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Sample records for accