; Wang, Maorong; Su, Changqing

2017-11-15

Much evidence suggested that quantitative analysis of bile acids (BAs), lysophosphatidylcholines (LPCs), and polyunsaturated fatty acids (PUFAs) in biofluids may be very useful for diagnosis and prevention of hepatobiliary disease with a non-invasive manner. However, simultaneously fast analysis of these metabolites has been challenging for their huge differences of physicochemical properties and concentration levels in biofluids. In this study, we present a liquid chromatography-mass spectrometry method with a high throughput analytical cycle (10min) to fast and accurately quantify fifteen potential biomarkers (eight BAs, four LPCs and three PUFAs) of hepatobiliary disease. The accuracy for the fifteen analytes in plasma and urine matrices was 80.45%-118.99% and 84.55%-112.66%, respectively. The intra- and inter- precisions for the fifteen analytes in plasma and urine matrices were all less than 20% and the lower limit of quantification (LLOQ) of analytes is up to 0.0283-8.2172nmol/L. Therefore, this method is fast, sensitive and accurate for the quantitative analysis of BAs, LPCs and PUFAs in biofluids. Moreover, the stability and concentration differences of the analytes in plasma and serum were evaluated, and the results demonstrated that LPCs is stable, but PUFAs is very unstable in freeze and thaw cycles, and the concentrations of the analytes in serum were slightly higher than those in plasma. We suggested plasma may be a kind of better bio-sample than serum using for quantitative analysis of metabolites in blood, due to the characteristics of plasma are more close to blood than those of serum. Copyright © 2017 Elsevier B.V. All rights reserved.

Remote In-Situ Quantitative Mineralogical Analysis Using XRD/XRF

NASA Technical Reports Server (NTRS)

Blake, D. F.; Bish, D.; Vaniman, D.; Chipera, S.; Sarrazin, P.; Collins, S. A.; Elliott, S. T.

2001-01-01

X-Ray Diffraction (XRD) is the most direct and accurate method for determining mineralogy. The CHEMIN XRD/XRF instrument has shown promising results on a variety of mineral and rock samples. Additional information is contained in the original extended abstract.

Photogrammetry of the Human Brain: A Novel Method for Three-Dimensional Quantitative Exploration of the Structural Connectivity in Neurosurgery and Neurosciences.

PubMed

De Benedictis, Alessandro; Nocerino, Erica; Menna, Fabio; Remondino, Fabio; Barbareschi, Mattia; Rozzanigo, Umberto; Corsini, Francesco; Olivetti, Emanuele; Marras, Carlo Efisio; Chioffi, Franco; Avesani, Paolo; Sarubbo, Silvio

2018-04-13

Anatomic awareness of the structural connectivity of the brain is mandatory for neurosurgeons, to select the most effective approaches for brain resections. Although standard microdissection is a validated technique to investigate the different white matter (WM) pathways and to verify the results of tractography, the possibility of interactive exploration of the specimens and reliable acquisition of quantitative information has not been described. Photogrammetry is a well-established technique allowing an accurate metrology on highly defined three-dimensional (3D) models. The aim of this work is to propose the application of the photogrammetric technique for supporting the 3D exploration and the quantitative analysis on the cerebral WM connectivity. The main perisylvian pathways, including the superior longitudinal fascicle and the arcuate fascicle were exposed using the Klingler technique. The photogrammetric acquisition followed each dissection step. The point clouds were registered to a reference magnetic resonance image of the specimen. All the acquisitions were coregistered into an open-source model. We analyzed 5 steps, including the cortical surface, the short intergyral fibers, the indirect posterior and anterior superior longitudinal fascicle, and the arcuate fascicle. The coregistration between the magnetic resonance imaging mesh and the point clouds models was highly accurate. Multiple measures of distances between specific cortical landmarks and WM tracts were collected on the photogrammetric model. Photogrammetry allows an accurate 3D reproduction of WM anatomy and the acquisition of unlimited quantitative data directly on the real specimen during the postdissection analysis. These results open many new promising neuroscientific and educational perspectives and also optimize the quality of neurosurgical treatments. Copyright © 2018 Elsevier Inc. All rights reserved.

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.

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.

A nonlinear generalization of the Savitzky-Golay filter and the quantitative analysis of saccades

PubMed Central

Dai, Weiwei; Selesnick, Ivan; Rizzo, John-Ross; Rucker, Janet; Hudson, Todd

2017-01-01

The Savitzky-Golay (SG) filter is widely used to smooth and differentiate time series, especially biomedical data. However, time series that exhibit abrupt departures from their typical trends, such as sharp waves or steps, which are of physiological interest, tend to be oversmoothed by the SG filter. Hence, the SG filter tends to systematically underestimate physiological parameters in certain situations. This article proposes a generalization of the SG filter to more accurately track abrupt deviations in time series, leading to more accurate parameter estimates (e.g., peak velocity of saccadic eye movements). The proposed filtering methodology models a time series as the sum of two component time series: a low-frequency time series for which the conventional SG filter is well suited, and a second time series that exhibits instantaneous deviations (e.g., sharp waves, steps, or more generally, discontinuities in a higher order derivative). The generalized SG filter is then applied to the quantitative analysis of saccadic eye movements. It is demonstrated that (a) the conventional SG filter underestimates the peak velocity of saccades, especially those of small amplitude, and (b) the generalized SG filter estimates peak saccadic velocity more accurately than the conventional filter. PMID:28813566

A nonlinear generalization of the Savitzky-Golay filter and the quantitative analysis of saccades.

PubMed

Dai, Weiwei; Selesnick, Ivan; Rizzo, John-Ross; Rucker, Janet; Hudson, Todd

2017-08-01

The Savitzky-Golay (SG) filter is widely used to smooth and differentiate time series, especially biomedical data. However, time series that exhibit abrupt departures from their typical trends, such as sharp waves or steps, which are of physiological interest, tend to be oversmoothed by the SG filter. Hence, the SG filter tends to systematically underestimate physiological parameters in certain situations. This article proposes a generalization of the SG filter to more accurately track abrupt deviations in time series, leading to more accurate parameter estimates (e.g., peak velocity of saccadic eye movements). The proposed filtering methodology models a time series as the sum of two component time series: a low-frequency time series for which the conventional SG filter is well suited, and a second time series that exhibits instantaneous deviations (e.g., sharp waves, steps, or more generally, discontinuities in a higher order derivative). The generalized SG filter is then applied to the quantitative analysis of saccadic eye movements. It is demonstrated that (a) the conventional SG filter underestimates the peak velocity of saccades, especially those of small amplitude, and (b) the generalized SG filter estimates peak saccadic velocity more accurately than the conventional filter.

1H NMR quantification in very dilute toxin solutions: application to anatoxin-a analysis.

PubMed

Dagnino, Denise; Schripsema, Jan

2005-08-01

A complete procedure is described for the extraction, detection and quantification of anatoxin-a in biological samples. Anatoxin-a is extracted from biomass by a routine acid base extraction. The extract is analysed by GC-MS, without the need of derivatization, with a detection limit of 0.5 ng. A method was developed for the accurate quantification of anatoxin-a in the standard solution to be used for the calibration of the GC analysis. 1H NMR allowed the accurate quantification of microgram quantities of anatoxin-a. The accurate quantification of compounds in standard solutions is rarely discussed, but for compounds like anatoxin-a (toxins with prices in the range of a million dollar a gram), of which generally only milligram quantities or less are available, this factor in the quantitative analysis is certainly not trivial. The method that was developed can easily be adapted for the accurate quantification of other toxins in very dilute solutions.

DEVELOPMENT OF AN IN SITU THERMAL EXTRACTION DETECTION SYSTEM (TEDS) FOR RAPID, ACCURATE, QUANTITATIVE ANALYSIS OF ENVIRONMENTAL POLLUTANTS IN THE SUBSURFACE - PHASE I

EPA Science Inventory

Ion Signature Technology, Inc. (IST) will develop and market a collection and analysis system that will retrieve soil-bound pollutants as well as soluble and non-soluble contaminants from groundwater as the probe is pushed by cone penetrometry of Geoprobe into the subsurface. ...

A Data-Processing System for Quantitative Analysis in Speech Production. CLCS Occasional Paper No. 17.

ERIC Educational Resources Information Center

Chasaide, Ailbhe Ni; Davis, Eugene

The data processing system used at Trinity College's Centre for Language and Communication Studies (Ireland) enables computer-automated collection and analysis of phonetic data and has many advantages for research on speech production. The system allows accurate handling of large quantities of data, eliminates many of the limitations of manual…

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.

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

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.

Quantitative analysis of drug distribution by ambient mass spectrometry imaging method with signal extinction normalization strategy and inkjet-printing technology.

PubMed

Luo, Zhigang; He, Jingjing; He, Jiuming; Huang, Lan; Song, Xiaowei; Li, Xin; Abliz, Zeper

2018-03-01

Quantitative mass spectrometry imaging (MSI) is a robust approach that provides both quantitative and spatial information for drug candidates' research. However, because of complicated signal suppression and interference, acquiring accurate quantitative information from MSI data remains a challenge, especially for whole-body tissue sample. Ambient MSI techniques using spray-based ionization appear to be ideal for pharmaceutical quantitative MSI analysis. However, it is more challenging, as it involves almost no sample preparation and is more susceptible to ion suppression/enhancement. Herein, based on our developed air flow-assisted desorption electrospray ionization (AFADESI)-MSI technology, an ambient quantitative MSI method was introduced by integrating inkjet-printing technology with normalization of the signal extinction coefficient (SEC) using the target compound itself. The method utilized a single calibration curve to quantify multiple tissue types. Basic blue 7 and an antitumor drug candidate (S-(+)-deoxytylophorinidine, CAT) were chosen to initially validate the feasibility and reliability of the quantitative MSI method. Rat tissue sections (heart, kidney, and brain) administered with CAT was then analyzed. The quantitative MSI analysis results were cross-validated by LC-MS/MS analysis data of the same tissues. The consistency suggests that the approach is able to fast obtain the quantitative MSI data without introducing interference into the in-situ environment of the tissue sample, and is potential to provide a high-throughput, economical and reliable approach for drug discovery and development. Copyright © 2017 Elsevier B.V. All rights reserved.

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.

Quantitative spectroscopy for the analysis of GOME data

NASA Technical Reports Server (NTRS)

Chance, K.

1997-01-01

Accurate analysis of the global ozone monitoring experiment (GOME) data to obtain atmospheric constituents requires reliable, traceable spectroscopic parameters for atmospheric absorption and scattering. Results are summarized for research that includes: the re-determination of Rayleigh scattering cross sections and phase functions for the 200 nm to 1000 nm range; the analysis of solar spectra to obtain a high-resolution reference spectrum with excellent absolute vacuum wavelength calibration; Ring effect cross sections and phase functions determined directly from accurate molecular parameters of N2 and O2; O2 A band line intensities and pressure broadening coefficients; and the analysis of absolute accuracies for ultraviolet and visible absorption cross sections of O3 and other trace species measurable by GOME.

Elucidating dynamic metabolic physiology through network integration of quantitative time-course metabolomics

DOE PAGES

Bordbar, Aarash; Yurkovich, James T.; Paglia, Giuseppe; ...

2017-04-07

In this study, the increasing availability of metabolomics data necessitates novel methods for deeper data analysis and interpretation. We present a flux balance analysis method that allows for the computation of dynamic intracellular metabolic changes at the cellular scale through integration of time-course absolute quantitative metabolomics. This approach, termed “unsteady-state flux balance analysis” (uFBA), is applied to four cellular systems: three dynamic and one steady-state as a negative control. uFBA and FBA predictions are contrasted, and uFBA is found to be more accurate in predicting dynamic metabolic flux states for red blood cells, platelets, and Saccharomyces cerevisiae. Notably, only uFBAmore » predicts that stored red blood cells metabolize TCA intermediates to regenerate important cofactors, such as ATP, NADH, and NADPH. These pathway usage predictions were subsequently validated through 13C isotopic labeling and metabolic flux analysis in stored red blood cells. Utilizing time-course metabolomics data, uFBA provides an accurate method to predict metabolic physiology at the cellular scale for dynamic systems.« less

Elucidating dynamic metabolic physiology through network integration of quantitative time-course metabolomics

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

Bordbar, Aarash; Yurkovich, James T.; Paglia, Giuseppe

In this study, the increasing availability of metabolomics data necessitates novel methods for deeper data analysis and interpretation. We present a flux balance analysis method that allows for the computation of dynamic intracellular metabolic changes at the cellular scale through integration of time-course absolute quantitative metabolomics. This approach, termed “unsteady-state flux balance analysis” (uFBA), is applied to four cellular systems: three dynamic and one steady-state as a negative control. uFBA and FBA predictions are contrasted, and uFBA is found to be more accurate in predicting dynamic metabolic flux states for red blood cells, platelets, and Saccharomyces cerevisiae. Notably, only uFBAmore » predicts that stored red blood cells metabolize TCA intermediates to regenerate important cofactors, such as ATP, NADH, and NADPH. These pathway usage predictions were subsequently validated through 13C isotopic labeling and metabolic flux analysis in stored red blood cells. Utilizing time-course metabolomics data, uFBA provides an accurate method to predict metabolic physiology at the cellular scale for dynamic systems.« less

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.

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.

Comparative Application of PLS and PCR Methods to Simultaneous Quantitative Estimation and Simultaneous Dissolution Test of Zidovudine - Lamivudine Tablets.

PubMed

Üstündağ, Özgür; Dinç, Erdal; Özdemir, Nurten; Tilkan, M Günseli

2015-01-01

In the development strategies of new drug products and generic drug products, the simultaneous in-vitro dissolution behavior of oral dosage formulations is the most important indication for the quantitative estimation of efficiency and biopharmaceutical characteristics of drug substances. This is to force the related field's scientists to improve very powerful analytical methods to get more reliable, precise and accurate results in the quantitative analysis and dissolution testing of drug formulations. In this context, two new chemometric tools, partial least squares (PLS) and principal component regression (PCR) were improved for the simultaneous quantitative estimation and dissolution testing of zidovudine (ZID) and lamivudine (LAM) in a tablet dosage form. The results obtained in this study strongly encourage us to use them for the quality control, the routine analysis and the dissolution test of the marketing tablets containing ZID and LAM drugs.

[Variable selection methods combined with local linear embedding theory used for optimization of near infrared spectral quantitative models].

PubMed

Hao, Yong; Sun, Xu-Dong; Yang, Qiang

2012-12-01

Variables selection strategy combined with local linear embedding (LLE) was introduced for the analysis of complex samples by using near infrared spectroscopy (NIRS). Three methods include Monte Carlo uninformation variable elimination (MCUVE), successive projections algorithm (SPA) and MCUVE connected with SPA were used for eliminating redundancy spectral variables. Partial least squares regression (PLSR) and LLE-PLSR were used for modeling complex samples. The results shown that MCUVE can both extract effective informative variables and improve the precision of models. Compared with PLSR models, LLE-PLSR models can achieve more accurate analysis results. MCUVE combined with LLE-PLSR is an effective modeling method for NIRS quantitative analysis.

Infrared Spectroscopy as a Versatile Analytical Tool for the Quantitative Determination of Antioxidants in Agricultural Products, Foods and Plants

PubMed Central

Cozzolino, Daniel

2015-01-01

Spectroscopic methods provide with very useful qualitative and quantitative information about the biochemistry and chemistry of antioxidants. Near infrared (NIR) and mid infrared (MIR) spectroscopy are considered as powerful, fast, accurate and non-destructive analytical tools that can be considered as a replacement of traditional chemical analysis. In recent years, several reports can be found in the literature demonstrating the usefulness of these methods in the analysis of antioxidants in different organic matrices. This article reviews recent applications of infrared (NIR and MIR) spectroscopy in the analysis of antioxidant compounds in a wide range of samples such as agricultural products, foods and plants. PMID:26783838

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.

Shot noise-limited Cramér-Rao bound and algorithmic sensitivity for wavelength shifting interferometry

NASA Astrophysics Data System (ADS)

Chen, Shichao; Zhu, Yizheng

2017-02-01

Sensitivity is a critical index to measure the temporal fluctuation of the retrieved optical pathlength in quantitative phase imaging system. However, an accurate and comprehensive analysis for sensitivity evaluation is still lacking in current literature. In particular, previous theoretical studies for fundamental sensitivity based on Gaussian noise models are not applicable to modern cameras and detectors, which are dominated by shot noise. In this paper, we derive two shot noiselimited theoretical sensitivities, Cramér-Rao bound and algorithmic sensitivity for wavelength shifting interferometry, which is a major category of on-axis interferometry techniques in quantitative phase imaging. Based on the derivations, we show that the shot noise-limited model permits accurate estimation of theoretical sensitivities directly from measured data. These results can provide important insights into fundamental constraints in system performance and can be used to guide system design and optimization. The same concepts can be generalized to other quantitative phase imaging techniques as well.

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%.

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.

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

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...

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.

The Application of SILAC Mouse in Human Body Fluid Proteomics Analysis Reveals Protein Patterns Associated with IgA Nephropathy.

PubMed

Zhao, Shilin; Li, Rongxia; Cai, Xiaofan; Chen, Wanjia; Li, Qingrun; Xing, Tao; Zhu, Wenjie; Chen, Y Eugene; Zeng, Rong; Deng, Yueyi

2013-01-01

Body fluid proteome is the most informative proteome from a medical viewpoint. But the lack of accurate quantitation method for complicated body fluid limited its application in disease research and biomarker discovery. To address this problem, we introduced a novel strategy, in which SILAC-labeled mouse serum was used as internal standard for human serum and urine proteome analysis. The SILAC-labeled mouse serum was mixed with human serum and urine, and multidimensional separation coupled with tandem mass spectrometry (IEF-LC-MS/MS) analysis was performed. The shared peptides between two species were quantified by their SILAC pairs, and the human-only peptides were quantified by mouse peptides with coelution. The comparison for the results from two replicate experiments indicated the high repeatability of our strategy. Then the urine from Immunoglobulin A nephropathy patients treated and untreated was compared by this quantitation strategy. Fifty-three peptides were found to be significantly changed between two groups, including both known diagnostic markers for IgAN and novel candidates, such as Complement C3, Albumin, VDBP, ApoA,1 and IGFBP7. In conclusion, we have developed a practical and accurate quantitation strategy for comparison of complicated human body fluid proteome. The results from such strategy could provide potential disease-related biomarkers for evaluation of treatment.

Direct Allocation Costing: Informed Management Decisions in a Changing Environment.

ERIC Educational Resources Information Center

Mancini, Cesidio G.; Goeres, Ernest R.

1995-01-01

It is argued that colleges and universities can use direct allocation costing to provide quantitative information needed for decision making. This method of analysis requires institutions to modify traditional ideas of costing, looking to the private sector for examples of accurate costing techniques. (MSE)

Quantitative analysis of Al-Si alloy using calibration free laser induced breakdown spectroscopy (CF-LIBS)

NASA Astrophysics Data System (ADS)

Shakeel, Hira; Haq, S. U.; Aisha, Ghulam; Nadeem, Ali

2017-06-01

The quantitative analysis of the standard aluminum-silicon alloy has been performed using calibration free laser induced breakdown spectroscopy (CF-LIBS). The plasma was produced using the fundamental harmonic (1064 nm) of the Nd: YAG laser and the emission spectra were recorded at 3.5 μs detector gate delay. The qualitative analysis of the emission spectra confirms the presence of Mg, Al, Si, Ti, Mn, Fe, Ni, Cu, Zn, Sn, and Pb in the alloy. The background subtracted and self-absorption corrected emission spectra were used for the estimation of plasma temperature as 10 100 ± 300 K. The plasma temperature and self-absorption corrected emission lines of each element have been used for the determination of concentration of each species present in the alloy. The use of corrected emission intensities and accurate evaluation of plasma temperature yield reliable quantitative analysis up to a maximum 2.2% deviation from reference sample concentration.

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.

Selection of reliable reference genes for quantitative real-time PCR gene expression analysis in Jute (Corchorus capsularis) under stress treatments

PubMed Central

Niu, Xiaoping; Qi, Jianmin; Zhang, Gaoyang; Xu, Jiantang; Tao, Aifen; Fang, Pingping; Su, Jianguang

2015-01-01

To accurately measure gene expression using quantitative reverse transcription PCR (qRT-PCR), reliable reference gene(s) are required for data normalization. Corchorus capsularis, an annual herbaceous fiber crop with predominant biodegradability and renewability, has not been investigated for the stability of reference genes with qRT-PCR. In this study, 11 candidate reference genes were selected and their expression levels were assessed using qRT-PCR. To account for the influence of experimental approach and tissue type, 22 different jute samples were selected from abiotic and biotic stress conditions as well as three different tissue types. The stability of the candidate reference genes was evaluated using geNorm, NormFinder, and BestKeeper programs, and the comprehensive rankings of gene stability were generated by aggregate analysis. For the biotic stress and NaCl stress subsets, ACT7 and RAN were suitable as stable reference genes for gene expression normalization. For the PEG stress subset, UBC, and DnaJ were sufficient for accurate normalization. For the tissues subset, four reference genes TUBβ, UBI, EF1α, and RAN were sufficient for accurate normalization. The selected genes were further validated by comparing expression profiles of WRKY15 in various samples, and two stable reference genes were recommended for accurate normalization of qRT-PCR data. Our results provide researchers with appropriate reference genes for qRT-PCR in C. capsularis, and will facilitate gene expression study under these conditions. PMID:26528312

Comparative analysis of monoclonal antibody N-glycosylation using stable isotope labelling and UPLC-fluorescence-MS.

PubMed

Millán Martín, Silvia; Delporte, Cédric; Farrell, Amy; Navas Iglesias, Natalia; McLoughlin, Niaobh; Bones, Jonathan

2015-03-07

A twoplex method using (12)C6 and (13)C6 stable isotope analogues (Δmass = 6 Da) of 2-aminobenzoic acid (2-AA) is described for quantitative analysis of N-glycans present on monoclonal antibodies and other glycoproteins using ultra performance liquid chromatography with sequential fluorescence and accurate mass tandem quadrupole time of flight (QToF) mass spectrometric detection.

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

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

Simultaneous quantitation of oxidized and reduced glutathione via LC-MS/MS: An insight into the redox state of hematopoietic stem cells.

PubMed

Carroll, Dustin; Howard, Diana; Zhu, Haining; Paumi, Christian M; Vore, Mary; Bondada, Subbarao; Liang, Ying; Wang, Chi; St Clair, Daret K

2016-08-01

Cellular redox balance plays a significant role in the regulation of hematopoietic stem-progenitor cell (HSC/MPP) self-renewal and differentiation. Unregulated changes in cellular redox homeostasis are associated with the onset of most hematological disorders. However, accurate measurement of the redox state in stem cells is difficult because of the scarcity of HSC/MPPs. Glutathione (GSH) constitutes the most abundant pool of cellular antioxidants. Thus, GSH metabolism may play a critical role in hematological disease onset and progression. A major limitation to studying GSH metabolism in HSC/MPPs has been the inability to measure quantitatively GSH concentrations in small numbers of HSC/MPPs. Current methods used to measure GSH levels not only rely on large numbers of cells, but also rely on the chemical/structural modification or enzymatic recycling of GSH and therefore are likely to measure only total glutathione content accurately. Here, we describe the validation of a sensitive method used for the direct and simultaneous quantitation of both oxidized and reduced GSH via liquid chromatography followed by tandem mass spectrometry (LC-MS/MS) in HSC/MPPs isolated from bone marrow. The lower limit of quantitation (LLOQ) was determined to be 5.0ng/mL for GSH and 1.0ng/mL for GSSG with lower limits of detection at 0.5ng/mL for both glutathione species. Standard addition analysis utilizing mouse bone marrow shows that this method is both sensitive and accurate with reproducible analyte recovery. This method combines a simple extraction with a platform for the high-throughput analysis, allows for efficient determination of GSH/GSSG concentrations within the HSC/MPP populations in mouse, chemotherapeutic treatment conditions within cell culture, and human normal/leukemia patient samples. The data implicate the importance of the modulation of GSH/GSSG redox couple in stem cells related diseases. Copyright © 2016 Elsevier Inc. All rights reserved.

[Rapid discriminating hogwash oil and edible vegetable oil using near infrared optical fiber spectrometer technique].

PubMed

Zhang, Bing-Fang; Yuan, Li-Bo; Kong, Qing-Ming; Shen, Wei-Zheng; Zhang, Bing-Xiu; Liu, Cheng-Hai

2014-10-01

In the present study, a new method using near infrared spectroscopy combined with optical fiber sensing technology was applied to the analysis of hogwash oil in blended oil. The 50 samples were a blend of frying oil and "nine three" soybean oil according to a certain volume ratio. The near infrared transmission spectroscopies were collected and the quantitative analysis model of frying oil was established by partial least squares (PLS) and BP artificial neural network The coefficients of determina- tion of calibration sets were 0.908 and 0.934 respectively. The coefficients of determination of validation sets were 0.961 and 0.952, the root mean square error of calibrations (RMSEC) was 0.184 and 0.136, and the root mean square error of predictions (RMSEP) was all 0.111 6. They conform to the model application requirement. At the same time, frying oil and qualified edible oil were identified with the principal component analysis (PCA), and the accurate rate was 100%. The experiment proved that near infrared spectral technology not only can quickly and accurately identify hogwash oil, but also can quantitatively detect hog- wash oil. This method has a wide application prospect in the detection of oil.

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.

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.

Accuracy Enhancement of Raman Spectroscopy Using Complementary Laser-Induced Breakdown Spectroscopy (LIBS) with Geologically Mixed Samples.

PubMed

Choi, Soojin; Kim, Dongyoung; Yang, Junho; Yoh, Jack J

2017-04-01

Quantitative Raman analysis was carried out with geologically mixed samples that have various matrices. In order to compensate the matrix effect in Raman shift, laser-induced breakdown spectroscopy (LIBS) analysis was performed. Raman spectroscopy revealed the geological materials contained in the mixed samples. However, the analysis of a mixture containing different matrices was inaccurate due to the weak signal of the Raman shift, interference, and the strong matrix effect. On the other hand, the LIBS quantitative analysis of atomic carbon and calcium in mixed samples showed high accuracy. In the case of the calcite and gypsum mixture, the coefficient of determination of atomic carbon using LIBS was 0.99, while the signal using Raman was less than 0.9. Therefore, the geological composition of the mixed samples is first obtained using Raman and the LIBS-based quantitative analysis is then applied to the Raman outcome in order to construct highly accurate univariate calibration curves. The study also focuses on a method to overcome matrix effects through the two complementary spectroscopic techniques of Raman spectroscopy and LIBS.

CMEIAS color segmentation: an improved computing technology to process color images for quantitative microbial ecology studies at single-cell resolution.

PubMed

Gross, Colin A; Reddy, Chandan K; Dazzo, Frank B

2010-02-01

Quantitative microscopy and digital image analysis are underutilized in microbial ecology largely because of the laborious task to segment foreground object pixels from background, especially in complex color micrographs of environmental samples. In this paper, we describe an improved computing technology developed to alleviate this limitation. The system's uniqueness is its ability to edit digital images accurately when presented with the difficult yet commonplace challenge of removing background pixels whose three-dimensional color space overlaps the range that defines foreground objects. Image segmentation is accomplished by utilizing algorithms that address color and spatial relationships of user-selected foreground object pixels. Performance of the color segmentation algorithm evaluated on 26 complex micrographs at single pixel resolution had an overall pixel classification accuracy of 99+%. Several applications illustrate how this improved computing technology can successfully resolve numerous challenges of complex color segmentation in order to produce images from which quantitative information can be accurately extracted, thereby gain new perspectives on the in situ ecology of microorganisms. Examples include improvements in the quantitative analysis of (1) microbial abundance and phylotype diversity of single cells classified by their discriminating color within heterogeneous communities, (2) cell viability, (3) spatial relationships and intensity of bacterial gene expression involved in cellular communication between individual cells within rhizoplane biofilms, and (4) biofilm ecophysiology based on ribotype-differentiated radioactive substrate utilization. The stand-alone executable file plus user manual and tutorial images for this color segmentation computing application are freely available at http://cme.msu.edu/cmeias/ . This improved computing technology opens new opportunities of imaging applications where discriminating colors really matter most, thereby strengthening quantitative microscopy-based approaches to advance microbial ecology in situ at individual single-cell resolution.

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.

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.

How to Combine ChIP with qPCR.

PubMed

Asp, Patrik

2018-01-01

Chromatin immunoprecipitation (ChIP) coupled with quantitative PCR (qPCR) has in the last 15 years become a basic mainstream tool in genomic research. Numerous commercially available ChIP kits, qPCR kits, and real-time PCR systems allow for quick and easy analysis of virtually anything chromatin-related as long as there is an available antibody. However, the highly accurate quantitative dimension added by using qPCR to analyze ChIP samples significantly raises the bar in terms of experimental accuracy, appropriate controls, data analysis, and data presentation. This chapter will address these potential pitfalls by providing protocols and procedures that address the difficulties inherent in ChIP-qPCR assays.

A new background subtraction method for Western blot densitometry band quantification through image analysis software.

PubMed

Gallo-Oller, Gabriel; Ordoñez, Raquel; Dotor, Javier

2018-06-01

Since its first description, Western blot has been widely used in molecular labs. It constitutes a multistep method that allows the detection and/or quantification of proteins from simple to complex protein mixtures. Western blot quantification method constitutes a critical step in order to obtain accurate and reproducible results. Due to the technical knowledge required for densitometry analysis together with the resources availability, standard office scanners are often used for the imaging acquisition of developed Western blot films. Furthermore, the use of semi-quantitative software as ImageJ (Java-based image-processing and analysis software) is clearly increasing in different scientific fields. In this work, we describe the use of office scanner coupled with the ImageJ software together with a new image background subtraction method for accurate Western blot quantification. The proposed method represents an affordable, accurate and reproducible approximation that could be used in the presence of limited resources availability. Copyright © 2018 Elsevier B.V. All rights reserved.

A Comparative Analysis of Selected Mechanical Aspects of the Ice Skating Stride.

ERIC Educational Resources Information Center

Marino, G. Wayne

This study quantitatively analyzes selected aspects of the skating strides of above-average and below-average ability skaters. Subproblems were to determine how stride length and stride rate are affected by changes in skating velocity, to ascertain whether the basic assumption that stride length accurately approximates horizontal movement of the…

Colorimetric analysis of saliva–alcohol test strips by smartphone-based instruments using machine-learning algorithms

USDA-ARS?s Scientific Manuscript database

Strip lateral flow assays, similar to a home pregnancy test, are used widely in food safety applications to provide rapid and accurate tests for the presence of specific foodborne pathogens or other contaminants. Though these tests are very rapid, they are not very sensitive, are not quantitative, a...

Development of Tripropellant CFD Design Code

NASA Technical Reports Server (NTRS)

Farmer, Richard C.; Cheng, Gary C.; Anderson, Peter G.

1998-01-01

A tripropellant, such as GO2/H2/RP-1, CFD design code has been developed to predict the local mixing of multiple propellant streams as they are injected into a rocket motor. The code utilizes real fluid properties to account for the mixing and finite-rate combustion processes which occur near an injector faceplate, thus the analysis serves as a multi-phase homogeneous spray combustion model. Proper accounting of the combustion allows accurate gas-side temperature predictions which are essential for accurate wall heating analyses. The complex secondary flows which are predicted to occur near a faceplate cannot be quantitatively predicted by less accurate methodology. Test cases have been simulated to describe an axisymmetric tripropellant coaxial injector and a 3-dimensional RP-1/LO2 impinger injector system. The analysis has been shown to realistically describe such injector combustion flowfields. The code is also valuable to design meaningful future experiments by determining the critical location and type of measurements needed.

Analysis of Biomass Sugars Using a Novel HPLC Method

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

Agblevor, F. A.; Hames, B. R.; Schell, D.

The precise quantitative analysis of biomass sugars is a very important step in the conversion of biomass feedstocks to fuels and chemicals. However, the most accurate method of biomass sugar analysis is based on the gas chromatography analysis of derivatized sugars either as alditol acetates or trimethylsilanes. The derivatization method is time consuming but the alternative high-performance liquid chromatography (HPLC) method cannot resolve most sugars found in biomass hydrolysates. We have demonstrated for the first time that by careful manipulation of the HPLC mobile phase, biomass monomeric sugars (arabinose, xylose, fructose, glucose, mannose, and galactose) can be analyzed quantitatively andmore » there is excellent baseline resolution of all the sugars. This method was demonstrated for standard sugars, pretreated corn stover liquid and solid fractions. Our method can also be used to analyze dimeric sugars (cellobiose and sucrose).« less

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

Composition and Quantitation of Microalgal Lipids by ERETIC 1H NMR Method

PubMed Central

Nuzzo, Genoveffa; Gallo, Carmela; d’Ippolito, Giuliana; Cutignano, Adele; Sardo, Angela; Fontana, Angelo

2013-01-01

Accurate characterization of biomass constituents is a crucial aspect of research in the biotechnological application of natural products. Here we report an efficient, fast and reproducible method for the identification and quantitation of fatty acids and complex lipids (triacylglycerols, glycolipids, phospholipids) in microalgae under investigation for the development of functional health products (probiotics, food ingredients, drugs, etc.) or third generation biofuels. The procedure consists of extraction of the biological matrix by modified Folch method and direct analysis of the resulting material by proton nuclear magnetic resonance (1H NMR). The protocol uses a reference electronic signal as external standard (ERETIC method) and allows assessment of total lipid content, saturation degree and class distribution in both high throughput screening of algal collection and metabolic analysis during genetic or culturing studies. As proof of concept, the methodology was applied to the analysis of three microalgal species (Thalassiosira weissflogii, Cyclotella cryptica and Nannochloropsis salina) which drastically differ for the qualitative and quantitative composition of their fatty acid-based lipids. PMID:24084790

Accounting for Limited Detection Efficiency and Localization Precision in Cluster Analysis in Single Molecule Localization Microscopy

PubMed Central

Shivanandan, Arun; Unnikrishnan, Jayakrishnan; Radenovic, Aleksandra

2015-01-01

Single Molecule Localization Microscopy techniques like PhotoActivated Localization Microscopy, with their sub-diffraction limit spatial resolution, have been popularly used to characterize the spatial organization of membrane proteins, by means of quantitative cluster analysis. However, such quantitative studies remain challenged by the techniques’ inherent sources of errors such as a limited detection efficiency of less than 60%, due to incomplete photo-conversion, and a limited localization precision in the range of 10 – 30nm, varying across the detected molecules, mainly depending on the number of photons collected from each. We provide analytical methods to estimate the effect of these errors in cluster analysis and to correct for them. These methods, based on the Ripley’s L(r) – r or Pair Correlation Function popularly used by the community, can facilitate potentially breakthrough results in quantitative biology by providing a more accurate and precise quantification of protein spatial organization. PMID:25794150

Computerized image analysis for quantitative neuronal phenotyping in zebrafish.

PubMed

Liu, Tianming; Lu, Jianfeng; Wang, Ye; Campbell, William A; Huang, Ling; Zhu, Jinmin; Xia, Weiming; Wong, Stephen T C

2006-06-15

An integrated microscope image analysis pipeline is developed for automatic analysis and quantification of phenotypes in zebrafish with altered expression of Alzheimer's disease (AD)-linked genes. We hypothesize that a slight impairment of neuronal integrity in a large number of zebrafish carrying the mutant genotype can be detected through the computerized image analysis method. Key functionalities of our zebrafish image processing pipeline include quantification of neuron loss in zebrafish embryos due to knockdown of AD-linked genes, automatic detection of defective somites, and quantitative measurement of gene expression levels in zebrafish with altered expression of AD-linked genes or treatment with a chemical compound. These quantitative measurements enable the archival of analyzed results and relevant meta-data. The structured database is organized for statistical analysis and data modeling to better understand neuronal integrity and phenotypic changes of zebrafish under different perturbations. Our results show that the computerized analysis is comparable to manual counting with equivalent accuracy and improved efficacy and consistency. Development of such an automated data analysis pipeline represents a significant step forward to achieve accurate and reproducible quantification of neuronal phenotypes in large scale or high-throughput zebrafish imaging studies.

Quantitative carbon detector for enhanced detection of molecules in foods, pharmaceuticals, cosmetics, flavors, and fuels.

PubMed

Beach, Connor A; Krumm, Christoph; Spanjers, Charles S; Maduskar, Saurabh; Jones, Andrew J; Dauenhauer, Paul J

2016-03-07

Analysis of trace compounds, such as pesticides and other contaminants, within consumer products, fuels, and the environment requires quantification of increasingly complex mixtures of difficult-to-quantify compounds. Many compounds of interest are non-volatile and exhibit poor response in current gas chromatography and flame ionization systems. Here we show the reaction of trimethylsilylated chemical analytes to methane using a quantitative carbon detector (QCD; the Polyarc™ reactor) within a gas chromatograph (GC), thereby enabling enhanced detection (up to 10×) of highly functionalized compounds including carbohydrates, acids, drugs, flavorants, and pesticides. Analysis of a complex mixture of compounds shows that the GC-QCD method exhibits faster and more accurate analysis of complex mixtures commonly encountered in everyday products and the environment.

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.

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.

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.

Standard Reference Line Combined with One-Point Calibration-Free Laser-Induced Breakdown Spectroscopy (CF-LIBS) to Quantitatively Analyze Stainless and Heat Resistant Steel.

PubMed

Fu, Hongbo; Wang, Huadong; Jia, Junwei; Ni, Zhibo; Dong, Fengzhong

2018-01-01

Due to the influence of major elements' self-absorption, scarce observable spectral lines of trace elements, and relative efficiency correction of experimental system, accurate quantitative analysis with calibration-free laser-induced breakdown spectroscopy (CF-LIBS) is in fact not easy. In order to overcome these difficulties, standard reference line (SRL) combined with one-point calibration (OPC) is used to analyze six elements in three stainless-steel and five heat-resistant steel samples. The Stark broadening and Saha - Boltzmann plot of Fe are used to calculate the electron density and the plasma temperature, respectively. In the present work, we tested the original SRL method, the SRL with the OPC method, and intercept with the OPC method. The final calculation results show that the latter two methods can effectively improve the overall accuracy of quantitative analysis and the detection limits of trace elements.

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

PubMed

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

2016-09-01

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

Absolute Quantification of Human Milk Caseins and the Whey/Casein Ratio during the First Year of Lactation.

PubMed

Liao, Yalin; Weber, Darren; Xu, Wei; Durbin-Johnson, Blythe P; Phinney, Brett S; Lönnerdal, Bo

2017-11-03

Whey proteins and caseins in breast milk provide bioactivities and also have different amino acid composition. Accurate determination of these two major protein classes provides a better understanding of human milk composition and function, and further aids in developing improved infant formulas based on bovine whey proteins and caseins. In this study, we implemented a LC-MS/MS quantitative analysis based on iBAQ label-free quantitation, to estimate absolute concentrations of α-casein, β-casein, and κ-casein in human milk samples (n = 88) collected between day 1 and day 360 postpartum. Total protein concentration ranged from 2.03 to 17.52 with a mean of 9.37 ± 3.65 g/L. Casein subunits ranged from 0.04 to 1.68 g/L (α-), 0.04 to 4.42 g/L (β-), and 0.10 to 1.72 g/L (α-), with β-casein having the highest average concentration among the three subunits. Calculated whey/casein ratio ranged from 45:55 to 97:3. Linear regression analyses show significant decreases in total protein, β-casein, κ-casein, total casein, and a significant increase of whey/casein ratio during the course of lactation. Our study presents a novel and accurate quantitative analysis of human milk casein content, demonstrating a lower casein content than earlier believed, which has implications for improved infants formulas.

Cardiac imaging: working towards fully-automated machine analysis & interpretation.

PubMed

Slomka, Piotr J; Dey, Damini; Sitek, Arkadiusz; Motwani, Manish; Berman, Daniel S; Germano, Guido

2017-03-01

Non-invasive imaging plays a critical role in managing patients with cardiovascular disease. Although subjective visual interpretation remains the clinical mainstay, quantitative analysis facilitates objective, evidence-based management, and advances in clinical research. This has driven developments in computing and software tools aimed at achieving fully automated image processing and quantitative analysis. In parallel, machine learning techniques have been used to rapidly integrate large amounts of clinical and quantitative imaging data to provide highly personalized individual patient-based conclusions. Areas covered: This review summarizes recent advances in automated quantitative imaging in cardiology and describes the latest techniques which incorporate machine learning principles. The review focuses on the cardiac imaging techniques which are in wide clinical use. It also discusses key issues and obstacles for these tools to become utilized in mainstream clinical practice. Expert commentary: Fully-automated processing and high-level computer interpretation of cardiac imaging are becoming a reality. Application of machine learning to the vast amounts of quantitative data generated per scan and integration with clinical data also facilitates a move to more patient-specific interpretation. These developments are unlikely to replace interpreting physicians but will provide them with highly accurate tools to detect disease, risk-stratify, and optimize patient-specific treatment. However, with each technological advance, we move further from human dependence and closer to fully-automated machine interpretation.

Recent Progress in the Remote Detection of Vapours and Gaseous Pollutants.

ERIC Educational Resources Information Center

Moffat, A. J.; And Others

Work has been continuing on the correlation spectrometry techniques described at previous remote sensing symposiums. Advances in the techniques are described which enable accurate quantitative measurements of diffused atmospheric gases to be made using controlled light sources, accurate quantitative measurements of gas clouds relative to…

Calibration method for spectroscopic systems

DOEpatents

Sandison, David R.

1998-01-01

Calibration spots of optically-characterized material placed in the field of view of a spectroscopic system allow calibration of the spectroscopic system. Response from the calibration spots is measured and used to calibrate for varying spectroscopic system operating parameters. The accurate calibration achieved allows quantitative spectroscopic analysis of responses taken at different times, different excitation conditions, and of different targets.

Calibration method for spectroscopic systems

DOEpatents

Sandison, D.R.

1998-11-17

Calibration spots of optically-characterized material placed in the field of view of a spectroscopic system allow calibration of the spectroscopic system. Response from the calibration spots is measured and used to calibrate for varying spectroscopic system operating parameters. The accurate calibration achieved allows quantitative spectroscopic analysis of responses taken at different times, different excitation conditions, and of different targets. 3 figs.

Selection of reference genes for RT-qPCR analysis in the monarch butterfly, Danaus plexippus (L.), a migrating bio-indicator

USDA-ARS?s Scientific Manuscript database

Quantitative real-time PCR (qRT-PCR) is a reliable and reproducible technique for measuring and evaluating changes in gene expression. To facilitate gene expression studies and obtain more accurate qRT-PCR data, normalization relative to stable housekeeping genes is required. In this study, expres...

An interactive method based on the live wire for segmentation of the breast in mammography images.

PubMed

Zewei, Zhang; Tianyue, Wang; Li, Guo; Tingting, Wang; Lu, Xu

2014-01-01

In order to improve accuracy of computer-aided diagnosis of breast lumps, the authors introduce an improved interactive segmentation method based on Live Wire. This paper presents the Gabor filters and FCM clustering algorithm is introduced to the Live Wire cost function definition. According to the image FCM analysis for image edge enhancement, we eliminate the interference of weak edge and access external features clear segmentation results of breast lumps through improving Live Wire on two cases of breast segmentation data. Compared with the traditional method of image segmentation, experimental results show that the method achieves more accurate segmentation of breast lumps and provides more accurate objective basis on quantitative and qualitative analysis of breast lumps.

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.

Qualitative and Quantitative Analysis of the Major Constituents in Chinese Medical Preparation Lianhua-Qingwen Capsule by UPLC-DAD-QTOF-MS

PubMed Central

Jia, Weina; Wang, Chunhua; Wang, Yuefei; Pan, Guixiang; Jiang, Miaomiao; Li, Zheng; Zhu, Yan

2015-01-01

Lianhua-Qingwen capsule (LQC) is a commonly used Chinese medical preparation to treat viral influenza and especially played a very important role in the fight against severe acute respiratory syndrome (SARS) in 2002-2003 in China. In this paper, a rapid ultraperformance liquid chromatography coupled with diode-array detector and quadrupole time-of-flight mass spectrometry (UPLC-DAD-QTOF-MS) method was established for qualitative and quantitative analysis of the major constituents of LQC. A total of 61 compounds including flavonoids, phenylpropanoids, anthraquinones, triterpenoids, iridoids, and other types of compounds were unambiguously or tentatively identified by comparing the retention times and accurate mass measurement with reference compounds or literature data. Among them, twelve representative compounds were further quantified as chemical markers in quantitative analysis, including salidroside, chlorogenic acid, forsythoside E, cryptochlorogenic acid, amygdalin, sweroside, hyperin, rutin, forsythoside A, phillyrin, rhein, and glycyrrhizic acid. The UPLC-DAD method was evaluated with linearity, limit of detection (LOD), limit of quantification (LOQ), precision, stability, repeatability, and recovery tests. The results showed that the developed quantitative method was linear, sensitive, and precise for the quality control of LQC. PMID:25654135

An operation support expert system based on on-line dynamics simulation and fuzzy reasoning for startup schedule optimization in fossil power plants

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

Matsumoto, H.; Eki, Y.; Kaji, A.

1993-12-01

An expert system which can support operators of fossil power plants in creating the optimum startup schedule and executing it accurately is described. The optimum turbine speed-up and load-up pattern is obtained through an iterative manner which is based on fuzzy resonating using quantitative calculations as plant dynamics models and qualitative knowledge as schedule optimization rules with fuzziness. The rules represent relationships between stress margins and modification rates of the schedule parameters. Simulations analysis proves that the system provides quick and accurate plant startups.

Total Protein Content Determination of Microalgal Biomass by Elemental Nitrogen Analysis and a Dedicated Nitrogen-to-Protein Conversion Factor

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

Laurens, Lieve M; Olstad-Thompson, Jessica L; Templeton, David W

Accurately determining protein content is important in the valorization of algal biomass in food, feed, and fuel markets, where these values are used for component balance calculations. Conversion of elemental nitrogen to protein is a well-accepted and widely practiced method, but depends on developing an applicable nitrogen-to-protein conversion factor. The methodology reported here covers the quantitative assessment of the total nitrogen content of algal biomass and a description of the methodology that underpins the accurate de novo calculation of a dedicated nitrogen-to-protein conversion factor.

An Image Analysis Method for the Precise Selection and Quantitation of Fluorescently Labeled Cellular Constituents

PubMed Central

Agley, Chibeza C.; Velloso, Cristiana P.; Lazarus, Norman R.

2012-01-01

The accurate measurement of the morphological characteristics of cells with nonuniform conformations presents difficulties. We report here a straightforward method using immunofluorescent staining and the commercially available imaging program Adobe Photoshop, which allows objective and precise information to be gathered on irregularly shaped cells. We have applied this measurement technique to the analysis of human muscle cells and their immunologically marked intracellular constituents, as these cells are prone to adopting a highly branched phenotype in culture. Use of this method can be used to overcome many of the long-standing limitations of conventional approaches for quantifying muscle cell size in vitro. In addition, wider applications of Photoshop as a quantitative and semiquantitative tool in immunocytochemistry are explored. PMID:22511600

Predicting ESI/MS Signal Change for Anions in Different Solvents.

PubMed

Kruve, Anneli; Kaupmees, Karl

2017-05-02

LC/ESI/MS is a technique widely used for qualitative and quantitative analysis in various fields. However, quantification is currently possible only for compounds for which the standard substances are available, as the ionization efficiency of different compounds in ESI source differs by orders of magnitude. In this paper we present an approach for quantitative LC/ESI/MS analysis without standard substances. This approach relies on accurately predicting the ionization efficiencies in ESI source based on a model, which uses physicochemical parameters of analytes. Furthermore, the model has been made transferable between different mobile phases and instrument setups by using a suitable set of calibration compounds. This approach has been validated both in flow injection and chromatographic mode with gradient elution.

Measurement of carbon distribution in nuclear fuel pin cladding specimens by means of a secondary ion mass spectrometer

NASA Astrophysics Data System (ADS)

Bart, Gerhard; Aerne, Ernst Tino; Burri, Martin; Zwicky, Hans-Urs

1986-11-01

Cladding carburization during irradiation of advanced mixed uranium plutonium carbide fast breeder reactor fuel is possibly a life limiting fuel pin factor. The quantitative assessment of such clad carbon embrittlement is difficult to perform by electron microprobe analysis because of sample surface contamination, and due to the very low energy of the carbon K α X-ray transition. The work presented here describes a method developed at the Swiss Federal Institute for Reactor Research (EIR) to use shielded secondary ion mass spectrometry (SIMS) as an accurate tool to determine radial distribution profiles of carbon in radioactive stainless steel fuel pin cladding. Compared with nuclear microprobe analysis (NMA) [1], which is also an accurate method for carbon analysis, the SIMS method distinguishes itself by its versatility for simultaneous determination of additional impurities.

A new strategy for statistical analysis-based fingerprint establishment: Application to quality assessment of Semen sojae praeparatum.

PubMed

Guo, Hui; Zhang, Zhen; Yao, Yuan; Liu, Jialin; Chang, Ruirui; Liu, Zhao; Hao, Hongyuan; Huang, Taohong; Wen, Jun; Zhou, Tingting

2018-08-30

Semen sojae praeparatum with homology of medicine and food is a famous traditional Chinese medicine. A simple and effective quality fingerprint analysis, coupled with chemometrics methods, was developed for quality assessment of Semen sojae praeparatum. First, similarity analysis (SA) and hierarchical clusting analysis (HCA) were applied to select the qualitative markers, which obviously influence the quality of Semen sojae praeparatum. 21 chemicals were selected and characterized by high resolution ion trap/time-of-flight mass spectrometry (LC-IT-TOF-MS). Subsequently, principal components analysis (PCA) and orthogonal partial least squares discriminant analysis (OPLS-DA) were conducted to select the quantitative markers of Semen sojae praeparatum samples from different origins. Moreover, 11 compounds with statistical significance were determined quantitatively, which provided an accurate and informative data for quality evaluation. This study proposes a new strategy for "statistic analysis-based fingerprint establishment", which would be a valuable reference for further study. Copyright © 2018 Elsevier Ltd. All rights reserved.

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.)

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

SearchLight: a freely available web-based quantitative spectral analysis tool (Conference Presentation)

NASA Astrophysics Data System (ADS)

Prabhat, Prashant; Peet, Michael; Erdogan, Turan

2016-03-01

In order to design a fluorescence experiment, typically the spectra of a fluorophore and of a filter set are overlaid on a single graph and the spectral overlap is evaluated intuitively. However, in a typical fluorescence imaging system the fluorophores and optical filters are not the only wavelength dependent variables - even the excitation light sources have been changing. For example, LED Light Engines may have a significantly different spectral response compared to the traditional metal-halide lamps. Therefore, for a more accurate assessment of fluorophore-to-filter-set compatibility, all sources of spectral variation should be taken into account simultaneously. Additionally, intuitive or qualitative evaluation of many spectra does not necessarily provide a realistic assessment of the system performance. "SearchLight" is a freely available web-based spectral plotting and analysis tool that can be used to address the need for accurate, quantitative spectral evaluation of fluorescence measurement systems. This tool is available at: http://searchlight.semrock.com/. Based on a detailed mathematical framework [1], SearchLight calculates signal, noise, and signal-to-noise ratio for multiple combinations of fluorophores, filter sets, light sources and detectors. SearchLight allows for qualitative and quantitative evaluation of the compatibility of filter sets with fluorophores, analysis of bleed-through, identification of optimized spectral edge locations for a set of filters under specific experimental conditions, and guidance regarding labeling protocols in multiplexing imaging assays. Entire SearchLight sessions can be shared with colleagues and collaborators and saved for future reference. [1] Anderson, N., Prabhat, P. and Erdogan, T., Spectral Modeling in Fluorescence Microscopy, http://www.semrock.com (2010).

HuMOVE: a low-invasive wearable monitoring platform in sexual medicine.

PubMed

Ciuti, Gastone; Nardi, Matteo; Valdastri, Pietro; Menciassi, Arianna; Basile Fasolo, Ciro; Dario, Paolo

2014-10-01

To investigate an accelerometer-based wearable system, named Human Movement (HuMOVE) platform, designed to enable quantitative and continuous measurement of sexual performance with minimal invasiveness and inconvenience for users. Design, implementation, and development of HuMOVE, a wearable platform equipped with an accelerometer sensor for monitoring inertial parameters for sexual performance assessment and diagnosis, were performed. The system enables quantitative measurement of movement parameters during sexual intercourse, meeting the requirements of wearability, data storage, sampling rate, and interfacing methods, which are fundamental for human sexual intercourse performance analysis. HuMOVE was validated through characterization using a controlled experimental test bench and evaluated in a human model during simulated sexual intercourse conditions. HuMOVE demonstrated to be a robust and quantitative monitoring platform and a reliable candidate for sexual performance evaluation and diagnosis. Characterization analysis on the controlled experimental test bench demonstrated an accurate correlation between the HuMOVE system and data from a reference displacement sensor. Experimental tests in the human model during simulated intercourse conditions confirmed the accuracy of the sexual performance evaluation platform and the effectiveness of the selected and derived parameters. The obtained outcomes also established the project expectations in terms of usability and comfort, evidenced by the questionnaires that highlighted the low invasiveness and acceptance of the device. To the best of our knowledge, HuMOVE platform is the first device for human sexual performance analysis compatible with sexual intercourse; the system has the potential to be a helpful tool for physicians to accurately classify sexual disorders, such as premature or delayed ejaculation. Copyright © 2014 Elsevier Inc. All rights reserved.

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

NASA Astrophysics Data System (ADS)

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

2018-01-01

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

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.

A quantitative method to measure biofilm removal efficiency from complex biomaterial surfaces using SEM and image analysis

NASA Astrophysics Data System (ADS)

Vyas, N.; Sammons, R. L.; Addison, O.; Dehghani, H.; Walmsley, A. D.

2016-09-01

Biofilm accumulation on biomaterial surfaces is a major health concern and significant research efforts are directed towards producing biofilm resistant surfaces and developing biofilm removal techniques. To accurately evaluate biofilm growth and disruption on surfaces, accurate methods which give quantitative information on biofilm area are needed, as current methods are indirect and inaccurate. We demonstrate the use of machine learning algorithms to segment biofilm from scanning electron microscopy images. A case study showing disruption of biofilm from rough dental implant surfaces using cavitation bubbles from an ultrasonic scaler is used to validate the imaging and analysis protocol developed. Streptococcus mutans biofilm was disrupted from sandblasted, acid etched (SLA) Ti discs and polished Ti discs. Significant biofilm removal occurred due to cavitation from ultrasonic scaling (p < 0.001). The mean sensitivity and specificity values for segmentation of the SLA surface images were 0.80 ± 0.18 and 0.62 ± 0.20 respectively and 0.74 ± 0.13 and 0.86 ± 0.09 respectively for polished surfaces. Cavitation has potential to be used as a novel way to clean dental implants. This imaging and analysis method will be of value to other researchers and manufacturers wishing to study biofilm growth and removal.

Quantitative 3D analysis of bone in hip osteoarthritis using clinical computed tomography.

PubMed

Turmezei, Tom D; Treece, Graham M; Gee, Andrew H; Fotiadou, Anastasia F; Poole, Kenneth E S

2016-07-01

To assess the relationship between proximal femoral cortical bone thickness and radiological hip osteoarthritis using quantitative 3D analysis of clinical computed tomography (CT) data. Image analysis was performed on clinical CT imaging data from 203 female volunteers with a technique called cortical bone mapping (CBM). Colour thickness maps were created for each proximal femur. Statistical parametric mapping was performed to identify statistically significant differences in cortical bone thickness that corresponded with the severity of radiological hip osteoarthritis. Kellgren and Lawrence (K&L) grade, minimum joint space width (JSW) and a novel CT-based osteophyte score were also blindly assessed from the CT data. For each increase in K&L grade, cortical thickness increased by up to 25 % in distinct areas of the superolateral femoral head-neck junction and superior subchondral bone plate. For increasing severity of CT osteophytes, the increase in cortical thickness was more circumferential, involving a wider portion of the head-neck junction, with up to a 7 % increase in cortical thickness per increment in score. Results were not significant for minimum JSW. These findings indicate that quantitative 3D analysis of the proximal femur can identify changes in cortical bone thickness relevant to structural hip osteoarthritis. • CT is being increasingly used to assess bony involvement in osteoarthritis • CBM provides accurate and reliable quantitative analysis of cortical bone thickness • Cortical bone is thicker at the superior femoral head-neck with worse osteoarthritis • Regions of increased thickness co-locate with impingement and osteophyte formation • Quantitative 3D bone analysis could enable clinical disease prediction and therapy development.

A comparison of 3D poly(ε-caprolactone) tissue engineering scaffolds produced with conventional and additive manufacturing techniques by means of quantitative analysis of SR μ-CT images

NASA Astrophysics Data System (ADS)

Brun, F.; Intranuovo, F.; Mohammadi, S.; Domingos, M.; Favia, P.; Tromba, G.

2013-07-01

The technique used to produce a 3D tissue engineering (TE) scaffold is of fundamental importance in order to guarantee its proper morphological characteristics. An accurate assessment of the resulting structural properties is therefore crucial in order to evaluate the effectiveness of the produced scaffold. Synchrotron radiation (SR) computed microtomography (μ-CT) combined with further image analysis seems to be one of the most effective techniques to this aim. However, a quantitative assessment of the morphological parameters directly from the reconstructed images is a non trivial task. This study considers two different poly(ε-caprolactone) (PCL) scaffolds fabricated with a conventional technique (Solvent Casting Particulate Leaching, SCPL) and an additive manufacturing (AM) technique (BioCell Printing), respectively. With the first technique it is possible to produce scaffolds with random, non-regular, rounded pore geometry. The AM technique instead is able to produce scaffolds with square-shaped interconnected pores of regular dimension. Therefore, the final morphology of the AM scaffolds can be predicted and the resulting model can be used for the validation of the applied imaging and image analysis protocols. It is here reported a SR μ-CT image analysis approach that is able to effectively and accurately reveal the differences in the pore- and throat-size distributions as well as connectivity of both AM and SCPL scaffolds.

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

Quantitative refractive index distribution of single cell by combining phase-shifting interferometry and AFM imaging.

PubMed

Zhang, Qinnan; Zhong, Liyun; Tang, Ping; Yuan, Yingjie; Liu, Shengde; Tian, Jindong; Lu, Xiaoxu

2017-05-31

Cell refractive index, an intrinsic optical parameter, is closely correlated with the intracellular mass and concentration. By combining optical phase-shifting interferometry (PSI) and atomic force microscope (AFM) imaging, we constructed a label free, non-invasive and quantitative refractive index of single cell measurement system, in which the accurate phase map of single cell was retrieved with PSI technique and the cell morphology with nanoscale resolution was achieved with AFM imaging. Based on the proposed AFM/PSI system, we achieved quantitative refractive index distributions of single red blood cell and Jurkat cell, respectively. Further, the quantitative change of refractive index distribution during Daunorubicin (DNR)-induced Jurkat cell apoptosis was presented, and then the content changes of intracellular biochemical components were achieved. Importantly, these results were consistent with Raman spectral analysis, indicating that the proposed PSI/AFM based refractive index system is likely to become a useful tool for intracellular biochemical components analysis measurement, and this will facilitate its application for revealing cell structure and pathological state from a new perspective.

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.

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

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

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 modelling is the most robust and reliable method to reconstruct accurate quantitative iodine-131 SPECT images.

Rapid Quantitative Determination of Squalene in Shark Liver Oils by Raman and IR Spectroscopy.

PubMed

Hall, David W; Marshall, Susan N; Gordon, Keith C; Killeen, Daniel P

2016-01-01

Squalene is sourced predominantly from shark liver oils and to a lesser extent from plants such as olives. It is used for the production of surfactants, dyes, sunscreen, and cosmetics. The economic value of shark liver oil is directly related to the squalene content, which in turn is highly variable and species-dependent. Presented here is a validated gas chromatography-mass spectrometry analysis method for the quantitation of squalene in shark liver oils, with an accuracy of 99.0 %, precision of 0.23 % (standard deviation), and linearity of >0.999. The method has been used to measure the squalene concentration of 16 commercial shark liver oils. These reference squalene concentrations were related to infrared (IR) and Raman spectra of the same oils using partial least squares regression. The resultant models were suitable for the rapid quantitation of squalene in shark liver oils, with cross-validation r (2) values of >0.98 and root mean square errors of validation of ≤4.3 % w/w. Independent test set validation of these models found mean absolute deviations of the 4.9 and 1.0 % w/w for the IR and Raman models, respectively. Both techniques were more accurate than results obtained by an industrial refractive index analysis method, which is used for rapid, cheap quantitation of squalene in shark liver oils. In particular, the Raman partial least squares regression was suited to quantitative squalene analysis. The intense and highly characteristic Raman bands of squalene made quantitative analysis possible irrespective of the lipid matrix.

Assessment of umbilical artery flow and fetal heart rate to predict delivery time in bitches.

PubMed

Giannico, Amália Turner; Garcia, Daniela Aparecida Ayres; Gil, Elaine Mayumi Ueno; Sousa, Marlos Gonçalves; Froes, Tilde Rodrigues

2016-10-15

The aim of this study was to quantitatively investigate the oscillation of the fetal heart rate (HR) in advance of normal delivery and whether this index could be used to indicate impending delivery. In addition, fetal HR oscillation and umbilical artery resistive index (RI) were correlated to determine if the combination of these parameters provided a more accurate prediction of the time of delivery. Sonographic evaluation was performed in 11 pregnant bitches to evaluate the fetal HR and umbilical artery RI at the following antepartum times: 120 to 96 hours, 72 to 48 hours, 24 to 12 hours, and 12 to 1 hours. Statistical analysis indicated a correlation between the oscillation of fetal HR and the umbilical artery RI. As delivery approached a considerable reduction in the umbilical artery RI was documented and greater oscillations between maximum and minimum HRs occurred. We conclude that the quantitative analysis of fetal HR oscillations may be used to predict the time of delivery in bitches. The combination of fetal HR and umbilical artery RI together may provide more accurate predictions of time of delivery. Copyright © 2016 Elsevier Inc. All rights reserved.

Simultaneous Quantification of Multiple Alternatively Spliced mRNA Transcripts Using Droplet Digital PCR.

PubMed

Sun, Bing; Zheng, Yun-Ling

2018-01-01

Currently there is no sensitive, precise, and reproducible method to quantitate alternative splicing of mRNA transcripts. Droplet digital™ PCR (ddPCR™) analysis allows for accurate digital counting for quantification of gene expression. Human telomerase reverse transcriptase (hTERT) is one of the essential components required for telomerase activity and for the maintenance of telomeres. Several alternatively spliced forms of hTERT mRNA in human primary and tumor cells have been reported in the literature. Using one pair of primers and two probes for hTERT, four alternatively spliced forms of hTERT (α-/β+, α+/β- single deletions, α-/β- double deletion, and nondeletion α+/β+) were accurately quantified through a novel analysis method via data collected from a single ddPCR reaction. In this chapter, we describe this ddPCR method that enables direct quantitative comparison of four alternatively spliced forms of the hTERT messenger RNA without the need for internal standards or multiple pairs of primers specific for each variant, eliminating the technical variation due to differential PCR amplification efficiency for different amplicons and the challenges of quantification using standard curves. This simple and straightforward method should have general utility for quantifying alternatively spliced gene transcripts.

Quantitative analysis of polypeptide pharmaceuticals by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

PubMed

Amini, Ahmad; Nilsson, Elin

2008-02-13

An accurate method based on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) has been developed for quantitative analysis of calcitonin and insulin in different commercially available pharmaceutical products. Tryptic peptides derived from these polypeptides were chemically modified at their C-terminal lysine-residues with 2-methoxy-4,5-dihydro-imidazole (light tagging) as standard and deuterated 2-methoxy-4,5-dihydro-imidazole (heavy tagging) as internal standard (IS). The heavy modified tryptic peptides (4D-Lys tag), differed by four atomic mass units from the corresponding light labelled counterparts (4H-Lys tag). The normalized peak areas (the ratio between the light and heavy tagged peptides) were used to construct a standard curve to determine the concentration of the analytes. The concentrations of calcitonin and insulin content of the analyzed pharmaceutical products were accurately determined, and less than 5% error was obtained between the present method and the manufacturer specified values. It was also found that the cysteine residues in CSNLSTCVLGK from tryptic calcitonin were converted to lanthionine by the loss of one sulfhydryl group during the labelling procedure.

Computed tomography in hypersensitivity pneumonitis: main findings, differential diagnosis and pitfalls.

PubMed

Dias, Olívia Meira; Baldi, Bruno Guedes; Pennati, Francesca; Aliverti, Andrea; Chate, Rodrigo Caruso; Sawamura, Márcio Valente Yamada; Carvalho, Carlos Roberto Ribeiro de; Albuquerque, André Luis Pereira de

2018-01-01

Hypersensitivity pneumonitis (HP) is a disease with variable clinical presentation in which inflammation in the lung parenchyma is caused by the inhalation of specific organic antigens or low molecular weight substances in genetically susceptible individuals. Alterations of the acute, subacute and chronic forms may eventually overlap, and the diagnosis based on temporality and presence of fibrosis (acute/inflammatory HP vs. chronic HP) seems to be more feasible and useful in clinical practice. Differential diagnosis of chronic HP with other interstitial fibrotic diseases is challenging due to the overlap of the clinical history, and the functional and imaging findings of these pathologies in the terminal stages. Areas covered: This article reviews the essential features of HP with emphasis on imaging features. Moreover, the main methodological limitations of high-resolution computed tomography (HRCT) interpretation are discussed, as well as new perspectives with volumetric quantitative CT analysis as a useful tool for retrieving detailed and accurate information from the lung parenchyma. Expert commentary: Mosaic attenuation is a prominent feature of this disease, but air trapping in chronic HP seems overestimated. Quantitative analysis has the potential to estimate the involvement of the pulmonary parenchyma more accurately and could correlate better with pulmonary function results.

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.

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.

An effective approach to quantitative analysis of ternary amino acids in foxtail millet substrate based on terahertz spectroscopy.

PubMed

Lu, Shao Hua; Li, Bao Qiong; Zhai, Hong Lin; Zhang, Xin; Zhang, Zhuo Yong

2018-04-25

Terahertz time-domain spectroscopy has been applied to many fields, however, it still encounters drawbacks in multicomponent mixtures analysis due to serious spectral overlapping. Here, an effective approach to quantitative analysis was proposed, and applied on the determination of the ternary amino acids in foxtail millet substrate. Utilizing three parameters derived from the THz-TDS, the images were constructed and the Tchebichef image moments were used to extract the information of target components. Then the quantitative models were obtained by stepwise regression. The correlation coefficients of leave-one-out cross-validation (R loo-cv 2 ) were more than 0.9595. As for external test set, the predictive correlation coefficients (R p 2 ) were more than 0.8026 and the root mean square error of prediction (RMSE p ) were less than 1.2601. Compared with the traditional methods (PLS and N-PLS methods), our approach is more accurate, robust and reliable, and can be a potential excellent approach to quantify multicomponent with THz-TDS spectroscopy. Copyright © 2017 Elsevier Ltd. All rights reserved.

Report on the analysis of common beverages spiked with gamma-hydroxybutyric acid (GHB) and gamma-butyrolactone (GBL) using NMR and the PURGE solvent-suppression technique.

PubMed

Lesar, Casey T; Decatur, John; Lukasiewicz, Elaan; Champeil, Elise

2011-10-10

In forensic evidence, the identification and quantitation of gamma-hydroxybutyric acid (GHB) in "spiked" beverages is challenging. In this report, we present the analysis of common alcoholic beverages found in clubs and bars spiked with gamma-hydroxybutyric acid (GHB) and gamma-butyrolactone (GBL). Our analysis of the spiked beverages consisted of using (1)H NMR with a water suppression method called Presaturation Utilizing Relaxation Gradients and Echoes (PURGE). The following beverages were analyzed: water, 10% ethanol in water, vodka-cranberry juice, rum and coke, gin and tonic, whisky and diet coke, white wine, red wine, and beer. The PURGE method allowed for the direct identification and quantitation of both compounds in all beverages except red and white wine where small interferences prevented accurate quantitation. The NMR method presented in this paper utilizes PURGE water suppression. Thanks to the use of a capillary internal standard, the method is fast, non-destructive, sensitive and requires no sample preparation which could disrupt the equilibrium between GHB and GBL. Published by Elsevier Ireland Ltd.

Image registration and analysis for quantitative myocardial perfusion: application to dynamic circular cardiac CT.

PubMed

Isola, A A; Schmitt, H; van Stevendaal, U; Begemann, P G; Coulon, P; Boussel, L; Grass, M

2011-09-21

Large area detector computed tomography systems with fast rotating gantries enable volumetric dynamic cardiac perfusion studies. Prospectively, ECG-triggered acquisitions limit the data acquisition to a predefined cardiac phase and thereby reduce x-ray dose and limit motion artefacts. Even in the case of highly accurate prospective triggering and stable heart rate, spatial misalignment of the cardiac volumes acquired and reconstructed per cardiac cycle may occur due to small motion pattern variations from cycle to cycle. These misalignments reduce the accuracy of the quantitative analysis of myocardial perfusion parameters on a per voxel basis. An image-based solution to this problem is elastic 3D image registration of dynamic volume sequences with variable contrast, as it is introduced in this contribution. After circular cone-beam CT reconstruction of cardiac volumes covering large areas of the myocardial tissue, the complete series is aligned with respect to a chosen reference volume. The results of the registration process and the perfusion analysis with and without registration are evaluated quantitatively in this paper. The spatial alignment leads to improved quantification of myocardial perfusion for three different pig data sets.

Optimal dimensionality reduction of complex dynamics: the chess game as diffusion on a free-energy landscape.

PubMed

Krivov, Sergei V

2011-07-01

Dimensionality reduction is ubiquitous in the analysis of complex dynamics. The conventional dimensionality reduction techniques, however, focus on reproducing the underlying configuration space, rather than the dynamics itself. The constructed low-dimensional space does not provide a complete and accurate description of the dynamics. Here I describe how to perform dimensionality reduction while preserving the essential properties of the dynamics. The approach is illustrated by analyzing the chess game--the archetype of complex dynamics. A variable that provides complete and accurate description of chess dynamics is constructed. The winning probability is predicted by describing the game as a random walk on the free-energy landscape associated with the variable. The approach suggests a possible way of obtaining a simple yet accurate description of many important complex phenomena. The analysis of the chess game shows that the approach can quantitatively describe the dynamics of processes where human decision-making plays a central role, e.g., financial and social dynamics.

Optimal dimensionality reduction of complex dynamics: The chess game as diffusion on a free-energy landscape

NASA Astrophysics Data System (ADS)

Krivov, Sergei V.

2011-07-01

Dimensionality reduction is ubiquitous in the analysis of complex dynamics. The conventional dimensionality reduction techniques, however, focus on reproducing the underlying configuration space, rather than the dynamics itself. The constructed low-dimensional space does not provide a complete and accurate description of the dynamics. Here I describe how to perform dimensionality reduction while preserving the essential properties of the dynamics. The approach is illustrated by analyzing the chess game—the archetype of complex dynamics. A variable that provides complete and accurate description of chess dynamics is constructed. The winning probability is predicted by describing the game as a random walk on the free-energy landscape associated with the variable. The approach suggests a possible way of obtaining a simple yet accurate description of many important complex phenomena. The analysis of the chess game shows that the approach can quantitatively describe the dynamics of processes where human decision-making plays a central role, e.g., financial and social dynamics.

Calibrating genomic and allelic coverage bias in single-cell sequencing.

PubMed

Zhang, Cheng-Zhong; Adalsteinsson, Viktor A; Francis, Joshua; Cornils, Hauke; Jung, Joonil; Maire, Cecile; Ligon, Keith L; Meyerson, Matthew; Love, J Christopher

2015-04-16

Artifacts introduced in whole-genome amplification (WGA) make it difficult to derive accurate genomic information from single-cell genomes and require different analytical strategies from bulk genome analysis. Here, we describe statistical methods to quantitatively assess the amplification bias resulting from whole-genome amplification of single-cell genomic DNA. Analysis of single-cell DNA libraries generated by different technologies revealed universal features of the genome coverage bias predominantly generated at the amplicon level (1-10 kb). The magnitude of coverage bias can be accurately calibrated from low-pass sequencing (∼0.1 × ) to predict the depth-of-coverage yield of single-cell DNA libraries sequenced at arbitrary depths. We further provide a benchmark comparison of single-cell libraries generated by multi-strand displacement amplification (MDA) and multiple annealing and looping-based amplification cycles (MALBAC). Finally, we develop statistical models to calibrate allelic bias in single-cell whole-genome amplification and demonstrate a census-based strategy for efficient and accurate variant detection from low-input biopsy samples.

Calibrating genomic and allelic coverage bias in single-cell sequencing

PubMed Central

Francis, Joshua; Cornils, Hauke; Jung, Joonil; Maire, Cecile; Ligon, Keith L.; Meyerson, Matthew; Love, J. Christopher

2016-01-01

Artifacts introduced in whole-genome amplification (WGA) make it difficult to derive accurate genomic information from single-cell genomes and require different analytical strategies from bulk genome analysis. Here, we describe statistical methods to quantitatively assess the amplification bias resulting from whole-genome amplification of single-cell genomic DNA. Analysis of single-cell DNA libraries generated by different technologies revealed universal features of the genome coverage bias predominantly generated at the amplicon level (1–10 kb). The magnitude of coverage bias can be accurately calibrated from low-pass sequencing (~0.1 ×) to predict the depth-of-coverage yield of single-cell DNA libraries sequenced at arbitrary depths. We further provide a benchmark comparison of single-cell libraries generated by multi-strand displacement amplification (MDA) and multiple annealing and looping-based amplification cycles (MALBAC). Finally, we develop statistical models to calibrate allelic bias in single-cell whole-genome amplification and demonstrate a census-based strategy for efficient and accurate variant detection from low-input biopsy samples. PMID:25879913

A sensitivity analysis of regional and small watershed hydrologic models

NASA Technical Reports Server (NTRS)

Ambaruch, R.; Salomonson, V. V.; Simmons, J. W.

1975-01-01

Continuous simulation models of the hydrologic behavior of watersheds are important tools in several practical applications such as hydroelectric power planning, navigation, and flood control. Several recent studies have addressed the feasibility of using remote earth observations as sources of input data for hydrologic models. The objective of the study reported here was to determine how accurately remotely sensed measurements must be to provide inputs to hydrologic models of watersheds, within the tolerances needed for acceptably accurate synthesis of streamflow by the models. The study objective was achieved by performing a series of sensitivity analyses using continuous simulation models of three watersheds. The sensitivity analysis showed quantitatively how variations in each of 46 model inputs and parameters affect simulation accuracy with respect to five different performance indices.

Cardiac imaging: working towards fully-automated machine analysis & interpretation

PubMed Central

Slomka, Piotr J; Dey, Damini; Sitek, Arkadiusz; Motwani, Manish; Berman, Daniel S; Germano, Guido

2017-01-01

Introduction Non-invasive imaging plays a critical role in managing patients with cardiovascular disease. Although subjective visual interpretation remains the clinical mainstay, quantitative analysis facilitates objective, evidence-based management, and advances in clinical research. This has driven developments in computing and software tools aimed at achieving fully automated image processing and quantitative analysis. In parallel, machine learning techniques have been used to rapidly integrate large amounts of clinical and quantitative imaging data to provide highly personalized individual patient-based conclusions. Areas covered This review summarizes recent advances in automated quantitative imaging in cardiology and describes the latest techniques which incorporate machine learning principles. The review focuses on the cardiac imaging techniques which are in wide clinical use. It also discusses key issues and obstacles for these tools to become utilized in mainstream clinical practice. Expert commentary Fully-automated processing and high-level computer interpretation of cardiac imaging are becoming a reality. Application of machine learning to the vast amounts of quantitative data generated per scan and integration with clinical data also facilitates a move to more patient-specific interpretation. These developments are unlikely to replace interpreting physicians but will provide them with highly accurate tools to detect disease, risk-stratify, and optimize patient-specific treatment. However, with each technological advance, we move further from human dependence and closer to fully-automated machine interpretation. PMID:28277804

Comparison of methods for the concentration of suspended sediment in river water for subsequent chemical analysis

USGS Publications Warehouse

Horowltz, A.J.

1986-01-01

Centrifugation, settling/centrifugation, and backflush-filtration procedures have been tested for the concentration of suspended sediment from water for subsequent trace-metal analysis. Either of the first two procedures is comparable with in-line filtration and can be carried out precisely, accurately, and with a facility that makes the procedures amenable to large-scale sampling and analysis programs. There is less potential for post-sampling alteration of suspended sediment-associated metal concentrations with the centrifugation procedure because sample stabilization is accomplished more rapidly than with settling/centrifugation. Sample preservation can be achieved by chilling. Suspended sediment associated metal levels can best be determined by direct analysis but can also be estimated from the difference between a set of unfiltered-digested and filtered subsamples. However, when suspended sediment concentrations (<150 mg/L) or trace-metal levels are low, the direct analysis approach makes quantitation more accurate and precise and can be accomplished with simpler analytical procedures.

Evaluating the dynamic response of in-flight thrust calculation techniques during throttle transients

NASA Technical Reports Server (NTRS)

Ray, Ronald J.

1994-01-01

New flight test maneuvers and analysis techniques for evaluating the dynamic response of in-flight thrust models during throttle transients have been developed and validated. The approach is based on the aircraft and engine performance relationship between thrust and drag. Two flight test maneuvers, a throttle step and a throttle frequency sweep, were developed and used in the study. Graphical analysis techniques, including a frequency domain analysis method, were also developed and evaluated. They provide quantitative and qualitative results. Four thrust calculation methods were used to demonstrate and validate the test technique. Flight test applications on two high-performance aircraft confirmed the test methods as valid and accurate. These maneuvers and analysis techniques were easy to implement and use. Flight test results indicate the analysis techniques can identify the combined effects of model error and instrumentation response limitations on the calculated thrust value. The methods developed in this report provide an accurate approach for evaluating, validating, or comparing thrust calculation methods for dynamic flight applications.

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.

Quantitative computed tomography for the prediction of pulmonary function after lung cancer surgery: a simple method using simulation software.

PubMed

Ueda, Kazuhiro; Tanaka, Toshiki; Li, Tao-Sheng; Tanaka, Nobuyuki; Hamano, Kimikazu

2009-03-01

The prediction of pulmonary functional reserve is mandatory in therapeutic decision-making for patients with resectable lung cancer, especially those with underlying lung disease. Volumetric analysis in combination with densitometric analysis of the affected lung lobe or segment with quantitative computed tomography (CT) helps to identify residual pulmonary function, although the utility of this modality needs investigation. The subjects of this prospective study were 30 patients with resectable lung cancer. A three-dimensional CT lung model was created with voxels representing normal lung attenuation (-600 to -910 Hounsfield units). Residual pulmonary function was predicted by drawing a boundary line between the lung to be preserved and that to be resected, directly on the lung model. The predicted values were correlated with the postoperative measured values. The predicted and measured values corresponded well (r=0.89, p<0.001). Although the predicted values corresponded with values predicted by simple calculation using a segment-counting method (r=0.98), there were two outliers whose pulmonary functional reserves were predicted more accurately by CT than by segment counting. The measured pulmonary functional reserves were significantly higher than the predicted values in patients with extensive emphysematous areas (<-910 Hounsfield units), but not in patients with chronic obstructive pulmonary disease. Quantitative CT yielded accurate prediction of functional reserve after lung cancer surgery and helped to identify patients whose functional reserves are likely to be underestimated. Hence, this modality should be utilized for patients with marginal pulmonary function.

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

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.

Advanced IR System For Supersonic Boundary Layer Transition Flight Experiment

NASA Technical Reports Server (NTRS)

Banks, Daniel W.

2008-01-01

Infrared thermography is a preferred method investigating transition in flight: a) Global and non-intrusive; b) Can also be used to visualize and characterize other fluid mechanic phenomena such as shock impingement, separation etc. F-15 based system was updated with new camera and digital video recorder to support high Reynolds number transition tests. Digital Recording improves image quality and analysis capability and allows for accurate quantitative (temperature) measurements and greater enhancement through image processing allows analysis of smaller scale phenomena.

Detection and Characterization of Boundary-Layer Transition in Flight at Supersonic Conditions Using Infrared Thermography

NASA Technical Reports Server (NTRS)

Banks, Daniel W.

2008-01-01

Infrared thermography is a powerful tool for investigating fluid mechanics on flight vehicles. (Can be used to visualize and characterize transition, shock impingement, separation etc.). Updated onboard F-15 based system was used to visualize supersonic boundary layer transition test article. (Tollmien-Schlichting and cross-flow dominant flow fields). Digital Recording improves image quality and analysis capability. (Allows accurate quantitative (temperature) measurements, Greater enhancement through image processing allows analysis of smaller scale phenomena).

A novel simple QSAR model for the prediction of anti-HIV activity using multiple linear regression analysis.

PubMed

Afantitis, Antreas; Melagraki, Georgia; Sarimveis, Haralambos; Koutentis, Panayiotis A; Markopoulos, John; Igglessi-Markopoulou, Olga

2006-08-01

A quantitative-structure activity relationship was obtained by applying Multiple Linear Regression Analysis to a series of 80 1-[2-hydroxyethoxy-methyl]-6-(phenylthio) thymine (HEPT) derivatives with significant anti-HIV activity. For the selection of the best among 37 different descriptors, the Elimination Selection Stepwise Regression Method (ES-SWR) was utilized. The resulting QSAR model (R (2) (CV) = 0.8160; S (PRESS) = 0.5680) proved to be very accurate both in training and predictive stages.

DIGE Analysis of Human Tissues.

PubMed

Gelfi, Cecilia; Capitanio, Daniele

2018-01-01

Two-dimensional difference gel electrophoresis (2-D DIGE) is an advanced and elegant gel electrophoretic analytical tool for comparative protein assessment. It is based on two-dimensional gel electrophoresis (2-DE) separation of fluorescently labeled protein extracts. The tagging procedures are designed to not interfere with the chemical properties of proteins with respect to their pI and electrophoretic mobility, once a proper labeling protocol is followed. The two-dye or three-dye systems can be adopted and their choice depends on specific applications. Furthermore, the use of an internal pooled standard makes 2-D DIGE a highly accurate quantitative method enabling multiple protein samples to be separated on the same two-dimensional gel. The image matching and cross-gel statistical analysis generates robust quantitative results making data validation by independent technologies successful.

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.

Variation in seed dormancy quantitative trait loci in Arabidopsis thaliana originating from one site.

PubMed

Silady, Rebecca A; Effgen, Sigi; Koornneef, Maarten; Reymond, Matthieu

2011-01-01

A Quantitative Trait Locus (QTL) analysis was performed using two novel Recombinant Inbred Line (RIL) populations, derived from the progeny between two Arabidopsis thaliana genotypes collected at the same site in Kyoto (Japan) crossed with the reference laboratory strain Landsberg erecta (Ler). We used these two RIL populations to determine the genetic basis of seed dormancy and flowering time, which are assumed to be the main traits controlling life history variation in Arabidopsis. The analysis revealed quantitative variation for seed dormancy that is associated with allelic variation at the seed dormancy QTL DOG1 (for Delay Of Germination 1) in one population and at DOG6 in both. These DOG QTL have been previously identified using mapping populations derived from accessions collected at different sites around the world. Genetic variation within a population may enhance its ability to respond accurately to variation within and between seasons. In contrast, variation for flowering time, which also segregated within each mapping population, is mainly governed by the same QTL.

Quantitation of sweet steviol glycosides by means of a HILIC-MS/MS-SIDA approach.

PubMed

Well, Caroline; Frank, Oliver; Hofmann, Thomas

2013-11-27

Meeting the rising consumer demand for natural food ingredients, steviol glycosides, the sweet principle of Stevia rebaudiana Bertoni (Bertoni), have recently been approved as food additives in the European Union. As regulatory constraints require sensitive methods to analyze the sweet-tasting steviol glycosides in foods and beverages, a HILIC-MS/MS method was developed enabling the accurate and reliable quantitation of the major steviol glycosides stevioside, rebaudiosides A-F, steviolbioside, rubusoside, and dulcoside A by using the corresponding deuterated 16,17-dihydrosteviol glycosides as suitable internal standards. This quantitation not only enables the analysis of the individual steviol glycosides in foods and beverages but also can support the optimization of breeding and postharvest downstream processing of Stevia plants to produce preferentially sweet and least bitter tasting Stevia extracts.

The Separation and Quantitation of Peptides with and without Oxidation of Methionine and Deamidation of Asparagine Using Hydrophilic Interaction Liquid Chromatography with Mass Spectrometry (HILIC-MS)

NASA Astrophysics Data System (ADS)

Badgett, Majors J.; Boyes, Barry; Orlando, Ron

2017-05-01

Peptides with deamidated asparagine residues and oxidized methionine residues are often not resolved sufficiently to allow quantitation of their native and modified forms using reversed phase (RP) chromatography. The accurate quantitation of these modifications is vital in protein biotherapeutic analysis because they can affect a protein's function, activity, and stability. We demonstrate here that hydrophilic interaction liquid chromatography (HILIC) adequately and predictably separates peptides with these modifications from their native counterparts. Furthermore, coefficients describing the extent of the hydrophilicity of these modifications have been derived and were incorporated into a previously made peptide retention prediction model that is capable of predicting the retention times of peptides with and without these modifications.

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.

The Separation and Quantitation of Peptides with and without Oxidation of Methionine and Deamidation of Asparagine Using Hydrophilic Interaction Liquid Chromatography with Mass Spectrometry (HILIC-MS).

PubMed

Badgett, Majors J; Boyes, Barry; Orlando, Ron

2017-05-01

Peptides with deamidated asparagine residues and oxidized methionine residues are often not resolved sufficiently to allow quantitation of their native and modified forms using reversed phase (RP) chromatography. The accurate quantitation of these modifications is vital in protein biotherapeutic analysis because they can affect a protein's function, activity, and stability. We demonstrate here that hydrophilic interaction liquid chromatography (HILIC) adequately and predictably separates peptides with these modifications from their native counterparts. Furthermore, coefficients describing the extent of the hydrophilicity of these modifications have been derived and were incorporated into a previously made peptide retention prediction model that is capable of predicting the retention times of peptides with and without these modifications. Graphical Abstract ᅟ.

Reliable enumeration of malaria parasites in thick blood films using digital image analysis.

PubMed

Frean, John A

2009-09-23

Quantitation of malaria parasite density is an important component of laboratory diagnosis of malaria. Microscopy of Giemsa-stained thick blood films is the conventional method for parasite enumeration. Accurate and reproducible parasite counts are difficult to achieve, because of inherent technical limitations and human inconsistency. Inaccurate parasite density estimation may have adverse clinical and therapeutic implications for patients, and for endpoints of clinical trials of anti-malarial vaccines or drugs. Digital image analysis provides an opportunity to improve performance of parasite density quantitation. Accurate manual parasite counts were done on 497 images of a range of thick blood films with varying densities of malaria parasites, to establish a uniformly reliable standard against which to assess the digital technique. By utilizing descriptive statistical parameters of parasite size frequency distributions, particle counting algorithms of the digital image analysis programme were semi-automatically adapted to variations in parasite size, shape and staining characteristics, to produce optimum signal/noise ratios. A reliable counting process was developed that requires no operator decisions that might bias the outcome. Digital counts were highly correlated with manual counts for medium to high parasite densities, and slightly less well correlated with conventional counts. At low densities (fewer than 6 parasites per analysed image) signal/noise ratios were compromised and correlation between digital and manual counts was poor. Conventional counts were consistently lower than both digital and manual counts. Using open-access software and avoiding custom programming or any special operator intervention, accurate digital counts were obtained, particularly at high parasite densities that are difficult to count conventionally. The technique is potentially useful for laboratories that routinely perform malaria parasite enumeration. The requirements of a digital microscope camera, personal computer and good quality staining of slides are potentially reasonably easy to meet.

Isotope-dilution gas chromatography-mass spectrometry method for the analysis of hydroxyurea.

PubMed

Garg, Uttam; Scott, David; Frazee, Clint; Kearns, Gregory; Neville, Kathleen

2015-06-01

Hydroxyurea is used in the treatment of various malignancies and sickle cell disease. There are limited studies on the pharmacokinetics of hydroxyurea, particularly in pediatric patients. An accurate, precise, and sensitive method is needed to support such studies and to monitor therapeutic adherence. We describe a novel gas chromatography-mass spectrometry (GC-MS) method for the determination of hydroxyurea concentration in plasma using stable labeled hydroxyurea C N2 as an internal standard. The method involved an organic extraction followed by the preparation of trimethylsilyl (TMS) derivatives of hydroxyurea for GC-MS selected ion-monitoring analysis. The following mass-to-charge (m/z) ratio ions for silated hydroxyurea and hydroxyurea C N2 were monitored: hydroxyurea-quantitative ion 277, qualifier ions 292 and 249; hydroxyurea C N2-quantitative ion 280, qualifier ion 295. This method was evaluated for reportable range, accuracy, within-run and between-run imprecisions, and limits of quantification. The reportable range for the method was 0.1-100 mcg/mL. All results were accurate within an allowable error of 15%. Within-run and between-run imprecisions were <15%. Samples were stable for at least 4 hours at room temperature, 2 months at -20°C, and 6 months at -70°C, and after 3 freeze/thaw cycles. Extraction efficiency for 1-, 5-, 10-, and 50-mcg/mL samples averaged 2.2%, 1.8%, 1.6%, and 1.4%, respectively. The isotope-dilution GC-MS method for analysis of hydroxyurea described here is accurate, sensitive, precise, and robust. Its characteristics make the method suitable for supporting pharmacokinetic studies and/or clinical therapeutic monitoring.

Tissue-based quantitative proteome analysis of human hepatocellular carcinoma using tandem mass tags.

PubMed

Megger, Dominik Andre; Rosowski, Kristin; Ahrens, Maike; Bracht, Thilo; Eisenacher, Martin; Schlaak, Jörg F; Weber, Frank; Hoffmann, Andreas-Claudius; Meyer, Helmut E; Baba, Hideo A; Sitek, Barbara

2017-03-01

Human hepatocellular carcinoma (HCC) is a severe malignant disease, and accurate and reliable diagnostic markers are still needed. This study was aimed for the discovery of novel marker candidates by quantitative proteomics. Proteomic differences between HCC and nontumorous liver tissue were studied by mass spectrometry. Among several significantly upregulated proteins, translocator protein 18 (TSPO) and Ras-related protein Rab-1A (RAB1A) were selected for verification by immunohistochemistry in an independent cohort. For RAB1A, a high accuracy for the discrimination of HCC and nontumorous liver tissue was observed. RAB1A was verified to be a potent biomarker candidate for HCC.

Quality evaluation of LC-MS/MS-based E. coli H antigen typing (MS-H) through label-free quantitative data analysis in a clinical sample setup.

PubMed

Cheng, Keding; Sloan, Angela; McCorrister, Stuart; Peterson, Lorea; Chui, Huixia; Drebot, Mike; Nadon, Celine; Knox, J David; Wang, Gehua

2014-12-01

The need for rapid and accurate H typing is evident during Escherichia coli outbreak situations. This study explores the transition of MS-H, a method originally developed for rapid H antigen typing of E. coli using LC-MS/MS of flagella digest of reference strains and some clinical strains, to E. coli isolates in clinical scenario through quantitative analysis and method validation. Motile and nonmotile strains were examined in batches to simulate clinical sample scenario. Various LC-MS/MS batch run procedures and MS-H typing rules were compared and summarized through quantitative analysis of MS-H data output for a standard method development. Label-free quantitative data analysis of MS-H typing was proven very useful for examining the quality of MS-H result and the effects of some sample carryovers from motile E. coli isolates. Based on this, a refined procedure and protein identification rule specific for clinical MS-H typing was established and validated. With LC-MS/MS batch run procedure and database search parameter unique for E. coli MS-H typing, the standard procedure maintained high accuracy and specificity in clinical situations, and its potential to be used in a clinical setting was clearly established. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Quantitative analysis of glycerophospholipids by LC-MS: acquisition, data handling, and interpretation

PubMed Central

Myers, David S.; Ivanova, Pavlina T.; Milne, Stephen B.; Brown, H. Alex

2012-01-01

As technology expands what it is possible to accurately measure, so too the challenges faced by modern mass spectrometry applications expand. A high level of accuracy in lipid quantitation across thousands of chemical species simultaneously is demanded. While relative changes in lipid amounts with varying conditions may provide initial insights or point to novel targets, there are many questions that require determination of lipid analyte absolute quantitation. Glycerophospholipids present a significant challenge in this regard, given the headgroup diversity, large number of possible acyl chain combinations, and vast range of ionization efficiency of species. Lipidomic output is being used more often not just for profiling of the masses of species, but also for highly-targeted flux-based measurements which put additional burdens on the quantitation pipeline. These first two challenges bring into sharp focus the need for a robust lipidomics workflow including deisotoping, differentiation from background noise, use of multiple internal standards per lipid class, and the use of a scriptable environment in order to create maximum user flexibility and maintain metadata on the parameters of the data analysis as it occurs. As lipidomics technology develops and delivers more output on a larger number of analytes, so must the sophistication of statistical post-processing also continue to advance. High-dimensional data analysis methods involving clustering, lipid pathway analysis, and false discovery rate limitation are becoming standard practices in a maturing field. PMID:21683157

Quantification of the methylation status of the PWS/AS imprinted region: comparison of two approaches based on bisulfite sequencing and methylation-sensitive MLPA.

PubMed

Dikow, Nicola; Nygren, Anders Oh; Schouten, Jan P; Hartmann, Carolin; Krämer, Nikola; Janssen, Bart; Zschocke, Johannes

2007-06-01

Standard methods used for genomic methylation analysis allow the detection of complete absence of either methylated or non-methylated alleles but are usually unable to detect changes in the proportion of methylated and unmethylated alleles. We compare two methods for quantitative methylation analysis, using the chromosome 15q11-q13 imprinted region as model. Absence of the non-methylated paternal allele in this region leads to Prader-Willi syndrome (PWS) whilst absence of the methylated maternal allele results in Angelman syndrome (AS). A proportion of AS is caused by mosaic imprinting defects which may be missed with standard methods and require quantitative analysis for their detection. Sequence-based quantitative methylation analysis (SeQMA) involves quantitative comparison of peaks generated through sequencing reactions after bisulfite treatment. It is simple, cost-effective and can be easily established for a large number of genes. However, our results support previous suggestions that methods based on bisulfite treatment may be problematic for exact quantification of methylation status. Methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) avoids bisulfite treatment. It detects changes in both CpG methylation as well as copy number of up to 40 chromosomal sequences in one simple reaction. Once established in a laboratory setting, the method is more accurate, reliable and less time consuming.

Predictive value of EEG in postanoxic encephalopathy: A quantitative model-based approach.

PubMed

Efthymiou, Evdokia; Renzel, Roland; Baumann, Christian R; Poryazova, Rositsa; Imbach, Lukas L

2017-10-01

The majority of comatose patients after cardiac arrest do not regain consciousness due to severe postanoxic encephalopathy. Early and accurate outcome prediction is therefore essential in determining further therapeutic interventions. The electroencephalogram is a standardized and commonly available tool used to estimate prognosis in postanoxic patients. The identification of pathological EEG patterns with poor prognosis relies however primarily on visual EEG scoring by experts. We introduced a model-based approach of EEG analysis (state space model) that allows for an objective and quantitative description of spectral EEG variability. We retrospectively analyzed standard EEG recordings in 83 comatose patients after cardiac arrest between 2005 and 2013 in the intensive care unit of the University Hospital Zürich. Neurological outcome was assessed one month after cardiac arrest using the Cerebral Performance Category. For a dynamic and quantitative EEG analysis, we implemented a model-based approach (state space analysis) to quantify EEG background variability independent from visual scoring of EEG epochs. Spectral variability was compared between groups and correlated with clinical outcome parameters and visual EEG patterns. Quantitative assessment of spectral EEG variability (state space velocity) revealed significant differences between patients with poor and good outcome after cardiac arrest: Lower mean velocity in temporal electrodes (T4 and T5) was significantly associated with poor prognostic outcome (p<0.005) and correlated with independently identified visual EEG patterns such as generalized periodic discharges (p<0.02). Receiver operating characteristic (ROC) analysis confirmed the predictive value of lower state space velocity for poor clinical outcome after cardiac arrest (AUC 80.8, 70% sensitivity, 15% false positive rate). Model-based quantitative EEG analysis (state space analysis) provides a novel, complementary marker for prognosis in postanoxic encephalopathy. Copyright © 2017 Elsevier B.V. All rights reserved.

Segmentation and Quantitative Analysis of Apoptosis of Chinese Hamster Ovary Cells from Fluorescence Microscopy Images.

PubMed

Du, Yuncheng; Budman, Hector M; Duever, Thomas A

2017-06-01

Accurate and fast quantitative analysis of living cells from fluorescence microscopy images is useful for evaluating experimental outcomes and cell culture protocols. An algorithm is developed in this work to automatically segment and distinguish apoptotic cells from normal cells. The algorithm involves three steps consisting of two segmentation steps and a classification step. The segmentation steps are: (i) a coarse segmentation, combining a range filter with a marching square method, is used as a prefiltering step to provide the approximate positions of cells within a two-dimensional matrix used to store cells' images and the count of the number of cells for a given image; and (ii) a fine segmentation step using the Active Contours Without Edges method is applied to the boundaries of cells identified in the coarse segmentation step. Although this basic two-step approach provides accurate edges when the cells in a given image are sparsely distributed, the occurrence of clusters of cells in high cell density samples requires further processing. Hence, a novel algorithm for clusters is developed to identify the edges of cells within clusters and to approximate their morphological features. Based on the segmentation results, a support vector machine classifier that uses three morphological features: the mean value of pixel intensities in the cellular regions, the variance of pixel intensities in the vicinity of cell boundaries, and the lengths of the boundaries, is developed for distinguishing apoptotic cells from normal cells. The algorithm is shown to be efficient in terms of computational time, quantitative analysis, and differentiation accuracy, as compared with the use of the active contours method without the proposed preliminary coarse segmentation step.

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.

Predicting Team Performance through Human Behavioral Sensing and Quantitative Workflow Instrumentation

DTIC Science & Technology

2016-07-27

make risk-informed decisions during serious games . Statistical models of intra- game performance were developed to determine whether behaviors in...specific facets of the gameplay workflow were predictive of analytical performance and games outcomes. A study of over seventy instrumented teams revealed...more accurate game decisions. 2 Keywords: Humatics · Serious Games · Human-System Interaction · Instrumentation · Teamwork · Communication Analysis

Quantitation of influenza virus using field flow fractionation and multi-angle light scattering for quantifying influenza A particles

PubMed Central

Bousse, Tatiana; Shore, David A.; Goldsmith, Cynthia S.; Hossain, M. Jaber; Jang, Yunho; Davis, Charles T.; Donis, Ruben O.; Stevens, James

2017-01-01

Summary Recent advances in instrumentation and data analysis in field flow fractionation and multi-angle light scattering (FFF-MALS) have enabled greater use of this technique to characterize and quantitate viruses. In this study, the FFF-MALS technique was applied to the characterization and quantitation of type A influenza virus particles to assess its usefulness for vaccine preparation. The use of FFF-MALS for quantitation and measurement of control particles provided data accurate to within 5% of known values, reproducible with a coefficient of variation of 1.9 %. The methods, sensitivity and limit of detection were established by analyzing different volumes of purified virus, which produced a linear regression with fitting value R2 of 0.99. FFF-MALS was further applied to detect and quantitate influenza virus in the supernatant of infected MDCK cells and allantoic fluids of infected eggs. FFF fractograms of the virus present in these different fluids revealed similar distribution of monomeric and oligomeric virions. However, the monomer fraction of cell grown virus has greater size variety. Notably, β-propialactone (BPL) inactivation of influenza viruses did not influence any of the FFF-MALS measurements. Quantitation analysis by FFF-MALS was compared to infectivity assays and real-time RT-PCR (qRT-PCR) and the limitations of each assay were discussed. PMID:23916678

Evaluation of the performance of high temperature conversion reactors for compound-specific oxygen stable isotope analysis.

PubMed

Hitzfeld, Kristina L; Gehre, Matthias; Richnow, Hans-Hermann

2017-05-01

In this study conversion conditions for oxygen gas chromatography high temperature conversion (HTC) isotope ratio mass spectrometry (IRMS) are characterised using qualitative mass spectrometry (IonTrap). It is shown that physical and chemical properties of a given reactor design impact HTC and thus the ability to accurately measure oxygen isotope ratios. Commercially available and custom-built tube-in-tube reactors were used to elucidate (i) by-product formation (carbon dioxide, water, small organic molecules), (ii) 2nd sources of oxygen (leakage, metal oxides, ceramic material), and (iii) required reactor conditions (conditioning, reduction, stability). The suitability of the available HTC approach for compound-specific isotope analysis of oxygen in volatile organic molecules like methyl tert-butyl ether is assessed. Main problems impeding accurate analysis are non-quantitative HTC and significant carbon dioxide by-product formation. An evaluation strategy combining mass spectrometric analysis of HTC products and IRMS 18 O/ 16 O monitoring for future method development is proposed.

Quantitative measurement and analysis for detection and treatment planning of developmental dysplasia of the hip

NASA Astrophysics Data System (ADS)

Liu, Xin; Lu, Hongbing; Chen, Hanyong; Zhao, Li; Shi, Zhengxing; Liang, Zhengrong

2009-02-01

Developmental dysplasia of the hip is a congenital hip joint malformation affecting the proximal femurs and acetabulum that are subluxatable, dislocatable, and dislocated. Conventionally, physicians made diagnoses and treatments only based on findings from two-dimensional (2D) images by manually calculating clinic parameters. However, anatomical complexity of the disease and the limitation of current standard procedures make accurate diagnosis quite difficultly. In this study, we developed a system that provides quantitative measurement of 3D clinical indexes based on computed tomography (CT) images. To extract bone structure from surrounding tissues more accurately, the system firstly segments the bone using a knowledge-based fuzzy clustering method, which is formulated by modifying the objective function of the standard fuzzy c-means algorithm with additive adaptation penalty. The second part of the system calculates automatically the clinical indexes, which are extended from 2D to 3D for accurate description of spatial relationship between femurs and acetabulum. To evaluate the system performance, experimental study based on 22 patients with unilateral or bilateral affected hip was performed. The results of 3D acetabulum index (AI) automatically provided by the system were validated by comparison with 2D results measured by surgeons manually. The correlation between the two results was found to be 0.622 (p<0.01).

Inconsistencies in reporting risk information: a pilot analysis of online news coverage of West Nile Virus.

PubMed

Birnbrauer, Kristina; Frohlich, Dennis Owen; Treise, Debbie

2017-09-01

West Nile Virus (WNV) has been reported as one of the worst epidemics in US history. This study sought to understand how WNV news stories were framed and how risk information was portrayed from its 1999 arrival in the US through the year 2012. The authors conducted a quantitative content analysis of online news articles obtained through Google News ( N = 428). The results of this analysis were compared to the CDC's ArboNET surveillance system. The following story frames were identified in this study: action, conflict, consequence, new evidence, reassurance and uncertainty, with the action frame appearing most frequently. Risk was communicated quantitatively without context in the majority of articles, and only in 2006, the year with the third-highest reported deaths, was risk reported with statistical accuracy. The results from the analysis indicated that at-risk communities were potentially under-informed as accurate risks were not communicated. This study offers evidence about how disease outbreaks are covered in relation to actual disease surveillance data.

Determination of left ventricular volume, ejection fraction, and myocardial mass by real-time three-dimensional echocardiography

NASA Technical Reports Server (NTRS)

Qin, J. X.; Shiota, T.; Thomas, J. D.

2000-01-01

Reconstructed three-dimensional (3-D) echocardiography is an accurate and reproducible method of assessing left ventricular (LV) functions. However, it has limitations for clinical study due to the requirement of complex computer and echocardiographic analysis systems, electrocardiographic/respiratory gating, and prolonged imaging times. Real-time 3-D echocardiography has a major advantage of conveniently visualizing the entire cardiac anatomy in three dimensions and of potentially accurately quantifying LV volumes, ejection fractions, and myocardial mass in patients even in the presence of an LV aneurysm. Although the image quality of the current real-time 3-D echocardiographic methods is not optimal, its widespread clinical application is possible because of the convenient and fast image acquisition. We review real-time 3-D echocardiographic image acquisition and quantitative analysis for the evaluation of LV function and LV mass.

Determination of left ventricular volume, ejection fraction, and myocardial mass by real-time three-dimensional echocardiography.

PubMed

Qin, J X; Shiota, T; Thomas, J D

2000-11-01

Reconstructed three-dimensional (3-D) echocardiography is an accurate and reproducible method of assessing left ventricular (LV) functions. However, it has limitations for clinical study due to the requirement of complex computer and echocardiographic analysis systems, electrocardiographic/respiratory gating, and prolonged imaging times. Real-time 3-D echocardiography has a major advantage of conveniently visualizing the entire cardiac anatomy in three dimensions and of potentially accurately quantifying LV volumes, ejection fractions, and myocardial mass in patients even in the presence of an LV aneurysm. Although the image quality of the current real-time 3-D echocardiographic methods is not optimal, its widespread clinical application is possible because of the convenient and fast image acquisition. We review real-time 3-D echocardiographic image acquisition and quantitative analysis for the evaluation of LV function and LV mass.

Human eyeball model reconstruction and quantitative analysis.

PubMed

Xing, Qi; Wei, Qi

2014-01-01

Determining shape of the eyeball is important to diagnose eyeball disease like myopia. In this paper, we present an automatic approach to precisely reconstruct three dimensional geometric shape of eyeball from MR Images. The model development pipeline involved image segmentation, registration, B-Spline surface fitting and subdivision surface fitting, neither of which required manual interaction. From the high resolution resultant models, geometric characteristics of the eyeball can be accurately quantified and analyzed. In addition to the eight metrics commonly used by existing studies, we proposed two novel metrics, Gaussian Curvature Analysis and Sphere Distance Deviation, to quantify the cornea shape and the whole eyeball surface respectively. The experiment results showed that the reconstructed eyeball models accurately represent the complex morphology of the eye. The ten metrics parameterize the eyeball among different subjects, which can potentially be used for eye disease diagnosis.

A novel visual-inertial monocular SLAM

NASA Astrophysics Data System (ADS)

Yue, Xiaofeng; Zhang, Wenjuan; Xu, Li; Liu, JiangGuo

2018-02-01

With the development of sensors and computer vision research community, cameras, which are accurate, compact, wellunderstood and most importantly cheap and ubiquitous today, have gradually been at the center of robot location. Simultaneous localization and mapping (SLAM) using visual features, which is a system getting motion information from image acquisition equipment and rebuild the structure in unknown environment. We provide an analysis of bioinspired flights in insects, employing a novel technique based on SLAM. Then combining visual and inertial measurements to get high accuracy and robustness. we present a novel tightly-coupled Visual-Inertial Simultaneous Localization and Mapping system which get a new attempt to address two challenges which are the initialization problem and the calibration problem. experimental results and analysis show the proposed approach has a more accurate quantitative simulation of insect navigation, which can reach the positioning accuracy of centimeter level.

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

Clinical significance of quantitative analysis of facial nerve enhancement on MRI in Bell's palsy.

PubMed

Song, Mee Hyun; Kim, Jinna; Jeon, Ju Hyun; Cho, Chang Il; Yoo, Eun Hye; Lee, Won-Sang; Lee, Ho-Ki

2008-11-01

Quantitative analysis of the facial nerve on the lesion side as well as the normal side, which allowed for more accurate measurement of facial nerve enhancement in patients with facial palsy, showed statistically significant correlation with the initial severity of facial nerve inflammation, although little prognostic significance was shown. This study investigated the clinical significance of quantitative measurement of facial nerve enhancement in patients with Bell's palsy by analyzing the enhancement pattern and correlating MRI findings with initial severity of facial palsy and clinical outcome. Facial nerve enhancement was measured quantitatively by using the region of interest on pre- and postcontrast T1-weighted images in 44 patients diagnosed with Bell's palsy. The signal intensity increase on the lesion side was first compared with that of the contralateral side and then correlated with the initial degree of facial palsy and prognosis. The lesion side showed significantly higher signal intensity increase compared with the normal side in all of the segments except for the mastoid segment. Signal intensity increase at the internal auditory canal and labyrinthine segments showed correlation with the initial degree of facial palsy but no significant difference was found between different prognostic groups.

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.

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.

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

Biomarkers identified by urinary metabonomics for noninvasive diagnosis of nutritional rickets.

PubMed

Wang, Maoqing; Yang, Xue; Ren, Lihong; Li, Songtao; He, Xuan; Wu, Xiaoyan; Liu, Tingting; Lin, Liqun; Li, Ying; Sun, Changhao

2014-09-05

Nutritional rickets is a worldwide public health problem; however, the current diagnostic methods retain shortcomings for accurate diagnosis of nutritional rickets. To identify urinary biomarkers associated with nutritional rickets and establish a noninvasive diagnosis method, urinary metabonomics analysis by ultra-performance liquid chromatography/quadrupole time-of-flight tandem mass spectrometry and multivariate statistical analysis were employed to investigate the metabolic alterations associated with nutritional rickets in 200 children with or without nutritional rickets. The pathophysiological changes and pathogenesis of nutritional rickets were illustrated by the identified biomarkers. By urinary metabolic profiling, 31 biomarkers of nutritional rickets were identified and five candidate biomarkers for clinical diagnosis were screened and identified by quantitative analysis and receiver operating curve analysis. Urinary levels of five candidate biomarkers were measured using mass spectrometry or commercial kits. In the validation step, the combination of phosphate and sebacic acid was able to give a noninvasive and accurate diagnostic with high sensitivity (94.0%) and specificity (71.2%). Furthermore, on the basis of the pathway analysis of biomarkers, our urinary metabonomics analysis gives new insight into the pathogenesis and pathophysiology of nutritional rickets.

Impact of TRMM and SSM/I Rainfall Assimilation on Global Analysis and QPF

NASA Technical Reports Server (NTRS)

Hou, Arthur; Zhang, Sara; Reale, Oreste

2002-01-01

Evaluation of QPF skills requires quantitatively accurate precipitation analyses. We show that assimilation of surface rain rates derived from the Tropical Rainfall Measuring Mission (TRMM) Microwave Imager and Special Sensor Microwave/Imager (SSM/I) improves quantitative precipitation estimates (QPE) and many aspects of global analyses. Short-range forecasts initialized with analyses with satellite rainfall data generally yield significantly higher QPF threat scores and better storm track predictions. These results were obtained using a variational procedure that minimizes the difference between the observed and model rain rates by correcting the moist physics tendency of the forecast model over a 6h assimilation window. In two case studies of Hurricanes Bonnie and Floyd, synoptic analysis shows that this procedure produces initial conditions with better-defined tropical storm features and stronger precipitation intensity associated with the storm.

Quantitative analysis and comparative study of four cities green pattern in API system on the background of big data

NASA Astrophysics Data System (ADS)

Xin, YANG; Si-qi, WU; Qi, ZHANG

2018-05-01

Beijing, London, Paris, New York are typical cities in the world, so comparative study of four cities green pattern is very important to find out gap and advantage and to learn from each other. The paper will provide basis and new ideas for development of metropolises in China. On the background of big data, API (Application Programming Interface) system can provide extensive and accurate basic data to study urban green pattern in different geographical environment in domestic and foreign. On the basis of this, Average nearest neighbor tool, Kernel density tool and Standard Ellipse tool in ArcGIS platform can process and summarize data and realize quantitative analysis of green pattern. The paper summarized uniqueness of four cities green pattern and reasons of formation on basis of numerical comparison.

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.

A review of empirical research related to the use of small quantitative samples in clinical outcome scale development.

PubMed

Houts, Carrie R; Edwards, Michael C; Wirth, R J; Deal, Linda S

2016-11-01

There has been a notable increase in the advocacy of using small-sample designs as an initial quantitative assessment of item and scale performance during the scale development process. This is particularly true in the development of clinical outcome assessments (COAs), where Rasch analysis has been advanced as an appropriate statistical tool for evaluating the developing COAs using a small sample. We review the benefits such methods are purported to offer from both a practical and statistical standpoint and detail several problematic areas, including both practical and statistical theory concerns, with respect to the use of quantitative methods, including Rasch-consistent methods, with small samples. The feasibility of obtaining accurate information and the potential negative impacts of misusing large-sample statistical methods with small samples during COA development are discussed.

Nanoparticle surface characterization and clustering through concentration-dependent surface adsorption modeling.

PubMed

Chen, Ran; Zhang, Yuntao; Sahneh, Faryad Darabi; Scoglio, Caterina M; Wohlleben, Wendel; Haase, Andrea; Monteiro-Riviere, Nancy A; Riviere, Jim E

2014-09-23

Quantitative characterization of nanoparticle interactions with their surrounding environment is vital for safe nanotechnological development and standardization. A recent quantitative measure, the biological surface adsorption index (BSAI), has demonstrated promising applications in nanomaterial surface characterization and biological/environmental prediction. This paper further advances the approach beyond the application of five descriptors in the original BSAI to address the concentration dependence of the descriptors, enabling better prediction of the adsorption profile and more accurate categorization of nanomaterials based on their surface properties. Statistical analysis on the obtained adsorption data was performed based on three different models: the original BSAI, a concentration-dependent polynomial model, and an infinite dilution model. These advancements in BSAI modeling showed a promising development in the application of quantitative predictive modeling in biological applications, nanomedicine, and environmental safety assessment of nanomaterials.

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

PubMed

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

2017-12-01

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

Leveraging unsupervised training sets for multi-scale compartmentalization in renal pathology

NASA Astrophysics Data System (ADS)

Lutnick, Brendon; Tomaszewski, John E.; Sarder, Pinaki

2017-03-01

Clinical pathology relies on manual compartmentalization and quantification of biological structures, which is time consuming and often error-prone. Application of computer vision segmentation algorithms to histopathological image analysis, in contrast, can offer fast, reproducible, and accurate quantitative analysis to aid pathologists. Algorithms tunable to different biologically relevant structures can allow accurate, precise, and reproducible estimates of disease states. In this direction, we have developed a fast, unsupervised computational method for simultaneously separating all biologically relevant structures from histopathological images in multi-scale. Segmentation is achieved by solving an energy optimization problem. Representing the image as a graph, nodes (pixels) are grouped by minimizing a Potts model Hamiltonian, adopted from theoretical physics, modeling interacting electron spins. Pixel relationships (modeled as edges) are used to update the energy of the partitioned graph. By iteratively improving the clustering, the optimal number of segments is revealed. To reduce computational time, the graph is simplified using a Cantor pairing function to intelligently reduce the number of included nodes. The classified nodes are then used to train a multiclass support vector machine to apply the segmentation over the full image. Accurate segmentations of images with as many as 106 pixels can be completed only in 5 sec, allowing for attainable multi-scale visualization. To establish clinical potential, we employed our method in renal biopsies to quantitatively visualize for the first time scale variant compartments of heterogeneous intra- and extraglomerular structures simultaneously. Implications of the utility of our method extend to fields such as oncology, genomics, and non-biological problems.

Characterization and quantitative analysis of surfactants in textile wastewater by liquid chromatography/quadrupole-time-of-flight mass spectrometry.

PubMed

González, Susana; Petrović, Mira; Radetic, Maja; Jovancic, Petar; Ilic, Vesna; Barceló, Damià

2008-05-01

A method based on the application of ultra-performance liquid chromatography (UPLC) coupled to hybrid quadrupole-time-of-flight mass spectrometry (QqTOF-MS) with an electrospray (ESI) interface has been developed for the screening and confirmation of several anionic and non-ionic surfactants: linear alkylbenzenesulfonates (LAS), alkylsulfate (AS), alkylethersulfate (AES), dihexyl sulfosuccinate (DHSS), alcohol ethoxylates (AEOs), coconut diethanolamide (CDEA), nonylphenol ethoxylates (NPEOs), and their degradation products (nonylphenol carboxylate (NPEC), octylphenol carboxylate (OPEC), 4-nonylphenol (NP), 4-octylphenol (OP) and NPEO sulfate (NPEO-SO4). The developed methodology permits reliable quantification combined with a high accuracy confirmation based on the accurate mass of the (de)protonated molecules in the TOFMS mode. For further confirmation of the identity of the detected compounds the QqTOF mode was used. Accurate masses of product ions obtained by performing collision-induced dissociation (CID) of the (de)protonated molecules of parent compounds were matched with the ions obtained for a standard solution. The method was applied for the quantitative analysis and high accuracy confirmation of surfactants in complex mixtures in effluents from the textile industry. Positive identification of the target compounds was based on accurate mass measurement of the base peak, at least one product ion and the LC retention time of the analyte compared with that of a standard. The most frequently surfactants found in these textile effluents were NPEO and NPEO-SO4 in concentrations ranging from 0.93 to 5.68 mg/L for NPEO and 0.06 to 4.30 mg/L for NPEO-SO4. AEOs were also identified.

Improving efficacy of metastatic tumor segmentation to facilitate early prediction of ovarian cancer patients' response to chemotherapy

NASA Astrophysics Data System (ADS)

Danala, Gopichandh; Wang, Yunzhi; Thai, Theresa; Gunderson, Camille C.; Moxley, Katherine M.; Moore, Kathleen; Mannel, Robert S.; Cheng, Samuel; Liu, Hong; Zheng, Bin; Qiu, Yuchen

2017-02-01

Accurate tumor segmentation is a critical step in the development of the computer-aided detection (CAD) based quantitative image analysis scheme for early stage prognostic evaluation of ovarian cancer patients. The purpose of this investigation is to assess the efficacy of several different methods to segment the metastatic tumors occurred in different organs of ovarian cancer patients. In this study, we developed a segmentation scheme consisting of eight different algorithms, which can be divided into three groups: 1) Region growth based methods; 2) Canny operator based methods; and 3) Partial differential equation (PDE) based methods. A number of 138 tumors acquired from 30 ovarian cancer patients were used to test the performance of these eight segmentation algorithms. The results demonstrate each of the tested tumors can be successfully segmented by at least one of the eight algorithms without the manual boundary correction. Furthermore, modified region growth, classical Canny detector, and fast marching, and threshold level set algorithms are suggested in the future development of the ovarian cancer related CAD schemes. This study may provide meaningful reference for developing novel quantitative image feature analysis scheme to more accurately predict the response of ovarian cancer patients to the chemotherapy at early stage.

An optimized method for neurotransmitters and their metabolites analysis in mouse hypothalamus by high performance liquid chromatography-Q Exactive hybrid quadrupole-orbitrap high-resolution accurate mass spectrometry.

PubMed

Yang, Zong-Lin; Li, Hui; Wang, Bing; Liu, Shu-Ying

2016-02-15

Neurotransmitters (NTs) and their metabolites are known to play an essential role in maintaining various physiological functions in nervous system. However, there are many difficulties in the detection of NTs together with their metabolites in biological samples. A new method for NTs and their metabolites detection by high performance liquid chromatography coupled with Q Exactive hybrid quadruple-orbitrap high-resolution accurate mass spectrometry (HPLC-HRMS) was established in this paper. This method was a great development of the applying of Q Exactive MS in the quantitative analysis. This method enabled a rapid quantification of ten compounds within 18min. Good linearity was obtained with a correlation coefficient above 0.99. The concentration range of the limit of detection (LOD) and the limit of quantitation (LOQ) level were 0.0008-0.05nmol/mL and 0.002-25.0nmol/mL respectively. Precisions (relative standard deviation, RSD) of this method were at 0.36-12.70%. Recovery ranges were between 81.83% and 118.04%. Concentrations of these compounds in mouse hypothalamus were detected by Q Exactive LC-MS technology with this method. Copyright © 2016 Elsevier B.V. All rights reserved.

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 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. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr09171c

A surface enhanced Raman scattering quantitative analytical platform for detection of trace Cu coupled the catalytic reaction and gold nanoparticle aggregation with label-free Victoria blue B molecular probe.

PubMed

Li, Chongning; Ouyang, Huixiang; Tang, Xueping; Wen, Guiqing; Liang, Aihui; Jiang, Zhiliang

2017-01-15

With development of economy and society, there is an urgent need to develop convenient and sensitive methods for detection of Cu 2+ pollution in water. In this article, a simple and sensitive SERS sensor was proposed to quantitative analysis of trace Cu 2+ in water. The SERS sensor platform was prepared a common gold nanoparticle (AuNP)-SiO 2 sol substrate platform by adsorbing HSA, coupling with the catalytic reaction of Cu 2+ -ascorbic acid (H 2 A)-dissolved oxygen, and using label-free Victoria blue B (VBB) as SERS molecular probes. The SERS sensor platform response to the AuNP aggregations by hydroxyl radicals (•OH) oxidizing from the Cu 2+ catalytic reaction, which caused the SERS signal enhancement. Therefore, by monitoring the increase of SERS signal, Cu 2+ in water can be determined accurately. The results show that the SERS sensor platforms owns a linear response with a range from 0.025 to 25μmol/L Cu 2+ , and with a detection limit of 0.008μmol/L. In addition, the SERS method demonstrated good specificity for Cu 2+ , which can determined accurately trace Cu 2+ in water samples, and good recovery and accuracy are obtained for the water samples. With its high selectivity and good accuracy, the sensitive SERS quantitative analysis method is expected to be a promising candidate for determining copper ions in environmental monitoring and food safety. Copyright © 2016 Elsevier B.V. All rights reserved.

Intraoperative perception and estimates on extent of resection during awake glioma surgery: overcoming the learning curve.

PubMed

Lau, Darryl; Hervey-Jumper, Shawn L; Han, Seunggu J; Berger, Mitchel S

2018-05-01

OBJECTIVE There is ample evidence that extent of resection (EOR) is associated with improved outcomes for glioma surgery. However, it is often difficult to accurately estimate EOR intraoperatively, and surgeon accuracy has yet to be reviewed. In this study, the authors quantitatively assessed the accuracy of intraoperative perception of EOR during awake craniotomy for tumor resection. METHODS A single-surgeon experience of performing awake craniotomies for tumor resection over a 17-year period was examined. Retrospective review of operative reports for quantitative estimation of EOR was recorded. Definitive EOR was based on postoperative MRI. Analysis of accuracy of EOR estimation was examined both as a general outcome (gross-total resection [GTR] or subtotal resection [STR]), and quantitatively (5% within EOR on postoperative MRI). Patient demographics, tumor characteristics, and surgeon experience were examined. The effects of accuracy on motor and language outcomes were assessed. RESULTS A total of 451 patients were included in the study. Overall accuracy of intraoperative perception of whether GTR or STR was achieved was 79.6%, and overall accuracy of quantitative perception of resection (within 5% of postoperative MRI) was 81.4%. There was a significant difference (p = 0.049) in accuracy for gross perception over the 17-year period, with improvement over the later years: 1997-2000 (72.6%), 2001-2004 (78.5%), 2005-2008 (80.7%), and 2009-2013 (84.4%). Similarly, there was a significant improvement (p = 0.015) in accuracy of quantitative perception of EOR over the 17-year period: 1997-2000 (72.2%), 2001-2004 (69.8%), 2005-2008 (84.8%), and 2009-2013 (93.4%). This improvement in accuracy is demonstrated by the significantly higher odds of correctly estimating quantitative EOR in the later years of the series on multivariate logistic regression. Insular tumors were associated with the highest accuracy of gross perception (89.3%; p = 0.034), but lowest accuracy of quantitative perception (61.1% correct; p < 0.001) compared with tumors in other locations. Even after adjusting for surgeon experience, this particular trend for insular tumors remained true. The absence of 1p19q co-deletion was associated with higher quantitative perception accuracy (96.9% vs 81.5%; p = 0.051). Tumor grade, recurrence, diagnosis, and isocitrate dehydrogenase-1 (IDH-1) status were not associated with accurate perception of EOR. Overall, new neurological deficits occurred in 8.4% of cases, and 42.1% of those new neurological deficits persisted after the 3-month follow-up. Correct quantitative perception was associated with lower postoperative motor deficits (2.4%) compared with incorrect perceptions (8.0%; p = 0.029). There were no detectable differences in language outcomes based on perception of EOR. CONCLUSIONS The findings from this study suggest that there is a learning curve associated with the ability to accurately assess intraoperative EOR during glioma surgery, and it may take more than a decade to be truly proficient. Understanding the factors associated with this ability to accurately assess EOR will provide safer surgeries while maximizing tumor resection.

Laplace Transform Based Radiative Transfer Studies

NASA Astrophysics Data System (ADS)

Hu, Y.; Lin, B.; Ng, T.; Yang, P.; Wiscombe, W.; Herath, J.; Duffy, D.

2006-12-01

Multiple scattering is the major uncertainty for data analysis of space-based lidar measurements. Until now, accurate quantitative lidar data analysis has been limited to very thin objects that are dominated by single scattering, where photons from the laser beam only scatter a single time with particles in the atmosphere before reaching the receiver, and simple linear relationship between physical property and lidar signal exists. In reality, multiple scattering is always a factor in space-based lidar measurement and it dominates space- based lidar returns from clouds, dust aerosols, vegetation canopy and phytoplankton. While multiple scattering are clear signals, the lack of a fast-enough lidar multiple scattering computation tool forces us to treat the signal as unwanted "noise" and use simple multiple scattering correction scheme to remove them. Such multiple scattering treatments waste the multiple scattering signals and may cause orders of magnitude errors in retrieved physical properties. Thus the lack of fast and accurate time-dependent radiative transfer tools significantly limits lidar remote sensing capabilities. Analyzing lidar multiple scattering signals requires fast and accurate time-dependent radiative transfer computations. Currently, multiple scattering is done with Monte Carlo simulations. Monte Carlo simulations take minutes to hours and are too slow for interactive satellite data analysis processes and can only be used to help system / algorithm design and error assessment. We present an innovative physics approach to solve the time-dependent radiative transfer problem. The technique utilizes FPGA based reconfigurable computing hardware. The approach is as following, 1. Physics solution: Perform Laplace transform on the time and spatial dimensions and Fourier transform on the viewing azimuth dimension, and convert the radiative transfer differential equation solving into a fast matrix inversion problem. The majority of the radiative transfer computation goes to matrix inversion processes, FFT and inverse Laplace transforms. 2. Hardware solutions: Perform the well-defined matrix inversion, FFT and Laplace transforms on highly parallel, reconfigurable computing hardware. This physics-based computational tool leads to accurate quantitative analysis of space-based lidar signals and improves data quality of current lidar mission such as CALIPSO. This presentation will introduce the basic idea of this approach, preliminary results based on SRC's FPGA-based Mapstation, and how we may apply it to CALIPSO data analysis.

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

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.

Nonlocal means-based speckle filtering for ultrasound images

PubMed Central

Coupé, Pierrick; Hellier, Pierre; Kervrann, Charles; Barillot, Christian

2009-01-01

In image processing, restoration is expected to improve the qualitative inspection of the image and the performance of quantitative image analysis techniques. In this paper, an adaptation of the Non Local (NL-) means filter is proposed for speckle reduction in ultrasound (US) images. Originally developed for additive white Gaussian noise, we propose to use a Bayesian framework to derive a NL-means filter adapted to a relevant ultrasound noise model. Quantitative results on synthetic data show the performances of the proposed method compared to well-established and state-of-the-art methods. Results on real images demonstrate that the proposed method is able to preserve accurately edges and structural details of the image. PMID:19482578

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.

3D Slicer as an Image Computing Platform for the Quantitative Imaging Network

PubMed Central

Fedorov, Andriy; Beichel, Reinhard; Kalpathy-Cramer, Jayashree; Finet, Julien; Fillion-Robin, Jean-Christophe; Pujol, Sonia; Bauer, Christian; Jennings, Dominique; Fennessy, Fiona; Sonka, Milan; Buatti, John; Aylward, Stephen; Miller, James V.; Pieper, Steve; Kikinis, Ron

2012-01-01

Quantitative analysis has tremendous but mostly unrealized potential in healthcare to support objective and accurate interpretation of the clinical imaging. In 2008, the National Cancer Institute began building the Quantitative Imaging Network (QIN) initiative with the goal of advancing quantitative imaging in the context of personalized therapy and evaluation of treatment response. Computerized analysis is an important component contributing to reproducibility and efficiency of the quantitative imaging techniques. The success of quantitative imaging is contingent on robust analysis methods and software tools to bring these methods from bench to bedside. 3D Slicer is a free open source software application for medical image computing. As a clinical research tool, 3D Slicer is similar to a radiology workstation that supports versatile visualizations but also provides advanced functionality such as automated segmentation and registration for a variety of application domains. Unlike a typical radiology workstation, 3D Slicer is free and is not tied to specific hardware. As a programming platform, 3D Slicer facilitates translation and evaluation of the new quantitative methods by allowing the biomedical researcher to focus on the implementation of the algorithm, and providing abstractions for the common tasks of data communication, visualization and user interface development. Compared to other tools that provide aspects of this functionality, 3D Slicer is fully open source and can be readily extended and redistributed. In addition, 3D Slicer is designed to facilitate the development of new functionality in the form of 3D Slicer extensions. In this paper, we present an overview of 3D Slicer as a platform for prototyping, development and evaluation of image analysis tools for clinical research applications. To illustrate the utility of the platform in the scope of QIN, we discuss several use cases of 3D Slicer by the existing QIN teams, and we elaborate on the future directions that can further facilitate development and validation of imaging biomarkers using 3D Slicer. PMID:22770690

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

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.

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.

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.

Qualitative and quantitative analysis of heparin and low molecular weight heparins using size exclusion chromatography with multiple angle laser scattering/refractive index and inductively coupled plasma/mass spectrometry detectors.

PubMed

Ouyang, Yilan; Zeng, Yangyang; Yi, Lin; Tang, Hong; Li, Duxin; Linhardt, Robert J; Zhang, Zhenqing

2017-11-03

Heparin, a highly sulfated glycosaminoglycan, has been used as a clinical anticoagulant over 80 years. Low molecular weight heparins (LMWHs), heparins partially depolymerized using different processes, are widely used as clinical anticoagulants. Qualitative molecular weight (MW) and quantitative mass content analysis are two important factors that contribute to LMWH quality control. Size exclusion chromatography (SEC), relying on multiple angle laser scattering (MALS)/refractive index (RI) detectors, has been developed for accurate analysis of heparin MW in the absence of standards. However, the cations, which ion-pair with the anionic polysaccharide chains of heparin and LMWHs, had not been considered in previous reports. In this study, SEC with MALS/RI and inductively coupled plasma/mass spectrometry detectors were used in a comprehensive analytical approach taking both anionic polysaccharide and ion-paired cations heparin products. This approach was also applied to quantitative analysis of heparin and LMWHs. Full profiles of MWs and mass recoveries for three commercial heparin/LMWH products, heparin sodium, enoxaparin sodium and nadroparin calcium, were obtained and all showed higher MWs than previously reported. This important improvement more precisely characterized the MW properties of heparin/LMWHs and potentially many other anionic polysaccharides. Copyright © 2017 Elsevier B.V. All rights reserved.

Recent Achievements in Characterizing the Histone Code and Approaches to Integrating Epigenomics and Systems Biology.

PubMed

Janssen, K A; Sidoli, S; Garcia, B A

2017-01-01

Functional epigenetic regulation occurs by dynamic modification of chromatin, including genetic material (i.e., DNA methylation), histone proteins, and other nuclear proteins. Due to the highly complex nature of the histone code, mass spectrometry (MS) has become the leading technique in identification of single and combinatorial histone modifications. MS has now overcome antibody-based strategies due to its automation, high resolution, and accurate quantitation. Moreover, multiple approaches to analysis have been developed for global quantitation of posttranslational modifications (PTMs), including large-scale characterization of modification coexistence (middle-down and top-down proteomics), which is not currently possible with any other biochemical strategy. Recently, our group and others have simplified and increased the effectiveness of analyzing histone PTMs by improving multiple MS methods and data analysis tools. This review provides an overview of the major achievements in the analysis of histone PTMs using MS with a focus on the most recent improvements. We speculate that the workflow for histone analysis at its state of the art is highly reliable in terms of identification and quantitation accuracy, and it has the potential to become a routine method for systems biology thanks to the possibility of integrating histone MS results with genomics and proteomics datasets. © 2017 Elsevier Inc. All rights reserved.

High and low frequency unfolded partial least squares regression based on empirical mode decomposition for quantitative analysis of fuel oil samples.

PubMed

Bian, Xihui; Li, Shujuan; Lin, Ligang; Tan, Xiaoyao; Fan, Qingjie; Li, Ming

2016-06-21

Accurate prediction of the model is fundamental to the successful analysis of complex samples. To utilize abundant information embedded over frequency and time domains, a novel regression model is presented for quantitative analysis of hydrocarbon contents in the fuel oil samples. The proposed method named as high and low frequency unfolded PLSR (HLUPLSR), which integrates empirical mode decomposition (EMD) and unfolded strategy with partial least squares regression (PLSR). In the proposed method, the original signals are firstly decomposed into a finite number of intrinsic mode functions (IMFs) and a residue by EMD. Secondly, the former high frequency IMFs are summed as a high frequency matrix and the latter IMFs and residue are summed as a low frequency matrix. Finally, the two matrices are unfolded to an extended matrix in variable dimension, and then the PLSR model is built between the extended matrix and the target values. Coupled with Ultraviolet (UV) spectroscopy, HLUPLSR has been applied to determine hydrocarbon contents of light gas oil and diesel fuels samples. Comparing with single PLSR and other signal processing techniques, the proposed method shows superiority in prediction ability and better model interpretation. Therefore, HLUPLSR method provides a promising tool for quantitative analysis of complex samples. Copyright © 2016 Elsevier B.V. All rights reserved.

[A novel approach to NIR spectral quantitative analysis: semi-supervised least-squares support vector regression machine].

PubMed

Li, Lin; Xu, Shuo; An, Xin; Zhang, Lu-Da

2011-10-01

In near infrared spectral quantitative analysis, the precision of measured samples' chemical values is the theoretical limit of those of quantitative analysis with mathematical models. However, the number of samples that can obtain accurately their chemical values is few. Many models exclude the amount of samples without chemical values, and consider only these samples with chemical values when modeling sample compositions' contents. To address this problem, a semi-supervised LS-SVR (S2 LS-SVR) model is proposed on the basis of LS-SVR, which can utilize samples without chemical values as well as those with chemical values. Similar to the LS-SVR, to train this model is equivalent to solving a linear system. Finally, the samples of flue-cured tobacco were taken as experimental material, and corresponding quantitative analysis models were constructed for four sample compositions' content(total sugar, reducing sugar, total nitrogen and nicotine) with PLS regression, LS-SVR and S2 LS-SVR. For the S2 LS-SVR model, the average relative errors between actual values and predicted ones for the four sample compositions' contents are 6.62%, 7.56%, 6.11% and 8.20%, respectively, and the correlation coefficients are 0.974 1, 0.973 3, 0.923 0 and 0.948 6, respectively. Experimental results show the S2 LS-SVR model outperforms the other two, which verifies the feasibility and efficiency of the S2 LS-SVR model.

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.

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

Determination of the aflatoxin AFB1 from corn by direct analysis in real time-mass spectrometry (DART-MS).

PubMed

Busman, Mark; Liu, Jihong; Zhong, Hongjian; Bobell, John R; Maragos, Chris M

2014-01-01

Direct analysis in real time (DART) ionisation coupled to a high-resolution mass spectrometer (MS) was used for screening of aflatoxins from a variety of surfaces and the rapid quantitative analysis of a common form of aflatoxin, AFB1, extracted from corn. Sample preparation procedure and instrument parameter settings were optimised to obtain sensitive and accurate determination of aflatoxin AFB1. 84:16 acetonitrile water extracts of corn were analysed by DART-MS. The lowest calibration level (LCL) for aflatoxin AFB1 was 4 μg kg⁻¹. Quantitative analysis was performed with the use of matrix-matched standards employing the ¹³C-labelled internal standard for AFB1. DART-MS of spiked corn extracts gave linear response in the range 4-1000 μg kg⁻¹. Good recoveries (94-110%) and repeatabilities (RSD = 0.7-6.9%) were obtained at spiking levels of 20 and 100 μg kg⁻¹ with the use of an isotope dilution technique. Trueness of data obtained for AFB1 in maize by DART-MS was demonstrated by analysis of corn certified reference materials.

EDXRF quantitative analysis of chromophore chemical elements in corundum samples.

PubMed

Bonizzoni, L; Galli, A; Spinolo, G; Palanza, V

2009-12-01

Corundum is a crystalline form of aluminum oxide (Al(2)O(3)) and is one of the rock-forming minerals. When aluminum oxide is pure, the mineral is colorless, but the presence of trace amounts of other elements such as iron, titanium, and chromium in the crystal lattice gives the typical colors (including blue, red, violet, pink, green, yellow, orange, gray, white, colorless, and black) of gemstone varieties. The starting point for our work is the quantitative evaluation of the concentration of chromophore chemical elements with a precision as good as possible to match the data obtained by different techniques as such as optical absorption photoluminescence. The aim is to give an interpretation of the absorption bands present in the NIR and visible ranges which do not involve intervalence charge transfer transitions (Fe(2+) --> Fe(3+) and Fe(2+) --> Ti(4+)), commonly considered responsible of the important features of the blue sapphire absorption spectra. So, we developed a method to evaluate as accurately as possible the autoabsorption effects and the secondary excitation effects which frequently are sources of relevant errors in the quantitative EDXRF analysis.

High-resolution dynamic imaging and quantitative analysis of lung cancer xenografts in nude mice using clinical PET/CT

PubMed Central

Wang, Ying Yi; Wang, Kai; Xu, Zuo Yu; Song, Yan; Wang, Chu Nan; Zhang, Chong Qing; Sun, Xi Lin; Shen, Bao Zhong

2017-01-01

Considering the general application of dedicated small-animal positron emission tomography/computed tomography is limited, an acceptable alternative in many situations might be clinical PET/CT. To estimate the feasibility of using clinical PET/CT with [F-18]-fluoro-2-deoxy-D-glucose for high-resolution dynamic imaging and quantitative analysis of cancer xenografts in nude mice. Dynamic clinical PET/CT scans were performed on xenografts for 60 min after injection with [F-18]-fluoro-2-deoxy-D-glucose. Scans were reconstructed with or without SharpIR method in two phases. And mice were sacrificed to extracting major organs and tumors, using ex vivo γ-counting as a reference. Strikingly, we observed that the image quality and the correlation between the all quantitive data from clinical PET/CT and the ex vivo counting was better with the SharpIR reconstructions than without. Our data demonstrate that clinical PET/CT scanner with SharpIR reconstruction is a valuable tool for imaging small animals in preclinical cancer research, offering dynamic imaging parameters, good image quality and accurate data quatification. PMID:28881772

High-resolution dynamic imaging and quantitative analysis of lung cancer xenografts in nude mice using clinical PET/CT.

PubMed

Wang, Ying Yi; Wang, Kai; Xu, Zuo Yu; Song, Yan; Wang, Chu Nan; Zhang, Chong Qing; Sun, Xi Lin; Shen, Bao Zhong

2017-08-08

Considering the general application of dedicated small-animal positron emission tomography/computed tomography is limited, an acceptable alternative in many situations might be clinical PET/CT. To estimate the feasibility of using clinical PET/CT with [F-18]-fluoro-2-deoxy-D-glucose for high-resolution dynamic imaging and quantitative analysis of cancer xenografts in nude mice. Dynamic clinical PET/CT scans were performed on xenografts for 60 min after injection with [F-18]-fluoro-2-deoxy-D-glucose. Scans were reconstructed with or without SharpIR method in two phases. And mice were sacrificed to extracting major organs and tumors, using ex vivo γ-counting as a reference. Strikingly, we observed that the image quality and the correlation between the all quantitive data from clinical PET/CT and the ex vivo counting was better with the SharpIR reconstructions than without. Our data demonstrate that clinical PET/CT scanner with SharpIR reconstruction is a valuable tool for imaging small animals in preclinical cancer research, offering dynamic imaging parameters, good image quality and accurate data quatification.

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.

New atom probe approaches to studying segregation in nanocrystalline materials.

PubMed

Samudrala, S K; Felfer, P J; Araullo-Peters, V J; Cao, Y; Liao, X Z; Cairney, J M

2013-09-01

Atom probe is a technique that is highly suited to the study of nanocrystalline materials. It can provide accurate atomic-scale information about the composition of grain boundaries in three dimensions. In this paper we have analysed the microstructure of a nanocrystalline super-duplex stainless steel prepared by high pressure torsion (HPT). Not all of the grain boundaries in this alloy display obvious segregation, making visualisation of the microstructure challenging. In addition, the grain boundaries present in the atom probe data acquired from this alloy have complex shapes that are curved at the scale of the dataset and the interfacial excess varies considerably over the boundaries, making the accurate characterisation of the distribution of solute challenging using existing analysis techniques. In this paper we present two new data treatment methods that allow the visualisation of boundaries with little or no segregation, the delineation of boundaries for further analysis and the quantitative analysis of Gibbsian interfacial excess at boundaries, including the capability of excess mapping. Copyright © 2013 Elsevier B.V. All rights reserved.

Quantification of urinary zwitterionic organic acids using weak-anion exchange chromatography with tandem MS detection.

PubMed

Bishop, Michael Jason; Crow, Brian S; Kovalcik, Kasey D; George, Joe; Bralley, James A

2007-04-01

A rapid and accurate quantitative method was developed and validated for the analysis of four urinary organic acids with nitrogen containing functional groups, formiminoglutamic acid (FIGLU), pyroglutamic acid (PYRGLU), 5-hydroxyindoleacetic acid (5-HIAA), and 2-methylhippuric acid (2-METHIP) by liquid chromatography tandem mass spectrometry (LC/MS/MS). The chromatography was developed using a weak anion-exchange amino column that provided mixed-mode retention of the analytes. The elution gradient relied on changes in mobile phase pH over a concave gradient, without the use of counter-ions or concentrated salt buffers. A simple sample preparation was used, only requiring the dilution of urine prior to instrumental analysis. The method was validated based on linearity (r2>or=0.995), accuracy (85-115%), precision (C.V.<12%), sample preparation stability (

Study on the application of MRF and the D-S theory to image segmentation of the human brain and quantitative analysis of the brain tissue

NASA Astrophysics Data System (ADS)

Guan, Yihong; Luo, Yatao; Yang, Tao; Qiu, Lei; Li, Junchang

2012-01-01

The features of the spatial information of Markov random field image was used in image segmentation. It can effectively remove the noise, and get a more accurate segmentation results. Based on the fuzziness and clustering of pixel grayscale information, we find clustering center of the medical image different organizations and background through Fuzzy cmeans clustering method. Then we find each threshold point of multi-threshold segmentation through two dimensional histogram method, and segment it. The features of fusing multivariate information based on the Dempster-Shafer evidence theory, getting image fusion and segmentation. This paper will adopt the above three theories to propose a new human brain image segmentation method. Experimental result shows that the segmentation result is more in line with human vision, and is of vital significance to accurate analysis and application of tissues.

A comparison of quantitative methods for clinical imaging with hyperpolarized (13)C-pyruvate.

PubMed

Daniels, Charlie J; McLean, Mary A; Schulte, Rolf F; Robb, Fraser J; Gill, Andrew B; McGlashan, Nicholas; Graves, Martin J; Schwaiger, Markus; Lomas, David J; Brindle, Kevin M; Gallagher, Ferdia A

2016-04-01

Dissolution dynamic nuclear polarization (DNP) enables the metabolism of hyperpolarized (13)C-labelled molecules, such as the conversion of [1-(13)C]pyruvate to [1-(13)C]lactate, to be dynamically and non-invasively imaged in tissue. Imaging of this exchange reaction in animal models has been shown to detect early treatment response and correlate with tumour grade. The first human DNP study has recently been completed, and, for widespread clinical translation, simple and reliable methods are necessary to accurately probe the reaction in patients. However, there is currently no consensus on the most appropriate method to quantify this exchange reaction. In this study, an in vitro system was used to compare several kinetic models, as well as simple model-free methods. Experiments were performed using a clinical hyperpolarizer, a human 3 T MR system, and spectroscopic imaging sequences. The quantitative methods were compared in vivo by using subcutaneous breast tumours in rats to examine the effect of pyruvate inflow. The two-way kinetic model was the most accurate method for characterizing the exchange reaction in vitro, and the incorporation of a Heaviside step inflow profile was best able to describe the in vivo data. The lactate time-to-peak and the lactate-to-pyruvate area under the curve ratio were simple model-free approaches that accurately represented the full reaction, with the time-to-peak method performing indistinguishably from the best kinetic model. Finally, extracting data from a single pixel was a robust and reliable surrogate of the whole region of interest. This work has identified appropriate quantitative methods for future work in the analysis of human hyperpolarized (13)C data. © 2016 The Authors. NMR in Biomedicine published by John Wiley & Sons Ltd.

Automated selected reaction monitoring data analysis workflow for large-scale targeted proteomic studies.

PubMed

Surinova, Silvia; Hüttenhain, Ruth; Chang, Ching-Yun; Espona, Lucia; Vitek, Olga; Aebersold, Ruedi

2013-08-01

Targeted proteomics based on selected reaction monitoring (SRM) mass spectrometry is commonly used for accurate and reproducible quantification of protein analytes in complex biological mixtures. Strictly hypothesis-driven, SRM assays quantify each targeted protein by collecting measurements on its peptide fragment ions, called transitions. To achieve sensitive and accurate quantitative results, experimental design and data analysis must consistently account for the variability of the quantified transitions. This consistency is especially important in large experiments, which increasingly require profiling up to hundreds of proteins over hundreds of samples. Here we describe a robust and automated workflow for the analysis of large quantitative SRM data sets that integrates data processing, statistical protein identification and quantification, and dissemination of the results. The integrated workflow combines three software tools: mProphet for peptide identification via probabilistic scoring; SRMstats for protein significance analysis with linear mixed-effect models; and PASSEL, a public repository for storage, retrieval and query of SRM data. The input requirements for the protocol are files with SRM traces in mzXML format, and a file with a list of transitions in a text tab-separated format. The protocol is especially suited for data with heavy isotope-labeled peptide internal standards. We demonstrate the protocol on a clinical data set in which the abundances of 35 biomarker candidates were profiled in 83 blood plasma samples of subjects with ovarian cancer or benign ovarian tumors. The time frame to realize the protocol is 1-2 weeks, depending on the number of replicates used in the experiment.

Asymptotic analysis of discrete schemes for non-equilibrium radiation diffusion

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

Cui, Xia, E-mail: cui_xia@iapcm.ac.cn; Yuan, Guang-wei; Shen, Zhi-jun

Motivated by providing well-behaved fully discrete schemes in practice, this paper extends the asymptotic analysis on time integration methods for non-equilibrium radiation diffusion in [2] to space discretizations. Therein studies were carried out on a two-temperature model with Larsen's flux-limited diffusion operator, both the implicitly balanced (IB) and linearly implicit (LI) methods were shown asymptotic-preserving. In this paper, we focus on asymptotic analysis for space discrete schemes in dimensions one and two. First, in construction of the schemes, in contrast to traditional first-order approximations, asymmetric second-order accurate spatial approximations are devised for flux-limiters on boundary, and discrete schemes with second-ordermore » accuracy on global spatial domain are acquired consequently. Then by employing formal asymptotic analysis, the first-order asymptotic-preserving property for these schemes and furthermore for the fully discrete schemes is shown. Finally, with the help of manufactured solutions, numerical tests are performed, which demonstrate quantitatively the fully discrete schemes with IB time evolution indeed have the accuracy and asymptotic convergence as theory predicts, hence are well qualified for both non-equilibrium and equilibrium radiation diffusion. - Highlights: • Provide AP fully discrete schemes for non-equilibrium radiation diffusion. • Propose second order accurate schemes by asymmetric approach for boundary flux-limiter. • Show first order AP property of spatially and fully discrete schemes with IB evolution. • Devise subtle artificial solutions; verify accuracy and AP property quantitatively. • Ideas can be generalized to 3-dimensional problems and higher order implicit schemes.« less

Single and two-shot quantitative phase imaging using Hilbert-Huang Transform based fringe pattern analysis

NASA Astrophysics Data System (ADS)

Trusiak, Maciej; Micó, Vicente; Patorski, Krzysztof; García-Monreal, Javier; Sluzewski, Lukasz; Ferreira, Carlos

2016-08-01

In this contribution we propose two Hilbert-Huang Transform based algorithms for fast and accurate single-shot and two-shot quantitative phase imaging applicable in both on-axis and off-axis configurations. In the first scheme a single fringe pattern containing information about biological phase-sample under study is adaptively pre-filtered using empirical mode decomposition based approach. Further it is phase demodulated by the Hilbert Spiral Transform aided by the Principal Component Analysis for the local fringe orientation estimation. Orientation calculation enables closed fringes efficient analysis and can be avoided using arbitrary phase-shifted two-shot Gram-Schmidt Orthonormalization scheme aided by Hilbert-Huang Transform pre-filtering. This two-shot approach is a trade-off between single-frame and temporal phase shifting demodulation. Robustness of the proposed techniques is corroborated using experimental digital holographic microscopy studies of polystyrene micro-beads and red blood cells. Both algorithms compare favorably with the temporal phase shifting scheme which is used as a reference method.

Analysis and Quantitation of Glycated Hemoglobin by Matrix Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry

NASA Astrophysics Data System (ADS)

Hattan, Stephen J.; Parker, Kenneth C.; Vestal, Marvin L.; Yang, Jane Y.; Herold, David A.; Duncan, Mark W.

2016-03-01

Measurement of glycated hemoglobin is widely used for the diagnosis and monitoring of diabetes mellitus. Matrix assisted laser desorption/ionization (MALDI) time of flight (TOF) mass spectrometry (MS) analysis of patient samples is used to demonstrate a method for quantitation of total glycation on the β-subunit of hemoglobin. The approach is accurate and calibrated with commercially available reference materials. Measurements were linear (R2 > 0.99) across the clinically relevant range of 4% to 20% glycation with coefficients of variation of ≤ 2.5%. Additional and independent measurements of glycation of the α-subunit of hemoglobin are used to validate β-subunit glycation measurements and distinguish hemoglobin variants. Results obtained by MALDI-TOF MS were compared with those obtained in a clinical laboratory using validated HPLC methodology. MALDI-TOF MS sample preparation was minimal and analysis times were rapid making the method an attractive alternative to methodologies currently in practice.

Inferring diagnosis and trajectory of wet age-related macular degeneration from OCT imagery of retina

NASA Astrophysics Data System (ADS)

Irvine, John M.; Ghadar, Nastaran; Duncan, Steve; Floyd, David; O'Dowd, David; Lin, Kristie; Chang, Tom

2017-03-01

Quantitative biomarkers for assessing the presence, severity, and progression of age-related macular degeneration (AMD) would benefit research, diagnosis, and treatment. This paper explores development of quantitative biomarkers derived from OCT imagery of the retina. OCT images for approximately 75 patients with Wet AMD, Dry AMD, and no AMD (healthy eyes) were analyzed to identify image features indicative of the patients' conditions. OCT image features provide a statistical characterization of the retina. Healthy eyes exhibit a layered structure, whereas chaotic patterns indicate the deterioration associated with AMD. Our approach uses wavelet and Frangi filtering, combined with statistical features that do not rely on image segmentation, to assess patient conditions. Classification analysis indicates clear separability of Wet AMD from other conditions, including Dry AMD and healthy retinas. The probability of correct classification of was 95.7%, as determined from cross validation. Similar classification analysis predicts the response of Wet AMD patients to treatment, as measured by the Best Corrected Visual Acuity (BCVA). A statistical model predicts BCVA from the imagery features with R2 = 0.846. Initial analysis of OCT imagery indicates that imagery-derived features can provide useful biomarkers for characterization and quantification of AMD: Accurate assessment of Wet AMD compared to other conditions; image-based prediction of outcome for Wet AMD treatment; and features derived from the OCT imagery accurately predict BCVA; unlike many methods in the literature, our techniques do not rely on segmentation of the OCT image. Next steps include larger scale testing and validation.

Determination of modafinil in plasma and urine by reversed phase high-performance liquid-chromatography.

PubMed

Schwertner, Harvey A; Kong, Suk Bin

2005-03-09

Modafinil (Provigil) is a new wake-promoting drug that is being used for the management of excessive sleepiness in patients with narcolepsy. It has pharmacological properties similar to that of amphetamine, but without some of the side effects associated with amphetamine-like stimulants. Since modafinil has the potential to be abused, accurate drug-screening methods are needed for its analysis. In this study, we developed a high-performance liquid-chromatographic procedure (HPLC) for the quantitative analysis of modafinil in plasma and urine. (Phenylthio)acetic acid was used as an internal standard for the analysis of both plasma and urine. Modafinil was extracted from urine and plasma with ethyl acetate and ethyl acetate-acetic acid (100:1, v/v), respectively, and analyzed on a C18 reverse phase column with methanol-water-acetic acid (500:500:1, v/v) as the mobile phase. Recoveries from urine and plasma were 80.0 and 98.9%, respectively and the limit of quantitation was 0.1 microg/mL at 233 nm. Forty-eight 2-h post-dose urine samples from sham controls and from individuals taking 200 or 400 mg of modafinil were analyzed without knowledge of drug administration. All 16-placebo urine samples and all 32 2-h post-dose urine samples were correctly classified. The analytical procedure is accurate and reproducible and can be used for therapeutic drug monitoring, pharmacokinetic studies, and drug abuse screening.

Mapping surface charge density of lipid bilayers by quantitative surface conductivity microscopy

PubMed Central

Klausen, Lasse Hyldgaard; Fuhs, Thomas; Dong, Mingdong

2016-01-01

Local surface charge density of lipid membranes influences membrane–protein interactions leading to distinct functions in all living cells, and it is a vital parameter in understanding membrane-binding mechanisms, liposome design and drug delivery. Despite the significance, no method has so far been capable of mapping surface charge densities under physiologically relevant conditions. Here, we use a scanning nanopipette setup (scanning ion-conductance microscope) combined with a novel algorithm to investigate the surface conductivity near supported lipid bilayers, and we present a new approach, quantitative surface conductivity microscopy (QSCM), capable of mapping surface charge density with high-quantitative precision and nanoscale resolution. The method is validated through an extensive theoretical analysis of the ionic current at the nanopipette tip, and we demonstrate the capacity of QSCM by mapping the surface charge density of model cationic, anionic and zwitterionic lipids with results accurately matching theoretical values. PMID:27561322

New horizons in mouse immunoinformatics: reliable in silico prediction of mouse class I histocompatibility major complex peptide binding affinity.

PubMed

Hattotuwagama, Channa K; Guan, Pingping; Doytchinova, Irini A; Flower, Darren R

2004-11-21

Quantitative structure-activity relationship (QSAR) analysis is a main cornerstone of modern informatic disciplines. Predictive computational models, based on QSAR technology, of peptide-major histocompatibility complex (MHC) binding affinity have now become a vital component of modern day computational immunovaccinology. Historically, such approaches have been built around semi-qualitative, classification methods, but these are now giving way to quantitative regression methods. The additive method, an established immunoinformatics technique for the quantitative prediction of peptide-protein affinity, was used here to identify the sequence dependence of peptide binding specificity for three mouse class I MHC alleles: H2-D(b), H2-K(b) and H2-K(k). As we show, in terms of reliability the resulting models represent a significant advance on existing methods. They can be used for the accurate prediction of T-cell epitopes and are freely available online ( http://www.jenner.ac.uk/MHCPred).

Mapping surface charge density of lipid bilayers by quantitative surface conductivity microscopy

NASA Astrophysics Data System (ADS)

Klausen, Lasse Hyldgaard; Fuhs, Thomas; Dong, Mingdong

2016-08-01

Local surface charge density of lipid membranes influences membrane-protein interactions leading to distinct functions in all living cells, and it is a vital parameter in understanding membrane-binding mechanisms, liposome design and drug delivery. Despite the significance, no method has so far been capable of mapping surface charge densities under physiologically relevant conditions. Here, we use a scanning nanopipette setup (scanning ion-conductance microscope) combined with a novel algorithm to investigate the surface conductivity near supported lipid bilayers, and we present a new approach, quantitative surface conductivity microscopy (QSCM), capable of mapping surface charge density with high-quantitative precision and nanoscale resolution. The method is validated through an extensive theoretical analysis of the ionic current at the nanopipette tip, and we demonstrate the capacity of QSCM by mapping the surface charge density of model cationic, anionic and zwitterionic lipids with results accurately matching theoretical values.

Mapping surface charge density of lipid bilayers by quantitative surface conductivity microscopy.

PubMed

Klausen, Lasse Hyldgaard; Fuhs, Thomas; Dong, Mingdong

2016-08-26

Local surface charge density of lipid membranes influences membrane-protein interactions leading to distinct functions in all living cells, and it is a vital parameter in understanding membrane-binding mechanisms, liposome design and drug delivery. Despite the significance, no method has so far been capable of mapping surface charge densities under physiologically relevant conditions. Here, we use a scanning nanopipette setup (scanning ion-conductance microscope) combined with a novel algorithm to investigate the surface conductivity near supported lipid bilayers, and we present a new approach, quantitative surface conductivity microscopy (QSCM), capable of mapping surface charge density with high-quantitative precision and nanoscale resolution. The method is validated through an extensive theoretical analysis of the ionic current at the nanopipette tip, and we demonstrate the capacity of QSCM by mapping the surface charge density of model cationic, anionic and zwitterionic lipids with results accurately matching theoretical values.

Development of a software for quantitative evaluation radiotherapy target and organ-at-risk segmentation comparison.

PubMed

Kalpathy-Cramer, Jayashree; Awan, Musaddiq; Bedrick, Steven; Rasch, Coen R N; Rosenthal, David I; Fuller, Clifton D

2014-02-01

Modern radiotherapy requires accurate region of interest (ROI) inputs for plan optimization and delivery. Target delineation, however, remains operator-dependent and potentially serves as a major source of treatment delivery error. In order to optimize this critical, yet observer-driven process, a flexible web-based platform for individual and cooperative target delineation analysis and instruction was developed in order to meet the following unmet needs: (1) an open-source/open-access platform for automated/semiautomated quantitative interobserver and intraobserver ROI analysis and comparison, (2) a real-time interface for radiation oncology trainee online self-education in ROI definition, and (3) a source for pilot data to develop and validate quality metrics for institutional and cooperative group quality assurance efforts. The resultant software, Target Contour Testing/Instructional Computer Software (TaCTICS), developed using Ruby on Rails, has since been implemented and proven flexible, feasible, and useful in several distinct analytical and research applications.

Quantitative Rainbow Schlieren Deflectometry as a Temperature Diagnostic for Spherical Flames

NASA Technical Reports Server (NTRS)

Feikema, Douglas A.

2004-01-01

Numerical analysis and experimental results are presented to define a method for quantitatively measuring the temperature distribution of a spherical diffusion flame using Rainbow Schlieren Deflectometry in microgravity. First, a numerical analysis is completed to show the method can suitably determine temperature in the presence of spatially varying species composition. Also, a numerical forward-backward inversion calculation is presented to illustrate the types of calculations and deflections to be encountered. Lastly, a normal gravity demonstration of temperature measurement in an axisymmetric laminar, diffusion flame using Rainbow Schlieren deflectometry is presented. The method employed in this paper illustrates the necessary steps for the preliminary design of a Schlieren system. The largest deflections for the normal gravity flame considered in this paper are 7.4 x 10(-4) radians which can be accurately measured with 2 meter focal length collimating and decollimating optics. The experimental uncertainty of deflection is less than 5 x 10(-5) radians.

Quantitative determination of the hydrolysis products of nitrogen mustards in human urine by liquid chromatography-electrospray ionization tandem mass spectrometry.

PubMed

Lemire, Sharon W; Ashley, David L; Calafat, Antonia M

2003-01-01

Nitrogen mustards are a public health concern because of their extreme vesicant properties and the possible exposure of workers during the destruction of chemical stockpiles. A sensitive, rapid, accurate, and precise analysis for the quantitation of ultratrace levels of N-ethyldiethanolamine (EDEA) and N-methyldiethanolamine (MDEA) in human urine as a means of assessing recent exposure to the nitrogen mustards bis(2-chloroethyl)ethylamine and bis(2-chloroethyl)methylamine, respectively, was developed. The method was based on solid-phase extraction, followed by analysis of the urine extract using isotope-dilution high-performance liquid chromatography-mass spectrometry with TurbolonSpray ionization and multiple-reaction monitoring. The method limits of detection were 0.41 ng/mL for EDEA and 0.96 ng/mL for MDEA in 1 mL of urine with coefficients of variation < 10% for both compounds.

From the street to the laboratory: analytical profiles of methoxetamine, 3-methoxyeticyclidine and 3-methoxyphencyclidine and their determination in three biological matrices.

PubMed

De Paoli, Giorgia; Brandt, Simon D; Wallach, Jason; Archer, Roland P; Pounder, Derrick J

2013-06-01

Three psychoactive arylcyclohexylamines, advertised as "research chemicals," were obtained from an online retailer and characterized by gas chromatography ion trap electron and chemical ionization mass spectrometry, nuclear magnetic resonance spectroscopy and diode array detection. The three phencyclidines were identified as 2-(ethylamino)-2-(3-methoxyphenyl)cyclohexanone (methoxetamine), N-ethyl-1-(3-methoxyphenyl)cyclohexanamine and 1-[1-(3-methoxyphenyl)cyclohexyl]piperidine. A qualitative/quantitative method of analysis was developed and validated using liquid chromatography (HPLC) electrospray tandem mass spectrometry and ultraviolet (UV) detection for the determination of these compounds in blood, urine and vitreous humor. HPLC-UV proved to be a robust, accurate and precise method for the qualitative and quantitative analysis of these substances in biological fluids (0.16-5.0 mg/L), whereas the mass spectrometer was useful as a confirmatory tool.

Principles of Metamorphic Petrology

NASA Astrophysics Data System (ADS)

Williams, Michael L.

2009-05-01

The field of metamorphic petrology has seen spectacular advances in the past decade, including new X-ray mapping techniques for characterizing metamorphic rocks and minerals, new internally consistent thermobarometers, new software for constructing and viewing phase diagrams, new methods to date metamorphic processes, and perhaps most significant, revised petrologic databases and the ability to calculate accurate phase diagrams and pseudosections. These tools and techniques provide new power and resolution for constraining pressure-temperature (P-T) histories and tectonic events. Two books have been fundamental for empowering petrologists and structural geologists during the past decade. Frank Spear's Metamorphic Phase Equilibria and Pressure-Temperature-Time Paths, published in 1993, builds on his seminal papers to provide a quantitative framework for P-T path analysis. Spear's book lays the foundation for modern quantitative metamorphic analysis. Cees Passchier and Rudolph Trouw's Microtectonics, published in 2005, with its superb photos and figures, provides the tools and the theory for interpreting deformation textures and inferring deformation processes.

Comparison of different approaches to quantitative adenovirus detection in stool specimens of hematopoietic stem cell transplant recipients.

PubMed

Kosulin, K; Dworzak, S; Lawitschka, A; Matthes-Leodolter, S; Lion, T

2016-12-01

Adenoviruses almost invariably proliferate in the gastrointestinal tract prior to dissemination, and critical threshold concentrations in stool correlate with the risk of viremia. Monitoring of adenovirus loads in stool may therefore be important for timely initiation of treatment in order to prevent invasive infection. Comparison of a manual DNA extraction kit in combination with a validated in-house PCR assay with automated extraction on the NucliSENS-EasyMAG device coupled with the Adenovirus R-gene kit (bioMérieux) for quantitative adenovirus analysis in stool samples. Stool specimens spiked with adenovirus concentrations in a range from 10E2-10E11 copies/g and 32 adenovirus-positive clinical stool specimens from pediatric stem cell transplant recipients were tested along with appropriate negative controls. Quantitative analysis of viral load in adenovirus-positive stool specimens revealed a median difference of 0.5 logs (range 0.1-2.2) between the detection systems tested and a difference of 0.3 logs (range 0.0-1.7) when the comparison was restricted to the PCR assays only. Spiking experiments showed a detection limit of 10 2 -10 3 adenovirus copies/g stool revealing a somewhat higher sensitivity offered by the automated extraction. The dynamic range of accurate quantitative analysis by both systems investigated was between 10 3 and 10 8 virus copies/g. The differences in quantitative analysis of adenovirus copy numbers between the systems tested were primarily attributable to the DNA extraction method used, while the qPCR assays revealed a high level of concordance. Both systems showed adequate performance for detection and monitoring of adenoviral load in stool specimens. Copyright © 2016 Elsevier B.V. All rights reserved.

Comparison of longitudinal excursion of a nerve-phantom model using quantitative ultrasound imaging and motion analysis system methods: A convergent validity study.

PubMed

Paquette, Philippe; El Khamlichi, Youssef; Lamontagne, Martin; Higgins, Johanne; Gagnon, Dany H

2017-08-01

Quantitative ultrasound imaging is gaining popularity in research and clinical settings to measure the neuromechanical properties of the peripheral nerves such as their capability to glide in response to body segment movement. Increasing evidence suggests that impaired median nerve longitudinal excursion is associated with carpal tunnel syndrome. To date, psychometric properties of longitudinal nerve excursion measurements using quantitative ultrasound imaging have not been extensively investigated. This study investigates the convergent validity of the longitudinal nerve excursion by comparing measures obtained using quantitative ultrasound imaging with those determined with a motion analysis system. A 38-cm long rigid nerve-phantom model was used to assess the longitudinal excursion in a laboratory environment. The nerve-phantom model, immersed in a 20-cm deep container filled with a gelatin-based solution, was moved 20 times using a linear forward and backward motion. Three light-emitting diodes were used to record nerve-phantom excursion with a motion analysis system, while a 5-cm linear transducer allowed simultaneous recording via ultrasound imaging. Both measurement techniques yielded excellent association ( r  = 0.99) and agreement (mean absolute difference between methods = 0.85 mm; mean relative difference between methods = 7.48 %). Small discrepancies were largely found when larger excursions (i.e. > 10 mm) were performed, revealing slight underestimation of the excursion by the ultrasound imaging analysis software. Quantitative ultrasound imaging is an accurate method to assess the longitudinal excursion of an in vitro nerve-phantom model and appears relevant for future research protocols investigating the neuromechanical properties of the peripheral nerves.

Development of a Fourier transform infrared spectroscopy coupled to UV-Visible analysis technique for aminosides and glycopeptides quantitation in antibiotic locks.

PubMed

Sayet, G; Sinegre, M; Ben Reguiga, M

2014-01-01

Antibiotic Lock technique maintains catheters' sterility in high-risk patients with long-term parenteral nutrition. In our institution, vancomycin, teicoplanin, amikacin and gentamicin locks are prepared in the pharmaceutical department. In order to insure patient safety and to comply to regulatory requirements, antibiotic locks are submitted to qualitative and quantitative assays prior to their release. The aim of this study was to develop an alternative quantitation technique for each of these 4 antibiotics, using a Fourier transform infrared (FTIR) coupled to UV-Visible spectroscopy and to compare results to HPLC or Immunochemistry assays. Prevalidation studies permitted to assess spectroscopic conditions used for antibiotic locks quantitation: FTIR/UV combinations were used for amikacin (1091-1115cm(-1) and 208-224nm), vancomycin (1222-1240cm(-1) and 276-280nm), and teicoplanin (1226-1230cm(-1) and 278-282nm). Gentamicin was quantified with FTIR only (1045-1169cm(-1) and 2715-2850cm(-1)) due to interferences in UV domain of parabens, preservatives present in the commercial brand used to prepare locks. For all AL, the method was linear (R(2)=0.996 to 0.999), accurate, repeatable (intraday RSD%: from 2.9 to 7.1% and inter-days RSD%: 2.9 to 5.1%) and precise. Compared to the reference methods, the FTIR/UV method appeared tightly correlated (Pearson factor: 97.4 to 99.9%) and did not show significant difference in recovery determinations. We developed a new simple reliable analysis technique for antibiotics quantitation in locks using an original association of FTIR and UV analysis, allowing a short time analysis to identify and quantify the studied antibiotics. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

A software package to improve image quality and isolation of objects of interest for quantitative stereology studies of rat hepatocarcinogenesis.

PubMed

Xu, Yihua; Pitot, Henry C

2006-03-01

In the studies of quantitative stereology of rat hepatocarcinogenesis, we have used image analysis technology (automatic particle analysis) to obtain data such as liver tissue area, size and location of altered hepatic focal lesions (AHF), and nuclei counts. These data are then used for three-dimensional estimation of AHF occurrence and nuclear labeling index analysis. These are important parameters for quantitative studies of carcinogenesis, for screening and classifying carcinogens, and for risk estimation. To take such measurements, structures or cells of interest should be separated from the other components based on the difference of color and density. Common background problems seen on the captured sample image such as uneven light illumination or color shading can cause severe problems in the measurement. Two application programs (BK_Correction and Pixel_Separator) have been developed to solve these problems. With BK_Correction, common background problems such as incorrect color temperature setting, color shading, and uneven light illumination background, can be corrected. With Pixel_Separator different types of objects can be separated from each other in relation to their color, such as seen with different colors in immunohistochemically stained slides. The resultant images of such objects separated from other components are then ready for particle analysis. Objects that have the same darkness but different colors can be accurately differentiated in a grayscale image analysis system after application of these programs.

Comparison of three‐dimensional analysis and stereological techniques for quantifying lithium‐ion battery electrode microstructures

PubMed Central

TAIWO, OLUWADAMILOLA O.; FINEGAN, DONAL P.; EASTWOOD, DAVID S.; FIFE, JULIE L.; BROWN, LEON D.; DARR, JAWWAD A.; LEE, PETER D.; BRETT, DANIEL J.L.

2016-01-01

Summary Lithium‐ion battery performance is intrinsically linked to electrode microstructure. Quantitative measurement of key structural parameters of lithium‐ion battery electrode microstructures will enable optimization as well as motivate systematic numerical studies for the improvement of battery performance. With the rapid development of 3‐D imaging techniques, quantitative assessment of 3‐D microstructures from 2‐D image sections by stereological methods appears outmoded; however, in spite of the proliferation of tomographic imaging techniques, it remains significantly easier to obtain two‐dimensional (2‐D) data sets. In this study, stereological prediction and three‐dimensional (3‐D) analysis techniques for quantitative assessment of key geometric parameters for characterizing battery electrode microstructures are examined and compared. Lithium‐ion battery electrodes were imaged using synchrotron‐based X‐ray tomographic microscopy. For each electrode sample investigated, stereological analysis was performed on reconstructed 2‐D image sections generated from tomographic imaging, whereas direct 3‐D analysis was performed on reconstructed image volumes. The analysis showed that geometric parameter estimation using 2‐D image sections is bound to be associated with ambiguity and that volume‐based 3‐D characterization of nonconvex, irregular and interconnected particles can be used to more accurately quantify spatially‐dependent parameters, such as tortuosity and pore‐phase connectivity. PMID:26999804

Comparison of three-dimensional analysis and stereological techniques for quantifying lithium-ion battery electrode microstructures.

PubMed

Taiwo, Oluwadamilola O; Finegan, Donal P; Eastwood, David S; Fife, Julie L; Brown, Leon D; Darr, Jawwad A; Lee, Peter D; Brett, Daniel J L; Shearing, Paul R

2016-09-01

Lithium-ion battery performance is intrinsically linked to electrode microstructure. Quantitative measurement of key structural parameters of lithium-ion battery electrode microstructures will enable optimization as well as motivate systematic numerical studies for the improvement of battery performance. With the rapid development of 3-D imaging techniques, quantitative assessment of 3-D microstructures from 2-D image sections by stereological methods appears outmoded; however, in spite of the proliferation of tomographic imaging techniques, it remains significantly easier to obtain two-dimensional (2-D) data sets. In this study, stereological prediction and three-dimensional (3-D) analysis techniques for quantitative assessment of key geometric parameters for characterizing battery electrode microstructures are examined and compared. Lithium-ion battery electrodes were imaged using synchrotron-based X-ray tomographic microscopy. For each electrode sample investigated, stereological analysis was performed on reconstructed 2-D image sections generated from tomographic imaging, whereas direct 3-D analysis was performed on reconstructed image volumes. The analysis showed that geometric parameter estimation using 2-D image sections is bound to be associated with ambiguity and that volume-based 3-D characterization of nonconvex, irregular and interconnected particles can be used to more accurately quantify spatially-dependent parameters, such as tortuosity and pore-phase connectivity. © 2016 The Authors. Journal of Microscopy published by John Wiley & Sons Ltd on behalf of Royal Microscopical Society.

Quantitative PCR: an appropriate tool to detect viable but not culturable Brettanomyces bruxellensis in wine.

PubMed

Willenburg, Elize; Divol, Benoit

2012-11-15

Quantitative PCR as a tool has been used to detect Brettanomyces bruxellensis directly from wine samples. Accurate and timely detection of this yeast is important to prevent unwanted spoilage of wines and beverages. The aim of this study was to distinguish differences between DNA and mRNA as template for the detection of this yeast. The study was also used to determine if it is possible to accurately detect cells in the viable but not culturable (VBNC) state of B. bruxellensis by qPCR. Several methods including traditional plating, epifluorescence counts and qPCR were used to amplify DNA and mRNA. It was observed that mRNA was a better template for the detection in terms of standard curve analysis and qPCR efficiencies. Various primers previously published were tested for their specificity, qPCR efficiency and accuracy of enumeration. A single primer set was selected which amplified a region of the actin-encoding gene. The detection limit for this assay was 10cellsmL(-1). B. bruxellensis could also be quantified in naturally contaminated wines with this assay. The mRNA gave a better indication of the viability of the cells which compared favourably to fluorescent microscopy and traditional cell counts. The ability of the assay to accurately estimate the number of cells in the VBNC state was also demonstrated. Copyright © 2012 Elsevier B.V. All rights reserved.

Protocol for Standardizing High-to-Moderate Abundance Protein Biomarker Assessments Through an MRM-with-Standard-Peptides Quantitative Approach.

PubMed

Percy, Andrew J; Yang, Juncong; Chambers, Andrew G; Mohammed, Yassene; Miliotis, Tasso; Borchers, Christoph H

2016-01-01

Quantitative mass spectrometry (MS)-based approaches are emerging as a core technology for addressing health-related queries in systems biology and in the biomedical and clinical fields. In several 'omics disciplines (proteomics included), an approach centered on selected or multiple reaction monitoring (SRM or MRM)-MS with stable isotope-labeled standards (SIS), at the protein or peptide level, has emerged as the most precise technique for quantifying and screening putative analytes in biological samples. To enable the widespread use of MRM-based protein quantitation for disease biomarker assessment studies and its ultimate acceptance for clinical analysis, the technique must be standardized to facilitate precise and accurate protein quantitation. To that end, we have developed a number of kits for assessing method/platform performance, as well as for screening proposed candidate protein biomarkers in various human biofluids. Collectively, these kits utilize a bottom-up LC-MS methodology with SIS peptides as internal standards and quantify proteins using regression analysis of standard curves. This chapter details the methodology used to quantify 192 plasma proteins of high-to-moderate abundance (covers a 6 order of magnitude range from 31 mg/mL for albumin to 18 ng/mL for peroxidredoxin-2), and a 21-protein subset thereof. We also describe the application of this method to patient samples for biomarker discovery and verification studies. Additionally, we introduce our recently developed Qualis-SIS software, which is used to expedite the analysis and assessment of protein quantitation data in control and patient samples.

Quantitative Assessment of Arrhythmia Using Non-linear Approach: A Non-invasive Prognostic Tool

NASA Astrophysics Data System (ADS)

Chakraborty, Monisha; Ghosh, Dipak

2017-12-01

Accurate prognostic tool to identify severity of Arrhythmia is yet to be investigated, owing to the complexity of the ECG signal. In this paper, we have shown that quantitative assessment of Arrhythmia is possible using non-linear technique based on "Hurst Rescaled Range Analysis". Although the concept of applying "non-linearity" for studying various cardiac dysfunctions is not entirely new, the novel objective of this paper is to identify the severity of the disease, monitoring of different medicine and their dose, and also to assess the efficiency of different medicine. The approach presented in this work is simple which in turn will help doctors in efficient disease management. In this work, Arrhythmia ECG time series are collected from MIT-BIH database. Normal ECG time series are acquired using POLYPARA system. Both time series are analyzed in thelight of non-linear approach following the method "Rescaled Range Analysis". The quantitative parameter, "Fractal Dimension" (D) is obtained from both types of time series. The major finding is that Arrhythmia ECG poses lower values of D as compared to normal. Further, this information can be used to access the severity of Arrhythmia quantitatively, which is a new direction of prognosis as well as adequate software may be developed for the use of medical practice.

Quantitative Assessment of Arrhythmia Using Non-linear Approach: A Non-invasive Prognostic Tool

NASA Astrophysics Data System (ADS)

Chakraborty, Monisha; Ghosh, Dipak

2018-04-01

Accurate prognostic tool to identify severity of Arrhythmia is yet to be investigated, owing to the complexity of the ECG signal. In this paper, we have shown that quantitative assessment of Arrhythmia is possible using non-linear technique based on "Hurst Rescaled Range Analysis". Although the concept of applying "non-linearity" for studying various cardiac dysfunctions is not entirely new, the novel objective of this paper is to identify the severity of the disease, monitoring of different medicine and their dose, and also to assess the efficiency of different medicine. The approach presented in this work is simple which in turn will help doctors in efficient disease management. In this work, Arrhythmia ECG time series are collected from MIT-BIH database. Normal ECG time series are acquired using POLYPARA system. Both time series are analyzed in thelight of non-linear approach following the method "Rescaled Range Analysis". The quantitative parameter, "Fractal Dimension" (D) is obtained from both types of time series. The major finding is that Arrhythmia ECG poses lower values of D as compared to normal. Further, this information can be used to access the severity of Arrhythmia quantitatively, which is a new direction of prognosis as well as adequate software may be developed for the use of medical practice.

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 across any fluvial system that can be used to analyse 3D digital outcrop data, and identify spatial attributes of sand bodies to identify their genetic origin and lithological component within fluvial reservoir systems, and the rock record. 3D quantitative analysis of major sand bodies have allowed more accurate width vs. thickness relationships within the La Serreta area, showing a vertical increase in width and channel-fill facies, and demonstrates a 22% increase of in-channel facies from previous interpretations. Additionally, identification of deposits that are products of a nodal avulsion event have been characterised and are interpreted to be the cause for the increase in width and channel-fill facies. Furthermore, analysis of the Pikeville and Hyden Fms contain sand bodies of stacked distributaries and palaeovalleys, as previously interpreted, and demonstrates that a 3D spatial approach to determine basin-wide architectural trends is integral to identifying the genetic origin, and preservation potential of sand bodies of both palaeovalleys and distributive fluvial systems. The resultant geostatistics assimilated in the thesis demonstrates the efficacy of integrated lidar studies of outcrop analogues, and provide empirical relationships which can be applied to subsurface analogues for reservoir model development and the distribution of both DFS and palaeovalley depositional systems in the rock record.

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...

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

PubMed Central

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

2012-01-01

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

Noninvasive Diagnosis of Nonalcoholic Fatty Liver Disease and Quantification of Liver Fat Using a New Quantitative Ultrasound Technique.

PubMed

Lin, Steven C; Heba, Elhamy; Wolfson, Tanya; Ang, Brandon; Gamst, Anthony; Han, Aiguo; Erdman, John W; O'Brien, William D; Andre, Michael P; Sirlin, Claude B; Loomba, Rohit

2015-07-01

Liver biopsy analysis is the standard method used to diagnose nonalcoholic fatty liver disease (NAFLD). Advanced magnetic resonance imaging is a noninvasive procedure that can accurately diagnose and quantify steatosis, but is expensive. Conventional ultrasound is more accessible but identifies steatosis with low levels of sensitivity, specificity, and quantitative accuracy, and results vary among technicians. A new quantitative ultrasound (QUS) technique can identify steatosis in animal models. We assessed the accuracy of QUS in the diagnosis and quantification of hepatic steatosis, comparing findings with those from magnetic resonance imaging proton density fat fraction (MRI-PDFF) analysis as a reference. We performed a prospective, cross-sectional analysis of a cohort of adults (N = 204) with NAFLD (MRI-PDFF, ≥5%) and without NAFLD (controls). Subjects underwent MRI-PDFF and QUS analyses of the liver on the same day at the University of California, San Diego, from February 2012 through March 2014. QUS parameters and backscatter coefficient (BSC) values were calculated. Patients were assigned randomly to training (n = 102; mean age, 51 ± 17 y; mean body mass index, 31 ± 7 kg/m(2)) and validation (n = 102; mean age, 49 ± 17 y; body mass index, 30 ± 6 kg/m(2)) groups; 69% of patients in each group had NAFLD. BSC (range, 0.00005-0.25 1/cm-sr) correlated with MRI-PDFF (Spearman ρ = 0.80; P < .0001). In the training group, the BSC analysis identified patients with NAFLD with an area under the curve value of 0.98 (95% confidence interval, 0.95-1.00; P < .0001). The optimal BSC cut-off value identified patients with NAFLD in the training and validation groups with 93% and 87% sensitivity, 97% and 91% specificity, 86% and 76% negative predictive values, and 99% and 95% positive predictive values, respectively. QUS measurements of BSC can accurately diagnose and quantify hepatic steatosis, based on a cross-sectional analysis that used MRI-PDFF as the reference. With further validation, QUS could be an inexpensive, widely available method to screen the general or at-risk population for NAFLD. Copyright © 2015 AGA Institute. Published by Elsevier Inc. All rights reserved.

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.

NMR-based metabolomic urinalysis: a rapid screening test for urinary tract infection.

PubMed

Lam, Ching-Wan; Law, Chun-Yiu; To, Kelvin Kai-Wang; Cheung, Stanley Kwok-Kuen; Lee, Kim-Chung; Sze, Kong-Hung; Leung, Ka-Fai; Yuen, Kwok-Yung

2014-09-25

Urinary tract infection (UTI) is one of the most common bacterial infections in humans; however, there is no accurate and fast quantitative test to detect UTI. Dipstick urinalysis is semi-quantitative with a limited diagnostic accuracy, while urine culture is accurate but takes time. We described a quantitative biochemical method for the diagnosis of bacteriuria using a single marker. We compared the urine metabolomes from 88 patients with bacterial UTI and 61 controls using (1)H NMR spectroscopy followed by principal component analysis (PCA) and orthogonal partial least squares-discriminant analysis (OPLS-DA). The biomarker identified was subsequently validated using independent samples. The urine acetic acid/creatinine (mmol/mmol) level was determined to be the most discriminatory marker for bacterial UTI with an area-under-receiver operating characteristic curve=0.97, sensitivity=91% and specificity=95% at the optimal cutoff 0.03 mmol/mmol. For validation, 60 samples were recruited prospectively. Using the optimal cutoff for acetic acid/creatinine, this method showed sensitivity=96%, specificity=94%, positive predictive value=92%, negative predictive value=97% and an overall accuracy=95%. The diagnostic performance was superior to dipstick urinalysis or microscopy. In addition, we also observed an increase of urinary trimethylamine (TMA) in patients with Escherichia coli-associated UTI. TMA is a mammalian-microbial co-metabolite and the high level of TMA generated is related to the bacterial enzyme, trimethylamine N-oxide (TMAO) reductase which reduces TMAO to TMA. Urine acetic acid is a neglected metabolite that can be used for rapid diagnosis of UTI and TMA can be used for etiologic diagnosis of UTI. With the introduction of NMR-based clinical analyzers to clinical laboratories, NMR-based urinalysis can be translated for clinical use. Copyright © 2014 Elsevier B.V. All rights reserved.

A method for rapid quantitative assessment of biofilms with biomolecular staining and image analysis

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

Larimer, Curtis J.; Winder, Eric M.; Jeters, Robert T.

Here, the accumulation of bacteria in surface attached biofilms, or biofouling, can be detrimental to human health, dental hygiene, and many industrial processes. A critical need in identifying and preventing the deleterious effects of biofilms is the ability to observe and quantify their development. Analytical methods capable of assessing early stage fouling are cumbersome or lab-confined, subjective, and qualitative. Herein, a novel photographic method is described that uses biomolecular staining and image analysis to enhance contrast of early stage biofouling. A robust algorithm was developed to objectively and quantitatively measure surface accumulation of Pseudomonas putida from photographs and results weremore » compared to independent measurements of cell density. Results from image analysis quantified biofilm growth intensity accurately and with approximately the same precision of the more laborious cell counting method. This simple method for early stage biofilm detection enables quantifiable measurement of surface fouling and is flexible enough to be applied from the laboratory to the field. Broad spectrum staining highlights fouling biomass, photography quickly captures a large area of interest, and image analysis rapidly quantifies fouling in the image.« less

A method for rapid quantitative assessment of biofilms with biomolecular staining and image analysis

DOE PAGES

Larimer, Curtis J.; Winder, Eric M.; Jeters, Robert T.; ...

2015-12-07

Here, the accumulation of bacteria in surface attached biofilms, or biofouling, can be detrimental to human health, dental hygiene, and many industrial processes. A critical need in identifying and preventing the deleterious effects of biofilms is the ability to observe and quantify their development. Analytical methods capable of assessing early stage fouling are cumbersome or lab-confined, subjective, and qualitative. Herein, a novel photographic method is described that uses biomolecular staining and image analysis to enhance contrast of early stage biofouling. A robust algorithm was developed to objectively and quantitatively measure surface accumulation of Pseudomonas putida from photographs and results weremore » compared to independent measurements of cell density. Results from image analysis quantified biofilm growth intensity accurately and with approximately the same precision of the more laborious cell counting method. This simple method for early stage biofilm detection enables quantifiable measurement of surface fouling and is flexible enough to be applied from the laboratory to the field. Broad spectrum staining highlights fouling biomass, photography quickly captures a large area of interest, and image analysis rapidly quantifies fouling in the image.« less

Application of high-resolution melting analysis for authenticity testing of valuable Dendrobium commercial products.

PubMed

Dong, Xiaoman; Jiang, Chao; Yuan, Yuan; Peng, Daiyin; Luo, Yuqin; Zhao, Yuyang; Huang, Luqi

2018-01-01

The accurate identification of botanical origin in commercial products is important to ensure food authenticity and safety for consumers. The Dendrobium species have long been commercialised as functional food supplements and herbal medicines in Asia. Three valuable Dendrobium species, namely Dendrobium officinale, D. huoshanense and D. moniliforme, are often mutually adulterated in trade products in pursuit of higher profit. In this paper, a rapid and reliable semi-quantitative method for identifying the botanical origin of Dendrobium products in terminal markets was developed using high-resolution melting (HRM) analysis with specific primer pairs to target the trnL-F region. The HRM analysis method detected amounts of D. moniliforme adulterants as low as 1% in D. huoshanense or D. officinale products. The results have demonstrated that HRM analysis is a fast and effective tool for the differentiation of these Dendrobium species both for their authenticity as well as for the semi-quantitative determination of the purity of their processed products. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Analysis of artifacts suggests DGGE should not be used for quantitative diversity analysis.

PubMed

Neilson, Julia W; Jordan, Fiona L; Maier, Raina M

2013-03-01

PCR-denaturing gradient gel electrophoresis (PCR-DGGE) is widely used in microbial ecology for the analysis of comparative community structure. However, artifacts generated during PCR-DGGE of mixed template communities impede the application of this technique to quantitative analysis of community diversity. The objective of the current study was to employ an artificial bacterial community to document and analyze artifacts associated with multiband signatures and preferential template amplification and to highlight their impacts on the use of this technique for quantitative diversity analysis. Six bacterial species (three Betaproteobacteria, two Alphaproteobacteria, and one Firmicutes) were amplified individually and in combinations with primers targeting the V7/V8 region of the 16S rRNA gene. Two of the six isolates produced multiband profiles demonstrating that band number does not correlate directly with α-diversity. Analysis of the multiple bands from one of these isolates confirmed that both bands had identical sequences which lead to the hypothesis that the multiband pattern resulted from two distinct structural conformations of the same amplicon. In addition, consistent preferential amplification was demonstrated following pairwise amplifications of the six isolates. DGGE and real time PCR analysis identified primer mismatch and PCR inhibition due to 16S rDNA secondary structure as the most probable causes of preferential amplification patterns. Reproducible DGGE community profiles generated in this study confirm that PCR-DGGE provides an excellent high-throughput tool for comparative community structure analysis, but that method-specific artifacts preclude its use for accurate comparative diversity analysis. Copyright © 2013 Elsevier B.V. All rights reserved.

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.

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.

Protein detection by Simple Western™ analysis.

PubMed

Harris, Valerie M

2015-01-01

Protein Simple© has taken a well-known protein detection method, the western blot, and revolutionized it. The Simple Western™ system uses capillary electrophoresis to identify and quantitate a protein of interest. Protein Simple© provides multiple detection apparatuses (Wes, Sally Sue, or Peggy Sue) that are suggested to save scientists valuable time by allowing the researcher to prepare the protein sample, load it along with necessary antibodies and substrates, and walk away. Within 3-5 h the protein will be separated by size, or charge, immuno-detection of target protein will be accurately quantitated, and results will be immediately made available. Using the Peggy Sue instrument, one study recently examined changes in MAPK signaling proteins in the sex-determining stage of gonadal development. Here the methodology is described.

Quantitative determination of a chemically modified hammerhead ribozyme in blood plasma using 96-well solid-phase extraction coupled with high-performance liquid chromatography or capillary gel electrophoresis.

PubMed

Bellon, L; Maloney, L; Zinnen, S P; Sandberg, J A; Johnson, K E

2000-08-01

Versatile bioanalytical assays to detect chemically stabilized hammerhead ribozyme and putative ribozyme metabolites from plasma are described. The extraction protocols presented are based on serial solid-phase extractions performed on a 96-well plate format and are compatible with either IEX-HPLC or CGE back-end analysis. A validation of both assays confirmed that both the HPLC and the CGE methods possess the required linearity, accuracy, and precision to accurately measure concentrations of hammerhead ribozyme extracted from plasma. These methods should be of general use to detect and quantitate ribozymes from other biological fluids such as serum and urine. Copyright 2000 Academic Press.

Spectroscopic database

NASA Technical Reports Server (NTRS)

Husson, N.; Barbe, A.; Brown, L. R.; Carli, B.; Goldman, A.; Pickett, H. M.; Roche, A. E.; Rothman, L. S.; Smith, M. A. H.

1985-01-01

Several aspects of quantitative atmospheric spectroscopy are considered, using a classification of the molecules according to the gas amounts in the stratosphere and upper troposphere, and reviews of quantitative atmospheric high-resolution spectroscopic measurements and field measurements systems are given. Laboratory spectroscopy and spectral analysis and prediction are presented with a summary of current laboratory spectroscopy capabilities. Spectroscopic data requirements for accurate derivation of atmospheric composition are discussed, where examples are given for space-based remote sensing experiments of the atmosphere: the ATMOS (Atmospheric Trace Molecule) and UARS (Upper Atmosphere Research Satellite) experiment. A review of the basic parameters involved in the data compilations; a summary of information on line parameter compilations already in existence; and a summary of current laboratory spectroscopy studies are used to assess the data base.

A disposable sampling device to collect volume-measured DBS directly from a fingerprick onto DBS paper.

PubMed

Lenk, Gabriel; Sandkvist, Sören; Pohanka, Anton; Stemme, Göran; Beck, Olof; Roxhed, Niclas

2015-01-01

DBS samples collected from a fingerprick typically vary in volume and homogeneity and hence make an accurate quantitative analysis of DBS samples difficult. We report a prototype which first defines a precise liquid volume and subsequently stores it to a conventional DBS matrix. Liquid volumes of 2.2 µl ± 7.1% (n = 21) for deionized water and 6.1 µl ± 8.8% (n = 15) for whole blood have been successfully metered and stored in DBS paper. The new method of collecting a defined volume of blood by DBS sampling has the potential to reduce assay bias for the quantitative evaluation of DBS samples while maintaining the simplicity of conventional DBS sampling.

Calibration and data collection protocols for reliable lattice parameter values in electron pair distribution function studies

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

Abeykoon, A. M. Milinda; Hu, Hefei; Wu, Lijun

2015-01-30

Different protocols for calibrating electron pair distribution function (ePDF) measurements are explored and described for quantitative studies on nanomaterials. It is found that the most accurate approach to determine the camera length is to use a standard calibration sample of Au nanoparticles from the National Institute of Standards and Technology. Different protocols for data collection are also explored, as are possible operational errors, to find the best approaches for accurate data collection for quantitative ePDF studies.

Calibration and data collection protocols for reliable lattice parameter values in electron pair distribution function (ePDF) studies

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

Abeykoon, A. M. Milinda; Hu, Hefei; Wu, Lijun

2015-02-01

We explore and describe different protocols for calibrating electron pair distribution function (ePDF) measurements for quantitative studies on nano-materials. We find the most accurate approach to determine the camera-length is to use a standard calibration sample of Au nanoparticles from National Institute of Standards and Technology. Different protocols for data collection are also explored, as are possible operational errors, to find the best approaches for accurate data collection for quantitative ePDF studies.

Quantification of fibre polymerization through Fourier space image analysis

PubMed Central

Nekouzadeh, Ali; Genin, Guy M.

2011-01-01

Quantification of changes in the total length of randomly oriented and possibly curved lines appearing in an image is a necessity in a wide variety of biological applications. Here, we present an automated approach based upon Fourier space analysis. Scaled, band-pass filtered power spectral densities of greyscale images are integrated to provide a quantitative measurement of the total length of lines of a particular range of thicknesses appearing in an image. A procedure is presented to correct for changes in image intensity. The method is most accurate for two-dimensional processes with fibres that do not occlude one another. PMID:24959096

Sifting noisy data for truths about noisy systems. Comment on "Extracting physics of life at the molecular level: A review of single-molecule data analyses" by W. Colomb and S.K. Sarkar

NASA Astrophysics Data System (ADS)

Flyvbjerg, Henrik; Mortensen, Kim I.

2015-06-01

With each new aspect of nature that becomes accessible to quantitative science, new needs arise for data analysis and mathematical modeling. The classical example is Tycho Brahe's accurate and comprehensive observations of planets, which made him hire Kepler for his mathematical skills to assist with the data analysis. We all learned what that lead to: Kepler's three laws of planetary motion, phenomenology in purely mathematical form. Newton built on this, and the scientific revolution was over, completed.

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

PubMed

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

2018-01-01

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

Simultaneous Estimation of Withaferin A and Z-Guggulsterone in Marketed Formulation by RP-HPLC.

PubMed

Agrawal, Poonam; Vegda, Rashmi; Laddha, Kirti

2015-07-01

A simple, rapid, precise and accurate high-performance liquid chromatography (HPLC) method was developed for simultaneous estimation of withaferin A and Z-guggulsterone in a polyherbal formulation containing Withania somnifera and Commiphora wightii. The chromatographic separation was achieved on a Purosphere RP-18 column (particle size 5 µm) with a mobile phase consisting of Solvent A (acetonitrile) and Solvent B (water) with the following gradients: 0-7 min, 50% A in B; 7-9 min, 50-80% A in B; 9-20 min, 80% A in B at a flow rate of 1 mL/min and detection at 235 nm. The marker compounds were well separated on the chromatogram within 20 min. The results obtained indicate accuracy and reliability of the developed simultaneous HPLC method for the quantification of withaferin A and Z-guggulsterone. The proposed method was found to be reproducible, specific, precise and accurate for simultaneous estimation of these marker compounds in a combined dosage form. The HPLC method was appropriate and the two markers are well resolved, enabling efficient quantitative analysis of withaferin A and Z-guggulsterone. The method can be successively used for quantitative analysis of these two marker constituents in combination of marketed polyherbal formulation. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Rapid and on-site analysis of illegal drugs on the nano-microscale using a deep ultraviolet-visible reflected optical fiber sensor.

PubMed

Li, Qiang; Qiu, Tian; Hao, Hongxia; Zhou, Hong; Wang, Tongzhou; Zhang, Ye; Li, Xin; Huang, Guoliang; Cheng, Jing

2012-04-07

A deep ultraviolet-visible (DUV-Vis) reflected optical fiber sensor was developed for use in a simple spectrophotometric detection system to detect the absorption of various illegal drugs at wavelengths between 180 and 800 nm. Quantitative analyses performed using the sensor revealed a high specificity and sensitivity for drug detection at a wavelength of approximately 200 nm. Using a double-absorption optical path length, extremely small sample volumes were used (32 to 160 nL), which allowed the use of minimal amounts of samples. A portable spectrophotometric system was established based on our optical fiber sensor for the on-site determination and quantitative analysis of common illegal drugs, such as 3,4-methylenedioxymethamphetamine (MDMA), ketamine hydrochloride, cocaine hydrochloride, diazepam, phenobarbital, and barbital. By analyzing the absorbance spectra, six different drugs were quantified at concentrations that ranged from 0.1 to 1000 μg mL(-1) (16 pg-0.16 μg). A novel Matching Algorithm of Spectra Space (MASS) was used to accurately distinguish between each drug in a mixture. As an important supplement to traditional methods, such as mass spectrometry or chromatography, our optical fiber sensor offers rapid and low-cost on-site detection using trace amounts of sample. This rapid and accurate analytical method has wide-ranging applications in forensic science, law enforcement, and medicine.

[Applications of 2D and 3D landscape pattern indices in landscape pattern analysis of mountainous area at county level].

PubMed

Lu, Chao; Qi, Wei; Li, Le; Sun, Yao; Qin, Tian-Tian; Wang, Na-Na

2012-05-01

Landscape pattern indices are the commonly used tools for the quantitative analysis of landscape pattern. However, the traditional 2D landscape pattern indices neglect the effects of terrain on landscape, existing definite limitations in quantitatively describing the landscape patterns in mountains areas. Taking the Qixia City, a typical mountainous and hilly region in Shandong Province of East China, as a case, this paper compared the differences between 2D and 3D landscape pattern indices in quantitatively describing the landscape patterns and their dynamic changes in mountainous areas. On the basis of terrain structure analysis, a set of landscape pattern indices were selected, including area and density (class area and mean patch size), edge and shape (edge density, landscape shape index, and fractal dimension of mean patch), diversity (Shannon's diversity index and evenness index) , and gathering and spread (contagion index). There existed obvious differences between the 3D class area, mean patch area, and edge density and the corresponding 2D indices, but no significant differences between the 3D landscape shape index, fractal dimension of mean patch, and Shannon' s diversity index and evenness index and the corresponding 2D indices. The 3D contagion index and 2D contagion index had no difference. Because the 3D landscape pattern indices were calculated by using patch surface area and surface perimeter whereas the 2D landscape pattern indices were calculated by adopting patch projective area and projective perimeter, the 3D landscape pattern indices could be relative accurate and efficient in describing the landscape area, density and borderline, in mountainous areas. However, there were no distinct differences in describing landscape shape, diversity, and gathering and spread between the 3D and 2D landscape pattern indices. Generally, by introducing 3D landscape pattern indices to topographic pattern, the description of landscape pattern and its dynamic change would be relatively accurate.

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.

Capillary nano-immunoassays: advancing quantitative proteomics analysis, biomarker assessment, and molecular diagnostics.

PubMed

Chen, Jin-Qiu; Wakefield, Lalage M; Goldstein, David J

2015-06-06

There is an emerging demand for the use of molecular profiling to facilitate biomarker identification and development, and to stratify patients for more efficient treatment decisions with reduced adverse effects. In the past decade, great strides have been made to advance genomic, transcriptomic and proteomic approaches to address these demands. While there has been much progress with these large scale approaches, profiling at the protein level still faces challenges due to limitations in clinical sample size, poor reproducibility, unreliable quantitation, and lack of assay robustness. A novel automated capillary nano-immunoassay (CNIA) technology has been developed. This technology offers precise and accurate measurement of proteins and their post-translational modifications using either charge-based or size-based separation formats. The system not only uses ultralow nanogram levels of protein but also allows multi-analyte analysis using a parallel single-analyte format for increased sensitivity and specificity. The high sensitivity and excellent reproducibility of this technology make it particularly powerful for analysis of clinical samples. Furthermore, the system can distinguish and detect specific protein post-translational modifications that conventional Western blot and other immunoassays cannot easily capture. This review will summarize and evaluate the latest progress to optimize the CNIA system for comprehensive, quantitative protein and signaling event characterization. It will also discuss how the technology has been successfully applied in both discovery research and clinical studies, for signaling pathway dissection, proteomic biomarker assessment, targeted treatment evaluation and quantitative proteomic analysis. Lastly, a comparison of this novel system with other conventional immuno-assay platforms is performed.

Joint Stochastic Inversion of Pre-Stack 3D Seismic Data and Well Logs for High Resolution Hydrocarbon Reservoir Characterization

NASA Astrophysics Data System (ADS)

Torres-Verdin, C.

2007-05-01

This paper describes the successful implementation of a new 3D AVA stochastic inversion algorithm to quantitatively integrate pre-stack seismic amplitude data and well logs. The stochastic inversion algorithm is used to characterize flow units of a deepwater reservoir located in the central Gulf of Mexico. Conventional fluid/lithology sensitivity analysis indicates that the shale/sand interface represented by the top of the hydrocarbon-bearing turbidite deposits generates typical Class III AVA responses. On the other hand, layer- dependent Biot-Gassmann analysis shows significant sensitivity of the P-wave velocity and density to fluid substitution. Accordingly, AVA stochastic inversion, which combines the advantages of AVA analysis with those of geostatistical inversion, provided quantitative information about the lateral continuity of the turbidite reservoirs based on the interpretation of inverted acoustic properties (P-velocity, S-velocity, density), and lithotype (sand- shale) distributions. The quantitative use of rock/fluid information through AVA seismic amplitude data, coupled with the implementation of co-simulation via lithotype-dependent multidimensional joint probability distributions of acoustic/petrophysical properties, yields accurate 3D models of petrophysical properties such as porosity and permeability. Finally, by fully integrating pre-stack seismic amplitude data and well logs, the vertical resolution of inverted products is higher than that of deterministic inversions methods.

Systems Toxicology: From Basic Research to Risk Assessment

PubMed Central

2014-01-01

Systems Toxicology is the integration of classical toxicology with quantitative analysis of large networks of molecular and functional changes occurring across multiple levels of biological organization. Society demands increasingly close scrutiny of the potential health risks associated with exposure to chemicals present in our everyday life, leading to an increasing need for more predictive and accurate risk-assessment approaches. Developing such approaches requires a detailed mechanistic understanding of the ways in which xenobiotic substances perturb biological systems and lead to adverse outcomes. Thus, Systems Toxicology approaches offer modern strategies for gaining such mechanistic knowledge by combining advanced analytical and computational tools. Furthermore, Systems Toxicology is a means for the identification and application of biomarkers for improved safety assessments. In Systems Toxicology, quantitative systems-wide molecular changes in the context of an exposure are measured, and a causal chain of molecular events linking exposures with adverse outcomes (i.e., functional and apical end points) is deciphered. Mathematical models are then built to describe these processes in a quantitative manner. The integrated data analysis leads to the identification of how biological networks are perturbed by the exposure and enables the development of predictive mathematical models of toxicological processes. This perspective integrates current knowledge regarding bioanalytical approaches, computational analysis, and the potential for improved risk assessment. PMID:24446777

Systems toxicology: from basic research to risk assessment.

PubMed

Sturla, Shana J; Boobis, Alan R; FitzGerald, Rex E; Hoeng, Julia; Kavlock, Robert J; Schirmer, Kristin; Whelan, Maurice; Wilks, Martin F; Peitsch, Manuel C

2014-03-17

Systems Toxicology is the integration of classical toxicology with quantitative analysis of large networks of molecular and functional changes occurring across multiple levels of biological organization. Society demands increasingly close scrutiny of the potential health risks associated with exposure to chemicals present in our everyday life, leading to an increasing need for more predictive and accurate risk-assessment approaches. Developing such approaches requires a detailed mechanistic understanding of the ways in which xenobiotic substances perturb biological systems and lead to adverse outcomes. Thus, Systems Toxicology approaches offer modern strategies for gaining such mechanistic knowledge by combining advanced analytical and computational tools. Furthermore, Systems Toxicology is a means for the identification and application of biomarkers for improved safety assessments. In Systems Toxicology, quantitative systems-wide molecular changes in the context of an exposure are measured, and a causal chain of molecular events linking exposures with adverse outcomes (i.e., functional and apical end points) is deciphered. Mathematical models are then built to describe these processes in a quantitative manner. The integrated data analysis leads to the identification of how biological networks are perturbed by the exposure and enables the development of predictive mathematical models of toxicological processes. This perspective integrates current knowledge regarding bioanalytical approaches, computational analysis, and the potential for improved risk assessment.

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

Quantitative analysis of detailed lignin monomer composition by pyrolysis-gas chromatography combined with preliminary acetylation of the samples.

PubMed

Sonoda, T; Ona, T; Yokoi, H; Ishida, Y; Ohtani, H; Tsuge, S

2001-11-15

Detailed quantitative analysis of lignin monomer composition comprising p-coumaryl, coniferyl, and sinapyl alcohol and p-coumaraldehyde, coniferaldehyde, and sinapaldehyde in plant has not been studied from every point mainly because of artifact formation during the lignin isolation procedure, partial loss of the lignin components inherent in the chemical degradative methods, and difficulty in the explanation of the complex spectra generally observed for the lignin components. Here we propose a new method to quantify lignin monomer composition in detail by pyrolysis-gas chromatography (Py-GC) using acetylated lignin samples. The lignin acetylation procedure would contribute to prevent secondary formation of cinnamaldehydes from the corresponding alcohol forms during pyrolysis, which are otherwise unavoidable in conventional Py-GC process to some extent. On the basis of the characteristic peaks on the pyrograms of the acetylated sample, lignin monomer compositions in various dehydrogenative polymers (DHP) as lignin model compounds were determined, taking even minor components such as cinnamaldehydes into consideration. The observed compositions by Py-GC were in good agreement with the supplied lignin monomer contents on DHP synthesis. The new Py-GC method combined with sample preacetylation allowed us an accurate quantitative analysis of detailed lignin monomer composition using a microgram order of extractive-free plant samples.

Establishment of a sensitive system for analysis of human vaginal microbiota on the basis of rRNA-targeted reverse transcription-quantitative PCR.

PubMed

Kurakawa, Takashi; Ogata, Kiyohito; Tsuji, Hirokazu; Kado, Yukiko; Takahashi, Takuya; Kida, Yumi; Ito, Masahiro; Okada, Nobuhiko; Nomoto, Koji

2015-04-01

Ten specific primer sets, for Lactobacillus gasseri, Lactobacillus crispatus, Atopobium vaginae, Gardnerella vaginalis, Mobiluncus curtisii, Chlamydia trachomatis/muridarum, Bifidobacterium longum subsp. longum, Bifidobacterium longum subsp. infantis, Bifidobacterium adolescentis, and Bifidobacterium angulatum, were developed for quantitative analysis of vaginal microbiota. rRNA-targeted reverse transcription-quantitative PCR (RT-qPCR) analysis of the vaginal samples from 12 healthy Japanese volunteers using the new primer sets together with 25 existing primer sets revealed the diversity of their vaginal microbiota: Lactobacilli such as L. crispatus, L. gasseri, Lactobacillus jensenii, Lactobacillus iners, and Lactobacillus vaginalis, as the major populations at 10(7) cells/ml vaginal fluid, were followed by facultative anaerobes such as Streptococcus and strict anaerobes at lower population levels of 10(4) cells/ml or less. Certain bacterial vaginosis (BV)-related bacteria, such as G. vaginalis, A. vaginae, M. curtisii, and Prevotella, were also detected in some subjects. Especially in one subject, both G. vaginalis and A. vaginae were detected at high population levels of 10(8.8) and 10(8.9) cells/ml vaginal fluid, suggesting that she is an asymptomatic BV patient. These results suggest that the RT-qPCR system is effective for accurate analysis of major vaginal commensals and diagnosis of several vaginal infections. Copyright © 2015 Elsevier B.V. All rights reserved.

Measuring laboratory-based influenza surveillance capacity: development of the 'International Influenza Laboratory Capacity Review' Tool.

PubMed

Muir-Paulik, S A; Johnson, L E A; Kennedy, P; Aden, T; Villanueva, J; Reisdorf, E; Humes, R; Moen, A C

2016-01-01

The 2005 International Health Regulations (IHR 2005) emphasized the importance of laboratory capacity to detect emerging diseases including novel influenza viruses. To support IHR 2005 requirements and the need to enhance influenza laboratory surveillance capacity, the Association of Public Health Laboratories (APHL) and the Centers for Disease Control and Prevention (CDC) Influenza Division developed the International Influenza Laboratory Capacity Review (Tool). Data from 37 assessments were reviewed and analyzed to verify that the quantitative analysis results accurately depicted a laboratory's capacity and capabilities. Subject matter experts in influenza and laboratory practice used an iterative approach to develop the Tool incorporating feedback and lessons learnt through piloting and implementation. To systematically analyze assessment data, a quantitative framework for analysis was added to the Tool. The review indicated that changes in scores consistently reflected enhanced or decreased capacity. The review process also validated the utility of adding a quantitative analysis component to the assessments and the benefit of establishing a baseline from which to compare future assessments in a standardized way. Use of the Tool has provided APHL, CDC and each assessed laboratory with a standardized analysis of the laboratory's capacity. The information generated is used to improve laboratory systems for laboratory testing and enhance influenza surveillance globally. We describe the development of the Tool and lessons learnt. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Fast and simultaneous determination of 12 polyphenols in apple peel and pulp by using chemometrics-assisted high-performance liquid chromatography with diode array detection.

PubMed

Wang, Tong; Wu, Hai-Long; Xie, Li-Xia; Zhu, Li; Liu, Zhi; Sun, Xiao-Dong; Xiao, Rong; Yu, Ru-Qin

2017-04-01

In this work, a smart chemometrics-enhanced strategy, high-performance liquid chromatography, and diode array detection coupled with second-order calibration method based on alternating trilinear decomposition algorithm was proposed to simultaneously quantify 12 polyphenols in different kinds of apple peel and pulp samples. The proposed strategy proved to be a powerful tool to solve the problems of coelution, unknown interferences, and chromatographic shifts in the process of high-performance liquid chromatography analysis, making it possible for the determination of 12 polyphenols in complex apple matrices within 10 min under simple conditions of elution. The average recoveries with standard deviations, and figures of merit including sensitivity, selectivity, limit of detection, and limit of quantitation were calculated to validate the accuracy of the proposed method. Compared to the quantitative analysis results from the classic high-performance liquid chromatography method, the statistical and graphical analysis showed that our proposed strategy obtained more reliable results. All results indicated that our proposed method used in the quantitative analysis of apple polyphenols was an accurate, fast, universal, simple, and green one, and it was expected to be developed as an attractive alternative method for simultaneous determination of multitargeted analytes in complex matrices. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

Quantitative DNA Methylation Analysis Identifies a Single CpG Dinucleotide Important for ZAP-70 Expression and Predictive of Prognosis in Chronic Lymphocytic Leukemia

PubMed Central

Claus, Rainer; Lucas, David M.; Stilgenbauer, Stephan; Ruppert, Amy S.; Yu, Lianbo; Zucknick, Manuela; Mertens, Daniel; Bühler, Andreas; Oakes, Christopher C.; Larson, Richard A.; Kay, Neil E.; Jelinek, Diane F.; Kipps, Thomas J.; Rassenti, Laura Z.; Gribben, John G.; Döhner, Hartmut; Heerema, Nyla A.; Marcucci, Guido; Plass, Christoph; Byrd, John C.

2012-01-01

Purpose Increased ZAP-70 expression predicts poor prognosis in chronic lymphocytic leukemia (CLL). Current methods for accurately measuring ZAP-70 expression are problematic, preventing widespread application of these tests in clinical decision making. We therefore used comprehensive DNA methylation profiling of the ZAP-70 regulatory region to identify sites important for transcriptional control. Patients and Methods High-resolution quantitative DNA methylation analysis of the entire ZAP-70 gene regulatory regions was conducted on 247 samples from patients with CLL from four independent clinical studies. Results Through this comprehensive analysis, we identified a small area in the 5′ regulatory region of ZAP-70 that showed large variability in methylation in CLL samples but was universally methylated in normal B cells. High correlation with mRNA and protein expression, as well as activity in promoter reporter assays, revealed that within this differentially methylated region, a single CpG dinucleotide and neighboring nucleotides are particularly important in ZAP-70 transcriptional regulation. Furthermore, by using clustering approaches, we identified a prognostic role for this site in four independent data sets of patients with CLL using time to treatment, progression-free survival, and overall survival as clinical end points. Conclusion Comprehensive quantitative DNA methylation analysis of the ZAP-70 gene in CLL identified important regions responsible for transcriptional regulation. In addition, loss of methylation at a specific single CpG dinucleotide in the ZAP-70 5′ regulatory sequence is a highly predictive and reproducible biomarker of poor prognosis in this disease. This work demonstrates the feasibility of using quantitative specific ZAP-70 methylation analysis as a relevant clinically applicable prognostic test in CLL. PMID:22564988

Patient-specific coronary blood supply territories for quantitative perfusion analysis

PubMed Central

Zakkaroff, Constantine; Biglands, John D.; Greenwood, John P.; Plein, Sven; Boyle, Roger D.; Radjenovic, Aleksandra; Magee, Derek R.

2018-01-01

Abstract Myocardial perfusion imaging, coupled with quantitative perfusion analysis, provides an important diagnostic tool for the identification of ischaemic heart disease caused by coronary stenoses. The accurate mapping between coronary anatomy and under-perfused areas of the myocardium is important for diagnosis and treatment. However, in the absence of the actual coronary anatomy during the reporting of perfusion images, areas of ischaemia are allocated to a coronary territory based on a population-derived 17-segment (American Heart Association) AHA model of coronary blood supply. This work presents a solution for the fusion of 2D Magnetic Resonance (MR) myocardial perfusion images and 3D MR angiography data with the aim to improve the detection of ischaemic heart disease. The key contribution of this work is a novel method for the mediated spatiotemporal registration of perfusion and angiography data and a novel method for the calculation of patient-specific coronary supply territories. The registration method uses 4D cardiac MR cine series spanning the complete cardiac cycle in order to overcome the under-constrained nature of non-rigid slice-to-volume perfusion-to-angiography registration. This is achieved by separating out the deformable registration problem and solving it through phase-to-phase registration of the cine series. The use of patient-specific blood supply territories in quantitative perfusion analysis (instead of the population-based model of coronary blood supply) has the potential of increasing the accuracy of perfusion analysis. Quantitative perfusion analysis diagnostic accuracy evaluation with patient-specific territories against the AHA model demonstrates the value of the mediated spatiotemporal registration in the context of ischaemic heart disease diagnosis. PMID:29392098

Automated classification of cell morphology by coherence-controlled holographic microscopy

NASA Astrophysics Data System (ADS)

Strbkova, Lenka; Zicha, Daniel; Vesely, Pavel; Chmelik, Radim

2017-08-01

In the last few years, classification of cells by machine learning has become frequently used in biology. However, most of the approaches are based on morphometric (MO) features, which are not quantitative in terms of cell mass. This may result in poor classification accuracy. Here, we study the potential contribution of coherence-controlled holographic microscopy enabling quantitative phase imaging for the classification of cell morphologies. We compare our approach with the commonly used method based on MO features. We tested both classification approaches in an experiment with nutritionally deprived cancer tissue cells, while employing several supervised machine learning algorithms. Most of the classifiers provided higher performance when quantitative phase features were employed. Based on the results, it can be concluded that the quantitative phase features played an important role in improving the performance of the classification. The methodology could be valuable help in refining the monitoring of live cells in an automated fashion. We believe that coherence-controlled holographic microscopy, as a tool for quantitative phase imaging, offers all preconditions for the accurate automated analysis of live cell behavior while enabling noninvasive label-free imaging with sufficient contrast and high-spatiotemporal phase sensitivity.

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.

The use of immunohistochemistry for biomarker assessment--can it compete with other technologies?

PubMed

Dunstan, Robert W; Wharton, Keith A; Quigley, Catherine; Lowe, Amanda

2011-10-01

A morphology-based assay such as immunohistochemistry (IHC) should be a highly effective means to define the expression of a target molecule of interest, especially if the target is a protein. However, over the past decade, IHC as a platform for biomarkers has been challenged by more quantitative molecular assays with reference standards but that lack morphologic context. For IHC to be considered a "top-tier" biomarker assay, it must provide truly quantitative data on par with non-morphologic assays, which means it needs to be run with reference standards. However, creating such standards for IHC will require optimizing all aspects of tissue collection, fixation, section thickness, morphologic criteria for assessment, staining processes, digitization of images, and image analysis. This will also require anatomic pathology to evolve from a discipline that is descriptive to one that is quantitative. A major step in this transformation will be replacing traditional ocular microscopes with computer monitors and whole slide images, for without digitization, there can be no accurate quantitation; without quantitation, there can be no standardization; and without standardization, the value of morphology-based IHC assays will not be realized.

Automated classification of cell morphology by coherence-controlled holographic microscopy.

PubMed

Strbkova, Lenka; Zicha, Daniel; Vesely, Pavel; Chmelik, Radim

2017-08-01

In the last few years, classification of cells by machine learning has become frequently used in biology. However, most of the approaches are based on morphometric (MO) features, which are not quantitative in terms of cell mass. This may result in poor classification accuracy. Here, we study the potential contribution of coherence-controlled holographic microscopy enabling quantitative phase imaging for the classification of cell morphologies. We compare our approach with the commonly used method based on MO features. We tested both classification approaches in an experiment with nutritionally deprived cancer tissue cells, while employing several supervised machine learning algorithms. Most of the classifiers provided higher performance when quantitative phase features were employed. Based on the results, it can be concluded that the quantitative phase features played an important role in improving the performance of the classification. The methodology could be valuable help in refining the monitoring of live cells in an automated fashion. We believe that coherence-controlled holographic microscopy, as a tool for quantitative phase imaging, offers all preconditions for the accurate automated analysis of live cell behavior while enabling noninvasive label-free imaging with sufficient contrast and high-spatiotemporal phase sensitivity. (2017) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE).

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.

Bidirectional Retroviral Integration Site PCR Methodology and Quantitative Data Analysis Workflow.

PubMed

Suryawanshi, Gajendra W; Xu, Song; Xie, Yiming; Chou, Tom; Kim, Namshin; Chen, Irvin S Y; Kim, Sanggu

2017-06-14

Integration Site (IS) assays are a critical component of the study of retroviral integration sites and their biological significance. In recent retroviral gene therapy studies, IS assays, in combination with next-generation sequencing, have been used as a cell-tracking tool to characterize clonal stem cell populations sharing the same IS. For the accurate comparison of repopulating stem cell clones within and across different samples, the detection sensitivity, data reproducibility, and high-throughput capacity of the assay are among the most important assay qualities. This work provides a detailed protocol and data analysis workflow for bidirectional IS analysis. The bidirectional assay can simultaneously sequence both upstream and downstream vector-host junctions. Compared to conventional unidirectional IS sequencing approaches, the bidirectional approach significantly improves IS detection rates and the characterization of integration events at both ends of the target DNA. The data analysis pipeline described here accurately identifies and enumerates identical IS sequences through multiple steps of comparison that map IS sequences onto the reference genome and determine sequencing errors. Using an optimized assay procedure, we have recently published the detailed repopulation patterns of thousands of Hematopoietic Stem Cell (HSC) clones following transplant in rhesus macaques, demonstrating for the first time the precise time point of HSC repopulation and the functional heterogeneity of HSCs in the primate system. The following protocol describes the step-by-step experimental procedure and data analysis workflow that accurately identifies and quantifies identical IS sequences.

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.

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.

A new measurement method of coatings thickness based on lock-in thermography

NASA Astrophysics Data System (ADS)

Zhang, Jin-Yu; Meng, Xiang-bin; Ma, Yong-chao

2016-05-01

Coatings have been widely used in modern industry and it plays an important role. Coatings thickness is directly related to the performance of the functional coatings, therefore, rapid and accurate coatings thickness inspection has great significance. Existing coatings thickness measurement method is difficult to achieve fast and accurate on-site non-destructive coatings inspection due to cost, accuracy, destruction during inspection and other reasons. This paper starts from the introduction of the principle of lock-in thermography, and then performs an in-depth study on the application of lock-in thermography in coatings inspection through numerical modeling and analysis. The numerical analysis helps explore the relationship between coatings thickness and phase, and the relationship lays the foundation for accurate calculation of coatings thickness. The author sets up a lock-in thermography inspection system and uses thermal barrier coatings specimens to conduct an experiment. The specimen coatings thickness is measured and calibrated to verify the quantitative inspection. Experiment results show that the lock-in thermography method can perform fast coatings inspection and the inspection accuracy is about 95%. Therefore, the method can meet the field testing requirements for engineering projects.

How little data is enough? Phase-diagram analysis of sparsity-regularized X-ray computed tomography

PubMed Central

Jørgensen, J. S.; Sidky, E. Y.

2015-01-01

We introduce phase-diagram analysis, a standard tool in compressed sensing (CS), to the X-ray computed tomography (CT) community as a systematic method for determining how few projections suffice for accurate sparsity-regularized reconstruction. In CS, a phase diagram is a convenient way to study and express certain theoretical relations between sparsity and sufficient sampling. We adapt phase-diagram analysis for empirical use in X-ray CT for which the same theoretical results do not hold. We demonstrate in three case studies the potential of phase-diagram analysis for providing quantitative answers to questions of undersampling. First, we demonstrate that there are cases where X-ray CT empirically performs comparably with a near-optimal CS strategy, namely taking measurements with Gaussian sensing matrices. Second, we show that, in contrast to what might have been anticipated, taking randomized CT measurements does not lead to improved performance compared with standard structured sampling patterns. Finally, we show preliminary results of how well phase-diagram analysis can predict the sufficient number of projections for accurately reconstructing a large-scale image of a given sparsity by means of total-variation regularization. PMID:25939620

How little data is enough? Phase-diagram analysis of sparsity-regularized X-ray computed tomography.

PubMed

Jørgensen, J S; Sidky, E Y

2015-06-13

We introduce phase-diagram analysis, a standard tool in compressed sensing (CS), to the X-ray computed tomography (CT) community as a systematic method for determining how few projections suffice for accurate sparsity-regularized reconstruction. In CS, a phase diagram is a convenient way to study and express certain theoretical relations between sparsity and sufficient sampling. We adapt phase-diagram analysis for empirical use in X-ray CT for which the same theoretical results do not hold. We demonstrate in three case studies the potential of phase-diagram analysis for providing quantitative answers to questions of undersampling. First, we demonstrate that there are cases where X-ray CT empirically performs comparably with a near-optimal CS strategy, namely taking measurements with Gaussian sensing matrices. Second, we show that, in contrast to what might have been anticipated, taking randomized CT measurements does not lead to improved performance compared with standard structured sampling patterns. Finally, we show preliminary results of how well phase-diagram analysis can predict the sufficient number of projections for accurately reconstructing a large-scale image of a given sparsity by means of total-variation regularization.

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 unavailable under MRM transition.

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 obtained using the automatic data processing described here compared to conventional methods.

Multivariate reference technique for quantitative analysis of fiber-optic tissue Raman spectroscopy.

PubMed

Bergholt, Mads Sylvest; Duraipandian, Shiyamala; Zheng, Wei; Huang, Zhiwei

2013-12-03

We report a novel method making use of multivariate reference signals of fused silica and sapphire Raman signals generated from a ball-lens fiber-optic Raman probe for quantitative analysis of in vivo tissue Raman measurements in real time. Partial least-squares (PLS) regression modeling is applied to extract the characteristic internal reference Raman signals (e.g., shoulder of the prominent fused silica boson peak (~130 cm(-1)); distinct sapphire ball-lens peaks (380, 417, 646, and 751 cm(-1))) from the ball-lens fiber-optic Raman probe for quantitative analysis of fiber-optic Raman spectroscopy. To evaluate the analytical value of this novel multivariate reference technique, a rapid Raman spectroscopy system coupled with a ball-lens fiber-optic Raman probe is used for in vivo oral tissue Raman measurements (n = 25 subjects) under 785 nm laser excitation powers ranging from 5 to 65 mW. An accurate linear relationship (R(2) = 0.981) with a root-mean-square error of cross validation (RMSECV) of 2.5 mW can be obtained for predicting the laser excitation power changes based on a leave-one-subject-out cross-validation, which is superior to the normal univariate reference method (RMSE = 6.2 mW). A root-mean-square error of prediction (RMSEP) of 2.4 mW (R(2) = 0.985) can also be achieved for laser power prediction in real time when we applied the multivariate method independently on the five new subjects (n = 166 spectra). We further apply the multivariate reference technique for quantitative analysis of gelatin tissue phantoms that gives rise to an RMSEP of ~2.0% (R(2) = 0.998) independent of laser excitation power variations. This work demonstrates that multivariate reference technique can be advantageously used to monitor and correct the variations of laser excitation power and fiber coupling efficiency in situ for standardizing the tissue Raman intensity to realize quantitative analysis of tissue Raman measurements in vivo, which is particularly appealing in challenging Raman endoscopic applications.

Quantitative analysis of glycated albumin in serum based on ATR-FTIR spectrum combined with SiPLS and SVM.

PubMed

Li, Yuanpeng; Li, Fucui; Yang, Xinhao; Guo, Liu; Huang, Furong; Chen, Zhenqiang; Chen, Xingdan; Zheng, Shifu

2018-08-05

A rapid quantitative analysis model for determining the glycated albumin (GA) content based on Attenuated total reflectance (ATR)-Fourier transform infrared spectroscopy (FTIR) combining with linear SiPLS and nonlinear SVM has been developed. Firstly, the real GA content in human serum was determined by GA enzymatic method, meanwhile, the ATR-FTIR spectra of serum samples from the population of health examination were obtained. The spectral data of the whole spectra mid-infrared region (4000-600 cm -1 ) and GA's characteristic region (1800-800 cm -1 ) were used as the research object of quantitative analysis. Secondly, several preprocessing steps including first derivative, second derivative, variable standardization and spectral normalization, were performed. Lastly, quantitative analysis regression models were established by using SiPLS and SVM respectively. The SiPLS modeling results are as follows: root mean square error of cross validation (RMSECV T ) = 0.523 g/L, calibration coefficient (R C ) = 0.937, Root Mean Square Error of Prediction (RMSEP T ) = 0.787 g/L, and prediction coefficient (R P ) = 0.938. The SVM modeling results are as follows: RMSECV T  = 0.0048 g/L, R C  = 0.998, RMSEP T  = 0.442 g/L, and R p  = 0.916. The results indicated that the model performance was improved significantly after preprocessing and optimization of characteristic regions. While modeling performance of nonlinear SVM was considerably better than that of linear SiPLS. Hence, the quantitative analysis model for GA in human serum based on ATR-FTIR combined with SiPLS and SVM is effective. And it does not need sample preprocessing while being characterized by simple operations and high time efficiency, providing a rapid and accurate method for GA content determination. Copyright © 2018 Elsevier B.V. All rights reserved.

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.

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.

Design and analysis of quantitative differential proteomics investigations using LC-MS technology.

PubMed

Bukhman, Yury V; Dharsee, Moyez; Ewing, Rob; Chu, Peter; Topaloglou, Thodoros; Le Bihan, Thierry; Goh, Theo; Duewel, Henry; Stewart, Ian I; Wisniewski, Jacek R; Ng, Nancy F

2008-02-01

Liquid chromatography-mass spectrometry (LC-MS)-based proteomics is becoming an increasingly important tool in characterizing the abundance of proteins in biological samples of various types and across conditions. Effects of disease or drug treatments on protein abundance are of particular interest for the characterization of biological processes and the identification of biomarkers. Although state-of-the-art instrumentation is available to make high-quality measurements and commercially available software is available to process the data, the complexity of the technology and data presents challenges for bioinformaticians and statisticians. Here, we describe a pipeline for the analysis of quantitative LC-MS data. Key components of this pipeline include experimental design (sample pooling, blocking, and randomization) as well as deconvolution and alignment of mass chromatograms to generate a matrix of molecular abundance profiles. An important challenge in LC-MS-based quantitation is to be able to accurately identify and assign abundance measurements to members of protein families. To address this issue, we implement a novel statistical method for inferring the relative abundance of related members of protein families from tryptic peptide intensities. This pipeline has been used to analyze quantitative LC-MS data from multiple biomarker discovery projects. We illustrate our pipeline here with examples from two of these studies, and show that the pipeline constitutes a complete workable framework for LC-MS-based differential quantitation. Supplementary material is available at http://iec01.mie.utoronto.ca/~thodoros/Bukhman/.

Target analysis of primary aromatic amines combined with a comprehensive screening of migrating substances in kitchen utensils by liquid chromatography-high resolution mass spectrometry.

PubMed

Sanchis, Yovana; Coscollà, Clara; Roca, Marta; Yusà, Vicent

2015-06-01

An analytical strategy including both the quantitative target analysis of 8 regulated primary aromatic amines (PAAs), as well as a comprehensive post-run target screening of 77 migrating substances, was developed for nylon utensils, using liquid chromatography-orbitrap-high resolution mass spectrometry (LC-HRMS) operating in full scan mode. The accurate mass data were acquired with a resolving power of 50,000 FWHM (scan speed, 2 Hz), and by alternating two acquisition events, ESI+ with and without fragmentation. The target method was validated after statistical optimization of the main ionization and fragmentation parameters. The quantitative method presented appropriate performance to be used in official monitoring with recoveries ranging from 78% to 112%, precision in terms of Relative Standard Deviation (RSD) was less than 15%, and the limits of quantification were between 2 and 2.5 µg kg(-1). For post-target screening, a customized theoretical database was built for food contact material migrants, including bisphenols, phthalates, and other amines. For identification purposes, accurate exact mass (<5 ppm) and some diagnostic ions including fragments were used. The strategy was applied to 10 real samples collected from different retailers in the Valencian Region (Spain) during 2014. Six out of eight target PAAs were detected in at least one sample in the target analysis. The most frequently detected compounds were 4,4'-methylenedianiline and aniline, with concentrations ranging from 2.4 to 19,715 µg kg(-1) and 2.5 to 283 µg kg(-1), respectively. Two phthalates were identified and confirmed in the post-run target screening analysis. Copyright © 2015 Elsevier B.V. All rights reserved.

Quantitative analysis of diagnosing pancreatic fibrosis using EUS-elastography (comparison with surgical specimens).

PubMed

Itoh, Yuya; Itoh, Akihiro; Kawashima, Hiroki; Ohno, Eizaburo; Nakamura, Yosuke; Hiramatsu, Takeshi; Sugimoto, Hiroyuki; Sumi, Hajime; Hayashi, Daijuro; Kuwahara, Takamichi; Morishima, Tomomasa; Funasaka, Kohei; Nakamura, Masanao; Miyahara, Ryoji; Ohmiya, Naoki; Katano, Yoshiaki; Ishigami, Masatoshi; Goto, Hidemi; Hirooka, Yoshiki

2014-07-01

An accurate diagnosis of pancreatic fibrosis is clinically important and may have potential for staging chronic pancreatitis. The aim of this study was to diagnose the grade of pancreatic fibrosis through a quantitative analysis of endoscopic ultrasound elastography (EUS-EG). From September 2004 to October 2010, 58 consecutive patients examined by EUS-EG for both pancreatic tumors and their upstream pancreas before pancreatectomy were enrolled. Preoperative EUS-EG images in the upstream pancreas were statistically quantified, and the results were retrospectively compared with postoperative histological fibrosis in the same area. For the quantification of EUS-EG images, 4 parameters (mean, standard deviation, skewness, and kurtosis) were calculated using novel software. Histological fibrosis was graded into 4 categories (normal, mild fibrosis, marked fibrosis, and severe fibrosis) according to a previously reported scoring system. The fibrosis grade in the upstream pancreas was normal in 24 patients, mild fibrosis in 19, marked fibrosis in 6, and severe fibrosis in 9. Fibrosis grade was significantly correlated with all 4 quantification parameters (mean r = -0.75, standard deviation r = -0.54, skewness r = 0.69, kurtosis r = 0.67). According to the receiver operating characteristic analysis, the mean was the most useful parameter for diagnosing pancreatic fibrosis. Using the mean, the area under the ROC curves for the diagnosis of mild or higher-grade fibrosis, marked or higher-grade fibrosis and severe fibrosis were 0.90, 0.90, and 0.90, respectively. An accurate diagnosis of pancreatic fibrosis may be possible by analyzing EUS-EG images.

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.

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.

A Quantitative Study of Oxygen as a Metabolic Regulator

NASA Technical Reports Server (NTRS)

Radhakrishnan, Krishnan; LaManna, Joseph C.; Cabera, Marco E.

2000-01-01

An acute reduction in oxygen delivery to a tissue is associated with metabolic changes aimed at maintaining ATP homeostasis. However, given the complexity of the human bio-energetic system, it is difficult to determine quantitatively how cellular metabolic processes interact to maintain ATP homeostasis during stress (e.g., hypoxia, ischemia, and exercise). In particular, we are interested in determining mechanisms relating cellular oxygen concentration to observed metabolic responses at the cellular, tissue, organ, and whole body levels and in quantifying how changes in tissue oxygen availability affect the pathways of ATP synthesis and the metabolites that control these pathways. In this study; we extend a previously developed mathematical model of human bioenergetics, to provide a physicochemical framework that permits quantitative understanding of oxygen as a metabolic regulator. Specifically, the enhancement - sensitivity analysis - permits studying the effects of variations in tissue oxygenation and parameters controlling cellular respiration on glycolysis, lactate production, and pyruvate oxidation. The analysis can distinguish between parameters that must be determined accurately and those that require less precision, based on their effects on model predictions. This capability may prove to be important in optimizing experimental design, thus reducing use of animals.

Sensitive and accurate identification of protein–DNA binding events in ChIP-chip assays using higher order derivative analysis

PubMed Central

Barrett, Christian L.; Cho, Byung-Kwan

2011-01-01

Immuno-precipitation of protein–DNA complexes followed by microarray hybridization is a powerful and cost-effective technology for discovering protein–DNA binding events at the genome scale. It is still an unresolved challenge to comprehensively, accurately and sensitively extract binding event information from the produced data. We have developed a novel strategy composed of an information-preserving signal-smoothing procedure, higher order derivative analysis and application of the principle of maximum entropy to address this challenge. Importantly, our method does not require any input parameters to be specified by the user. Using genome-scale binding data of two Escherichia coli global transcription regulators for which a relatively large number of experimentally supported sites are known, we show that ∼90% of known sites were resolved to within four probes, or ∼88 bp. Over half of the sites were resolved to within two probes, or ∼38 bp. Furthermore, we demonstrate that our strategy delivers significant quantitative and qualitative performance gains over available methods. Such accurate and sensitive binding site resolution has important consequences for accurately reconstructing transcriptional regulatory networks, for motif discovery, for furthering our understanding of local and non-local factors in protein–DNA interactions and for extending the usefulness horizon of the ChIP-chip platform. PMID:21051353

Rapid and precise determination of total sulphur in soda-lime-silica glasses.

PubMed

Beesley, W J; Chamberlain, B R

1974-04-01

A method is described for the determination of total sulphur in small amounts of soda-lime-silica glasses (100 mg or less). The crushed glass is mixed with vanadium pentoxide and decomposed at 1450 degrees under oxygen. The sulphur is quantitatively removed from the glass and determined by a conductometric technique. The method is standardized by accurately injecting sulphur dioxide into the furnace tube. The analysis time is about 10 min and the overall precision (2s) is of the order of 5%.

Sunspot analysis and prediction

NASA Technical Reports Server (NTRS)

Steyer, C. C.

1971-01-01

An attempt is made to develop an accurate functional representation, using common trigonometric functions, of all existing sunspot data, both quantitative and qualitative, ancient and modern. It is concluded that the three periods of high sunspot activity (1935 to 1970, 1835 to 1870, and 1755 to 1790) are independent populations. It is also concluded that these populations have long periods of approximately 400, 500, and 610 years, respectively. The difficulties in assuming a periodicity of seven 11-year cycles of approximately 80 years are discussed.

CLICK: The new USGS center for LIDAR information coordination and knowledge

USGS Publications Warehouse

Stoker, Jason M.; Greenlee, Susan K.; Gesch, Dean B.; Menig, Jordan C.

2006-01-01

Elevation data is rapidly becoming an important tool for the visualization and analysis of geographic information. The creation and display of three-dimensional models representing bare earth, vegetation, and structures have become major requirements for geographic research in the past few years. Light Detection and Ranging (lidar) has been increasingly accepted as an effective and accurate technology for acquiring high-resolution elevation data for bare earth, vegetation, and structures. Lidar is an active remote sensing system that records the distance, or range, of a laser fi red from an airborne or space borne platform such as an airplane, helicopter or satellite to objects or features on the Earth’s surface. By converting lidar data into bare ground topography and vegetation or structural morphologic information, extremely accurate, high-resolution elevation models can be derived to visualize and quantitatively represent scenes in three dimensions. In addition to high-resolution digital elevation models (Evans et al., 2001), other lidar-derived products include quantitative estimates of vegetative features such as canopy height, canopy closure, and biomass (Lefsky et al., 2002), and models of urban areas such as building footprints and three-dimensional city models (Maas, 2001).

Antibiotic Resistome: Improving Detection and Quantification Accuracy for Comparative Metagenomics.

PubMed

Elbehery, Ali H A; Aziz, Ramy K; Siam, Rania

2016-04-01

The unprecedented rise of life-threatening antibiotic resistance (AR), combined with the unparalleled advances in DNA sequencing of genomes and metagenomes, has pushed the need for in silico detection of the resistance potential of clinical and environmental metagenomic samples through the quantification of AR genes (i.e., genes conferring antibiotic resistance). Therefore, determining an optimal methodology to quantitatively and accurately assess AR genes in a given environment is pivotal. Here, we optimized and improved existing AR detection methodologies from metagenomic datasets to properly consider AR-generating mutations in antibiotic target genes. Through comparative metagenomic analysis of previously published AR gene abundance in three publicly available metagenomes, we illustrate how mutation-generated resistance genes are either falsely assigned or neglected, which alters the detection and quantitation of the antibiotic resistome. In addition, we inspected factors influencing the outcome of AR gene quantification using metagenome simulation experiments, and identified that genome size, AR gene length, total number of metagenomics reads and selected sequencing platforms had pronounced effects on the level of detected AR. In conclusion, our proposed improvements in the current methodologies for accurate AR detection and resistome assessment show reliable results when tested on real and simulated metagenomic datasets.

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.

Detection of blur artifacts in histopathological whole-slide images of endomyocardial biopsies.

PubMed

Hang Wu; Phan, John H; Bhatia, Ajay K; Cundiff, Caitlin A; Shehata, Bahig M; Wang, May D

2015-01-01

Histopathological whole-slide images (WSIs) have emerged as an objective and quantitative means for image-based disease diagnosis. However, WSIs may contain acquisition artifacts that affect downstream image feature extraction and quantitative disease diagnosis. We develop a method for detecting blur artifacts in WSIs using distributions of local blur metrics. As features, these distributions enable accurate classification of WSI regions as sharp or blurry. We evaluate our method using over 1000 portions of an endomyocardial biopsy (EMB) WSI. Results indicate that local blur metrics accurately detect blurry image regions.

Band-limited Green's Functions for Quantitative Evaluation of Acoustic Emission Using the Finite Element Method

NASA Technical Reports Server (NTRS)

Leser, William P.; Yuan, Fuh-Gwo; Leser, William P.

2013-01-01

A method of numerically estimating dynamic Green's functions using the finite element method is proposed. These Green's functions are accurate in a limited frequency range dependent on the mesh size used to generate them. This range can often match or exceed the frequency sensitivity of the traditional acoustic emission sensors. An algorithm is also developed to characterize an acoustic emission source by obtaining information about its strength and temporal dependence. This information can then be used to reproduce the source in a finite element model for further analysis. Numerical examples are presented that demonstrate the ability of the band-limited Green's functions approach to determine the moment tensor coefficients of several reference signals to within seven percent, as well as accurately reproduce the source-time function.

A Stereo Imaging Velocimetry Technique for Analyzing Structure of Flame Balls at Low Lewis-Number (SOFBALL) Data

NASA Technical Reports Server (NTRS)

McDowell, Mark; Gray, Elizabeth

2008-01-01

Stereo Imaging Velocimetry (SIV) is a NASA Glenn Research Center (GRC) developed fluid physics technique for measuring threedimensional (3-D) velocities in any optically transparent fluid that can be seeded with tracer particles. SIV provides a means to measure 3-D fluid velocities quantitatively and qualitatively at many points. This technique provides full-field 3-D analysis of any optically clear fluid or gas experiment using standard off-the-shelf CCD cameras to provide accurate and reproducible 3-D velocity profiles for experiments that require 3-D analysis. A flame ball is a steady flame in a premixed combustible atmosphere which, due to the transport properties (low Lewis-number) of the mixture, does not propagate but is instead supplied by diffusive transport of the reactants, forming a premixed flame. This flame geometry presents a unique environment for testing combustion theory. We present our analysis of flame ball phenomena utilizing SIV technology in order to accurately calculate the 3-D position of a flame ball(s) during an experiment, which can be used as a direct comparison of numerical simulations.

Evaluation of simulation-based scatter correction for 3-D PET cardiac imaging

NASA Astrophysics Data System (ADS)

Watson, C. C.; Newport, D.; Casey, M. E.; deKemp, R. A.; Beanlands, R. S.; Schmand, M.

1997-02-01

Quantitative imaging of the human thorax poses one of the most difficult challenges for three-dimensional (3-D) (septaless) positron emission tomography (PET), due to the strong attenuation of the annihilation radiation and the large contribution of scattered photons to the data. In [/sup 18/F] fluorodeoxyglucose (FDG) studies of the heart with the patient's arms in the field of view, the contribution of scattered events can exceed 50% of the total detected coincidences. Accurate correction for this scatter component is necessary for meaningful quantitative image analysis and tracer kinetic modeling. For this reason, the authors have implemented a single-scatter simulation technique for scatter correction in positron volume imaging. Here, they describe this algorithm and present scatter correction results from human and chest phantom studies.

Contact inspection of Si nanowire with SEM voltage contrast

NASA Astrophysics Data System (ADS)

Ohashi, Takeyoshi; Yamaguchi, Atsuko; Hasumi, Kazuhisa; Ikota, Masami; Lorusso, Gian; Horiguchi, Naoto

2018-03-01

A methodology to evaluate the electrical contact between nanowire (NW) and source/drain (SD) in NW FETs was investigated with SEM voltage contrast (VC). The electrical defects were robustly detected by VC. The validity of the inspection result was verified by TEM physical observations. Moreover, estimation of the parasitic resistance and capacitance was achieved from the quantitative analysis of VC images which were acquired with different scan conditions of electron beam (EB). A model considering the dynamics of EB-induce charging was proposed to calculate the VC. The resistance and capacitance can be determined by comparing the model-based VC with experimentally obtained VC. Quantitative estimation of resistance and capacitance would be valuable not only for more accurate inspection, but also for identification of the defect point.

Fatigue crack identification method based on strain amplitude changing

NASA Astrophysics Data System (ADS)

Guo, Tiancai; Gao, Jun; Wang, Yonghong; Xu, Youliang

2017-09-01

Aiming at the difficulties in identifying the location and time of crack initiation in the castings of helicopter transmission system during fatigue tests, by introducing the classification diagnostic criteria of similar failure mode to find out the similarity of fatigue crack initiation among castings, an engineering method and quantitative criterion for detecting fatigue cracks based on strain amplitude changing is proposed. This method is applied on the fatigue test of a gearbox housing, whose results indicates: during the fatigue test, the system alarms when SC strain meter reaches the quantitative criterion. The afterwards check shows that a fatigue crack less than 5mm is found at the corresponding location of SC strain meter. The test result proves that the method can provide accurate test data for strength life analysis.

A simultaneous screening and quantitative method for the multiresidue analysis of pesticides in spices using ultra-high performance liquid chromatography-high resolution (Orbitrap) mass spectrometry.

PubMed

Goon, Arnab; Khan, Zareen; Oulkar, Dasharath; Shinde, Raviraj; Gaikwad, Suresh; Banerjee, Kaushik

2018-01-12

A novel screening and quantitation method is reported for non-target multiresidue analysis of pesticides using ultra-HPLC-quadrupole-Orbitrap mass spectrometry in spice matrices, including black pepper, cardamom, chili, coriander, cumin, and turmeric. The method involved sequential full-scan (resolution = 70,000), and variable data independent acquisition (vDIA) with nine consecutive fragmentation events (resolution = 17,500). Samples were extracted by the QuEChERS method. The introduction of an SPE-based clean-up step through hydrophilic-lipophilic-balance (HLB) cartridges proved advantageous in minimizing the false negatives. For coriander, cumin, chili, and cardamom, the screening detection limit was largely at 2 ng/g, while it was 5 ng/g for black pepper, and turmeric. When the method was quantitatively validated for 199 pesticides, the limit of quantification (LOQ) was mostly at 10 ng/g (excluding black pepper, and turmeric with LOQ = 20 ng/g) with recoveries within 70-120%, and precision-RSDs <20%. Furthermore, the method allowed the identification of suspected non-target analytes through retrospective search of the accurate mass of the compound-specific precursor and product ions. Compared to LC-MS/MS, the quantitative performance of this Orbitrap-MS method had agreements in residue values between 78-100%. Copyright © 2017 Elsevier B.V. All rights reserved.

Quantification of mitral valve morphology with three-dimensional echocardiography--can measurement lead to better management?

PubMed

Lee, Alex Pui-Wai; Fang, Fang; Jin, Chun-Na; Kam, Kevin Ka-Ho; Tsui, Gary K W; Wong, Kenneth K Y; Looi, Jen-Li; Wong, Randolph H L; Wan, Song; Sun, Jing Ping; Underwood, Malcolm J; Yu, Cheuk-Man

2014-01-01

The mitral valve (MV) has complex 3-dimensional (3D) morphology and motion. Advance in real-time 3D echocardiography (RT3DE) has revolutionized clinical imaging of the MV by providing clinicians with realistic visualization of the valve. Thus far, RT3DE of the MV structure and dynamics has adopted an approach that depends largely on subjective and qualitative interpretation of the 3D images of the valve, rather than objective and reproducible measurement. RT3DE combined with image-processing computer techniques provides precise segmentation and reliable quantification of the complex 3D morphology and rapid motion of the MV. This new approach to imaging may provide additional quantitative descriptions that are useful in diagnostic and therapeutic decision-making. Quantitative analysis of the MV using RT3DE has increased our understanding of the pathologic mechanism of degenerative, ischemic, functional, and rheumatic MV disease. Most recently, 3D morphologic quantification has entered into clinical use to provide more accurate diagnosis of MV disease and for planning surgery and transcatheter interventions. Current limitations of this quantitative approach to MV imaging include labor-intensiveness during image segmentation and lack of a clear definition of the clinical significance of many of the morphologic parameters. This review summarizes the current development and applications of quantitative analysis of the MV morphology using RT3DE.

Patient-specific analysis of post-operative aortic hemodynamics: a focus on thoracic endovascular repair (TEVAR)

NASA Astrophysics Data System (ADS)

Auricchio, F.; Conti, M.; Lefieux, A.; Morganti, S.; Reali, A.; Sardanelli, F.; Secchi, F.; Trimarchi, S.; Veneziani, A.

2014-10-01

The purpose of this study is to quantitatively evaluate the impact of endovascular repair on aortic hemodynamics. The study addresses the assessment of post-operative hemodynamic conditions of a real clinical case through patient-specific analysis, combining accurate medical image analysis and advanced computational fluid-dynamics (CFD). Although the main clinical concern was firstly directed to the endoluminal protrusion of the prosthesis, the CFD simulations have demonstrated that there are two other important areas where the local hemodynamics is impaired and a disturbed blood flow is present: the first one is the ostium of the subclavian artery, which is partially closed by the graft; the second one is the stenosis of the distal thoracic aorta. Besides the clinical relevance of these specific findings, this study highlights how CFD analyses allow to observe important flow effects resulting from the specific features of patient vessel geometries. Consequently, our results demonstrate the potential impact of computational biomechanics not only on the basic knowledge of physiopathology, but also on the clinical practice, thanks to a quantitative extraction of knowledge made possible by merging medical data and mathematical models.

Adduct simplification in the analysis of cyanobacterial toxins by matrix-assisted laser desorption/ionization mass spectrometry.

PubMed

Howard, Karen L; Boyer, Gregory L

2007-01-01

A novel method for simplifying adduct patterns to improve the detection and identification of peptide toxins using matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry is presented. Addition of 200 microM zinc sulfate heptahydrate (ZnSO(4) . 7H(2)O) to samples prior to spotting on the target enhances detection of the protonated molecule while suppressing competing adducts. This produces a highly simplified spectrum with the potential to enhance quantitative analysis, particularly for complex samples. The resulting improvement in total signal strength and reduction in the coefficient of variation (from 31.1% to 5.2% for microcystin-LR) further enhance the potential for sensitive and accurate quantitation. Other potential additives tested, including 18-crown-6 ether, alkali metal salts (lithium chloride, sodium chloride, potassium chloride), and other transition metal salts (silver chloride, silver nitrate, copper(II) nitrate, copper(II) sulfate, zinc acetate), were unable to achieve comparable results. Application of this technique to the analysis of several microcystins, potent peptide hepatotoxins from cyanobacteria, is illustrated. Copyright (c) 2007 John Wiley & Sons, Ltd.

[Rapid determination of volatile organic compounds in workplace air by protable gas chromatography-mass spectrometer].

PubMed

Zhu, H B; Su, C J; Tang, H F; Ruan, Z; Liu, D H; Wang, H; Qian, Y L

2017-10-20

Objective: To establish a method for rapid determination of 47 volatile organic compounds in the air of workplace using portable gas chromatography - mass spectrometer(GC - MS). Methods: The mixed standard gas with different concentration levels was made by using the static gas distribution method with the high purity nitrogen as dilution gas. The samples were injected into the GC - MS by a hand - held probe. Retention time and characteristic ion were used for qualitative analysis,and the internal standard method was usd for quantitation. Results: The 47 poisonous substances were separated and determined well. The linear range of this method was 0.2 - 16.0 mg/m(3),and the relative standard deviation of 45 volatile ovganic compounds was 3.8% - 15.8%. The average recovery was 79.3% - 119.0%. Conclusion: The method is simple,accurate,sensitive,has good separation effect,short analysis period, can be used for qualitative and quantitative analysis of volatile organic compounds in the workplace, and also supports the rapid identification and detection of occupational hazards.

A Workstation for Interactive Display and Quantitative Analysis of 3-D and 4-D Biomedical Images

PubMed Central

Robb, R.A.; Heffeman, P.B.; Camp, J.J.; Hanson, D.P.

1986-01-01

The capability to extract objective and quantitatively accurate information from 3-D radiographic biomedical images has not kept pace with the capabilities to produce the images themselves. This is rather an ironic paradox, since on the one hand the new 3-D and 4-D imaging capabilities promise significant potential for providing greater specificity and sensitivity (i.e., precise objective discrimination and accurate quantitative measurement of body tissue characteristics and function) in clinical diagnostic and basic investigative imaging procedures than ever possible before, but on the other hand, the momentous advances in computer and associated electronic imaging technology which have made these 3-D imaging capabilities possible have not been concomitantly developed for full exploitation of these capabilities. Therefore, we have developed a powerful new microcomputer-based system which permits detailed investigations and evaluation of 3-D and 4-D (dynamic 3-D) biomedical images. The system comprises a special workstation to which all the information in a large 3-D image data base is accessible for rapid display, manipulation, and measurement. The system provides important capabilities for simultaneously representing and analyzing both structural and functional data and their relationships in various organs of the body. This paper provides a detailed description of this system, as well as some of the rationale, background, theoretical concepts, and practical considerations related to system implementation. ImagesFigure 5Figure 7Figure 8Figure 9Figure 10Figure 11Figure 12Figure 13Figure 14Figure 15Figure 16

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

Garcia-Mateo, Carlos, E-mail: cgm@cenim.csic.es

Since the major strengthening mechanisms in nanocrystalline bainitic steels arise from the exceptionally small size of the bainitc ferrite plate, accurate determination of this parameter is fundamental for quantitative relating the microstructure to the mechanical properties. In this work, the thickness of the bainitic ferrite subunits obtained by different bainitic heat treatments was determined in two steels, with carbon contents of 0.3 and 0.7 wt.%, from SEM and TEM micrographs. As these measurements were made on 2D images taken from random sections, the method includes some stereological correction factors to obtain accurate information. Finally, the determined thicknesses of bainitic ferritemore » plates were compared with the crystallite size calculated from the analysis of X-ray diffraction peak broadening. Although in some case the values obtained for crystallite size and plate thickness can be similar, this study confirms that indeed they are two different parameters. - Highlights: •Bainitic microstructure in a nanostructured and sub-micron steel •Bainitic ferrite plate thickness measured by SEM and TEM •Crystallite size determined by X-ray analysis.« less

When the Sun's Away, N2O5 Comes Out to Play: An Updated Analysis of Ambient N2O5 Heterogeneous Chemistry

NASA Astrophysics Data System (ADS)

McDuffie, E. E.; Brown, S. S.

2017-12-01

The heterogeneous chemistry of N2O5 impacts the budget of tropospheric oxidants, which directly controls air quality at Earth's surface. The reaction between gas-phase N2O5 and aerosol particles occurs largely at night, and is therefore more important during the less-intensively-studied winter season. Though N2O5-aerosol interactions are vital for the accurate understanding and simulation of tropospheric chemistry and air quality, many uncertainties persist in our understanding of how various environmental factors influence the reaction rate and probability. Quantitative and accurate evaluation of these factors directly improves the predictive capabilities of atmospheric models, used to inform mitigation strategies for wintertime air pollution. In an update to last year's presentation, The Wintertime Fate of N2O5: Observations and Box Model Analysis for the 2015 WINTER Aircraft Campaign, this presentation will focus on recent field results regarding new information about N2O5 heterogeneous chemistry and future research directions.

[Computer aided diagnosis model for lung tumor based on ensemble convolutional neural network].

PubMed

Wang, Yuanyuan; Zhou, Tao; Lu, Huiling; Wu, Cuiying; Yang, Pengfei

2017-08-01

The convolutional neural network (CNN) could be used on computer-aided diagnosis of lung tumor with positron emission tomography (PET)/computed tomography (CT), which can provide accurate quantitative analysis to compensate for visual inertia and defects in gray-scale sensitivity, and help doctors diagnose accurately. Firstly, parameter migration method is used to build three CNNs (CT-CNN, PET-CNN, and PET/CT-CNN) for lung tumor recognition in CT, PET, and PET/CT image, respectively. Then, we aimed at CT-CNN to obtain the appropriate model parameters for CNN training through analysis the influence of model parameters such as epochs, batchsize and image scale on recognition rate and training time. Finally, three single CNNs are used to construct ensemble CNN, and then lung tumor PET/CT recognition was completed through relative majority vote method and the performance between ensemble CNN and single CNN was compared. The experiment results show that the ensemble CNN is better than single CNN on computer-aided diagnosis of lung tumor.

Performance improvement of the one-dot lateral flow immunoassay for aflatoxin B1 by using a smartphone-based reading system.

PubMed

Lee, Sangdae; Kim, Giyoung; Moon, Jihea

2013-04-18

This study was conducted to develop a simple, rapid, and accurate lateral flow immunoassay (LFIA) detection method for point-of-care diagnosis. The one-dot LFIA for aflatoxin B1 (AFB1) was based on the modified competitive binding format using competition between AFB1 and colloidal gold-AFB1-BSA conjugate for antibody binding sites in the test zone. A Smartphone-based reading system consisting of a Samsung Galaxy S2 Smartphone, a LFIA reader, and a Smartphone application for the image acquisition and data analysis. The detection limit of one-dot LFIA for AFB1 is 5 μg/kg. This method provided semi-quantitative analysis of AFB1 samples in the range of 5 to 1,000 μg/kg. Using combination of the one-dot LFIA and the Smartphone-based reading system, it is possible to conduct a more fast and accurate point-of-care diagnosis.

Performance Improvement of the One-Dot Lateral Flow Immunoassay for Aflatoxin B1 by Using a Smartphone-Based Reading System

PubMed Central

Lee, Sangdae; Kim, Giyoung; Moon, Jihea

2013-01-01

This study was conducted to develop a simple, rapid, and accurate lateral flow immunoassay (LFIA) detection method for point-of-care diagnosis. The one-dot LFIA for aflatoxin B1 (AFB1) was based on the modified competitive binding format using competition between AFB1 and colloidal gold-AFB1-BSA conjugate for antibody binding sites in the test zone. A Smartphone-based reading system consisting of a Samsung Galaxy S2 Smartphone, a LFIA reader, and a Smartphone application for the image acquisition and data analysis. The detection limit of one-dot LFIA for AFB1 is 5 μg/kg. This method provided semi-quantitative analysis of AFB1 samples in the range of 5 to 1,000 μg/kg. Using combination of the one-dot LFIA and the Smartphone-based reading system, it is possible to conduct a more fast and accurate point-of-care diagnosis. PMID:23598499

Validation of Bayesian analysis of compartmental kinetic models in medical imaging.

PubMed

Sitek, Arkadiusz; Li, Quanzheng; El Fakhri, Georges; Alpert, Nathaniel M

2016-10-01

Kinetic compartmental analysis is frequently used to compute physiologically relevant quantitative values from time series of images. In this paper, a new approach based on Bayesian analysis to obtain information about these parameters is presented and validated. The closed-form of the posterior distribution of kinetic parameters is derived with a hierarchical prior to model the standard deviation of normally distributed noise. Markov chain Monte Carlo methods are used for numerical estimation of the posterior distribution. Computer simulations of the kinetics of F18-fluorodeoxyglucose (FDG) are used to demonstrate drawing statistical inferences about kinetic parameters and to validate the theory and implementation. Additionally, point estimates of kinetic parameters and covariance of those estimates are determined using the classical non-linear least squares approach. Posteriors obtained using methods proposed in this work are accurate as no significant deviation from the expected shape of the posterior was found (one-sided P>0.08). It is demonstrated that the results obtained by the standard non-linear least-square methods fail to provide accurate estimation of uncertainty for the same data set (P<0.0001). The results of this work validate new methods for a computer simulations of FDG kinetics. Results show that in situations where the classical approach fails in accurate estimation of uncertainty, Bayesian estimation provides an accurate information about the uncertainties in the parameters. Although a particular example of FDG kinetics was used in the paper, the methods can be extended for different pharmaceuticals and imaging modalities. Copyright © 2016 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

Ultrasound hepatic/renal ratio and hepatic attenuation rate for quantifying liver fat content.

PubMed

Zhang, Bo; Ding, Fang; Chen, Tian; Xia, Liang-Hua; Qian, Juan; Lv, Guo-Yi

2014-12-21

To establish and validate a simple quantitative assessment method for nonalcoholic fatty liver disease (NAFLD) based on a combination of the ultrasound hepatic/renal ratio and hepatic attenuation rate. A total of 170 subjects were enrolled in this study. All subjects were examined by ultrasound and (1)H-magnetic resonance spectroscopy ((1)H-MRS) on the same day. The ultrasound hepatic/renal echo-intensity ratio and ultrasound hepatic echo-intensity attenuation rate were obtained from ordinary ultrasound images using the MATLAB program. Correlation analysis revealed that the ultrasound hepatic/renal ratio and hepatic echo-intensity attenuation rate were significantly correlated with (1)H-MRS liver fat content (ultrasound hepatic/renal ratio: r = 0.952, P = 0.000; hepatic echo-intensity attenuation r = 0.850, P = 0.000). The equation for predicting liver fat content by ultrasound (quantitative ultrasound model) is: liver fat content (%) = 61.519 × ultrasound hepatic/renal ratio + 167.701 × hepatic echo-intensity attenuation rate -26.736. Spearman correlation analysis revealed that the liver fat content ratio of the quantitative ultrasound model was positively correlated with serum alanine aminotransferase, aspartate aminotransferase, and triglyceride, but negatively correlated with high density lipoprotein cholesterol. Receiver operating characteristic curve analysis revealed that the optimal point for diagnosing fatty liver was 9.15% in the quantitative ultrasound model. Furthermore, in the quantitative ultrasound model, fatty liver diagnostic sensitivity and specificity were 94.7% and 100.0%, respectively, showing that the quantitative ultrasound model was better than conventional ultrasound methods or the combined ultrasound hepatic/renal ratio and hepatic echo-intensity attenuation rate. If the (1)H-MRS liver fat content had a value < 15%, the sensitivity and specificity of the ultrasound quantitative model would be 81.4% and 100%, which still shows that using the model is better than the other methods. The quantitative ultrasound model is a simple, low-cost, and sensitive tool that can accurately assess hepatic fat content in clinical practice. It provides an easy and effective parameter for the early diagnosis of mild hepatic steatosis and evaluation of the efficacy of NAFLD treatment.

Quantitative 3D reconstruction of airway and pulmonary vascular trees using HRCT

NASA Astrophysics Data System (ADS)

Wood, Susan A.; Hoford, John D.; Hoffman, Eric A.; Zerhouni, Elias A.; Mitzner, Wayne A.

1993-07-01

Accurate quantitative measurements of airway and vascular dimensions are essential to evaluate function in the normal and diseased lung. In this report, a novel method is described for three-dimensional extraction and analysis of pulmonary tree structures using data from High Resolution Computed Tomography (HRCT). Serially scanned two-dimensional slices of the lower left lobe of isolated dog lungs were stacked to create a volume of data. Airway and vascular trees were three-dimensionally extracted using a three dimensional seeded region growing algorithm based on difference in CT number between wall and lumen. To obtain quantitative data, we reduced each tree to its central axis. From the central axis, branch length is measured as the distance between two successive branch points, branch angle is measured as the angle produced by two daughter branches, and cross sectional area is measured from a plane perpendicular to the central axis point. Data derived from these methods can be used to localize and quantify structural differences both during changing physiologic conditions and in pathologic lungs.

The diagnostic capability of laser induced fluorescence in the characterization of excised breast tissues

NASA Astrophysics Data System (ADS)

Galmed, A. H.; Elshemey, Wael M.

2017-08-01

Differentiating between normal, benign and malignant excised breast tissues is one of the major worldwide challenges that need a quantitative, fast and reliable technique in order to avoid personal errors in diagnosis. Laser induced fluorescence (LIF) is a promising technique that has been applied for the characterization of biological tissues including breast tissue. Unfortunately, only few studies have adopted a quantitative approach that can be directly applied for breast tissue characterization. This work provides a quantitative means for such characterization via introduction of several LIF characterization parameters and determining the diagnostic accuracy of each parameter in the differentiation between normal, benign and malignant excised breast tissues. Extensive analysis on 41 lyophilized breast samples using scatter diagrams, cut-off values, diagnostic indices and receiver operating characteristic (ROC) curves, shows that some spectral parameters (peak height and area under the peak) are superior for characterization of normal, benign and malignant breast tissues with high sensitivity (up to 0.91), specificity (up to 0.91) and accuracy ranking (highly accurate).

A multi-center study benchmarks software tools for label-free proteome quantification

PubMed Central

Gillet, Ludovic C; Bernhardt, Oliver M.; MacLean, Brendan; Röst, Hannes L.; Tate, Stephen A.; Tsou, Chih-Chiang; Reiter, Lukas; Distler, Ute; Rosenberger, George; Perez-Riverol, Yasset; Nesvizhskii, Alexey I.; Aebersold, Ruedi; Tenzer, Stefan

2016-01-01

The consistent and accurate quantification of proteins by mass spectrometry (MS)-based proteomics depends on the performance of instruments, acquisition methods and data analysis software. In collaboration with the software developers, we evaluated OpenSWATH, SWATH2.0, Skyline, Spectronaut and DIA-Umpire, five of the most widely used software methods for processing data from SWATH-MS (sequential window acquisition of all theoretical fragment ion spectra), a method that uses data-independent acquisition (DIA) for label-free protein quantification. We analyzed high-complexity test datasets from hybrid proteome samples of defined quantitative composition acquired on two different MS instruments using different SWATH isolation windows setups. For consistent evaluation we developed LFQbench, an R-package to calculate metrics of precision and accuracy in label-free quantitative MS, and report the identification performance, robustness and specificity of each software tool. Our reference datasets enabled developers to improve their software tools. After optimization, all tools provided highly convergent identification and reliable quantification performance, underscoring their robustness for label-free quantitative proteomics. PMID:27701404

A multicenter study benchmarks software tools for label-free proteome quantification.

PubMed

Navarro, Pedro; Kuharev, Jörg; Gillet, Ludovic C; Bernhardt, Oliver M; MacLean, Brendan; Röst, Hannes L; Tate, Stephen A; Tsou, Chih-Chiang; Reiter, Lukas; Distler, Ute; Rosenberger, George; Perez-Riverol, Yasset; Nesvizhskii, Alexey I; Aebersold, Ruedi; Tenzer, Stefan

2016-11-01

Consistent and accurate quantification of proteins by mass spectrometry (MS)-based proteomics depends on the performance of instruments, acquisition methods and data analysis software. In collaboration with the software developers, we evaluated OpenSWATH, SWATH 2.0, Skyline, Spectronaut and DIA-Umpire, five of the most widely used software methods for processing data from sequential window acquisition of all theoretical fragment-ion spectra (SWATH)-MS, which uses data-independent acquisition (DIA) for label-free protein quantification. We analyzed high-complexity test data sets from hybrid proteome samples of defined quantitative composition acquired on two different MS instruments using different SWATH isolation-window setups. For consistent evaluation, we developed LFQbench, an R package, to calculate metrics of precision and accuracy in label-free quantitative MS and report the identification performance, robustness and specificity of each software tool. Our reference data sets enabled developers to improve their software tools. After optimization, all tools provided highly convergent identification and reliable quantification performance, underscoring their robustness for label-free quantitative proteomics.

Quantitative analysis of urea in human urine and serum by 1H nuclear magnetic resonance†

PubMed Central

Liu, Lingyan; Mo, Huaping; Wei, Siwei

2016-01-01

A convenient and fast method for quantifying urea in biofluids is demonstrated using NMR analysis and the solvent water signal as a concentration reference. The urea concentration can be accurately determined with errors less than 3% between 1 mM and 50 mM, and less than 2% above 50 mM in urine and serum. The method is promising for various applications with advantages of simplicity, high accuracy, and fast non-destructive detection. With an ability to measure other metabolites simultaneously, this NMR method is also likely to find applications in metabolic profiling and system biology. PMID:22179722

Concentrations of platinum group elements in 122 U.S. coal samples

USGS Publications Warehouse

Oman, C.L.; Finkelman, R.B.; Tewalt, S.J.

1997-01-01

Analysis of more than 13,000 coal samples by semi-quantitative optical emission spectroscopy (OES) indicates that concentrations of the platinum group elements (iridium, palladium, platinum, osmium, rhodium, and ruthenium) are less than 1 ppm in the ash, the limit of detection for this method of analysis. In order to accurately determine the concentration of the platinum group elements (PGE) in coal, additional data were obtained by inductively coupled plasma mass spectroscopy, an analytical method having part-per-billion (ppb) detection limits for these elements. These data indicate that the PGE in coal occur in concentrations on the order of 1 ppb or less.

Quantitative interpretations of Visible-NIR reflectance spectra of blood.

PubMed

Serebrennikova, Yulia M; Smith, Jennifer M; Huffman, Debra E; Leparc, German F; García-Rubio, Luis H

2008-10-27

This paper illustrates the implementation of a new theoretical model for rapid quantitative analysis of the Vis-NIR diffuse reflectance spectra of blood cultures. This new model is based on the photon diffusion theory and Mie scattering theory that have been formulated to account for multiple scattering populations and absorptive components. This study stresses the significance of the thorough solution of the scattering and absorption problem in order to accurately resolve for optically relevant parameters of blood culture components. With advantages of being calibration-free and computationally fast, the new model has two basic requirements. First, wavelength-dependent refractive indices of the basic chemical constituents of blood culture components are needed. Second, multi-wavelength measurements or at least the measurements of characteristic wavelengths equal to the degrees of freedom, i.e. number of optically relevant parameters, of blood culture system are required. The blood culture analysis model was tested with a large number of diffuse reflectance spectra of blood culture samples characterized by an extensive range of the relevant parameters.

Note: An automated image analysis method for high-throughput classification of surface-bound bacterial cell motions.

PubMed

Shen, Simon; Syal, Karan; Tao, Nongjian; Wang, Shaopeng

2015-12-01

We present a Single-Cell Motion Characterization System (SiCMoCS) to automatically extract bacterial cell morphological features from microscope images and use those features to automatically classify cell motion for rod shaped motile bacterial cells. In some imaging based studies, bacteria cells need to be attached to the surface for time-lapse observation of cellular processes such as cell membrane-protein interactions and membrane elasticity. These studies often generate large volumes of images. Extracting accurate bacterial cell morphology features from these images is critical for quantitative assessment. Using SiCMoCS, we demonstrated simultaneous and automated motion tracking and classification of hundreds of individual cells in an image sequence of several hundred frames. This is a significant improvement from traditional manual and semi-automated approaches to segmenting bacterial cells based on empirical thresholds, and a first attempt to automatically classify bacterial motion types for motile rod shaped bacterial cells, which enables rapid and quantitative analysis of various types of bacterial motion.

Minimizing target interference in PK immunoassays: new approaches for low-pH-sample treatment.

PubMed

Partridge, Michael A; Pham, John; Dziadiv, Olena; Luong, Onson; Rafique, Ashique; Sumner, Giane; Torri, Albert

2013-08-01

Quantitating total levels of monoclonal antibody (mAb) biotherapeutics in serum using ELISA may be hindered by soluble targets. We developed two low-pH-sample-pretreatment techniques to minimize target interference. The first procedure involves sample pretreatment at pH <3.0 before neutralization and analysis in a target capture ELISA. Careful monitoring of acidification time is required to minimize potential impact on mAb detection. The second approach involves sample dilution into mild acid (pH ∼4.5) before transferring to an anti-human capture-antibody-coated plate without neutralization. Analysis of target-drug and drug-capture antibody interactions at pH 4.5 indicated that the capture antibody binds to the drug, while the drug and the target were dissociated. Using these procedures, total biotherapeutic levels were accurately measured when soluble target was >30-fold molar excess. These techniques provide alternatives for quantitating mAb biotherapeutics in the presence of a target when standard acid-dissociation procedures are ineffective.

Recovering the dynamics of root growth and development using novel image acquisition and analysis methods

PubMed Central

Wells, Darren M.; French, Andrew P.; Naeem, Asad; Ishaq, Omer; Traini, Richard; Hijazi, Hussein; Bennett, Malcolm J.; Pridmore, Tony P.

2012-01-01

Roots are highly responsive to environmental signals encountered in the rhizosphere, such as nutrients, mechanical resistance and gravity. As a result, root growth and development is very plastic. If this complex and vital process is to be understood, methods and tools are required to capture the dynamics of root responses. Tools are needed which are high-throughput, supporting large-scale experimental work, and provide accurate, high-resolution, quantitative data. We describe and demonstrate the efficacy of the high-throughput and high-resolution root imaging systems recently developed within the Centre for Plant Integrative Biology (CPIB). This toolset includes (i) robotic imaging hardware to generate time-lapse datasets from standard cameras under infrared illumination and (ii) automated image analysis methods and software to extract quantitative information about root growth and development both from these images and via high-resolution light microscopy. These methods are demonstrated using data gathered during an experimental study of the gravitropic response of Arabidopsis thaliana. PMID:22527394

Genotype-phenotype association study via new multi-task learning model

PubMed Central

Huo, Zhouyuan; Shen, Dinggang

2018-01-01

Research on the associations between genetic variations and imaging phenotypes is developing with the advance in high-throughput genotype and brain image techniques. Regression analysis of single nucleotide polymorphisms (SNPs) and imaging measures as quantitative traits (QTs) has been proposed to identify the quantitative trait loci (QTL) via multi-task learning models. Recent studies consider the interlinked structures within SNPs and imaging QTs through group lasso, e.g. ℓ2,1-norm, leading to better predictive results and insights of SNPs. However, group sparsity is not enough for representing the correlation between multiple tasks and ℓ2,1-norm regularization is not robust either. In this paper, we propose a new multi-task learning model to analyze the associations between SNPs and QTs. We suppose that low-rank structure is also beneficial to uncover the correlation between genetic variations and imaging phenotypes. Finally, we conduct regression analysis of SNPs and QTs. Experimental results show that our model is more accurate in prediction than compared methods and presents new insights of SNPs. PMID:29218896

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.

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.

Recovering the dynamics of root growth and development using novel image acquisition and analysis methods.

PubMed

Wells, Darren M; French, Andrew P; Naeem, Asad; Ishaq, Omer; Traini, Richard; Hijazi, Hussein I; Hijazi, Hussein; Bennett, Malcolm J; Pridmore, Tony P

2012-06-05

Roots are highly responsive to environmental signals encountered in the rhizosphere, such as nutrients, mechanical resistance and gravity. As a result, root growth and development is very plastic. If this complex and vital process is to be understood, methods and tools are required to capture the dynamics of root responses. Tools are needed which are high-throughput, supporting large-scale experimental work, and provide accurate, high-resolution, quantitative data. We describe and demonstrate the efficacy of the high-throughput and high-resolution root imaging systems recently developed within the Centre for Plant Integrative Biology (CPIB). This toolset includes (i) robotic imaging hardware to generate time-lapse datasets from standard cameras under infrared illumination and (ii) automated image analysis methods and software to extract quantitative information about root growth and development both from these images and via high-resolution light microscopy. These methods are demonstrated using data gathered during an experimental study of the gravitropic response of Arabidopsis thaliana.

Augmented multivariate image analysis applied to quantitative structure-activity relationship modeling of the phytotoxicities of benzoxazinone herbicides and related compounds on problematic weeds.

PubMed

Freitas, Mirlaine R; Matias, Stella V B G; Macedo, Renato L G; Freitas, Matheus P; Venturin, Nelson

2013-09-11

Two of major weeds affecting cereal crops worldwide are Avena fatua L. (wild oat) and Lolium rigidum Gaud. (rigid ryegrass). Thus, development of new herbicides against these weeds is required; in line with this, benzoxazinones, their degradation products, and analogues have been shown to be important allelochemicals and natural herbicides. Despite earlier structure-activity studies demonstrating that hydrophobicity (log P) of aminophenoxazines correlates to phytotoxicity, our findings for a series of benzoxazinone derivatives do not show any relationship between phytotoxicity and log P nor with other two usual molecular descriptors. On the other hand, a quantitative structure-activity relationship (QSAR) analysis based on molecular graphs representing structural shape, atomic sizes, and colors to encode other atomic properties performed very accurately for the prediction of phytotoxicities of these compounds against wild oat and rigid ryegrass. Therefore, these QSAR models can be used to estimate the phytotoxicity of new congeners of benzoxazinone herbicides toward A. fatua L. and L. rigidum Gaud.

Fast and accurate determination of arsenobetaine in fish tissues using accelerated solvent extraction and HPLC-ICP-MS determination.

PubMed

Wahlen, Raimund

2004-04-01

A high-performance liquid chromatography-inductively coupled plasma-mass spectrometry (HPLC-ICP-MS) method has been developed for the fast and accurate analysis of arsenobetaine (AsB) in fish samples extracted by accelerated solvent extraction. The combined extraction and analysis approach is validated using certified reference materials for AsB in fish and during a European intercomparison exercise with a blind sample. Up to six species of arsenic (As) can be separated and quantitated in the extracts within a 10-min isocratic elution. The method is optimized so as to minimize time-consuming sample preparation steps and allow for automated extraction and analysis of large sample batches. A comparison of standard addition and external calibration show no significant difference in the results obtained, which indicates that the LC-ICP-MS method is not influenced by severe matrix effects. The extraction procedure can process up to 24 samples in an automated manner, yet the robustness of the developed HPLC-ICP-MS approach is highlighted by the capability to run more than 50 injections per sequence, which equates to a total run-time of more than 12 h. The method can therefore be used to rapidly and accurately assess the proportion of nontoxic AsB in fish samples with high total As content during toxicological screening studies.

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, to a lesser degree, of potassium from the cortex to the nucleus. Development of galactose-induced cataract was heterogeneous by morphological criteria, beginning at the lens equator and spreading from the cortex into the nucleus. However, the loss of potassium and increase in sodium concentration occurred at early stages in both the cortex and nucleus cells, possibly because these cells are interconnected by gap junctions. There is a local alteration in elemental content prior to morphologically demonstrable cataract formation.(ABSTRACT TRUNCATED AT 400 WORDS)

Genetic analysis of PAX3 for diagnosis of Waardenburg syndrome type I.

PubMed

Matsunaga, Tatsuo; Mutai, Hideki; Namba, Kazunori; Morita, Noriko; Masuda, Sawako

2013-04-01

PAX3 genetic analysis increased the diagnostic accuracy for Waardenburg syndrome type I (WS1). Analysis of the three-dimensional (3D) structure of PAX3 helped verify the pathogenicity of a missense mutation, and multiple ligation-dependent probe amplification (MLPA) analysis of PAX3 increased the sensitivity of genetic diagnosis in patients with WS1. Clinical diagnosis of WS1 is often difficult in individual patients with isolated, mild, or non-specific symptoms. The objective of the present study was to facilitate the accurate diagnosis of WS1 through genetic analysis of PAX3 and to expand the spectrum of known PAX3 mutations. In two Japanese families with WS1, we conducted a clinical evaluation of symptoms and genetic analysis, which involved direct sequencing, MLPA analysis, quantitative PCR of PAX3, and analysis of the predicted 3D structure of PAX3. The normal-hearing control group comprised 92 subjects who had normal hearing according to pure tone audiometry. In one family, direct sequencing of PAX3 identified a heterozygous mutation, p.I59F. Analysis of PAX3 3D structures indicated that this mutation distorted the DNA-binding site of PAX3. In the other family, MLPA analysis and subsequent quantitative PCR detected a large, heterozygous deletion spanning 1759-2554 kb that eliminated 12-18 genes including a whole PAX3 gene.

Cardiovascular magnetic resonance of myocardial edema using a short inversion time inversion recovery (STIR) black-blood technique: Diagnostic accuracy of visual and semi-quantitative assessment

PubMed Central

2012-01-01

Background The short inversion time inversion recovery (STIR) black-blood technique has been used to visualize myocardial edema, and thus to differentiate acute from chronic myocardial lesions. However, some cardiovascular magnetic resonance (CMR) groups have reported variable image quality, and hence the diagnostic value of STIR in routine clinical practice has been put into question. The aim of our study was to analyze image quality and diagnostic performance of STIR using a set of pulse sequence parameters dedicated to edema detection, and to discuss possible factors that influence image quality. We hypothesized that STIR imaging is an accurate and robust way of detecting myocardial edema in non-selected patients with acute myocardial infarction. Methods Forty-six consecutive patients with acute myocardial infarction underwent CMR (day 4.5, +/- 1.6) including STIR for the assessment of myocardial edema and late gadolinium enhancement (LGE) for quantification of myocardial necrosis. Thirty of these patients underwent a follow-up CMR at approximately six months (195 +/- 39 days). Both STIR and LGE images were evaluated separately on a segmental basis for image quality as well as for presence and extent of myocardial hyper-intensity, with both visual and semi-quantitative (threshold-based) analysis. LGE was used as a reference standard for localization and extent of myocardial necrosis (acute) or scar (chronic). Results Image quality of STIR images was rated as diagnostic in 99.5% of cases. At the acute stage, the sensitivity and specificity of STIR to detect infarcted segments on visual assessment was 95% and 78% respectively, and on semi-quantitative assessment was 99% and 83%, respectively. STIR differentiated acutely from chronically infarcted segments with a sensitivity of 95% by both methods and with a specificity of 99% by visual assessment and 97% by semi-quantitative assessment. The extent of hyper-intense areas on acute STIR images was 85% larger than those on LGE images, with a larger myocardial salvage index in reperfused than in non-reperfused infarcts (p = 0.035). Conclusions STIR with appropriate pulse sequence settings is accurate in detecting acute myocardial infarction (MI) and distinguishing acute from chronic MI with both visual and semi-quantitative analysis. Due to its unique technical characteristics, STIR should be regarded as an edema-weighted rather than a purely T2-weighted technique. PMID:22455461

Studying flow close to an interface by total internal reflection fluorescence cross-correlation spectroscopy: Quantitative data analysis

NASA Astrophysics Data System (ADS)

Schmitz, R.; Yordanov, S.; Butt, H. J.; Koynov, K.; Dünweg, B.

2011-12-01

Total internal reflection fluorescence cross-correlation spectroscopy (TIR-FCCS) has recently [S. Yordanov , Optics ExpressOPEXFF1094-408710.1364/OE.17.021149 17, 21149 (2009)] been established as an experimental method to probe hydrodynamic flows near surfaces, on length scales of tens of nanometers. Its main advantage is that fluorescence occurs only for tracer particles close to the surface, thus resulting in high sensitivity. However, the measured correlation functions provide only rather indirect information about the flow parameters of interest, such as the shear rate and the slip length. In the present paper, we show how to combine detailed and fairly realistic theoretical modeling of the phenomena by Brownian dynamics simulations with accurate measurements of the correlation functions, in order to establish a quantitative method to retrieve the flow properties from the experiments. First, Brownian dynamics is used to sample highly accurate correlation functions for a fixed set of model parameters. Second, these parameters are varied systematically by means of an importance-sampling Monte Carlo procedure in order to fit the experiments. This provides the optimum parameter values together with their statistical error bars. The approach is well suited for massively parallel computers, which allows us to do the data analysis within moderate computing times. The method is applied to flow near a hydrophilic surface, where the slip length is observed to be smaller than 10nm, and, within the limitations of the experiments and the model, indistinguishable from zero.

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.

An importance-performance analysis of hospital information system attributes: A nurses' perspective.

PubMed

Cohen, Jason F; Coleman, Emma; Kangethe, Matheri J

2016-02-01

Health workers have numerous concerns about hospital IS (HIS) usage. Addressing these concerns requires understanding the system attributes most important to their satisfaction and productivity. Following a recent HIS implementation, our objective was to identify priorities for managerial intervention based on user evaluations of the performance of the HIS attributes as well as the relative importance of these attributes to user satisfaction and productivity outcomes. We collected data along a set of attributes representing system quality, data quality, information quality, and service quality from 154 nurse users. Their quantitative responses were analysed using the partial least squares approach followed by an importance-performance analysis. Qualitative responses were analysed using thematic analysis to triangulate and supplement the quantitative findings. Two system quality attributes (responsiveness and ease of learning), one information quality attribute (detail), one service quality attribute (sufficient support), and three data quality attributes (records complete, accurate and never missing) were identified as high priorities for intervention. Our application of importance-performance analysis is unique in HIS evaluation and we have illustrated its utility for identifying those system attributes for which underperformance is not acceptable to users and therefore should be high priorities for intervention. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Sensitive and quantitative measurement of gene expression directly from a small amount of whole blood.

PubMed

Zheng, Zhi; Luo, Yuling; McMaster, Gary K

2006-07-01

Accurate and precise quantification of mRNA in whole blood is made difficult by gene expression changes during blood processing, and by variations and biases introduced by sample preparations. We sought to develop a quantitative whole-blood mRNA assay that eliminates blood purification, RNA isolation, reverse transcription, and target amplification while providing high-quality data in an easy assay format. We performed single- and multiplex gene expression analysis with multiple hybridization probes to capture mRNA directly from blood lysate and used branched DNA to amplify the signal. The 96-well plate singleplex assay uses chemiluminescence detection, and the multiplex assay combines Luminex-encoded beads with fluorescent detection. The single- and multiplex assays could quantitatively measure as few as 6000 and 24,000 mRNA target molecules (0.01 and 0.04 amoles), respectively, in up to 25 microL of whole blood. Both formats had CVs < 10% and dynamic ranges of 3-4 logs. Assay sensitivities allowed quantitative measurement of gene expression in the minority of cells in whole blood. The signals from whole-blood lysate correlated well with signals from purified RNA of the same sample, and absolute mRNA quantification results from the assay were similar to those obtained by quantitative reverse transcription-PCR. Both single- and multiplex assay formats were compatible with common anticoagulants and PAXgene-treated samples; however, PAXgene preparations induced expression of known antiapoptotic genes in whole blood. Both the singleplex and the multiplex branched DNA assays can quantitatively measure mRNA expression directly from small volumes of whole blood. The assay offers an alternative to current technologies that depend on RNA isolation and is amenable to high-throughput gene expression analysis of whole blood.

Semi-quantitative analysis of salivary gland scintigraphy in Sjögren's syndrome diagnosis: a first-line tool.

PubMed

Angusti, Tiziana; Pilati, Emanuela; Parente, Antonella; Carignola, Renato; Manfredi, Matteo; Cauda, Simona; Pizzigati, Elena; Dubreuil, Julien; Giammarile, Francesco; Podio, Valerio; Skanjeti, Andrea

2017-09-01

The aim of this study was the assessment of semi-quantified salivary gland dynamic scintigraphy (SGdS) parameters independently and in an integrated way in order to predict primary Sjögren's syndrome (pSS). Forty-six consecutive patients (41 females; age 61 ± 11 years) with sicca syndrome were studied by SGdS after injection of 200 MBq of pertechnetate. In sixteen patients, pSS was diagnosed, according to American-European Consensus Group criteria (AECGc). Semi-quantitative parameters (uptake (UP) and excretion fraction (EF)) were obtained for each gland. ROC curves were used to determine the best cut-off value. The area under the curve (AUC) was used to estimate the accuracy of each semi-quantitative analysis. To assess the correlation between scintigraphic results and disease severity, semi-quantitative parameters were plotted versus Sjögren's syndrome disease activity index (ESSDAI). A nomogram was built to perform an integrated evaluation of all the scintigraphic semi-quantitative data. Both UP and EF of salivary glands were significantly lower in pSS patients compared to those in non-pSS (p < 0.001). ROC curve showed significantly large AUC for both the parameters (p < 0.05). Parotid UP and submandibular EF, assessed by univariated and multivariate logistic regression, showed a significant and independent correlation with pSS diagnosis (p value <0.05). No correlation was found between SGdS semi-quantitative parameters and ESSDAI. The proposed nomogram accuracy was 87%. SGdS is an accurate and reproducible tool for the diagnosis of pSS. ESSDAI was not shown to be correlated with SGdS data. SGdS should be the first-line imaging technique in patients with suspected pSS.

Quantitative fluorescence in intracranial tumor: implications for ALA-induced PpIX as an intraoperative biomarker

PubMed Central

Valdés, Pablo A.; Leblond, Frederic; Kim, Anthony; Harris, Brent T.; Wilson, Brian C.; Fan, Xiaoyao; Tosteson, Tor D.; Hartov, Alex; Ji, Songbai; Erkmen, Kadir; Simmons, Nathan E.; Paulsen, Keith D.; Roberts, David W.

2011-01-01

Object Accurate discrimination between tumor and normal tissue is crucial for optimal tumor resection. Qualitative fluorescence of protoporphyrin IX (PpIX), synthesized endogenously following δ-aminolevulinic acid (ALA) administration, has been used for this purpose in high-grade glioma (HGG). The authors show that diagnostically significant but visually imperceptible concentrations of PpIX can be quantitatively measured in vivo and used to discriminate normal from neoplastic brain tissue across a range of tumor histologies. Methods The authors studied 14 patients with diagnoses of low-grade glioma (LGG), HGG, meningioma, and metastasis under an institutional review board–approved protocol for fluorescence-guided resection. The primary aim of the study was to compare the diagnostic capabilities of a highly sensitive, spectrally resolved quantitative fluorescence approach to conventional fluorescence imaging for detection of neoplastic tissue in vivo. Results A significant difference in the quantitative measurements of PpIX concentration occurred in all tumor groups compared with normal brain tissue. Receiver operating characteristic (ROC) curve analysis of PpIX concentration as a diagnostic variable for detection of neoplastic tissue yielded a classification efficiency of 87% (AUC = 0.95, specificity = 92%, sensitivity = 84%) compared with 66% (AUC = 0.73, specificity = 100%, sensitivity = 47%) for conventional fluorescence imaging (p < 0.0001). More than 81% (57 of 70) of the quantitative fluorescence measurements that were below the threshold of the surgeon's visual perception were classified correctly in an analysis of all tumors. Conclusions These findings are clinically profound because they demonstrate that ALA-induced PpIX is a targeting biomarker for a variety of intracranial tumors beyond HGGs. This study is the first to measure quantitative ALA-induced PpIX concentrations in vivo, and the results have broad implications for guidance during resection of intracranial tumors. PMID:21438658

99mTc-sestamibi scintigraphy used to evaluate tumor response to neoadjuvant chemotherapy in locally advanced breast cancer: A quantitative analysis

PubMed Central

KOGA, KATIA HIROMOTO; MORIGUCHI, SONIA MARTA; NETO, JORGE NAHÁS; PERES, STELA VERZINHASSE; SILVA, EDUARDO TINÓIS DA; SARRI, ALMIR JOSÉ; MICHELIN, ODAIR CARLITO; MARQUES, MARIANGELA ESTHER ALENCAR; GRIVA, BEATRIZ LOTUFO

2010-01-01

To evaluate the tumor response to neoadjuvant chemotherapy, 99mTc-sestamibi breast scintigraphy was proposed as a quantitative method. Fifty-five patients with ductal carcinoma were studied. They underwent breast scintigraphy before and after neoadjuvant chemotherapy, along with clinical assessment and surgical specimen analysis. The regions of interest on the lesion and contralateral breast were identified, and the pixel counts were used to evaluate lesion uptake in relation to background radiation. The ratio of these counts before to after neoadjuvant chemotherapy was assessed. The decrease in uptake rate due to chemotherapy characterized the scintigraphy tumor response. The Kruskal-Wallis test was used to compare the mean scintigraphic tumor response and histological type. Dunn’s multiple comparison test was used to detect differences between histological types. The Mann-Whitney test was used to compare means between quantitative and qualitative variables: scintigraphic tumor response vs. clinical response and uptake before chemotherapy vs. scintigraphic tumor response. The Spearman’s test was used to correlate the quantitative variables of clinical reduction in tumor size and scintigraphic tumor response. All of the variables compared presented significant differences. The change in 99mTc-sestamibi uptake noted on breast scintigraphy, before to after neoadjuvant chemotherapy, may be used as an effective method for evaluating the response to neoadjuvant chemotherapy, since this quantification reflects the biological behavior of the tumor towards the chemotherapy regimen. Furthermore, additional analysis on the uptake rate before chemotherapy may accurately predict treatment response. PMID:22966312

Image-derived input function with factor analysis and a-priori information.

PubMed

Simončič, Urban; Zanotti-Fregonara, Paolo

2015-02-01

Quantitative PET studies often require the cumbersome and invasive procedure of arterial cannulation to measure the input function. This study sought to minimize the number of necessary blood samples by developing a factor-analysis-based image-derived input function (IDIF) methodology for dynamic PET brain studies. IDIF estimation was performed as follows: (a) carotid and background regions were segmented manually on an early PET time frame; (b) blood-weighted and tissue-weighted time-activity curves (TACs) were extracted with factor analysis; (c) factor analysis results were denoised and scaled using the voxels with the highest blood signal; (d) using population data and one blood sample at 40 min, whole-blood TAC was estimated from postprocessed factor analysis results; and (e) the parent concentration was finally estimated by correcting the whole-blood curve with measured radiometabolite concentrations. The methodology was tested using data from 10 healthy individuals imaged with [(11)C](R)-rolipram. The accuracy of IDIFs was assessed against full arterial sampling by comparing the area under the curve of the input functions and by calculating the total distribution volume (VT). The shape of the image-derived whole-blood TAC matched the reference arterial curves well, and the whole-blood area under the curves were accurately estimated (mean error 1.0±4.3%). The relative Logan-V(T) error was -4.1±6.4%. Compartmental modeling and spectral analysis gave less accurate V(T) results compared with Logan. A factor-analysis-based IDIF for [(11)C](R)-rolipram brain PET studies that relies on a single blood sample and population data can be used for accurate quantification of Logan-V(T) values.

A new application of continuous wavelet transform to overlapping chromatograms for the quantitative analysis of amiloride hydrochloride and hydrochlorothiazide in tablets by ultra-performance liquid chromatography.

PubMed

Dinç, Erdal; Büker, Eda

2012-01-01

A new application of continuous wavelet transform (CWT) to overlapping peaks in a chromatogram was developed for the quantitative analysis of amiloride hydrochloride (AML) and hydrochlorothiazide (HCT) in tablets. Chromatographic analysis was done by using an ACQUITY ultra-performance LC (UPLC) BEH C18 column (50 x 2.1 mm id, 1.7 pm particle size) and a mobile phase consisting of methanol-0.1 M acetic acid (21 + 79, v/v) at a constant flow rate of 0.3 mL/min with diode array detection at 274 nm. The overlapping chromatographic peaks of the calibration set consisting of AML and HCT mixtures were recorded rapidly by using an ACQUITY UPLC H-Class system. The overlapping UPLC data vectors of AML and HCT drugs and their samples were processed by CWT signal processing methods. The calibration graphs for AML and HCT were computed from the relationship between concentration and areas of chromatographic CWT peaks. The applicability and validity of the improved UPLC-CWT approaches were confirmed by recovery studies and the standard addition technique. The proposed UPLC-CWT methods were applied to the determination of AML and HCT in tablets. The experimental results indicated that the suggested UPLC-CWT signal processing provides accurate and precise results for industrial QC and quantitative evaluation of AML-HCT tablets.

Surface complexation and precipitate geometry for aqueous Zn(II) sorption on ferrihydrite: II. XANES analysis and simulation

USGS Publications Warehouse

Waychunas, G.A.; Fuller, C.C.; Davis, J.A.; Rehr, J.J.

2003-01-01

X-ray absorption near-edge spectroscopy (XANES) analysis of sorption complexes has the advantages of high sensitivity (10- to 20-fold greater than extended X-ray absorption fine structure [EXAFS] analysis) and relative ease and speed of data collection (because of the short k-space range). It is thus a potentially powerful tool for characterization of environmentally significant surface complexes and precipitates at very low surface coverages. However, quantitative analysis has been limited largely to "fingerprint" comparison with model spectra because of the difficulty of obtaining accurate multiple-scattering amplitudes for small clusters with high confidence. In the present work, calculations of the XANES for 50- to 200-atom clusters of structure from Zn model compounds using the full multiple-scattering code Feff 8.0 accurately replicate experimental spectra and display features characteristic of specific first-neighbor anion coordination geometry and second-neighbor cation geometry and number. Analogous calculations of the XANES for small molecular clusters indicative of precipitation and sorption geometries for aqueous Zn on ferrihydrite, and suggested by EXAFS analysis, are in good agreement with observed spectral trends with sample composition, with Zn-oxygen coordination and with changes in second-neighbor cation coordination as a function of sorption coverage. Empirical analysis of experimental XANES features further verifies the validity of the calculations. The findings agree well with a complete EXAFS analysis previously reported for the same sample set, namely, that octahedrally coordinated aqueous Zn2+ species sorb as a tetrahedral complex on ferrihydrite with varying local geometry depending on sorption density. At significantly higher densities but below those at which Zn hydroxide is expected to precipitate, a mainly octahedral coordinated Zn2+ precipitate is observed. An analysis of the multiple scattering paths contributing to the XANES demonstrates the importance of scattering paths involving the anion sublattice. We also describe the specific advantages of complementary quantitative XANES and EXAFS analysis and estimate limits on the extent of structural information obtainable from XANES analysis. ?? 2003 Elsevier Science Ltd.

Development and application of a multi-targeting reference plasmid as calibrator for analysis of five genetically modified soybean events.

PubMed

Pi, Liqun; Li, Xiang; Cao, Yiwei; Wang, Canhua; Pan, Liangwen; Yang, Litao

2015-04-01

Reference materials are important in accurate analysis of genetically modified organism (GMO) contents in food/feeds, and development of novel reference plasmid is a new trend in the research of GMO reference materials. Herein, we constructed a novel multi-targeting plasmid, pSOY, which contained seven event-specific sequences of five GM soybeans (MON89788-5', A2704-12-3', A5547-127-3', DP356043-5', DP305423-3', A2704-12-5', and A5547-127-5') and sequence of soybean endogenous reference gene Lectin. We evaluated the specificity, limit of detection and quantification, and applicability of pSOY in both qualitative and quantitative PCR analyses. The limit of detection (LOD) was as low as 20 copies in qualitative PCR, and the limit of quantification (LOQ) in quantitative PCR was 10 copies. In quantitative real-time PCR analysis, the PCR efficiencies of all event-specific and Lectin assays were higher than 90%, and the squared regression coefficients (R(2)) were more than 0.999. The quantification bias varied from 0.21% to 19.29%, and the relative standard deviations were from 1.08% to 9.84% in simulated samples analysis. All the results demonstrated that the developed multi-targeting plasmid, pSOY, was a credible substitute of matrix reference materials, and could be used as a reliable reference calibrator in the identification and quantification of multiple GM soybean events.

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

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 analysis. Conclusions Fluorescence-guided resection may be a useful adjunct in the resection of skull base meningiomas. The use of a quantitative intraoperative probe to detect PpIX concentration allows more accurate determination of neoplastic tissue in meningiomas than visible fluorescence and is readily applicable in areas, such as the skull base, where complete resection is critical but difficult because of the vital structures surrounding the pathology. PMID:21529179

Quantitative characterization of metastatic disease in the spine. Part I. Semiautomated segmentation using atlas-based deformable registration and the level set method

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

Hardisty, M.; Gordon, L.; Agarwal, P.

2007-08-15

Quantitative assessment of metastatic disease in bone is often considered immeasurable and, as such, patients with skeletal metastases are often excluded from clinical trials. In order to effectively quantify the impact of metastatic tumor involvement in the spine, accurate segmentation of the vertebra is required. Manual segmentation can be accurate but involves extensive and time-consuming user interaction. Potential solutions to automating segmentation of metastatically involved vertebrae are demons deformable image registration and level set methods. The purpose of this study was to develop a semiautomated method to accurately segment tumor-bearing vertebrae using the aforementioned techniques. By maintaining morphology of anmore » atlas, the demons-level set composite algorithm was able to accurately differentiate between trans-cortical tumors and surrounding soft tissue of identical intensity. The algorithm successfully segmented both the vertebral body and trabecular centrum of tumor-involved and healthy vertebrae. This work validates our approach as equivalent in accuracy to an experienced user.« less

Her-2/neu expression in node-negative breast cancer: direct tissue quantitation by computerized image analysis and association of overexpression with increased risk of recurrent disease.

PubMed

Press, M F; Pike, M C; Chazin, V R; Hung, G; Udove, J A; Markowicz, M; Danyluk, J; Godolphin, W; Sliwkowski, M; Akita, R

1993-10-15

The HER-2/neu proto-oncogene (also known as c-erb B-2) is homologous with, but distinct from, the epidermal growth factor receptor. Amplification of this gene in node-positive breast cancers has been shown to correlate with both earlier relapse and shorter overall survival. In node-negative breast cancer patients, the subgroup for which accurate prognostic data could make a significant contribution to treatment decisions, the prognostic utility of HER-2/neu amplification and/or overexpression has been controversial. The purpose of this report is to address the issues surrounding this controversy and to evaluate the prognostic utility of overexpression in a carefully followed group of patients using appropriately characterized reagents and methods. In this report we present data from a study of HER-2/neu expression designed specifically to test whether or not overexpression is associated with an increased risk of recurrence in node-negative breast cancers. From a cohort of 704 women with node-negative breast cancer who experienced recurrent disease (relapsed cases) 105 were matched with 105 women with no recurrence (disease-free controls) after the equivalent follow-up period. Immunohistochemistry was used to assess HER-2/neu expression in archival tissue blocks from both relapsed cases and their matched disease-free controls. Importantly, a series of molecularly characterized breast cancer specimens were used to confirm that the antibody used was of sufficient sensitivity and specificity to identify those cancers overexpressing the HER-2/neu protein in this formalin-fixed, paraffin-embedded tissue cohort. In addition, a quantitative approach was developed to more accurately assess the amount of HER-2/neu protein identified by immunostaining tumor tissue. This was done using a purified HER-2/neu protein synthesized in a bacterial expression vector and protein lysates derived from a series of cell lines, engineered to express a defined range of HER-2/neu oncoprotein levels. By using cells with defined expression levels as calibration material, computerized image analysis of immunohistochemical staining could be used to determine the amount of oncoprotein product in these cell lines as well as in human breast cancer specimens. Quantitation of the amount of HER-2/neu protein product determined by computerized image analysis of immunohistochemical assays correlated very closely with quantitative analysis of a series of molecularly characterized breast cancer cell lines and breast cancer tissue specimens.(ABSTRACT TRUNCATED AT 400 WORDS)

Analytical validation of quantitative immunohistochemical assays of tumor infiltrating lymphocyte biomarkers.

PubMed

Singh, U; Cui, Y; Dimaano, N; Mehta, S; Pruitt, S K; Yearley, J; Laterza, O F; Juco, J W; Dogdas, B

2018-06-04

Tumor infiltrating lymphocytes (TIL), especially T-cells, have both prognostic and therapeutic applications. The presence of CD8+ effector T-cells and the ratio of CD8+ cells to FOXP3+ regulatory T-cells have been used as biomarkers of disease prognosis to predict response to various immunotherapies. Blocking the interaction between inhibitory receptors on T-cells and their ligands with therapeutic antibodies including atezolizumab, nivolumab, pembrolizumab and tremelimumab increases the immune response against cancer cells and has shown significant improvement in clinical benefits and survival in several different tumor types. The improved clinical outcome is presumed to be associated with a higher tumor infiltration; therefore, it is thought that more accurate methods for measuring the amount of TIL could assist prognosis and predict treatment response. We have developed and validated quantitative immunohistochemistry (IHC) assays for CD3, CD8 and FOXP3 for immunophenotyping T-lymphocytes in tumor tissue. Various types of formalin fixed, paraffin embedded (FFPE) tumor tissues were immunolabeled with anti-CD3, anti-CD8 and anti-FOXP3 antibodies using an IHC autostainer. The tumor area of stained tissues, including the invasive margin of the tumor, was scored by a pathologist (visual scoring) and by computer-based quantitative image analysis. Two image analysis scores were obtained for the staining of each biomarker: the percent positive cells in the tumor area and positive cells/mm 2 tumor area. Comparison of visual vs. image analysis scoring methods using regression analysis showed high correlation and indicated that quantitative image analysis can be used to score the number of positive cells in IHC stained slides. To demonstrate that the IHC assays produce consistent results in normal daily testing, we evaluated the specificity, sensitivity and reproducibility of the IHC assays using both visual and image analysis scoring methods. We found that CD3, CD8 and FOXP3 IHC assays met the fit-for-purpose analytical acceptance validation criteria and that they can be used to support clinical studies.

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

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

Spatial delineation, fluid-lithology characterization, and petrophysical modeling of deepwater Gulf of Mexico reservoirs though joint AVA deterministic and stochastic inversion of three-dimensional partially-stacked seismic amplitude data and well logs

NASA Astrophysics Data System (ADS)

Contreras, Arturo Javier

This dissertation describes a novel Amplitude-versus-Angle (AVA) inversion methodology to quantitatively integrate pre-stack seismic data, well logs, geologic data, and geostatistical information. Deterministic and stochastic inversion algorithms are used to characterize flow units of deepwater reservoirs located in the central Gulf of Mexico. A detailed fluid/lithology sensitivity analysis was conducted to assess the nature of AVA effects in the study area. Standard AVA analysis indicates that the shale/sand interface represented by the top of the hydrocarbon-bearing turbidite deposits generate typical Class III AVA responses. Layer-dependent Biot-Gassmann analysis shows significant sensitivity of the P-wave velocity and density to fluid substitution, indicating that presence of light saturating fluids clearly affects the elastic response of sands. Accordingly, AVA deterministic and stochastic inversions, which combine the advantages of AVA analysis with those of inversion, have provided quantitative information about the lateral continuity of the turbidite reservoirs based on the interpretation of inverted acoustic properties and fluid-sensitive modulus attributes (P-Impedance, S-Impedance, density, and LambdaRho, in the case of deterministic inversion; and P-velocity, S-velocity, density, and lithotype (sand-shale) distributions, in the case of stochastic inversion). The quantitative use of rock/fluid information through AVA seismic data, coupled with the implementation of co-simulation via lithotype-dependent multidimensional joint probability distributions of acoustic/petrophysical properties, provides accurate 3D models of petrophysical properties such as porosity, permeability, and water saturation. Pre-stack stochastic inversion provides more realistic and higher-resolution results than those obtained from analogous deterministic techniques. Furthermore, 3D petrophysical models can be more accurately co-simulated from AVA stochastic inversion results. By combining AVA sensitivity analysis techniques with pre-stack stochastic inversion, geologic data, and awareness of inversion pitfalls, it is possible to substantially reduce the risk in exploration and development of conventional and non-conventional reservoirs. From the final integration of deterministic and stochastic inversion results with depositional models and analogous examples, the M-series reservoirs have been interpreted as stacked terminal turbidite lobes within an overall fan complex (the Miocene MCAVLU Submarine Fan System); this interpretation is consistent with previous core data interpretations and regional stratigraphic/depositional studies.

Quantitative X-ray mapping, scatter diagrams and the generation of correction maps to obtain more information about your material

NASA Astrophysics Data System (ADS)

Wuhrer, R.; Moran, K.

2014-03-01

Quantitative X-ray mapping with silicon drift detectors and multi-EDS detector systems have become an invaluable analysis technique and one of the most useful methods of X-ray microanalysis today. The time to perform an X-ray map has reduced considerably with the ability to map minor and trace elements very accurately due to the larger detector area and higher count rate detectors. Live X-ray imaging can now be performed with a significant amount of data collected in a matter of minutes. A great deal of information can be obtained from X-ray maps. This includes; elemental relationship or scatter diagram creation, elemental ratio mapping, chemical phase mapping (CPM) and quantitative X-ray maps. In obtaining quantitative x-ray maps, we are able to easily generate atomic number (Z), absorption (A), fluorescence (F), theoretical back scatter coefficient (η), and quantitative total maps from each pixel in the image. This allows us to generate an image corresponding to each factor (for each element present). These images allow the user to predict and verify where they are likely to have problems in our images, and are especially helpful to look at possible interface artefacts. The post-processing techniques to improve the quantitation of X-ray map data and the development of post processing techniques for improved characterisation are covered in this paper.

[The qualitative analysis and quantitative analysis of purification of salvianolic acids by macroreticular resin].

PubMed

Fang, Xin-sheng; Tan, Xiao-mei

2005-09-01

To purify salvianolic acids by macroreticular resin,then mensurate the contents of salvianolic acids and analyse the chromatogram with HPLC. Make salvianolic acids with macroreticular resin; mensurate the content of Salvianolic acids with UV spestrophotometry: the control compound is protocaechuic aldehyde, and the wavelength is 281 nm. Analysis the chromatogram with HPLC, and compare the chromatogram in different technics: zorbax ODS column (4.6 mm x 250 mm, 5 microm), mobilephase: 1% aceticacid-water and methanol in different proportions, the wavelength is 281 nm. The contents of salvianolic acids is 53.8%; HPLC chromatogram indicate that the method is reasonable to make salvianolic acids. Determination of contents and HPLC chromatogram can control the quality of Salvianolic acids more accurately.

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. This flexibility and excitation accuracy is key to multicolour applications and future adaptation of the instrument to address the application requirements and newly emerging dyes.

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.

Visualization techniques to aid in the analysis of multi-spectral astrophysical data sets

NASA Technical Reports Server (NTRS)

Brugel, Edward W.; Domik, Gitta O.; Ayres, Thomas R.

1993-01-01

The goal of this project was to support the scientific analysis of multi-spectral astrophysical data by means of scientific visualization. Scientific visualization offers its greatest value if it is not used as a method separate or alternative to other data analysis methods but rather in addition to these methods. Together with quantitative analysis of data, such as offered by statistical analysis, image or signal processing, visualization attempts to explore all information inherent in astrophysical data in the most effective way. Data visualization is one aspect of data analysis. Our taxonomy as developed in Section 2 includes identification and access to existing information, preprocessing and quantitative analysis of data, visual representation and the user interface as major components to the software environment of astrophysical data analysis. In pursuing our goal to provide methods and tools for scientific visualization of multi-spectral astrophysical data, we therefore looked at scientific data analysis as one whole process, adding visualization tools to an already existing environment and integrating the various components that define a scientific data analysis environment. As long as the software development process of each component is separate from all other components, users of data analysis software are constantly interrupted in their scientific work in order to convert from one data format to another, or to move from one storage medium to another, or to switch from one user interface to another. We also took an in-depth look at scientific visualization and its underlying concepts, current visualization systems, their contributions, and their shortcomings. The role of data visualization is to stimulate mental processes different from quantitative data analysis, such as the perception of spatial relationships or the discovery of patterns or anomalies while browsing through large data sets. Visualization often leads to an intuitive understanding of the meaning of data values and their relationships by sacrificing accuracy in interpreting the data values. In order to be accurate in the interpretation, data values need to be measured, computed on, and compared to theoretical or empirical models (quantitative analysis). If visualization software hampers quantitative analysis (which happens with some commercial visualization products), its use is greatly diminished for astrophysical data analysis. The software system STAR (Scientific Toolkit for Astrophysical Research) was developed as a prototype during the course of the project to better understand the pragmatic concerns raised in the project. STAR led to a better understanding on the importance of collaboration between astrophysicists and computer scientists.

Quantitative, multiplexed workflow for deep analysis of human blood plasma and biomarker discovery by mass spectrometry.

PubMed

Keshishian, Hasmik; Burgess, Michael W; Specht, Harrison; Wallace, Luke; Clauser, Karl R; Gillette, Michael A; Carr, Steven A

2017-08-01

Proteomic characterization of blood plasma is of central importance to clinical proteomics and particularly to biomarker discovery studies. The vast dynamic range and high complexity of the plasma proteome have, however, proven to be serious challenges and have often led to unacceptable tradeoffs between depth of coverage and sample throughput. We present an optimized sample-processing pipeline for analysis of the human plasma proteome that provides greatly increased depth of detection, improved quantitative precision and much higher sample analysis throughput as compared with prior methods. The process includes abundant protein depletion, isobaric labeling at the peptide level for multiplexed relative quantification and ultra-high-performance liquid chromatography coupled to accurate-mass, high-resolution tandem mass spectrometry analysis of peptides fractionated off-line by basic pH reversed-phase (bRP) chromatography. The overall reproducibility of the process, including immunoaffinity depletion, is high, with a process replicate coefficient of variation (CV) of <12%. Using isobaric tags for relative and absolute quantitation (iTRAQ) 4-plex, >4,500 proteins are detected and quantified per patient sample on average, with two or more peptides per protein and starting from as little as 200 μl of plasma. The approach can be multiplexed up to 10-plex using tandem mass tags (TMT) reagents, further increasing throughput, albeit with some decrease in the number of proteins quantified. In addition, we provide a rapid protocol for analysis of nonfractionated depleted plasma samples analyzed in 10-plex. This provides ∼600 quantified proteins for each of the ten samples in ∼5 h of instrument time.

Determination of dasatinib in the tablet dosage form by ultra high performance liquid chromatography, capillary zone electrophoresis, and sequential injection analysis.

PubMed

Gonzalez, Aroa Garcia; Taraba, Lukáš; Hraníček, Jakub; Kozlík, Petr; Coufal, Pavel

2017-01-01

Dasatinib is a novel oral prescription drug proposed for treating adult patients with chronic myeloid leukemia. Three analytical methods, namely ultra high performance liquid chromatography, capillary zone electrophoresis, and sequential injection analysis, were developed, validated, and compared for determination of the drug in the tablet dosage form. The total analysis time of optimized ultra high performance liquid chromatography and capillary zone electrophoresis methods was 2.0 and 2.2 min, respectively. Direct ultraviolet detection with detection wavelength of 322 nm was employed in both cases. The optimized sequential injection analysis method was based on spectrophotometric detection of dasatinib after a simple colorimetric reaction with folin ciocalteau reagent forming a blue-colored complex with an absorbance maximum at 745 nm. The total analysis time was 2.5 min. The ultra high performance liquid chromatography method provided the lowest detection and quantitation limits and the most precise and accurate results. All three newly developed methods were demonstrated to be specific, linear, sensitive, precise, and accurate, providing results satisfactorily meeting the requirements of the pharmaceutical industry, and can be employed for the routine determination of the active pharmaceutical ingredient in the tablet dosage form. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Analysis of selected sugars and sugar phosphates in mouse heart tissue by reductive amination and liquid chromatography-electrospray ionization mass spectrometry.

PubMed

Han, Jun; Tschernutter, Vera; Yang, Juncong; Eckle, Tobias; Borchers, Christoph H

2013-06-18

Sensitive and reliable analysis of sugars and sugar phosphates in tissues and cells is essential for many biological and cell engineering studies. However, the successful analysis of these endogenous compounds in biological samples by liquid chromatography/electrospray ionization mass spectrometry (LC/ESI-MS) is often difficult because of their poor chromatographic retention properties in reversed-phase LC, the complex biological matrices, and the ionization suppression in ESI. This situation is further complicated by the existence of their multiple structural isomers in vivo. This work describes the combination of reductive amination using 3-amino-9-ethylcarbazole, with a new LC approach using a pentafluorophenyl core-shell ultrahigh performance (UP) LC column and methylphosphonic acid as an efficient tail-sweeping reagent for improved chromatographic separation. This new method was used for selected detection and accurate quantitation of the major free and phosphorylated reducing sugars in mouse heart tissue. Among the detected compounds, accurate quantitation of glyceraldehyde, ribose, glucose, glycerylaldehyde-3-phosphate, ribose-5-phosphate, glucose-6-phosphate, and mannose-6-phosphate was achieved by UPLC/multiple-reaction monitoring (MRM)-MS, with analytical accuracies ranging from 87.4% to 109.4% and CVs of ≤8.5% (n = 6). To demonstrate isotope-resolved metabolic profiling, we used UPLC/quadrupole time-of-flight (QTOF)-MS to analyze the isotope distribution patterns of C3 to C6 free and phosphorylated reducing sugars in heart tissues from (13)C-labeled wild type and knockout mice. In conclusion, the preanalytical derivatization-LC/ESI-MS method has resulted in selective determination of free and phosphorylated reducing sugars without the interferences from their nonreducing structural isomers in mouse heart tissue, with analytical sensitivities in the femtomole to low picomole range.

Comprehensive analytical strategy for biomonitoring of pesticides in urine by liquid chromatography–orbitrap high resolution masss pectrometry.

PubMed

Roca, M; Leon, N; Pastor, A; Yusà, V

2014-12-29

In this study we propose an analytical strategy that combines a target approach for the quantitative analysis of contemporary pesticide metabolites with a comprehensive post-target screening for the identification of biomarkers of exposure to environmental contaminants in urine using liquid chromatography coupled to high-resolution mass spectrometry (LC–HRMS). The quantitative method for the target analysis of 29 urinary metabolites of organophosphate (OP) insecticides, synthetic pyrethroids, herbicides and fungicides was validated after a previous statistical optimization of the main factors governing the ion source ionization and a fragmentation study using the high energy collision dissociation (HCD) cell. The full scan accurate mass data were acquired with a resolving power of 50,000 FWHM (scan speed, 2 Hz), in both ESI+ and ESI− modes, and with and without HCD-fragmentation. The method – LOQ was lower than 3.2 μg L−1 for the majority of the analytes. For post-target screening a customized theoretical database was built, for the identification of 60 metabolites including pesticides, PAHs, phenols, and other metabolites of environmental pollutants. For identification purposes, accurate exact mass with less than 5 ppm, and diagnostic ions including isotopes and/or fragments were used. The analytical strategy was applied to 20 urine sample collected from children living in Valencia Region. Eleven target metabolites were detected with concentrations ranging from 1.18 to 131 μg L−1. Likewise, several compounds were tentatively identified in the post-target analysis belonging to the families of phthalates, phenols and parabenes. The proposed strategy is suitable for the determination of target pesticide biomarkers in urine in the framework of biomonitoring studies, and appropriate for the identification of other non-target metabolites.

Peripheral Quantitative CT (pQCT) Using a Dedicated Extremity Cone-Beam CT Scanner

PubMed Central

Muhit, A. A.; Arora, S.; Ogawa, M.; Ding, Y.; Zbijewski, W.; Stayman, J. W.; Thawait, G.; Packard, N.; Senn, R.; Yang, D.; Yorkston, J.; Bingham, C.O.; Means, K.; Carrino, J. A.; Siewerdsen, J. H.

2014-01-01

Purpose We describe the initial assessment of the peripheral quantitative CT (pQCT) imaging capabilities of a cone-beam CT (CBCT) scanner dedicated to musculoskeletal extremity imaging. The aim is to accurately measure and quantify bone and joint morphology using information automatically acquired with each CBCT scan, thereby reducing the need for a separate pQCT exam. Methods A prototype CBCT scanner providing isotropic, sub-millimeter spatial resolution and soft-tissue contrast resolution comparable or superior to standard multi-detector CT (MDCT) has been developed for extremity imaging, including the capability for weight-bearing exams and multi-mode (radiography, fluoroscopy, and volumetric) imaging. Assessment of pQCT performance included measurement of bone mineral density (BMD), morphometric parameters of subchondral bone architecture, and joint space analysis. Measurements employed phantoms, cadavers, and patients from an ongoing pilot study imaged with the CBCT prototype (at various acquisition, calibration, and reconstruction techniques) in comparison to MDCT (using pQCT protocols for analysis of BMD) and micro-CT (for analysis of subchondral morphometry). Results The CBCT extremity scanner yielded BMD measurement within ±2–3% error in both phantom studies and cadaver extremity specimens. Subchondral bone architecture (bone volume fraction, trabecular thickness, degree of anisotropy, and structure model index) exhibited good correlation with gold standard micro-CT (error ~5%), surpassing the conventional limitations of spatial resolution in clinical MDCT scanners. Joint space analysis demonstrated the potential for sensitive 3D joint space mapping beyond that of qualitative radiographic scores in application to non-weight-bearing versus weight-bearing lower extremities and assessment of phalangeal joint space integrity in the upper extremities. Conclusion The CBCT extremity scanner demonstrated promising initial results in accurate pQCT analysis from images acquired with each CBCT scan. Future studies will include improved x-ray scatter correction and image reconstruction techniques to further improve accuracy and to correlate pQCT metrics with known pathology. PMID:25076823

Changes in body composition of neonatal piglets during growth

USDA-ARS?s Scientific Manuscript database

During studies of neonatal piglet growth it is important to be able to accurately assess changes in body composition. Previous studies have demonstrated that quantitative magnetic resonance (QMR) provides precise and accurate measurements of total body fat mass, lean mass and total body water in non...

Deep Learning for Brain MRI Segmentation: State of the Art and Future Directions.

PubMed

Akkus, Zeynettin; Galimzianova, Alfiia; Hoogi, Assaf; Rubin, Daniel L; Erickson, Bradley J

2017-08-01

Quantitative analysis of brain MRI is routine for many neurological diseases and conditions and relies on accurate segmentation of structures of interest. Deep learning-based segmentation approaches for brain MRI are gaining interest due to their self-learning and generalization ability over large amounts of data. As the deep learning architectures are becoming more mature, they gradually outperform previous state-of-the-art classical machine learning algorithms. This review aims to provide an overview of current deep learning-based segmentation approaches for quantitative brain MRI. First we review the current deep learning architectures used for segmentation of anatomical brain structures and brain lesions. Next, the performance, speed, and properties of deep learning approaches are summarized and discussed. Finally, we provide a critical assessment of the current state and identify likely future developments and trends.

Optical demodulation system for digitally encoded suspension array in fluoroimmunoassay

NASA Astrophysics Data System (ADS)

He, Qinghua; Li, Dongmei; He, Yonghong; Guan, Tian; Zhang, Yilong; Shen, Zhiyuan; Chen, Xuejing; Liu, Siyu; Lu, Bangrong; Ji, Yanhong

2017-09-01

A laser-induced breakdown spectroscopy and fluorescence spectroscopy-coupled optical system is reported to demodulate digitally encoded suspension array in fluoroimmunoassay. It takes advantage of the plasma emissions of assembled elemental materials to digitally decode the suspension array, providing a more stable and accurate recognition to target biomolecules. By separating the decoding procedure of suspension array and adsorption quantity calculation of biomolecules into two independent channels, the cross talk between decoding and label signals in traditional methods had been successfully avoided, which promoted the accuracy of both processes and realized more sensitive quantitative detection of target biomolecules. We carried a multiplexed detection of several types of anti-IgG to verify the quantitative analysis performance of the system. A limit of detection of 1.48×10-10 M was achieved, demonstrating the detection sensitivity of the optical demodulation system.

Quantitative analysis of matrine in liquid crystalline nanoparticles by HPLC.

PubMed

Peng, Xinsheng; Li, Baohong; Hu, Min; Ling, Yahao; Tian, Yuan; Zhou, Yanxing; Zhou, Yanfang

2014-01-01

A reversed-phase high-performance liquid chromatographic method has been developed to quantitatively determine matrine in liquid crystal nanoparticles. The chromatographic method is carried out using an isocratic system. The mobile phase was composed of methanol-PBS(pH6.8)-triethylamine (50 : 50 : 0.1%) with a flow rate of 1 mL/min with SPD-20A UV/vis detector and the detection wavelength was at 220 nm. The linearity of matrine is in the range of 1.6 to 200.0  μ g/mL. The regression equation is y = 10706x - 2959 (R (2) = 1.0). The average recovery is 101.7%; RSD = 2.22%  (n = 9). This method provides a simple and accurate strategy to determine matrine in liquid crystalline nanoparticle.

Size Dependent Mechanical Properties of Monolayer Densely Arranged Polystyrene Nanospheres.

PubMed

Huang, Peng; Zhang, Lijing; Yan, Qingfeng; Guo, Dan; Xie, Guoxin

2016-12-13

In contrast to macroscopic materials, the mechanical properties of polymer nanospheres show fascinating scientific and application values. However, the experimental measurements of individual nanospheres and quantitative analysis of theoretical mechanisms remain less well performed and understood. We provide a highly efficient and accurate method with monolayer densely arranged honeycomb polystyrene (PS) nanospheres for the quantitatively mechanical characterization of individual nanospheres on the basis of atomic force microscopy (AFM) nanoindentation. The efficiency is improved by 1-2 orders, and the accuracy is also enhanced almost by half-order. The elastic modulus measured in the experiments increases with decreasing radius to the smallest nanospheres (25-35 nm in radius). A core-shell model is introduced to predict the size dependent elasticity of PS nanospheres, and the theoretical prediction agrees reasonably well with the experimental results and also shows a peak modulus value.

[Quality evaluation of Artemisiae Argyi Folium based on fingerprint analysis and quantitative analysis of multicomponents].

PubMed

Guo, Long; Jiao, Qian; Zhang, Dan; Liu, Ai-Peng; Wang, Qian; Zheng, Yu-Guang

2018-03-01

Artemisiae Argyi Folium, the dried leaves of Artemisia argyi, has been widely used in traditional Chinese and folk medicines for treatment of hemorrhage, pain, and skin itch. Phytochemical studies indicated that volatile oil, organic acid and flavonoids were the main bioactive components in Artemisiae Argyi Folium. Compared to the volatile compounds, the research of nonvolatile compounds in Artemisiae Argyi Folium are limited. In the present study, an accurate and reliable fingerprint approach was developed using HPLC for quality control of Artemisiae Argyi Folium. A total of 10 common peaks were marked，and the similarity of all the Artemisiae Argyi Folium samples was above 0.940. The established fingerprint method could be used for quality control of Artemisiae Argyi Folium. Furthermore, an HPLC method was applied for simultaneous determination of seven bioactive compounds including five organic acids and two flavonoids in Artemisiae Argyi Folium and Artemisiae Lavandulaefoliae Folium samples. Moreover, chemometrics methods such as hierarchical clustering analysis and principal component analysis were performed to compare and discriminate the Artemisiae Argyi Folium and Artemisiae Lavandulaefoliae Folium based on the quantitative data of analytes. The results indicated that simultaneous quantification of multicomponents coupled with chemometrics analysis could be a well-acceptable strategy to identify and evaluate the quality of Artemisiae Argyi Folium. Copyright© by the Chinese Pharmaceutical Association.

Identification of suitable reference genes for hepatic microRNA quantitation.

PubMed

Lamba, Vishal; Ghodke-Puranik, Yogita; Guan, Weihua; Lamba, Jatinder K

2014-03-07

MicroRNAs (miRNAs) are short (~22 nt) endogenous RNAs that play important roles in regulating expression of a wide variety of genes involved in different cellular processes. Alterations in microRNA expression patterns have been associated with a number of human diseases. Accurate quantitation of microRNA levels is important for their use as biomarkers and in determining their functions. Real time PCR is the gold standard and the most frequently used technique for miRNA quantitation. Real time PCR data analysis includes normalizing the amplification data to suitable endogenous control/s to ensure that microRNA quantitation is not affected by the variability that is potentially introduced at different experimental steps. U6 (RNU6A) and RNU6B are two commonly used endogenous controls in microRNA quantitation. The present study was designed to investigate inter-individual variability and gender differences in hepatic microRNA expression as well as to identify the best endogenous control/s that could be used for normalization of real-time expression data in liver samples. We used Taqman based real time PCR to quantitate hepatic expression levels of 22 microRNAs along with U6 and RNU6B in 50 human livers samples (25 M, 25 F). To identify the best endogenous controls for use in data analysis, we evaluated the amplified candidates for their stability (least variability) in expression using two commonly used software programs: Normfinder and GeNormplus, Both Normfinder and GeNormplus identified U6 to be among the least stable of all the candidates analyzed, and RNU6B was also not among the top genes in stability. mir-152 and mir-23b were identified to be the two most stable candidates by both Normfinder and GeNormplus in our analysis, and were used as endogenous controls for normalization of hepatic miRNA levels. Measurements of microRNA stability indicate that U6 and RNU6B are not suitable for use as endogenous controls for normalizing microRNA relative quantitation data in hepatic tissue, and their use can led to possibly erroneous conclusions.

A systematic study on the influencing parameters and improvement of quantitative analysis of multi-component with single marker method using notoginseng as research subject.

PubMed

Wang, Chao-Qun; Jia, Xiu-Hong; Zhu, Shu; Komatsu, Katsuko; Wang, Xuan; Cai, Shao-Qing

2015-03-01

A new quantitative analysis of multi-component with single marker (QAMS) method for 11 saponins (ginsenosides Rg1, Rb1, Rg2, Rh1, Rf, Re and Rd; notoginsenosides R1, R4, Fa and K) in notoginseng was established, when 6 of these saponins were individually used as internal referring substances to investigate the influences of chemical structure, concentrations of quantitative components, and purities of the standard substances on the accuracy of the QAMS method. The results showed that the concentration of the analyte in sample solution was the major influencing parameter, whereas the other parameters had minimal influence on the accuracy of the QAMS method. A new method for calculating the relative correction factors by linear regression was established (linear regression method), which demonstrated to decrease standard method differences of the QAMS method from 1.20%±0.02% - 23.29%±3.23% to 0.10%±0.09% - 8.84%±2.85% in comparison with the previous method. And the differences between external standard method and the QAMS method using relative correction factors calculated by linear regression method were below 5% in the quantitative determination of Rg1, Re, R1, Rd and Fa in 24 notoginseng samples and Rb1 in 21 notoginseng samples. And the differences were mostly below 10% in the quantitative determination of Rf, Rg2, R4 and N-K (the differences of these 4 constituents bigger because their contents lower) in all the 24 notoginseng samples. The results indicated that the contents assayed by the new QAMS method could be considered as accurate as those assayed by external standard method. In addition, a method for determining applicable concentration ranges of the quantitative components assayed by QAMS method was established for the first time, which could ensure its high accuracy and could be applied to QAMS methods of other TCMs. The present study demonstrated the practicability of the application of the QAMS method for the quantitative analysis of multi-component and the quality control of TCMs and TCM prescriptions. Copyright © 2014 Elsevier B.V. All rights reserved.

Detailed mechanism of benzene oxidation

NASA Technical Reports Server (NTRS)

Bittker, David A.

1987-01-01

A detailed quantitative mechanism for the oxidation of benzene in both argon and nitrogen diluted systems is presented. Computed ignition delay time for argon diluted mixtures are in satisfactory agreement with experimental results for a wide range of initial conditions. An experimental temperature versus time profile for a nitrogen diluted oxidation was accurately matched and several concentration profiles were matched qualitatively. Application of sensitivity analysis has given approximate rate constant expressions for the two dominant heat release reactions, the oxidation of C6H5 and C5H5 radicals by molecular oxygen.

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,…

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...

A novel mesh processing based technique for 3D plant analysis

PubMed Central

2012-01-01

Background In recent years, imaging based, automated, non-invasive, and non-destructive high-throughput plant phenotyping platforms have become popular tools for plant biology, underpinning the field of plant phenomics. Such platforms acquire and record large amounts of raw data that must be accurately and robustly calibrated, reconstructed, and analysed, requiring the development of sophisticated image understanding and quantification algorithms. The raw data can be processed in different ways, and the past few years have seen the emergence of two main approaches: 2D image processing and 3D mesh processing algorithms. Direct image quantification methods (usually 2D) dominate the current literature due to comparative simplicity. However, 3D mesh analysis provides the tremendous potential to accurately estimate specific morphological features cross-sectionally and monitor them over-time. Result In this paper, we present a novel 3D mesh based technique developed for temporal high-throughput plant phenomics and perform initial tests for the analysis of Gossypium hirsutum vegetative growth. Based on plant meshes previously reconstructed from multi-view images, the methodology involves several stages, including morphological mesh segmentation, phenotypic parameters estimation, and plant organs tracking over time. The initial study focuses on presenting and validating the accuracy of the methodology on dicotyledons such as cotton but we believe the approach will be more broadly applicable. This study involved applying our technique to a set of six Gossypium hirsutum (cotton) plants studied over four time-points. Manual measurements, performed for each plant at every time-point, were used to assess the accuracy of our pipeline and quantify the error on the morphological parameters estimated. Conclusion By directly comparing our automated mesh based quantitative data with manual measurements of individual stem height, leaf width and leaf length, we obtained the mean absolute errors of 9.34%, 5.75%, 8.78%, and correlation coefficients 0.88, 0.96, and 0.95 respectively. The temporal matching of leaves was accurate in 95% of the cases and the average execution time required to analyse a plant over four time-points was 4.9 minutes. The mesh processing based methodology is thus considered suitable for quantitative 4D monitoring of plant phenotypic features. PMID:22553969

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.

A Model of Risk Analysis in Analytical Methodology for Biopharmaceutical Quality Control.

PubMed

Andrade, Cleyton Lage; Herrera, Miguel Angel De La O; Lemes, Elezer Monte Blanco

2018-01-01

One key quality control parameter for biopharmaceutical products is the analysis of residual cellular DNA. To determine small amounts of DNA (around 100 pg) that may be in a biologically derived drug substance, an analytical method should be sensitive, robust, reliable, and accurate. In principle, three techniques have the ability to measure residual cellular DNA: radioactive dot-blot, a type of hybridization; threshold analysis; and quantitative polymerase chain reaction. Quality risk management is a systematic process for evaluating, controlling, and reporting of risks that may affects method capabilities and supports a scientific and practical approach to decision making. This paper evaluates, by quality risk management, an alternative approach to assessing the performance risks associated with quality control methods used with biopharmaceuticals, using the tool hazard analysis and critical control points. This tool provides the possibility to find the steps in an analytical procedure with higher impact on method performance. By applying these principles to DNA analysis methods, we conclude that the radioactive dot-blot assay has the largest number of critical control points, followed by quantitative polymerase chain reaction, and threshold analysis. From the analysis of hazards (i.e., points of method failure) and the associated method procedure critical control points, we conclude that the analytical methodology with the lowest risk for performance failure for residual cellular DNA testing is quantitative polymerase chain reaction. LAY ABSTRACT: In order to mitigate the risk of adverse events by residual cellular DNA that is not completely cleared from downstream production processes, regulatory agencies have required the industry to guarantee a very low level of DNA in biologically derived pharmaceutical products. The technique historically used was radioactive blot hybridization. However, the technique is a challenging method to implement in a quality control laboratory: It is laborious, time consuming, semi-quantitative, and requires a radioisotope. Along with dot-blot hybridization, two alternatives techniques were evaluated: threshold analysis and quantitative polymerase chain reaction. Quality risk management tools were applied to compare the techniques, taking into account the uncertainties, the possibility of circumstances or future events, and their effects upon method performance. By illustrating the application of these tools with DNA methods, we provide an example of how they can be used to support a scientific and practical approach to decision making and can assess and manage method performance risk using such tools. This paper discusses, considering the principles of quality risk management, an additional approach to the development and selection of analytical quality control methods using the risk analysis tool hazard analysis and critical control points. This tool provides the possibility to find the method procedural steps with higher impact on method reliability (called critical control points). Our model concluded that the radioactive dot-blot assay has the larger number of critical control points, followed by quantitative polymerase chain reaction and threshold analysis. Quantitative polymerase chain reaction is shown to be the better alternative analytical methodology in residual cellular DNA analysis. © PDA, Inc. 2018.

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

Quantitative Analysis of Subcellular Distribution of the SUMO Conjugation System by Confocal Microscopy Imaging.

PubMed

Mas, Abraham; Amenós, Montse; Lois, L Maria

2016-01-01

Different studies point to an enrichment in SUMO conjugation in the cell nucleus, although non-nuclear SUMO targets also exist. In general, the study of subcellular localization of proteins is essential for understanding their function within a cell. Fluorescence microscopy is a powerful tool for studying subcellular protein partitioning in living cells, since fluorescent proteins can be fused to proteins of interest to determine their localization. Subcellular distribution of proteins can be influenced by binding to other biomolecules and by posttranslational modifications. Sometimes these changes affect only a portion of the protein pool or have a partial effect, and a quantitative evaluation of fluorescence images is required to identify protein redistribution among subcellular compartments. In order to obtain accurate data about the relative subcellular distribution of SUMO conjugation machinery members, and to identify the molecular determinants involved in their localization, we have applied quantitative confocal microscopy imaging. In this chapter, we will describe the fluorescent protein fusions used in these experiments, and how to measure, evaluate, and compare average fluorescence intensities in cellular compartments by image-based analysis. We show the distribution of some components of the Arabidopsis SUMOylation machinery in epidermal onion cells and how they change their distribution in the presence of interacting partners or even when its activity is affected.

Smartphone based visual and quantitative assays on upconversional paper sensor.

PubMed

Mei, Qingsong; Jing, Huarong; Li, You; Yisibashaer, Wuerzha; Chen, Jian; Nan Li, Bing; Zhang, Yong

2016-01-15

The integration of smartphone with paper sensors recently has been gain increasing attentions because of the achievement of quantitative and rapid analysis. However, smartphone based upconversional paper sensors have been restricted by the lack of effective methods to acquire luminescence signals on test paper. Herein, by the virtue of 3D printing technology, we exploited an auxiliary reusable device, which orderly assembled a 980nm mini-laser, optical filter and mini-cavity together, for digitally imaging the luminescence variations on test paper and quantitative analyzing pesticide thiram by smartphone. In detail, copper ions decorated NaYF4:Yb/Tm upconversion nanoparticles were fixed onto filter paper to form test paper, and the blue luminescence on it would be quenched after additions of thiram through luminescence resonance energy transfer mechanism. These variations could be monitored by the smartphone camera, and then the blue channel intensities of obtained colored images were calculated to quantify amounts of thiram through a self-written Android program installed on the smartphone, offering a reliable and accurate detection limit of 0.1μM for the system. This work provides an initial demonstration of integrating upconversion nanosensors with smartphone digital imaging for point-of-care analysis on a paper-based platform. Copyright © 2015 Elsevier B.V. All rights reserved.

Application of scenario analysis and multiagent technique in land-use planning: a case study on Sanjiang wetlands.

PubMed

Yu, Huan; Ni, Shi-Jun; Kong, Bo; He, Zheng-Wei; Zhang, Cheng-Jiang; Zhang, Shu-Qing; Pan, Xin; Xia, Chao-Xu; Li, Xuan-Qiong

2013-01-01

Land-use planning has triggered debates on social and environmental values, in which two key questions will be faced: one is how to see different planning simulation results instantaneously and apply the results back to interactively assist planning work; the other is how to ensure that the planning simulation result is scientific and accurate. To answer these questions, the objective of this paper is to analyze whether and how a bridge can be built between qualitative and quantitative approaches for land-use planning work and to find out a way to overcome the gap that exists between the ability to construct computer simulation models to aid integrated land-use plan making and the demand for them by planning professionals. The study presented a theoretical framework of land-use planning based on scenario analysis (SA) method and multiagent system (MAS) simulation integration and selected freshwater wetlands in the Sanjiang Plain of China as a case study area. Study results showed that MAS simulation technique emphasizing quantitative process effectively compensated for the SA method emphasizing qualitative process, which realized the organic combination of qualitative and quantitative land-use planning work, and then provided a new idea and method for the land-use planning and sustainable managements of land resources.

Application of Scenario Analysis and Multiagent Technique in Land-Use Planning: A Case Study on Sanjiang Wetlands

PubMed Central

Ni, Shi-Jun; He, Zheng-Wei; Zhang, Cheng-Jiang; Zhang, Shu-Qing; Pan, Xin; Xia, Chao-Xu; Li, Xuan-Qiong

2013-01-01

Land-use planning has triggered debates on social and environmental values, in which two key questions will be faced: one is how to see different planning simulation results instantaneously and apply the results back to interactively assist planning work; the other is how to ensure that the planning simulation result is scientific and accurate. To answer these questions, the objective of this paper is to analyze whether and how a bridge can be built between qualitative and quantitative approaches for land-use planning work and to find out a way to overcome the gap that exists between the ability to construct computer simulation models to aid integrated land-use plan making and the demand for them by planning professionals. The study presented a theoretical framework of land-use planning based on scenario analysis (SA) method and multiagent system (MAS) simulation integration and selected freshwater wetlands in the Sanjiang Plain of China as a case study area. Study results showed that MAS simulation technique emphasizing quantitative process effectively compensated for the SA method emphasizing qualitative process, which realized the organic combination of qualitative and quantitative land-use planning work, and then provided a new idea and method for the land-use planning and sustainable managements of land resources. PMID:23818816

Simultaneous determination of eight major steroids from Polyporus umbellatus by high-performance liquid chromatography coupled with mass spectrometry detections.

PubMed

Zhao, Ying-yong; Cheng, Xian-long; Zhang, Yongmin; Zhao, Ye; Lin, Rui-chao; Sun, Wen-ji

2010-02-01

Polyporus umbellatus is a widely used diuretic herbal medicine. In this study, a high-performance liquid chromatography coupled with atmospheric pressure chemical ionization-mass spectrometric detection (HPLC-APCI-MS) method was developed for qualitative and quantitative analysis of steroids, as well as for the quality control of Polyporus umbellatus. The selectivity, reproducibility and sensitivity were compared with HPLC with photodiode array detection and evaporative light scattering detection (ELSD). Selective ion monitoring in positive mode was used for qualitative and quantitative analysis of eight major components and beta-ecdysterone was used as the internal standard. Limits of detection and quantification fell in the ranges 7-21 and 18-63 ng/mL for the eight analytes with an injection of 10 microL samples, and all calibration curves showed good linear regression (r(2) > 0.9919) within the test range. The quantitative results demonstrated that samples from different localities showed different qualities. Advantages, in comparison with conventional HPLC-diode array detection and HPLC-ELSD, are that reliable identification of target compounds could be achieved by accurate mass measurements along with characteristic retention time, and the great enhancement in selectivity and sensitivity allows identification and quantification of low levels of constituents in complex Polyporus umbellatus matrixes. (c) 2009 John Wiley & Sons, Ltd.

Find Pairs: The Module for Protein Quantification of the PeakQuant Software Suite

PubMed Central

Eisenacher, Martin; Kohl, Michael; Wiese, Sebastian; Hebeler, Romano; Meyer, Helmut E.

2012-01-01

Abstract Accurate quantification of proteins is one of the major tasks in current proteomics research. To address this issue, a wide range of stable isotope labeling techniques have been developed, allowing one to quantitatively study thousands of proteins by means of mass spectrometry. In this article, the FindPairs module of the PeakQuant software suite is detailed. It facilitates the automatic determination of protein abundance ratios based on the automated analysis of stable isotope-coded mass spectrometric data. Furthermore, it implements statistical methods to determine outliers due to biological as well as technical variance of proteome data obtained in replicate experiments. This provides an important means to evaluate the significance in obtained protein expression data. For demonstrating the high applicability of FindPairs, we focused on the quantitative analysis of proteome data acquired in 14N/15N labeling experiments. We further provide a comprehensive overview of the features of the FindPairs software, and compare these with existing quantification packages. The software presented here supports a wide range of proteomics applications, allowing one to quantitatively assess data derived from different stable isotope labeling approaches, such as 14N/15N labeling, SILAC, and iTRAQ. The software is publicly available at http://www.medizinisches-proteom-center.de/software and free for academic use. PMID:22909347

Electron paramagnetic resonance oximetry as a quantitative method to measure cellular respiration: a consideration of oxygen diffusion interference.

PubMed

Presley, Tennille; Kuppusamy, Periannan; Zweier, Jay L; Ilangovan, Govindasamy

2006-12-15

Electron paramagnetic resonance (EPR) oximetry is being widely used to measure the oxygen consumption of cells, mitochondria, and submitochondrial particles. However, further improvement of this technique, in terms of data analysis, is required to use it as a quantitative tool. Here, we present a new approach for quantitative analysis of cellular respiration using EPR oximetry. The course of oxygen consumption by cells in suspension has been observed to have three distinct zones: pO(2)-independent respiration at higher pO(2) ranges, pO(2)-dependent respiration at low pO(2) ranges, and a static equilibrium with no change in pO(2) at very low pO(2) values. The approach here enables one to comprehensively analyze all of the three zones together-where the progression of O(2) diffusion zones around each cell, their overlap within time, and their potential impact on the measured pO(2) data are considered. The obtained results agree with previously established methods such as high-resolution respirometry measurements. Additionally, it is also demonstrated how the diffusion limitations can depend on cell density and consumption rate. In conclusion, the new approach establishes a more accurate and meaningful model to evaluate the EPR oximetry data on cellular respiration to quantify related parameters using EPR oximetry.

Quantitative ROESY analysis of computational models: structural studies of citalopram and β-cyclodextrin complexes by (1) H-NMR and computational methods.

PubMed

Ali, Syed Mashhood; Shamim, Shazia

2015-07-01

Complexation of racemic citalopram with β-cyclodextrin (β-CD) in aqueous medium was investigated to determine atom-accurate structure of the inclusion complexes. (1) H-NMR chemical shift change data of β-CD cavity protons in the presence of citalopram confirmed the formation of 1 : 1 inclusion complexes. ROESY spectrum confirmed the presence of aromatic ring in the β-CD cavity but whether one of the two or both rings was not clear. Molecular mechanics and molecular dynamic calculations showed the entry of fluoro-ring from wider side of β-CD cavity as the most favored mode of inclusion. Minimum energy computational models were analyzed for their accuracy in atomic coordinates by comparison of calculated and experimental intermolecular ROESY peak intensities, which were not found in agreement. Several least energy computational models were refined and analyzed till calculated and experimental intensities were compatible. The results demonstrate that computational models of CD complexes need to be analyzed for atom-accuracy and quantitative ROESY analysis is a promising method. Moreover, the study also validates that the quantitative use of ROESY is feasible even with longer mixing times if peak intensity ratios instead of absolute intensities are used. Copyright © 2015 John Wiley & Sons, Ltd.

Quantitative monitoring of activity-dependent bulk endocytosis of synaptic vesicle membrane by fluorescent dextran imaging

PubMed Central

Clayton, Emma Louise; Cousin, Michael Alan

2012-01-01

Activity-dependent bulk endocytosis (ADBE) is the dominant synaptic vesicle (SV) retrieval mode in central nerve terminals during periods of intense neuronal activity. Despite this fact there are very few real time assays that report the activity of this critical SV retrieval mode. In this paper we report a simple and quantitative assay of ADBE using uptake of large flourescent dextrans as fluid phase markers. We show that almost all dextran uptake occurs in nerve terminals, using co-localisation with the fluorescent probe FM1-43. We also demonstrate that accumulated dextran cannot be unloaded by neuronal stimulation, indicating its specific loading into bulk endosomes and not SVs. Quantification of dextran uptake was achieved by using thresholding analysis to count the number of loaded nerve terminals, since monitoring the average fluorescence intensity of these nerve terminals did not accurately report the extent of ADBE. Using this analysis we showed that dextran uptake occurs very soon after stimulation and that it does not persist when stimulation terminates. Thus we have devised a simple and quantitative method to monitor ADBE in living neurones, which will be ideal for real time screening of small molecule inhibitors of this key SV retrieval mode. PMID:19766140

An automated gas chromatography time-of-flight mass spectrometry instrument for the quantitative analysis of halocarbons in air

NASA Astrophysics Data System (ADS)

Obersteiner, F.; Bönisch, H.; Engel, A.

2016-01-01

We present the characterization and application of a new gas chromatography time-of-flight mass spectrometry instrument (GC-TOFMS) for the quantitative analysis of halocarbons in air samples. The setup comprises three fundamental enhancements compared to our earlier work (Hoker et al., 2015): (1) full automation, (2) a mass resolving power R = m/Δm of the TOFMS (Tofwerk AG, Switzerland) increased up to 4000 and (3) a fully accessible data format of the mass spectrometric data. Automation in combination with the accessible data allowed an in-depth characterization of the instrument. Mass accuracy was found to be approximately 5 ppm in mean after automatic recalibration of the mass axis in each measurement. A TOFMS configuration giving R = 3500 was chosen to provide an R-to-sensitivity ratio suitable for our purpose. Calculated detection limits are as low as a few femtograms by means of the accurate mass information. The precision for substance quantification was 0.15 % at the best for an individual measurement and in general mainly determined by the signal-to-noise ratio of the chromatographic peak. Detector non-linearity was found to be insignificant up to a mixing ratio of roughly 150 ppt at 0.5 L sampled volume. At higher concentrations, non-linearities of a few percent were observed (precision level: 0.2 %) but could be attributed to a potential source within the detection system. A straightforward correction for those non-linearities was applied in data processing, again by exploiting the accurate mass information. Based on the overall characterization results, the GC-TOFMS instrument was found to be very well suited for the task of quantitative halocarbon trace gas observation and a big step forward compared to scanning, quadrupole MS with low mass resolving power and a TOFMS technique reported to be non-linear and restricted by a small dynamical range.

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

Chemical Fingerprint and Quantitative Analysis for the Quality Evaluation of Platycladi cacumen by Ultra-performance Liquid Chromatography Coupled with Hierarchical Cluster Analysis.

PubMed

Shan, Mingqiu; Li, Sam Fong Yau; Yu, Sheng; Qian, Yan; Guo, Shuchen; Zhang, Li; Ding, Anwei

2018-01-01

Platycladi cacumen (dried twigs and leaves of Platycladus orientalis (L.) Franco) is a frequently utilized Chinese medicinal herb. To evaluate the quality of the phytomedcine, an ultra-performance liquid chromatographic method with diode array detection was established for chemical fingerprinting and quantitative analysis. In this study, 27 batches of P. cacumen from different regions were collected for analysis. A chemical fingerprint with 20 common peaks was obtained using Similarity Evaluation System for Chromatographic Fingerprint of Traditional Chinese Medicine (Version 2004A). Among these 20 components, seven flavonoids (myricitrin, isoquercitrin, quercitrin, afzelin, cupressuflavone, amentoflavone and hinokiflavone) were identified and determined simultaneously. In the method validation, the seven analytes showed good regressions (R ≥ 0.9995) within linear ranges and good recoveries from 96.4% to 103.3%. Furthermore, with the contents of these seven flavonoids, hierarchical clustering analysis was applied to distinguish the 27 batches into five groups. The chemometric results showed that these groups were almost consistent with geographical positions and climatic conditions of the production regions. Integrating fingerprint analysis, simultaneous determination and hierarchical clustering analysis, the established method is rapid, sensitive, accurate and readily applicable, and also provides a significant foundation for quality control of P. cacumen efficiently. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

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.

Limitations of commonly used internal controls for real-time RT-PCR analysis of renal epithelial-mesenchymal cell transition.

PubMed

Elberg, Gerard; Elberg, Dorit; Logan, Charlotte J; Chen, Lijuan; Turman, Martin A

2006-01-01

Progressive renal fibrotic disease is accompanied by the massive accumulation of myofibroblasts as defined by alpha smooth muscle actin (alphaSMA) expression. We quantitated gene expression using real-time RT-PCR analysis during conversion of primary cultured human renal tubular cells (RTC) to myofibroblasts after treatment with transforming growth factor-beta1 (TGF-beta1). We report herein the limitations of commonly used reference genes for mRNA quantitation. We determined the expression of alphaSMA and megakaryoblastic leukemia-1 (MKL1), a transcriptional regulator of alphaSMA, by quantitative real-time PCR using three common internal controls, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), cyclophilin A and 18S rRNA. Expression of GAPDH mRNA and cyclophilin A mRNA, and to a lesser extent, 18S rRNA levels varied over time in culture and with exposure to TGF-beta1. Thus, depending on which reference gene was used, TGF-beta1 appeared to have different effects on expression of MKL1 and alphaSMA. RTC converting to myofibroblasts in primary culture is a valuable system to study renal fibrosis in humans. However, variability in expression of reference genes with TGF-beta1 treatment illustrates the need to validate mRNA quantitation with multiple reference genes to provide accurate interpretation of fibrosis studies in the absence of a universal internal standard for mRNA expression. 2006 S. Karger AG, Basel.

Quantitative Analysis of the KSHV Transcriptome Following Primary Infection of Blood and Lymphatic Endothelial Cells

PubMed Central

Bruce, A. Gregory; Barcy, Serge; DiMaio, Terri; Gan, Emilia; Garrigues, H. Jacques; Lagunoff, Michael; Rose, Timothy M.

2017-01-01

The transcriptome of the Kaposi’s sarcoma-associated herpesvirus (KSHV/HHV8) after primary latent infection of human blood (BEC), lymphatic (LEC) and immortalized (TIME) endothelial cells was analyzed using RNAseq, and compared to long-term latency in BCBL-1 lymphoma cells. Naturally expressed transcripts were obtained without artificial induction, and a comprehensive annotation of the KSHV genome was determined. A set of unique coding sequence (UCDS) features and a process to resolve overlapping transcripts were developed to accurately quantitate transcript levels from specific promoters. Similar patterns of KSHV expression were detected in BCBL-1 cells undergoing long-term latent infections and in primary latent infections of both BEC and LEC cultures. High expression levels of poly-adenylated nuclear (PAN) RNA and spliced and unspliced transcripts encoding the K12 Kaposin B/C complex and associated microRNA region were detected, with an elevated expression of a large set of lytic genes in all latently infected cultures. Quantitation of non-overlapping regions of transcripts across the complete KSHV genome enabled for the first time accurate evaluation of the KSHV transcriptome associated with viral latency in different cell types. Hierarchical clustering applied to a gene correlation matrix identified modules of co-regulated genes with similar correlation profiles, which corresponded with biological and functional similarities of the encoded gene products. Gene modules were differentially upregulated during latency in specific cell types indicating a role for cellular factors associated with differentiated and/or proliferative states of the host cell to influence viral gene expression. PMID:28335496

Early Oscillation Detection for Hybrid DC/DC Converter Fault Diagnosis

NASA Technical Reports Server (NTRS)

Wang, Bright L.

2011-01-01

This paper describes a novel fault detection technique for hybrid DC/DC converter oscillation diagnosis. The technique is based on principles of feedback control loop oscillation and RF signal modulations, and Is realized by using signal spectral analysis. Real-circuit simulation and analytical study reveal critical factors of the oscillation and indicate significant correlations between the spectral analysis method and the gain/phase margin method. A stability diagnosis index (SDI) is developed as a quantitative measure to accurately assign a degree of stability to the DC/DC converter. This technique Is capable of detecting oscillation at an early stage without interfering with DC/DC converter's normal operation and without limitations of probing to the converter.

Automated analysis of plethysmograms for functional studies of hemodynamics

NASA Astrophysics Data System (ADS)

Zatrudina, R. Sh.; Isupov, I. B.; Gribkov, V. Yu.

2018-04-01

The most promising method for the quantitative determination of cardiovascular tone indicators and of cerebral hemodynamics indicators is the method of impedance plethysmography. The accurate determination of these indicators requires the correct identification of the characteristic points in the thoracic impedance plethysmogram and the cranial impedance plethysmogram respectively. An algorithm for automatic analysis of these plethysmogram is presented. The algorithm is based on the hard temporal relationships between the phases of the cardiac cycle and the characteristic points of the plethysmogram. The proposed algorithm does not require estimation of initial data and selection of processing parameters. Use of the method on healthy subjects showed a very low detection error of characteristic points.

Stochastic resonance algorithm applied to quantitative analysis for weak chromatographic signals of alkyl halides and alkyl benzenes in water samples.

PubMed

Xiang, Suyun; Wang, Wei; Xia, Jia; Xiang, Bingren; Ouyang, Pingkai

2009-09-01

The stochastic resonance algorithm is applied to the trace analysis of alkyl halides and alkyl benzenes in water samples. Compared to encountering a single signal when applying the algorithm, the optimization of system parameters for a multicomponent is more complex. In this article, the resolution of adjacent chromatographic peaks is first involved in the optimization of parameters. With the optimized parameters, the algorithm gave an ideal output with good resolution as well as enhanced signal-to-noise ratio. Applying the enhanced signals, the method extended the limit of detection and exhibited good linearity, which ensures accurate determination of the multicomponent.

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…

Breath analysis with broadly tunable quantum cascade lasers.

PubMed

Wörle, Katharina; Seichter, Felicia; Wilk, Andreas; Armacost, Chris; Day, Tim; Godejohann, Matthias; Wachter, Ulrich; Vogt, Josef; Radermacher, Peter; Mizaikoff, Boris

2013-03-05

With the availability of broadly tunable external cavity quantum cascade lasers (EC-QCLs), particularly bright mid-infrared (MIR; 3-20 μm) light sources are available offering high spectral brightness along with an analytically relevant spectral tuning range of >2 μm. Accurate isotope ratio determination of (12)CO2 and (13)CO2 in exhaled breath is of critical importance in the field of breath analysis, which may be addressed via measurements in the MIR spectral regime. Here, we combine for the first time an EC-QCL tunable across the (12)CO2/(13)CO2 spectral band with a miniaturized hollow waveguide gas cell for quantitatively determining the (12)CO2/(13)CO2 ratio within the exhaled breath of mice. Due to partially overlapping spectral features, these studies are augmented by appropriate multivariate data evaluation and calibration techniques based on partial least-squares regression along with optimized data preprocessing. Highly accurate determinations of the isotope ratio within breath samples collected from a mouse intensive care unit validated via hyphenated gas chromatography-mass spectrometry confirm the viability of IR-HWG-EC-QCL sensing techniques for isotope-selective exhaled breath analysis.

Determination of phosphate in natural waters by activation analysis of tungstophosphoric acid

USGS Publications Warehouse

Allen, Herbert E.; Hahn, Richard B.

1969-01-01

Activation analysis may be used to determine quantitatively traces of phosphate in natural waters. Methods based on the reaction 31P(n,γ)32P are subject to interference by sulfur and chlorine which give rise to 32P through n,p and n,α reactions. If the ratio of phosphorus to sulfur or chlorine is small, as it is in most natural waters, accurate analyses by these methods are difficult to achieve. In the activation analysis method, molybdate and tungstate ions are added to samples containing phosphate ion to form tungstomolybdophosphoric acid. The complex is extracted with 2,6-dimethyl-4-heptanone. After activation of an aliquot of the organic phase for 1 hour at a flux of 1013 neutrons per cm2, per second, the gamma spectrum is essentially that of tungsten-187. The induced activity is proportional to the concentration of phosphate in the sample. A test of the method showed it to give accurate results at concentrations of 4 to at least 200 p.p.b. of phosphorus when an aliquot of 100 μl. was activated. By suitable reagent purification, counting for longer times, and activation of larger aliquots, the detection limit could be lowered several hundredfold.

A new LC-MS based method to quantitate exogenous recombinant transferrin in cerebrospinal fluid: a potential approach for pharmacokinetic studies of transferrin-based therapeutics in the central nervous system

PubMed Central

Wang, Shunhai; Bobst, Cedric E.; Kaltashov, Igor A.

2018-01-01

Transferrin (Tf) is an 80 kDa iron-binding protein which is viewed as a promising drug carrier to target the central nervous system due to its ability to penetrate the blood-brain barrier (BBB). Among the many challenges during the development of Tf-based therapeutics, sensitive and accurate quantitation of the administered Tf in cerebrospinal fluid (CSF) remains particularly difficult due to the presence of abundant endogenous Tf. Herein, we describe the development of a new LC-MS based method for sensitive and accurate quantitation of exogenous recombinant human Tf in rat CSF. By taking advantage of a His-tag present in recombinant Tf and applying Ni affinity purification, the exogenous hTf can be greatly enriched from rat CSF, despite the presence of the abundant endogenous protein. Additionally, we applied a newly developed O18-labeling technique that can generate internal standards at the protein level, which greatly improved the accuracy and robustness of quantitation. The developed method was investigated for linearity, accuracy, precision and lower limit of quantitation, all of which met the commonly accepted criteria for bioanalytical method validation. PMID:26307718

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

Monitoring the injured brain: registered, patient specific atlas models to improve accuracy of recovered brain saturation values

NASA Astrophysics Data System (ADS)

Clancy, Michael; Belli, Antonio; Davies, David; Lucas, Samuel J. E.; Su, Zhangjie; Dehghani, Hamid

2015-07-01

The subject of superficial contamination and signal origins remains a widely debated topic in the field of Near Infrared Spectroscopy (NIRS), yet the concept of using the technology to monitor an injured brain, in a clinical setting, poses additional challenges concerning the quantitative accuracy of recovered parameters. Using high density diffuse optical tomography probes, quantitatively accurate parameters from different layers (skin, bone and brain) can be recovered from subject specific reconstruction models. This study assesses the use of registered atlas models for situations where subject specific models are not available. Data simulated from subject specific models were reconstructed using the 8 registered atlas models implementing a regional (layered) parameter recovery in NIRFAST. A 3-region recovery based on the atlas model yielded recovered brain saturation values which were accurate to within 4.6% (percentage error) of the simulated values, validating the technique. The recovered saturations in the superficial regions were not quantitatively accurate. These findings highlight differences in superficial (skin and bone) layer thickness between the subject and atlas models. This layer thickness mismatch was propagated through the reconstruction process decreasing the parameter accuracy.

Robust and fast characterization of OCT-based optical attenuation using a novel frequency-domain algorithm for brain cancer detection

NASA Astrophysics Data System (ADS)

Yuan, Wu; Kut, Carmen; Liang, Wenxuan; Li, Xingde

2017-03-01

Cancer is known to alter the local optical properties of tissues. The detection of OCT-based optical attenuation provides a quantitative method to efficiently differentiate cancer from non-cancer tissues. In particular, the intraoperative use of quantitative OCT is able to provide a direct visual guidance in real time for accurate identification of cancer tissues, especially these without any obvious structural layers, such as brain cancer. However, current methods are suboptimal in providing high-speed and accurate OCT attenuation mapping for intraoperative brain cancer detection. In this paper, we report a novel frequency-domain (FD) algorithm to enable robust and fast characterization of optical attenuation as derived from OCT intensity images. The performance of this FD algorithm was compared with traditional fitting methods by analyzing datasets containing images from freshly resected human brain cancer and from a silica phantom acquired by a 1310 nm swept-source OCT (SS-OCT) system. With graphics processing unit (GPU)-based CUDA C/C++ implementation, this new attenuation mapping algorithm can offer robust and accurate quantitative interpretation of OCT images in real time during brain surgery.

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

Numerical simulation of magmatic hydrothermal systems

USGS Publications Warehouse

Ingebritsen, S.E.; Geiger, S.; Hurwitz, S.; Driesner, T.

2010-01-01

The dynamic behavior of magmatic hydrothermal systems entails coupled and nonlinear multiphase flow, heat and solute transport, and deformation in highly heterogeneous media. Thus, quantitative analysis of these systems depends mainly on numerical solution of coupled partial differential equations and complementary equations of state (EOS). The past 2 decades have seen steady growth of computational power and the development of numerical models that have eliminated or minimized the need for various simplifying assumptions. Considerable heuristic insight has been gained from process-oriented numerical modeling. Recent modeling efforts employing relatively complete EOS and accurate transport calculations have revealed dynamic behavior that was damped by linearized, less accurate models, including fluid property control of hydrothermal plume temperatures and three-dimensional geometries. Other recent modeling results have further elucidated the controlling role of permeability structure and revealed the potential for significant hydrothermally driven deformation. Key areas for future reSearch include incorporation of accurate EOS for the complete H2O-NaCl-CO2 system, more realistic treatment of material heterogeneity in space and time, realistic description of large-scale relative permeability behavior, and intercode benchmarking comparisons. Copyright 2010 by the American Geophysical Union.

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

NASA Astrophysics Data System (ADS)

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

2013-02-01

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

Multifactorial Optimization of Contrast-Enhanced Nanofocus Computed Tomography for Quantitative Analysis of Neo-Tissue Formation in Tissue Engineering Constructs.

PubMed

Sonnaert, Maarten; Kerckhofs, Greet; Papantoniou, Ioannis; Van Vlierberghe, Sandra; Boterberg, Veerle; Dubruel, Peter; Luyten, Frank P; Schrooten, Jan; Geris, Liesbet

2015-01-01

To progress the fields of tissue engineering (TE) and regenerative medicine, development of quantitative methods for non-invasive three dimensional characterization of engineered constructs (i.e. cells/tissue combined with scaffolds) becomes essential. In this study, we have defined the most optimal staining conditions for contrast-enhanced nanofocus computed tomography for three dimensional visualization and quantitative analysis of in vitro engineered neo-tissue (i.e. extracellular matrix containing cells) in perfusion bioreactor-developed Ti6Al4V constructs. A fractional factorial 'design of experiments' approach was used to elucidate the influence of the staining time and concentration of two contrast agents (Hexabrix and phosphotungstic acid) and the neo-tissue volume on the image contrast and dataset quality. Additionally, the neo-tissue shrinkage that was induced by phosphotungstic acid staining was quantified to determine the operating window within which this contrast agent can be accurately applied. For Hexabrix the staining concentration was the main parameter influencing image contrast and dataset quality. Using phosphotungstic acid the staining concentration had a significant influence on the image contrast while both staining concentration and neo-tissue volume had an influence on the dataset quality. The use of high concentrations of phosphotungstic acid did however introduce significant shrinkage of the neo-tissue indicating that, despite sub-optimal image contrast, low concentrations of this staining agent should be used to enable quantitative analysis. To conclude, design of experiments allowed us to define the most optimal staining conditions for contrast-enhanced nanofocus computed tomography to be used as a routine screening tool of neo-tissue formation in Ti6Al4V constructs, transforming it into a robust three dimensional quality control methodology.

A novel LCMSMS method for quantitative measurement of short-chain fatty acids in human stool derivatized with 12C- and 13C-labelled aniline.

PubMed

Chan, James Chun Yip; Kioh, Dorinda Yan Qin; Yap, Gaik Chin; Lee, Bee Wah; Chan, Eric Chun Yong

2017-05-10

A novel liquid chromatography tandem mass spectrometry (LCMSMS) method for the quantitative measurement of gut microbial-derived short-chain fatty acids (SCFAs) in human infant stool has been developed and validated. Baseline chromatographic resolution was achieved for 12 SCFAs (acetic, butyric, caproic, 2,2-dimethylbutyric, 2-ethylbutyric, isobutyric, isovaleric, 2-methylbutyric, 4-methylvaleric, propionic, pivalic and valeric acids) within an analysis time of 15min. A novel sequential derivatization of endogenous and spiked SCFAs in stool via 12 C- and 13 C-aniline respectively, facilitated the accurate quantitation of 12 C-aniline derivatized endogenous SCFAs based on calibration of exogenously 13 C-derivatized SCFAs. Optimized quenching of derivatization agents prior to LCMSMS analysis further reduced to negligible levels the confounding chromatographic peak due to in-line derivatization of unquenched aniline with residual acetic acid present within the LCMS system. The effect of residual acetic acid, a common LCMS modifier, in analysis of SCFAs has not been addressed in previous SCFA assays. For the first time, a total of 9 SCFAs (acetic, butyric, caproic, isobutyric, isovaleric, 2-methylbutyric, 4-methylvaleric, propionic and valeric acids) were detected and quantitated in 107 healthy infant stool samples. The abundance and diversity of SCFAs in infant stool vary temporally from 3 weeks onwards and stabilize towards the end of 12 months. This in turn reflects the maturation of infant SCFA-producing gut microbiota community. In summary, this novel method is applicable to future studies that investigate the biological roles of SCFAs in paediatric health and diseases. Copyright © 2017 Elsevier B.V. All rights reserved.

A Focused Multiple Reaction Monitoring (MRM) Quantitative Method for Bioactive Grapevine Stilbenes by Ultra-High-Performance Liquid Chromatography Coupled to Triple-Quadrupole Mass Spectrometry (UHPLC-QqQ).

PubMed

Hurtado-Gaitán, Elías; Sellés-Marchart, Susana; Martínez-Márquez, Ascensión; Samper-Herrero, Antonio; Bru-Martínez, Roque

2017-03-07

Grapevine stilbenes are a family of polyphenols which derive from trans -resveratrol having antifungal and antimicrobial properties, thus being considered as phytoalexins. In addition to their diverse bioactive properties in animal models, they highlight a strong potential in human health maintenance and promotion. Due to this relevance, highly-specific qualitative and quantitative methods of analysis are necessary to accurately analyze stilbenes in different matrices derived from grapevine. Here, we developed a rapid, sensitive, and specific analysis method using ultra-high-performance liquid chromatography coupled to triple-quadrupole mass spectrometry (UHPLC-QqQ) in MRM mode to detect and quantify five grapevine stilbenes, trans -resveratrol, trans -piceid, trans -piceatannol, trans -pterostilbene, and trans -ε-viniferin, whose interest in relation to human health is continuously growing. The method was optimized to minimize in-source fragmentation of piceid and to avoid co-elution of cis -piceid and trans -resveratrol, as both are detected with resveratrol transitions. The applicability of the developed method of stilbene analysis was tested successfully in different complex matrices including cellular extracts of Vitis vinifera cell cultures, reaction media of biotransformation assays, and red wine.

Recent trends in analytical procedures in forensic toxicology.

PubMed

Van Bocxlaer, Jan F

2005-12-01

Forensic toxicology is a very demanding discipline,heavily dependent on good analytical techniques. That is why new trends appear continuously. In the past years. LC-MS has revolutionized target compound analysis and has become the trend, also in toxicology. In LC-MS screening analysis, things are less straightforward and several approaches exist. One promising approach based on accurate LC-MSTOF mass measurements and elemental formula based library searches is discussed. This way of screening has already proven its applicability but at the same time it became obvious that a single accurate mass measurement lacks some specificity when using large compound libraries. CE too is a reemerging approach. The increasingly polar and ionic molecules encountered make it a worthwhile addition to e.g. LC, as illustrated for the analysis of GHB. A third recent trend is the use of MALDI mass spectrometry for small molecules. It is promising for its ease-of-use and high throughput. Unfortunately, re-ports of disappointment but also accomplishment, e.g. the quantitative analysis of LSD as discussed here, alternate, and it remains to be seen whether MALDI really will establish itself. Indeed, not all new trends will prove themselves but the mere fact that many appear in the world of analytical toxicology nowadays is, in itself, encouraging for the future of (forensic) toxicology.

Understanding the detection of carbon in austenitic high-Mn steel using atom probe tomography.

PubMed

Marceau, R K W; Choi, P; Raabe, D

2013-09-01

A high-Mn TWIP steel having composition Fe-22Mn-0.6C (wt%) is considered in this study, where the need for accurate and quantitative analysis of clustering and short-range ordering by atom probe analysis requires a better understanding of the detection of carbon in this system. Experimental measurements reveal that a high percentage of carbon atoms are detected as molecular ion species and on multiple hit events, which is discussed with respect to issues such as optimal experimental parameters, correlated field evaporation and directional walk/migration of carbon atoms at the surface of the specimen tip during analysis. These phenomena impact the compositional and spatial accuracy of the atom probe measurement and thus require careful consideration for further cluster-finding analysis. Copyright © 2013 Elsevier B.V. All rights reserved.

Real time myocardial contrast echocardiography during supine bicycle stress and continuous infusion of contrast agent. Cutoff values for myocardial contrast replenishment discriminating abnormal myocardial perfusion.

PubMed

Miszalski-Jamka, Tomasz; Kuntz-Hehner, Stefanie; Schmidt, Harald; Hammerstingl, Christoph; Tiemann, Klaus; Ghanem, Alexander; Troatz, Clemens; Lüderitz, Berndt; Omran, Heyder

2007-07-01

Myocardial contrast echocardiography (MCE) is a new imaging modality for diagnosing coronary artery disease (CAD). The aim of our study was to evaluate feasibility of qualitative myocardial contrast replenishment (RP) assessment during supine bicycle stress MCE and find out cutoff values for such analysis, which could allow accurate detection of CAD. Forty-four consecutive patients, scheduled for coronary angiography (CA) underwent supine bicycle stress two-dimensional echocardiography (2DE). During the same session, MCE was performed at peak stress and post stress. Ultrasound contrast agent (SonoVue) was administered in continuous mode using an infusion pump (BR-INF 100, Bracco Research). Seventeen-segment model of left ventricle was used in analysis. MCE was assessed off-line in terms of myocardial contrast opacification and RP. RP was evaluated on the basis of the number of cardiac cycles required to refill the segment with contrast after its prior destruction with high-power frames. Determination of cutoff values for RP assessment was performed by means of reference intervals and receiver operating characteristic analysis. Quantitative CA was carried out using CAAS system. MCE could be assessed in 42 patients. CA revealed CAD in 25 patients. Calculated cutoff values for RP-analysis (peak-stress RP >3 cardiac cycles and difference between peak stress and post stress RP >0 cardiac cycles) provided sensitive (88%) and accurate (88%) detection of CAD. Sensitivity and accuracy of 2DE were 76% and 79%, respectively. Qualitative RP-analysis based on the number of cardiac cycles required to refill myocardium with contrast is feasible during supine bicycle stress MCE and enables accurate detection of CAD.

Accurate quantification of chromosomal lesions via short tandem repeat analysis using minimal amounts of DNA

PubMed Central

Jann, Johann-Christoph; Nowak, Daniel; Nolte, Florian; Fey, Stephanie; Nowak, Verena; Obländer, Julia; Pressler, Jovita; Palme, Iris; Xanthopoulos, Christina; Fabarius, Alice; Platzbecker, Uwe; Giagounidis, Aristoteles; Götze, Katharina; Letsch, Anne; Haase, Detlef; Schlenk, Richard; Bug, Gesine; Lübbert, Michael; Ganser, Arnold; Germing, Ulrich; Haferlach, Claudia; Hofmann, Wolf-Karsten; Mossner, Maximilian

2017-01-01

Background Cytogenetic aberrations such as deletion of chromosome 5q (del(5q)) represent key elements in routine clinical diagnostics of haematological malignancies. Currently established methods such as metaphase cytogenetics, FISH or array-based approaches have limitations due to their dependency on viable cells, high costs or semi-quantitative nature. Importantly, they cannot be used on low abundance DNA. We therefore aimed to establish a robust and quantitative technique that overcomes these shortcomings. Methods For precise determination of del(5q) cell fractions, we developed an inexpensive multiplex-PCR assay requiring only nanograms of DNA that simultaneously measures allelic imbalances of 12 independent short tandem repeat markers. Results Application of this method to n=1142 samples from n=260 individuals revealed strong intermarker concordance (R²=0.77–0.97) and reproducibility (mean SD: 1.7%). Notably, the assay showed accurate quantification via standard curve assessment (R²>0.99) and high concordance with paired FISH measurements (R²=0.92) even with subnanogram amounts of DNA. Moreover, cytogenetic response was reliably confirmed in del(5q) patients with myelodysplastic syndromes treated with lenalidomide. While the assay demonstrated good diagnostic accuracy in receiver operating characteristic analysis (area under the curve: 0.97), we further observed robust correlation between bone marrow and peripheral blood samples (R²=0.79), suggesting its potential suitability for less-invasive clonal monitoring. Conclusions In conclusion, we present an adaptable tool for quantification of chromosomal aberrations, particularly in problematic samples, which should be easily applicable to further tumour entities. PMID:28600436

Estimation of whole body fat from appendicular soft tissue from peripheral quantitative computed tomography in adolescent girls

PubMed Central

Lee, Vinson R.; Blew, Rob M.; Farr, Josh N.; Tomas, Rita; Lohman, Timothy G.; Going, Scott B.

2013-01-01

Objective Assess the utility of peripheral quantitative computed tomography (pQCT) for estimating whole body fat in adolescent girls. Research Methods and Procedures Our sample included 458 girls (aged 10.7 ± 1.1y, mean BMI = 18.5 ± 3.3 kg/m2) who had DXA scans for whole body percent fat (DXA %Fat). Soft tissue analysis of pQCT scans provided thigh and calf subcutaneous percent fat and thigh and calf muscle density (muscle fat content surrogates). Anthropometric variables included weight, height and BMI. Indices of maturity included age and maturity offset. The total sample was split into validation (VS; n = 304) and cross-validation (CS; n = 154) samples. Linear regression was used to develop prediction equations for estimating DXA %Fat from anthropometric variables and pQCT-derived soft tissue components in VS and the best prediction equation was applied to CS. Results Thigh and calf SFA %Fat were positively correlated with DXA %Fat (r = 0.84 to 0.85; p <0.001) and thigh and calf muscle densities were inversely related to DXA %Fat (r = −0.30 to −0.44; p < 0.001). The best equation for estimating %Fat included thigh and calf SFA %Fat and thigh and calf muscle density (adj. R2 = 0.90; SEE = 2.7%). Bland-Altman analysis in CS showed accurate estimates of percent fat (adj. R2 = 0.89; SEE = 2.7%) with no bias. Discussion Peripheral QCT derived indices of adiposity can be used to accurately estimate whole body percent fat in adolescent girls. PMID:25147482

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

NASA Astrophysics Data System (ADS)

Pu, Fei; Yang, Bingye; Ke, Caihuan

2015-07-01

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

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

Movement Correction Method for Human Brain PET Images: Application to Quantitative Analysis of Dynamic [18F]-FDDNP Scans

PubMed Central

Wardak, Mirwais; Wong, Koon-Pong; Shao, Weber; Dahlbom, Magnus; Kepe, Vladimir; Satyamurthy, Nagichettiar; Small, Gary W.; Barrio, Jorge R.; Huang, Sung-Cheng

2010-01-01

Head movement during a PET scan (especially, dynamic scan) can affect both the qualitative and quantitative aspects of an image, making it difficult to accurately interpret the results. The primary objective of this study was to develop a retrospective image-based movement correction (MC) method and evaluate its implementation on dynamic [18F]-FDDNP PET images of cognitively intact controls and patients with Alzheimer’s disease (AD). Methods Dynamic [18F]-FDDNP PET images, used for in vivo imaging of beta-amyloid plaques and neurofibrillary tangles, were obtained from 12 AD and 9 age-matched controls. For each study, a transmission scan was first acquired for attenuation correction. An accurate retrospective MC method that corrected for transmission-emission misalignment as well as emission-emission misalignment was applied to all studies. No restriction was assumed for zero movement between the transmission scan and first emission scan. Logan analysis with cerebellum as the reference region was used to estimate various regional distribution volume ratio (DVR) values in the brain before and after MC. Discriminant analysis was used to build a predictive model for group membership, using data with and without MC. Results MC improved the image quality and quantitative values in [18F]-FDDNP PET images. In this subject population, medial temporal (MTL) did not show a significant difference between controls and AD before MC. However, after MC, significant differences in DVR values were seen in frontal, parietal, posterior cingulate (PCG), MTL, lateral temporal (LTL), and global between the two groups (P < 0.05). In controls and AD, the variability of regional DVR values (as measured by the coefficient of variation) decreased on average by >18% after MC. Mean DVR separation between controls and ADs was higher in frontal, MTL, LTL and global after MC. Group classification by discriminant analysis based on [18F]-FDDNP DVR values was markedly improved after MC. Conclusion The streamlined and easy to use MC method presented in this work significantly improves the image quality and the measured tracer kinetics of [18F]-FDDNP PET images. The proposed MC method has the potential to be applied to PET studies on patients having other disorders (e.g., Down syndrome and Parkinson’s disease) and to brain PET scans with other molecular imaging probes. PMID:20080894

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.

Estimation of L-dopa from Mucuna pruriens LINN and formulations containing M. pruriens by HPTLC method.

PubMed

Modi, Ketan Pravinbhai; Patel, Natvarlal Manilal; Goyal, Ramesh Kishorilal

2008-03-01

A selective, precise, and accurate high-performance thin-layer chromatographic (HPTLC) method has been developed for the analysis of L-dopa in Mucuna pruriens seed extract and its formulations. The method involves densitometric evaluation of L-dopa after resolving it by HPTLC on silica gel plates with n-butanol-acetic acid-water (4.0+1.0+1.0, v/v) as the mobile phase. Densitometric analysis of L-dopa was carried out in the absorbance mode at 280 nm. The relationship between the concentration of L-dopa and corresponding peak areas was found to be linear in the range of 100 to 1200 ng/spot. The method was validated for precision (inter and intraday), repeatability, and accuracy. Mean recovery was 100.30%. The relative standard deviation (RSD) values of the precision were found to be in the range 0.64-1.52%. In conclusion, the proposed TLC method was found to be precise, specific and accurate and can be used for identification and quantitative determination of L-dopa in herbal extract and its formulations.

Non-lambertian reflectance modeling and shape recovery of faces using tensor splines.

PubMed

Kumar, Ritwik; Barmpoutis, Angelos; Banerjee, Arunava; Vemuri, Baba C

2011-03-01

Modeling illumination effects and pose variations of a face is of fundamental importance in the field of facial image analysis. Most of the conventional techniques that simultaneously address both of these problems work with the Lambertian assumption and thus fall short of accurately capturing the complex intensity variation that the facial images exhibit or recovering their 3D shape in the presence of specularities and cast shadows. In this paper, we present a novel Tensor-Spline-based framework for facial image analysis. We show that, using this framework, the facial apparent BRDF field can be accurately estimated while seamlessly accounting for cast shadows and specularities. Further, using local neighborhood information, the same framework can be exploited to recover the 3D shape of the face (to handle pose variation). We quantitatively validate the accuracy of the Tensor Spline model using a more general model based on the mixture of single-lobed spherical functions. We demonstrate the effectiveness of our technique by presenting extensive experimental results for face relighting, 3D shape recovery, and face recognition using the Extended Yale B and CMU PIE benchmark data sets.

Low-dose CT for quantitative analysis in acute respiratory distress syndrome

PubMed Central

2013-01-01

Introduction The clinical use of serial quantitative computed tomography (CT) to characterize lung disease and guide the optimization of mechanical ventilation in patients with acute respiratory distress syndrome (ARDS) is limited by the risk of cumulative radiation exposure and by the difficulties and risks related to transferring patients to the CT room. We evaluated the effects of tube current-time product (mAs) variations on quantitative results in healthy lungs and in experimental ARDS in order to support the use of low-dose CT for quantitative analysis. Methods In 14 sheep chest CT was performed at baseline and after the induction of ARDS via intravenous oleic acid injection. For each CT session, two consecutive scans were obtained applying two different mAs: 60 mAs was paired with 140, 15 or 7.5 mAs. All other CT parameters were kept unaltered (tube voltage 120 kVp, collimation 32 × 0.5 mm, pitch 0.85, matrix 512 × 512, pixel size 0.625 × 0.625 mm). Quantitative results obtained at different mAs were compared via Bland-Altman analysis. Results Good agreement was observed between 60 mAs and 140 mAs and between 60 mAs and 15 mAs (all biases less than 1%). A further reduction of mAs to 7.5 mAs caused an increase in the bias of poorly aerated and nonaerated tissue (-2.9% and 2.4%, respectively) and determined a significant widening of the limits of agreement for the same compartments (-10.5% to 4.8% for poorly aerated tissue and -5.9% to 10.8% for nonaerated tissue). Estimated mean effective dose at 140, 60, 15 and 7.5 mAs corresponded to 17.8, 7.4, 2.0 and 0.9 mSv, respectively. Image noise of scans performed at 140, 60, 15 and 7.5 mAs corresponded to 10, 16, 38 and 74 Hounsfield units, respectively. Conclusions A reduction of effective dose up to 70% has been achieved with minimal effects on lung quantitative results. Low-dose computed tomography provides accurate quantitative results and could be used to characterize lung compartment distribution and possibly monitor time-course of ARDS with a lower risk of exposure to ionizing radiation. A further radiation dose reduction is associated with lower accuracy in quantitative results. PMID:24004842

Quantitative analysis of low-density SNP data for parentage assignment and estimation of family contributions to pooled samples.

PubMed

Henshall, John M; Dierens, Leanne; Sellars, Melony J

2014-09-02

While much attention has focused on the development of high-density single nucleotide polymorphism (SNP) assays, the costs of developing and running low-density assays have fallen dramatically. This makes it feasible to develop and apply SNP assays for agricultural species beyond the major livestock species. Although low-cost low-density assays may not have the accuracy of the high-density assays widely used in human and livestock species, we show that when combined with statistical analysis approaches that use quantitative instead of discrete genotypes, their utility may be improved. The data used in this study are from a 63-SNP marker Sequenom® iPLEX Platinum panel for the Black Tiger shrimp, for which high-density SNP assays are not currently available. For quantitative genotypes that could be estimated, in 5% of cases the most likely genotype for an individual at a SNP had a probability of less than 0.99. Matrix formulations of maximum likelihood equations for parentage assignment were developed for the quantitative genotypes and also for discrete genotypes perturbed by an assumed error term. Assignment rates that were based on maximum likelihood with quantitative genotypes were similar to those based on maximum likelihood with perturbed genotypes but, for more than 50% of cases, the two methods resulted in individuals being assigned to different families. Treating genotypes as quantitative values allows the same analysis framework to be used for pooled samples of DNA from multiple individuals. Resulting correlations between allele frequency estimates from pooled DNA and individual samples were consistently greater than 0.90, and as high as 0.97 for some pools. Estimates of family contributions to the pools based on quantitative genotypes in pooled DNA had a correlation of 0.85 with estimates of contributions from DNA-derived pedigree. Even with low numbers of SNPs of variable quality, parentage testing and family assignment from pooled samples are sufficiently accurate to provide useful information for a breeding program. Treating genotypes as quantitative values is an alternative to perturbing genotypes using an assumed error distribution, but can produce very different results. An understanding of the distribution of the error is required for SNP genotyping platforms.

Validation of HPLC and UV spectrophotometric methods for the determination of meropenem in pharmaceutical dosage form.

PubMed

Mendez, Andreas S L; Steppe, Martin; Schapoval, Elfrides E S

2003-12-04

A high-performance liquid chromatographic method and a UV spectrophotometric method for the quantitative determination of meropenem, a highly active carbapenem antibiotic, in powder for injection were developed in present work. The parameters linearity, precision, accuracy, specificity, robustness, limit of detection and limit of quantitation were studied according to International Conference on Harmonization guidelines. Chromatography was carried out by reversed-phase technique on an RP-18 column with a mobile phase composed of 30 mM monobasic phosphate buffer and acetonitrile (90:10; v/v), adjusted to pH 3.0 with orthophosphoric acid. The UV spectrophotometric method was performed at 298 nm. The samples were prepared in water and the stability of meropenem in aqueous solution at 4 and 25 degrees C was studied. The results were satisfactory with good stability after 24 h at 4 degrees C. Statistical analysis by Student's t-test showed no significant difference between the results obtained by the two methods. The proposed methods are highly sensitive, precise and accurate and can be used for the reliable quantitation of meropenem in pharmaceutical dosage form.

A preamplification approach to GMO detection in processed foods.

PubMed

Del Gaudio, S; Cirillo, A; Di Bernardo, G; Galderisi, U; Cipollaro, M

2010-03-01

DNA is widely used as a target for GMO analysis because of its stability and high detectability. Real-time PCR is the method routinely used in most analytical laboratories due to its quantitative performance and great sensitivity. Accurate DNA detection and quantification is dependent on the specificity and sensitivity of the amplification protocol as well as on the quality and quantity of the DNA used in the PCR reaction. In order to enhance the sensitivity of real-time PCR and consequently expand the number of analyzable target genes, we applied a preamplification technique to processed foods where DNA can be present in low amounts and/or in degraded forms thereby affecting the reliability of qualitative and quantitative results. The preamplification procedure utilizes a pool of primers targeting genes of interest and is followed by real-time PCR reactions specific for each gene. An improvement of Ct values was found comparing preamplified vs. non-preamplified DNA. The strategy reported in the present study will be also applicable to other fields requiring quantitative DNA testing by real-time PCR.

Targeted proteomics coming of age - SRM, PRM and DIA performance evaluated from a core facility perspective.

PubMed

Kockmann, Tobias; Trachsel, Christian; Panse, Christian; Wahlander, Asa; Selevsek, Nathalie; Grossmann, Jonas; Wolski, Witold E; Schlapbach, Ralph

2016-08-01

Quantitative mass spectrometry is a rapidly evolving methodology applied in a large number of omics-type research projects. During the past years, new designs of mass spectrometers have been developed and launched as commercial systems while in parallel new data acquisition schemes and data analysis paradigms have been introduced. Core facilities provide access to such technologies, but also actively support the researchers in finding and applying the best-suited analytical approach. In order to implement a solid fundament for this decision making process, core facilities need to constantly compare and benchmark the various approaches. In this article we compare the quantitative accuracy and precision of current state of the art targeted proteomics approaches single reaction monitoring (SRM), parallel reaction monitoring (PRM) and data independent acquisition (DIA) across multiple liquid chromatography mass spectrometry (LC-MS) platforms, using a readily available commercial standard sample. All workflows are able to reproducibly generate accurate quantitative data. However, SRM and PRM workflows show higher accuracy and precision compared to DIA approaches, especially when analyzing low concentrated analytes. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

GLS-Finder: A Platform for Fast Profiling of Glucosinolates in Brassica Vegetables.

PubMed

Sun, Jianghao; Zhang, Mengliang; Chen, Pei

2016-06-01

Mass spectrometry combined with related tandem techniques has become the most popular method for plant secondary metabolite characterization. We introduce a new strategy based on in-database searching, mass fragmentation behavior study, formula predicting for fast profiling of glucosinolates, a class of important compounds in brassica vegetables. A MATLAB script-based expert system computer program, "GLS-Finder", was developed. It is capable of qualitative and semi-quantitative analyses of glucosinolates in samples using data generated by ultrahigh-performance liquid chromatography-high-resolution accurate mass with multi-stage mass fragmentation (UHPLC-HRAM/MS(n)). A suite of bioinformatic tools was integrated into the "GLS-Finder" to perform raw data deconvolution, peak alignment, glucosinolate putative assignments, semi-quantitation, and unsupervised principal component analysis (PCA). GLS-Finder was successfully applied to identify intact glucosinolates in 49 commonly consumed Brassica vegetable samples in the United States. It is believed that this work introduces a new way of fast data processing and interpretation for qualitative and quantitative analyses of glucosinolates, where great efficacy was improved in comparison to identification manually.

Effect of Diffusion Limitations on Multianalyte Determination from Biased Biosensor Response

PubMed Central

Baronas, Romas; Kulys, Juozas; Lančinskas, Algirdas; Žilinskas, Antanas

2014-01-01

The optimization-based quantitative determination of multianalyte concentrations from biased biosensor responses is investigated under internal and external diffusion-limited conditions. A computational model of a biocatalytic amperometric biosensor utilizing a mono-enzyme-catalyzed (nonspecific) competitive conversion of two substrates was used to generate pseudo-experimental responses to mixtures of compounds. The influence of possible perturbations of the biosensor signal, due to a white noise- and temperature-induced trend, on the precision of the concentration determination has been investigated for different configurations of the biosensor operation. The optimization method was found to be suitable and accurate enough for the quantitative determination of the concentrations of the compounds from a given biosensor transient response. The computational experiments showed a complex dependence of the precision of the concentration estimation on the relative thickness of the outer diffusion layer, as well as on whether the biosensor operates under diffusion- or kinetics-limited conditions. When the biosensor response is affected by the induced exponential trend, the duration of the biosensor action can be optimized for increasing the accuracy of the quantitative analysis. PMID:24608006

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.

Biological Matrix Effects in Quantitative Tandem Mass Spectrometry-Based Analytical Methods: Advancing Biomonitoring

PubMed Central

Panuwet, Parinya; Hunter, Ronald E.; D’Souza, Priya E.; Chen, Xianyu; Radford, Samantha A.; Cohen, Jordan R.; Marder, M. Elizabeth; Kartavenka, Kostya; Ryan, P. Barry; Barr, Dana Boyd

2015-01-01

The ability to quantify levels of target analytes in biological samples accurately and precisely, in biomonitoring, involves the use of highly sensitive and selective instrumentation such as tandem mass spectrometers and a thorough understanding of highly variable matrix effects. Typically, matrix effects are caused by co-eluting matrix components that alter the ionization of target analytes as well as the chromatographic response of target analytes, leading to reduced or increased sensitivity of the analysis. Thus, before the desired accuracy and precision standards of laboratory data are achieved, these effects must be characterized and controlled. Here we present our review and observations of matrix effects encountered during the validation and implementation of tandem mass spectrometry-based analytical methods. We also provide systematic, comprehensive laboratory strategies needed to control challenges posed by matrix effects in order to ensure delivery of the most accurate data for biomonitoring studies assessing exposure to environmental toxicants. PMID:25562585

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.

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 functions and how these functions were acquired in cells from different organisms or species. A public web interface of PLAST is available at http://plast.bii.a-star.edu.sg.

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 functions and how these functions were acquired in cells from different organisms or species. A public web interface of PLAST is available at http://plast.bii.a-star.edu.sg. PMID:24603469

SPECHT - single-stage phosphopeptide enrichment and stable-isotope chemical tagging: quantitative phosphoproteomics of insulin action in muscle.

PubMed

Kettenbach, Arminja N; Sano, Hiroyuki; Keller, Susanna R; Lienhard, Gustav E; Gerber, Scott A

2015-01-30

The study of cellular signaling remains a significant challenge for translational and clinical research. In particular, robust and accurate methods for quantitative phosphoproteomics in tissues and tumors represent significant hurdles for such efforts. In the present work, we design, implement and validate a method for single-stage phosphopeptide enrichment and stable isotope chemical tagging, or SPECHT, that enables the use of iTRAQ, TMT and/or reductive dimethyl-labeling strategies to be applied to phosphoproteomics experiments performed on primary tissue. We develop and validate our approach using reductive dimethyl-labeling and HeLa cells in culture, and find these results indistinguishable from data generated from more traditional SILAC-labeled HeLa cells mixed at the cell level. We apply the SPECHT approach to the quantitative analysis of insulin signaling in a murine myotube cell line and muscle tissue, identify known as well as new phosphorylation events, and validate these phosphorylation sites using phospho-specific antibodies. Taken together, our work validates chemical tagging post-single-stage phosphoenrichment as a general strategy for studying cellular signaling in primary tissues. Through the use of a quantitatively reproducible, proteome-wide phosphopeptide enrichment strategy, we demonstrated the feasibility of post-phosphopeptide purification chemical labeling and tagging as an enabling approach for quantitative phosphoproteomics of primary tissues. Using reductive dimethyl labeling as a generalized chemical tagging strategy, we compared the performance of post-phosphopeptide purification chemical tagging to the well established community standard, SILAC, in insulin-stimulated tissue culture cells. We then extended our method to the analysis of low-dose insulin signaling in murine muscle tissue, and report on the analytical and biological significance of our results. Copyright © 2014 Elsevier B.V. All rights reserved.

Quantitative study of FORC diagrams in thermally corrected Stoner- Wohlfarth nanoparticles systems

NASA Astrophysics Data System (ADS)

De Biasi, E.; Curiale, J.; Zysler, R. D.

2016-12-01

The use of FORC diagrams is becoming increasingly popular among researchers devoted to magnetism and magnetic materials. However, a thorough interpretation of this kind of diagrams, in order to achieve quantitative information, requires an appropriate model of the studied system. For that reason most of the FORC studies are used for a qualitative analysis. In magnetic systems thermal fluctuations "blur" the signatures of the anisotropy, volume and particle interactions distributions, therefore thermal effects in nanoparticles systems conspire against a proper interpretation and analysis of these diagrams. Motivated by this fact, we have quantitatively studied the degree of accuracy of the information extracted from FORC diagrams for the special case of single-domain thermal corrected Stoner- Wohlfarth (easy axes along the external field orientation) nanoparticles systems. In this work, the starting point is an analytical model that describes the behavior of a magnetic nanoparticles system as a function of field, anisotropy, temperature and measurement time. In order to study the quantitative degree of accuracy of our model, we built FORC diagrams for different archetypical cases of magnetic nanoparticles. Our results show that from the quantitative information obtained from the diagrams, under the hypotheses of the proposed model, is possible to recover the features of the original system with accuracy above 95%. This accuracy is improved at low temperatures and also it is possible to access to the anisotropy distribution directly from the FORC coercive field profile. Indeed, our simulations predict that the volume distribution plays a secondary role being the mean value and its deviation the only important parameters. Therefore it is possible to obtain an accurate result for the inversion and interaction fields despite the features of the volume distribution.

Surrogate matrix and surrogate analyte approaches for definitive quantitation of endogenous biomolecules.

PubMed

Jones, Barry R; Schultz, Gary A; Eckstein, James A; Ackermann, Bradley L

2012-10-01

Quantitation of biomarkers by LC-MS/MS is complicated by the presence of endogenous analytes. This challenge is most commonly overcome by calibration using an authentic standard spiked into a surrogate matrix devoid of the target analyte. A second approach involves use of a stable-isotope-labeled standard as a surrogate analyte to allow calibration in the actual biological matrix. For both methods, parallelism between calibration standards and the target analyte in biological matrix must be demonstrated in order to ensure accurate quantitation. In this communication, the surrogate matrix and surrogate analyte approaches are compared for the analysis of five amino acids in human plasma: alanine, valine, methionine, leucine and isoleucine. In addition, methodology based on standard addition is introduced, which enables a robust examination of parallelism in both surrogate analyte and surrogate matrix methods prior to formal validation. Results from additional assays are presented to introduce the standard-addition methodology and to highlight the strengths and weaknesses of each approach. For the analysis of amino acids in human plasma, comparable precision and accuracy were obtained by the surrogate matrix and surrogate analyte methods. Both assays were well within tolerances prescribed by regulatory guidance for validation of xenobiotic assays. When stable-isotope-labeled standards are readily available, the surrogate analyte approach allows for facile method development. By comparison, the surrogate matrix method requires greater up-front method development; however, this deficit is offset by the long-term advantage of simplified sample analysis.

Evaluation of laser diode thermal desorption-tandem mass spectrometry (LDTD-MS-MS) in forensic toxicology.

PubMed

Bynum, Nichole D; Moore, Katherine N; Grabenauer, Megan

2014-10-01

Many forensic laboratories experience backlogs due to increased drug-related cases. Laser diode thermal desorption (LDTD) has demonstrated its applicability in other scientific areas by providing data comparable with instrumentation, such as liquid chromatography-tandem mass spectrometry, in less time. LDTD-MS-MS was used to validate 48 compounds in drug-free human urine and blood for screening or quantitative analysis. Carryover, interference, limit of detection, limit of quantitation, matrix effect, linearity, precision and accuracy and stability were evaluated. Quantitative analysis indicated that LDTD-MS-MS produced precise and accurate results with the average overall within-run precision in urine and blood represented by a %CV <14.0 and <7.0, respectively. The accuracy for all drugs in urine ranged from 88.9 to 104.5% and 91.9 to 107.1% in blood. Overall, LDTD has the potential for use in forensic toxicology but before it can be successfully implemented that there are some challenges that must be addressed. Although the advantages of the LDTD system include minimal maintenance and rapid analysis (∼10 s per sample) which makes it ideal for high-throughput forensic laboratories, a major disadvantage is its inability or difficulty analyzing isomers and isobars due to the lack of chromatography without the use of high-resolution MS; therefore, it would be best implemented as a screening technique. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

A Quantitative Comparison of Single-Dye Tracking Analysis Tools Using Monte Carlo Simulations

PubMed Central

McColl, James; Irvine, Kate L.; Davis, Simon J.; Gay, Nicholas J.; Bryant, Clare E.; Klenerman, David

2013-01-01

Single-particle tracking (SPT) is widely used to study processes from membrane receptor organization to the dynamics of RNAs in living cells. While single-dye labeling strategies have the benefit of being minimally invasive, this comes at the expense of data quality; typically a data set of short trajectories is obtained and analyzed by means of the mean square displacements (MSD) or the distribution of the particles’ displacements in a set time interval (jump distance, JD). To evaluate the applicability of both approaches, a quantitative comparison of both methods under typically encountered experimental conditions is necessary. Here we use Monte Carlo simulations to systematically compare the accuracy of diffusion coefficients (D-values) obtained for three cases: one population of diffusing species, two populations with different D-values, and a population switching between two D-values. For the first case we find that the MSD gives more or equally accurate results than the JD analysis (relative errors of D-values <6%). If two diffusing species are present or a particle undergoes a motion change, the JD analysis successfully distinguishes both species (relative error <5%). Finally we apply the JD analysis to investigate the motion of endogenous LPS receptors in live macrophages before and after treatment with methyl-β-cyclodextrin and latrunculin B. PMID:23737978

A quantitative comparison of single-dye tracking analysis tools using Monte Carlo simulations.

PubMed

Weimann, Laura; Ganzinger, Kristina A; McColl, James; Irvine, Kate L; Davis, Simon J; Gay, Nicholas J; Bryant, Clare E; Klenerman, David

2013-01-01

Single-particle tracking (SPT) is widely used to study processes from membrane receptor organization to the dynamics of RNAs in living cells. While single-dye labeling strategies have the benefit of being minimally invasive, this comes at the expense of data quality; typically a data set of short trajectories is obtained and analyzed by means of the mean square displacements (MSD) or the distribution of the particles' displacements in a set time interval (jump distance, JD). To evaluate the applicability of both approaches, a quantitative comparison of both methods under typically encountered experimental conditions is necessary. Here we use Monte Carlo simulations to systematically compare the accuracy of diffusion coefficients (D-values) obtained for three cases: one population of diffusing species, two populations with different D-values, and a population switching between two D-values. For the first case we find that the MSD gives more or equally accurate results than the JD analysis (relative errors of D-values <6%). If two diffusing species are present or a particle undergoes a motion change, the JD analysis successfully distinguishes both species (relative error <5%). Finally we apply the JD analysis to investigate the motion of endogenous LPS receptors in live macrophages before and after treatment with methyl-β-cyclodextrin and latrunculin B.

Development of quantitative security optimization approach for the picture archives and carrying system between a clinic and a rehabilitation center

NASA Astrophysics Data System (ADS)

Haneda, Kiyofumi; Kajima, Toshio; Koyama, Tadashi; Muranaka, Hiroyuki; Dojo, Hirofumi; Aratani, Yasuhiko

2002-05-01

The target of our study is to analyze the level of necessary security requirements, to search for suitable security measures and to optimize security distribution to every portion of the medical practice. Quantitative expression must be introduced to our study, if possible, to enable simplified follow-up security procedures and easy evaluation of security outcomes or results. Using fault tree analysis (FTA), system analysis showed that system elements subdivided into groups by details result in a much more accurate analysis. Such subdivided composition factors greatly depend on behavior of staff, interactive terminal devices, kinds of services provided, and network routes. Security measures were then implemented based on the analysis results. In conclusion, we identified the methods needed to determine the required level of security and proposed security measures for each medical information system, and the basic events and combinations of events that comprise the threat composition factors. Methods for identifying suitable security measures were found and implemented. Risk factors for each basic event, a number of elements for each composition factor, and potential security measures were found. Methods to optimize the security measures for each medical information system were proposed, developing the most efficient distribution of risk factors for basic events.

Investigation of the "true" extraction recovery of analytes from multiple types of tissues and its impact on tissue bioanalysis using two model compounds.

PubMed

Yuan, Long; Ma, Li; Dillon, Lisa; Fancher, R Marcus; Sun, Huadong; Zhu, Mingshe; Lehman-McKeeman, Lois; Aubry, Anne-Françoise; Ji, Qin C

2016-11-16

LC-MS/MS has been widely applied to the quantitative analysis of tissue samples. However, one key remaining issue is that the extraction recovery of analyte from spiked tissue calibration standard and quality control samples (QCs) may not accurately represent the "true" recovery of analyte from incurred tissue samples. This may affect the accuracy of LC-MS/MS tissue bioanalysis. Here, we investigated whether the recovery determined using tissue QCs by LC-MS/MS can accurately represent the "true" recovery from incurred tissue samples using two model compounds: BMS-986104, a S1P 1 receptor modulator drug candidate, and its phosphate metabolite, BMS-986104-P. We first developed a novel acid and surfactant assisted protein precipitation method for the extraction of BMS-986104 and BMS-986104-P from rat tissues, and determined their recoveries using tissue QCs by LC-MS/MS. We then used radioactive incurred samples from rats dosed with 3 H-labeled BMS-986104 to determine the absolute total radioactivity recovery in six different tissues. The recoveries determined using tissue QCs and incurred samples matched with each other very well. The results demonstrated that, in this assay, tissue QCs accurately represented the incurred tissue samples to determine the "true" recovery, and LC-MS/MS assay was accurate for tissue bioanalysis. Another aspect we investigated is how the tissue QCs should be prepared to better represent the incurred tissue samples. We compared two different QC preparation methods (analyte spiked in tissue homogenates or in intact tissues) and demonstrated that the two methods had no significant difference when a good sample preparation was in place. The developed assay showed excellent accuracy and precision, and was successfully applied to the quantitative determination of BMS-986104 and BMS-986104-P in tissues in a rat toxicology study. Copyright © 2016 Elsevier B.V. All rights reserved.

Quantitative analysis of time-resolved microwave conductivity data

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

Reid, Obadiah G.; Moore, David T.; Li, Zhen

Flash-photolysis time-resolved microwave conductivity (fp-TRMC) is a versatile, highly sensitive technique for studying the complex photoconductivity of solution, solid, and gas-phase samples. The purpose of this paper is to provide a standard reference work for experimentalists interested in using microwave conductivity methods to study functional electronic materials, describing how to conduct and calibrate these experiments in order to obtain quantitative results. The main focus of the paper is on calculating the calibration factor, K, which is used to connect the measured change in microwave power absorption to the conductance of the sample. We describe the standard analytical formulae that havemore » been used in the past, and compare them to numerical simulations. This comparison shows that the most widely used analytical analysis of fp-TRMC data systematically under-estimates the transient conductivity by ~60%. We suggest a more accurate semi-empirical way of calibrating these experiments. However, we emphasize that the full numerical calculation is necessary to quantify both transient and steady-state conductance for arbitrary sample properties and geometry.« less

Quantitative analysis of time-resolved microwave conductivity data

DOE PAGES

Reid, Obadiah G.; Moore, David T.; Li, Zhen; ...

2017-11-10

Flash-photolysis time-resolved microwave conductivity (fp-TRMC) is a versatile, highly sensitive technique for studying the complex photoconductivity of solution, solid, and gas-phase samples. The purpose of this paper is to provide a standard reference work for experimentalists interested in using microwave conductivity methods to study functional electronic materials, describing how to conduct and calibrate these experiments in order to obtain quantitative results. The main focus of the paper is on calculating the calibration factor, K, which is used to connect the measured change in microwave power absorption to the conductance of the sample. We describe the standard analytical formulae that havemore » been used in the past, and compare them to numerical simulations. This comparison shows that the most widely used analytical analysis of fp-TRMC data systematically under-estimates the transient conductivity by ~60%. We suggest a more accurate semi-empirical way of calibrating these experiments. However, we emphasize that the full numerical calculation is necessary to quantify both transient and steady-state conductance for arbitrary sample properties and geometry.« less

Quantitative analysis of red wine tannins using Fourier-transform mid-infrared spectrometry.

PubMed

Fernandez, Katherina; Agosin, Eduardo

2007-09-05

Tannin content and composition are critical quality components of red wines. No spectroscopic method assessing these phenols in wine has been described so far. We report here a new method using Fourier transform mid-infrared (FT-MIR) spectroscopy and chemometric techniques for the quantitative analysis of red wine tannins. Calibration models were developed using protein precipitation and phloroglucinolysis as analytical reference methods. After spectra preprocessing, six different predictive partial least-squares (PLS) models were evaluated, including the use of interval selection procedures such as iPLS and CSMWPLS. PLS regression with full-range (650-4000 cm(-1)), second derivative of the spectra and phloroglucinolysis as the reference method gave the most accurate determination for tannin concentration (RMSEC = 2.6%, RMSEP = 9.4%, r = 0.995). The prediction of the mean degree of polymerization (mDP) of the tannins also gave a reasonable prediction (RMSEC = 6.7%, RMSEP = 10.3%, r = 0.958). These results represent the first step in the development of a spectroscopic methodology for the quantification of several phenolic compounds that are critical for wine quality.

Geochemical variations of rare earth elements in Marcellus shale flowback waters and multiple-source cores in the Appalachian Basin

NASA Astrophysics Data System (ADS)

Noack, C.; Jain, J.; Hakala, A.; Schroeder, K.; Dzombak, D. A.; Karamalidis, A.

2013-12-01

Rare earth elements (REE) - encompassing the naturally occurring lanthanides, yttrium, and scandium - are potential tracers for subsurface groundwater-brine flows and geochemical processes. Application of these elements as naturally occurring tracers during shale gas development is reliant on accurate quantitation of trace metals in hypersaline brines. We have modified and validated a liquid-liquid technique for extraction and pre-concentration of REE from saline produced waters from shale gas extraction wells with quantitative analysis by ICP-MS. This method was used to analyze time-series samples of Marcellus shale flowback and produced waters. Additionally, the total REE content of core samples of various strata throughout the Appalachian Basin were determined using HF/HNO3 digestion and ICP-MS analysis. A primary goal of the study is to elucidate systematic geochemical variations as a function of location or shale characteristics. Statistical testing will be performed to study temporal variability of inter-element relationships and explore associations between REE abundance and major solution chemistry. The results of these analyses and discussion of their significance will be presented.

In-house validation of a method for determination of silver nanoparticles in chicken meat based on asymmetric flow field-flow fractionation and inductively coupled plasma mass spectrometric detection.

PubMed

Loeschner, Katrin; Navratilova, Jana; Grombe, Ringo; Linsinger, Thomas P J; Købler, Carsten; Mølhave, Kristian; Larsen, Erik H

2015-08-15

Nanomaterials are increasingly used in food production and packaging, and validated methods for detection of nanoparticles (NPs) in foodstuffs need to be developed both for regulatory purposes and product development. Asymmetric flow field-flow fractionation with inductively coupled plasma mass spectrometric detection (AF(4)-ICP-MS) was applied for quantitative analysis of silver nanoparticles (AgNPs) in a chicken meat matrix following enzymatic sample preparation. For the first time an analytical validation of nanoparticle detection in a food matrix by AF(4)-ICP-MS has been carried out and the results showed repeatable and intermediately reproducible determination of AgNP mass fraction and size. The findings demonstrated the potential of AF(4)-ICP-MS for quantitative analysis of NPs in complex food matrices for use in food monitoring and control. The accurate determination of AgNP size distribution remained challenging due to the lack of certified size standards. Copyright © 2015 Elsevier Ltd. All rights reserved.

Characterization of Colloidal Quantum Dot Ligand Exchange by X-ray Photoelectron Spectroscopy

NASA Astrophysics Data System (ADS)

Atewologun, Ayomide; Ge, Wangyao; Stiff-Roberts, Adrienne D.

2013-05-01

Colloidal quantum dots (CQDs) are chemically synthesized semiconductor nanoparticles with size-dependent wavelength tunability. Chemical synthesis of CQDs involves the attachment of long organic surface ligands to prevent aggregation; however, these ligands also impede charge transport. Therefore, it is beneficial to exchange longer surface ligands for shorter ones for optoelectronic devices. Typical characterization techniques used to analyze surface ligand exchange include Fourier-transform infrared spectroscopy, x-ray diffraction, transmission electron microscopy, and nuclear magnetic resonance spectroscopy, yet these techniques do not provide a simultaneously direct, quantitative, and sensitive method for evaluating surface ligands on CQDs. In contrast, x-ray photoelectron spectroscopy (XPS) can provide nanoscale sensitivity for quantitative analysis of CQD surface ligand exchange. A unique aspect of this work is that a fingerprint is identified for shorter surface ligands by resolving the regional XPS spectrum corresponding to different types of carbon bonds. In addition, a deposition technique known as resonant infrared matrix-assisted pulsed laser evaporation is used to improve the CQD film uniformity such that stronger XPS signals are obtained, enabling more accurate analysis of the ligand exchange process.

Partial volume correction and image segmentation for accurate measurement of standardized uptake value of grey matter in the brain.

PubMed

Bural, Gonca; Torigian, Drew; Basu, Sandip; Houseni, Mohamed; Zhuge, Ying; Rubello, Domenico; Udupa, Jayaram; Alavi, Abass

2015-12-01

Our aim was to explore a novel quantitative method [based upon an MRI-based image segmentation that allows actual calculation of grey matter, white matter and cerebrospinal fluid (CSF) volumes] for overcoming the difficulties associated with conventional techniques for measuring actual metabolic activity of the grey matter. We included four patients with normal brain MRI and fluorine-18 fluorodeoxyglucose (F-FDG)-PET scans (two women and two men; mean age 46±14 years) in this analysis. The time interval between the two scans was 0-180 days. We calculated the volumes of grey matter, white matter and CSF by using a novel segmentation technique applied to the MRI images. We measured the mean standardized uptake value (SUV) representing the whole metabolic activity of the brain from the F-FDG-PET images. We also calculated the white matter SUV from the upper transaxial slices (centrum semiovale) of the F-FDG-PET images. The whole brain volume was calculated by summing up the volumes of the white matter, grey matter and CSF. The global cerebral metabolic activity was calculated by multiplying the mean SUV with total brain volume. The whole brain white matter metabolic activity was calculated by multiplying the mean SUV for the white matter by the white matter volume. The global cerebral metabolic activity only reflects those of the grey matter and the white matter, whereas that of the CSF is zero. We subtracted the global white matter metabolic activity from that of the whole brain, resulting in the global grey matter metabolism alone. We then divided the grey matter global metabolic activity by grey matter volume to accurately calculate the SUV for the grey matter alone. The brain volumes ranged between 1546 and 1924 ml. The mean SUV for total brain was 4.8-7. Total metabolic burden of the brain ranged from 5565 to 9617. The mean SUV for white matter was 2.8-4.1. On the basis of these measurements we generated the grey matter SUV, which ranged from 8.1 to 11.3. The accurate metabolic activity of the grey matter can be calculated using the novel segmentation technique that we applied to MRI. By combining these quantitative data with those generated from F-FDG-PET images we were able to calculate the accurate metabolic activity of the grey matter. These types of measurements will be of great value in accurate analysis of the data from patients with neuropsychiatric disorders.

Dataglove measurement of joint angles in sign language handshapes

PubMed Central

Eccarius, Petra; Bour, Rebecca; Scheidt, Robert A.

2012-01-01

In sign language research, we understand little about articulatory factors involved in shaping phonemic boundaries or the amount (and articulatory nature) of acceptable phonetic variation between handshapes. To date, there exists no comprehensive analysis of handshape based on the quantitative measurement of joint angles during sign production. The purpose of our work is to develop a methodology for collecting and visualizing quantitative handshape data in an attempt to better understand how handshapes are produced at a phonetic level. In this pursuit, we seek to quantify the flexion and abduction angles of the finger joints using a commercial data glove (CyberGlove; Immersion Inc.). We present calibration procedures used to convert raw glove signals into joint angles. We then implement those procedures and evaluate their ability to accurately predict joint angle. Finally, we provide examples of how our recording techniques might inform current research questions. PMID:23997644

Development and Validation of an Enzymatic Method To Determine Stevioside Content from Stevia rebaudiana.

PubMed

Udompaisarn, Somsiri; Arthan, Dumrongkiet; Somana, Jamorn

2017-04-19

An enzymatic method for specific determination of stevioside content was established. Recombinant β-glucosidase BT_3567 (rBT_3567) from Bacteroides thetaiotaomicron HB-13 exhibited selective hydrolysis of stevioside at β-1,2-glycosidic bond to yield rubusoside and glucose. Coupling of this enzyme with glucose oxidase and peroxidase allowed for quantitation of stevioside content in Stevia samples by using a colorimetric-based approach. The series of reactions for stevioside determination can be completed within 1 h at 37 °C. Stevioside determination using the enzymatic assay strongly correlated with results obtained from HPLC quantitation (r 2 = 0.9629, n = 16). The percentages of coefficient variation (CV) of within day (n = 12) and between days (n = 12) assays were lower than 5%, and accuracy ranges were 95-105%. This analysis demonstrates that the enzymatic method developed in this study is specific, easy to perform, accurate, and yields reproducible results.

Label-free distinguishing between neurons and glial cells based on two-photon excited fluorescence signal of neuron perinuclear granules

NASA Astrophysics Data System (ADS)

Du, Huiping; Jiang, Liwei; Wang, Xingfu; Liu, Gaoqiang; Wang, Shu; Zheng, Liqin; Li, Lianhuang; Zhuo, Shuangmu; Zhu, Xiaoqin; Chen, Jianxin

2016-08-01

Neurons and glial cells are two critical cell types of brain tissue. Their accurate identification is important for the diagnosis of psychiatric disorders such as depression and schizophrenia. In this paper, distinguishing between neurons and glial cells by using the two-photon excited fluorescence (TPEF) signals of intracellular intrinsic sources was performed. TPEF microscopy combined with TUJ-1 and GFAP immunostaining and quantitative image analysis demonstrated that the perinuclear granules of neurons in the TPEF images of brain tissue and the primary cultured cortical cells were a unique characteristic of neurons compared to glial cells which can become a quantitative feature to distinguish neurons from glial cells. With the development of miniaturized TPEF microscope (‘two-photon fiberscopes’) imaging devices, TPEF microscopy can be developed into an effective diagnostic and monitoring tool for psychiatric disorders such as depression and schizophrenia.

Simultaneous determination of the HIV nucleoside analogue reverse transcriptase inhibitors lamivudine, didanosine, stavudine, zidovudine and abacavir in human plasma by reversed phase high performance liquid chromatography.

PubMed

Verweij-van Wissen, C P W G M; Aarnoutse, R E; Burger, D M

2005-02-25

A reversed phase high performance liquid chromatography method was developed for the simultaneous quantitative determination of the nucleoside reverse transcriptase inhibitors (NRTIs) lamivudine, didanosine, stavudine, zidovudine and abacavir in plasma. The method involved solid-phase extraction with Oasis MAX cartridges from plasma, followed by high performance liquid chromatography with a SymmetryShield RP 18 column and ultraviolet detection set at a wavelength of 260 nm. The assay was validated over the concentration range of 0.015-5 mg/l for all five NRTIs. The average accuracies for the assay were 92-102%, inter- and intra-day coefficients of variation (CV) were <2.5% and extraction recoveries were higher than 97%. This method proved to be simple, accurate and precise, and is currently in use in our laboratory for the quantitative analysis of NRTIs in plasma.

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

A software suite for the generation and comparison of peptide arrays from sets of data collected by liquid chromatography-mass spectrometry.

PubMed

Li, Xiao-jun; Yi, Eugene C; Kemp, Christopher J; Zhang, Hui; Aebersold, Ruedi

2005-09-01

There is an increasing interest in the quantitative proteomic measurement of the protein contents of substantially similar biological samples, e.g. for the analysis of cellular response to perturbations over time or for the discovery of protein biomarkers from clinical samples. Technical limitations of current proteomic platforms such as limited reproducibility and low throughput make this a challenging task. A new LC-MS-based platform is able to generate complex peptide patterns from the analysis of proteolyzed protein samples at high throughput and represents a promising approach for quantitative proteomics. A crucial component of the LC-MS approach is the accurate evaluation of the abundance of detected peptides over many samples and the identification of peptide features that can stratify samples with respect to their genetic, physiological, or environmental origins. We present here a new software suite, SpecArray, that generates a peptide versus sample array from a set of LC-MS data. A peptide array stores the relative abundance of thousands of peptide features in many samples and is in a format identical to that of a gene expression microarray. A peptide array can be subjected to an unsupervised clustering analysis to stratify samples or to a discriminant analysis to identify discriminatory peptide features. We applied the SpecArray to analyze two sets of LC-MS data: one was from four repeat LC-MS analyses of the same glycopeptide sample, and another was from LC-MS analysis of serum samples of five male and five female mice. We demonstrate through these two study cases that the SpecArray software suite can serve as an effective software platform in the LC-MS approach for quantitative proteomics.

Quantitative assessment of hematopoietic chimerism by quantitative real-time polymerase chain reaction of sequence polymorphism systems after hematopoietic stem cell transplantation.

PubMed

Qin, Xiao-ying; Li, Guo-xuan; Qin, Ya-zhen; Wang, Yu; Wang, Feng-rong; Liu, Dai-hong; Xu, Lan-ping; Chen, Huan; Han, Wei; Wang, Jing-zhi; Zhang, Xiao-hui; Li, Jin-lan; Li, Ling-di; Liu, Kai-yan; Huang, Xiao-jun

2011-08-01

Analysis of changes in recipient and donor hematopoietic cell origin is extremely useful to monitor the effect of hematopoietic stem cell transplantation (HSCT) and sequential adoptive immunotherapy by donor lymphocyte infusions. We developed a sensitive, reliable and rapid real-time PCR method based on sequence polymorphism systems to quantitatively assess the hematopoietic chimerism after HSCT. A panel of 29 selected sequence polymorphism (SP) markers was screened by real-time PCR in 101 HSCT patients with leukemia and other hematological diseases. The chimerism kinetics of bone marrow samples of 8 HSCT patients in remission and relapse situations were followed longitudinally. Recipient genotype discrimination was possible in 97.0% (98 of 101) with a mean number of 2.5 (1-7) informative markers per recipient/donor pair. Using serial dilutions of plasmids containing specific SP markers, the linear correlation (r) of 0.99, the slope between -3.2 and -3.7 and the sensitivity of 0.1% were proved reproducible. By this method, it was possible to very accurately detect autologous signals in the range from 0.1% to 30%. The accuracy of the method in the very important range of autologous signals below 5% was extraordinarily high (standard deviation <1.85%), which might significantly improve detection accuracy of changes in autologous signals early in the post-transplantation course of follow-up. The main advantage of the real-time PCR method over short tandem repeat PCR chimerism assays is the absence of PCR competition and plateau biases, with demonstrated greater sensitivity and linearity. Finally, we prospectively analyzed bone marrow samples of 8 patients who received allografts and presented the chimerism kinetics of remission and relapse situations that illustrated the sensitivity level and the promising clinical application of this method. This SP-based real-time PCR assay provides a rapid, sensitive, and accurate quantitative assessment of mixed chimerism that can be useful in predicting graft rejection and early relapse.

Visualization techniques to aid in the analysis of multispectral astrophysical data sets

NASA Technical Reports Server (NTRS)

Brugel, E. W.; Domik, Gitta O.; Ayres, T. R.

1993-01-01

The goal of this project was to support the scientific analysis of multi-spectral astrophysical data by means of scientific visualization. Scientific visualization offers its greatest value if it is not used as a method separate or alternative to other data analysis methods but rather in addition to these methods. Together with quantitative analysis of data, such as offered by statistical analysis, image or signal processing, visualization attempts to explore all information inherent in astrophysical data in the most effective way. Data visualization is one aspect of data analysis. Our taxonomy as developed in Section 2 includes identification and access to existing information, preprocessing and quantitative analysis of data, visual representation and the user interface as major components to the software environment of astrophysical data analysis. In pursuing our goal to provide methods and tools for scientific visualization of multi-spectral astrophysical data, we therefore looked at scientific data analysis as one whole process, adding visualization tools to an already existing environment and integrating the various components that define a scientific data analysis environment. As long as the software development process of each component is separate from all other components, users of data analysis software are constantly interrupted in their scientific work in order to convert from one data format to another, or to move from one storage medium to another, or to switch from one user interface to another. We also took an in-depth look at scientific visualization and its underlying concepts, current visualization systems, their contributions and their shortcomings. The role of data visualization is to stimulate mental processes different from quantitative data analysis, such as the perception of spatial relationships or the discovery of patterns or anomalies while browsing through large data sets. Visualization often leads to an intuitive understanding of the meaning of data values and their relationships by sacrificing accuracy in interpreting the data values. In order to be accurate in the interpretation, data values need to be measured, computed on, and compared to theoretical or empirical models (quantitative analysis). If visualization software hampers quantitative analysis (which happens with some commercial visualization products), its use is greatly diminished for astrophysical data analysis. The software system STAR (Scientific Toolkit for Astrophysical Research) was developed as a prototype during the course of the project to better understand the pragmatic concerns raised in the project. STAR led to a better understanding on the importance of collaboration between astrophysicists and computer scientists. Twenty-one examples of the use of visualization for astrophysical data are included with this report. Sixteen publications related to efforts performed during or initiated through work on this project are listed at the end of this report.

Accuracy and precision of pseudo-continuous arterial spin labeling perfusion during baseline and hypercapnia: a head-to-head comparison with ¹⁵O H₂O positron emission tomography.

PubMed

Heijtel, D F R; Mutsaerts, H J M M; Bakker, E; Schober, P; Stevens, M F; Petersen, E T; van Berckel, B N M; Majoie, C B L M; Booij, J; van Osch, M J P; Vanbavel, E; Boellaard, R; Lammertsma, A A; Nederveen, A J

2014-05-15

Measurements of the cerebral blood flow (CBF) and cerebrovascular reactivity (CVR) provide useful information about cerebrovascular condition and regional metabolism. Pseudo-continuous arterial spin labeling (pCASL) is a promising non-invasive MRI technique to quantitatively measure the CBF, whereas additional hypercapnic pCASL measurements are currently showing great promise to quantitatively assess the CVR. However, the introduction of pCASL at a larger scale awaits further evaluation of the exact accuracy and precision compared to the gold standard. (15)O H₂O positron emission tomography (PET) is currently regarded as the most accurate and precise method to quantitatively measure both CBF and CVR, though it is one of the more invasive methods as well. In this study we therefore assessed the accuracy and precision of quantitative pCASL-based CBF and CVR measurements by performing a head-to-head comparison with (15)O H₂O PET, based on quantitative CBF measurements during baseline and hypercapnia. We demonstrate that pCASL CBF imaging is accurate during both baseline and hypercapnia with respect to (15)O H₂O PET with a comparable precision. These results pave the way for quantitative usage of pCASL MRI in both clinical and research settings. Copyright © 2014 Elsevier Inc. All rights reserved.

Usefulness of a Dual Macro- and Micro-Energy-Dispersive X-Ray Fluorescence Spectrometer to Develop Quantitative Methodologies for Historic Mortar and Related Materials Characterization.

PubMed

García-Florentino, Cristina; Maguregui, Maite; Romera-Fernández, Miriam; Queralt, Ignasi; Margui, Eva; Madariaga, Juan Manuel

2018-05-01

Wavelength dispersive X-ray fluorescence (WD-XRF) spectrometry has been widely used for elemental quantification of mortars and cements. In this kind of instrument, samples are usually prepared as pellets or fused beads and the whole volume of sample is measured at once. In this work, the usefulness of a dual energy dispersive X-ray fluorescence spectrometer (ED-XRF), working at two lateral resolutions (1 mm and 25 μm) for macro and microanalysis respectively, to develop quantitative methods for the elemental characterization of mortars and concretes is demonstrated. A crucial step before developing any quantitative method with this kind of spectrometers is to verify the homogeneity of the standards at these two lateral resolutions. This new ED-XRF quantitative method also demonstrated the importance of matrix effects in the accuracy of the results being necessary to use Certified Reference Materials as standards. The results obtained with the ED-XRF quantitative method were compared with the ones obtained with two WD-XRF quantitative methods employing two different sample preparation strategies (pellets and fused beads). The selected ED-XRF and both WD-XRF quantitative methods were applied to the analysis of real mortars. The accuracy of the ED-XRF results turn out to be similar to the one achieved by WD-XRF, except for the lightest elements (Na and Mg). The results described in this work proved that μ-ED-XRF spectrometers can be used not only for acquiring high resolution elemental map distributions, but also to perform accurate quantitative studies avoiding the use of more sophisticated WD-XRF systems or the acid extraction/alkaline fusion required as destructive pretreatment in Inductively coupled plasma mass spectrometry based procedures.

Colorimetric microdetermination of captopril in pure form and in pharmaceutical formulations

NASA Astrophysics Data System (ADS)

Shama, Sayed Ahmed; El-Sayed Amin, Alla; Omara, Hany

2006-11-01

A simple, rapid, accurate, precise and sensitive colorimetric method for the determination of captopril (CAP) in bulk sample and in dosage forms is described. The method is based on oxidation of the drug by potassium permanganate in acidic medium and determination of the unreacted oxidant by measuring the decrease in absorbance for five different dyes; methylene blue (MB); acid blue 74 (AB), acid red 73 (AR), amaranth dye (AM) and acid orange 7 (AO) at a suitable λmax (660, 610, 510, 520, and 485 nm), respectively. Regression analysis of Beer's plots showed good correlation in the concentration ranges (0.4 12.5, 0.3 10, 0.5 11, 0.4 8.3 and 0.5 9.3 μg ml-1), respectively. The apparent molar absorbtivity, Sandell sensitivity, detection and quantitation limits were calculated. For more accurate results, Ringbom optimum concentration ranges were 0.5 12, 0.5 9.6, 0.6 10.5, 0.5 8.0 and 0.7 9.0 μg ml-1, respectively. The validity of the proposed method was tested by analyzing in pure and dosage forms containing CAP whether alone or in combination with hydrochlorothiazide. Statistical analysis of the results reflects that the proposed procedures are precise, accurate and easily applicable for the determination of CAP in pure form and in pharmaceutical preparations. Also, the stability constant was determined and the free energy change was calculated potentiometrically.

A feasible, economical, and accurate analytical method for simultaneous determination of six alkaloid markers in Aconiti Lateralis Radix Praeparata from different manufacturing sources and processing ways.

PubMed

Zhang, Yi-Bei; DA, Juan; Zhang, Jing-Xian; Li, Shang-Rong; Chen, Xin; Long, Hua-Li; Wang, Qiu-Rong; Cai, Lu-Ying; Yao, Shuai; Hou, Jin-Jun; Wu, Wan-Ying; Guo, De-An

2017-04-01

Aconiti Lateralis Radix Praeparata (Fuzi) is a commonly used traditional Chinese medicine in clinic for its potency in restoring yang and rescuing from collapse. Aconiti alkaloids, mainly including monoester-diterpenoidaconitines (MDAs) and diester-diterpenoidaconitines (DDAs), are considered to act as both bioactive and toxic constituents. In the present study, a feasible, economical, and accurate HPLC method for simultaneous determination of six alkaloid markers using the Single Standard for Determination of Multi-Components (SSDMC) method was developed and fully validated. Benzoylmesaconine was used as the unique reference standard. This method was proven as accurate (recovery varying between 97.5%-101.8%, RSD < 3%), precise (RSD 0.63%-2.05%), and linear (R > 0.999 9) over the concentration ranges, and subsequently applied to quantitative evaluation of 62 batches of samples, among which 45 batches were from good manufacturing practice (GMP) facilities and 17 batches from the drug market. The contents were then analyzed by principal component analysis (PCA) and homogeneity test. The present study provided valuable information for improving the quality standard of Aconiti Lateralis Radix Praeparata. The developed method also has the potential in analysis of other Aconitum species, such as Aconitum carmichaelii (prepared parent root) and Aconitum kusnezoffii (prepared root). Copyright © 2017 China Pharmaceutical University. Published by Elsevier B.V. All rights reserved.

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…

An optimized color transformation for the analysis of digital images of hematoxylin & eosin stained slides.

PubMed

Zarella, Mark D; Breen, David E; Plagov, Andrei; Garcia, Fernando U

2015-01-01

Hematoxylin and eosin (H&E) staining is ubiquitous in pathology practice and research. As digital pathology has evolved, the reliance of quantitative methods that make use of H&E images has similarly expanded. For example, cell counting and nuclear morphometry rely on the accurate demarcation of nuclei from other structures and each other. One of the major obstacles to quantitative analysis of H&E images is the high degree of variability observed between different samples and different laboratories. In an effort to characterize this variability, as well as to provide a substrate that can potentially mitigate this factor in quantitative image analysis, we developed a technique to project H&E images into an optimized space more appropriate for many image analysis procedures. We used a decision tree-based support vector machine learning algorithm to classify 44 H&E stained whole slide images of resected breast tumors according to the histological structures that are present. This procedure takes an H&E image as an input and produces a classification map of the image that predicts the likelihood of a pixel belonging to any one of a set of user-defined structures (e.g., cytoplasm, stroma). By reducing these maps into their constituent pixels in color space, an optimal reference vector is obtained for each structure, which identifies the color attributes that maximally distinguish one structure from other elements in the image. We show that tissue structures can be identified using this semi-automated technique. By comparing structure centroids across different images, we obtained a quantitative depiction of H&E variability for each structure. This measurement can potentially be utilized in the laboratory to help calibrate daily staining or identify troublesome slides. Moreover, by aligning reference vectors derived from this technique, images can be transformed in a way that standardizes their color properties and makes them more amenable to image processing.

Liquid-Crystal Point-Diffraction Interferometer for Wave-Front Measurements

NASA Technical Reports Server (NTRS)

Mercer, Carolyn R.; Creath, Katherine

1996-01-01

A new instrument, the liquid-crystal point-diffraction interferometer (LCPDI), is developed for the measurement of phase objects. This instrument maintains the compact, robust design of Linnik's point-diffraction interferometer and adds to it a phase-stepping capability for quantitative interferogram analysis. The result is a compact, simple to align, environmentally insensitive interferometer capable of accurately measuring optical wave fronts with very high data density and with automated data reduction. We describe the theory and design of the LCPDI. A focus shift was measured with the LCPDI, and the results are compared with theoretical results,

Thermal Imaging with Novel Infrared Focal Plane Arrays and Quantitative Analysis of Thermal Imagery

NASA Technical Reports Server (NTRS)

Gunapala, S. D.; Rafol, S. B.; Bandara, S. V.; Liu, J. K.; Mumolo, J. M.; Soibel, A.; Ting, D. Z.; Tidrow, Meimei

2012-01-01

We have developed a single long-wavelength infrared (LWIR) quantum well infrared photodetector (QWIP) camera for thermography. This camera has been used to measure the temperature profile of patients. A pixel coregistered simultaneously reading mid-wavelength infrared (MWIR)/LWIR dual-band QWIP camera was developed to improve the accuracy of temperature measurements especially with objects with unknown emissivity. Even the dualband measurement can provide inaccurate results due to the fact that emissivity is a function of wavelength. Thus we have been developing a four-band QWIP camera for accurate temperature measurement of remote object.

Fabrication of 10nm diameter carbon nanopores

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

Radenovic, Aleksandra; Trepagnier, Eliane; Csencsits, Roseann

2008-09-25

The addition of carbon to samples, during imaging, presents a barrier to accurate TEM analysis, the controlled deposition of hydrocarbons by a focused electron beam can be a useful technique for local nanometer-scale sculpting of material. Here we use hydrocarbon deposition to form nanopores from larger focused ion beam (FIB) holes in silicon nitride membranes. Using this method, we close 100-200nm diameter holes to diameters of 10nm and below, with deposition rates of 0.6nm per minute. I-V characteristics of electrolytic flow through these nanopores agree quantitatively with a one dimensional model at all examined salt concentrations.

Simulating Initial and Progressive Failure of Open-Hole Composite Laminates under Tension

NASA Astrophysics Data System (ADS)

Guo, Zhangxin; Zhu, Hao; Li, Yongcun; Han, Xiaoping; Wang, Zhihua

2016-12-01

A finite element (FE) model is developed for the progressive failure analysis of fiber reinforced polymer laminates. The failure criterion for fiber and matrix failure is implemented in the FE code Abaqus using user-defined material subroutine UMAT. The gradual degradation of the material properties is controlled by the individual fracture energies of fiber and matrix. The failure and damage in composite laminates containing a central hole subjected to uniaxial tension are simulated. The numerical results show that the damage model can be used to accurately predicte the progressive failure behaviour both qualitatively and quantitatively.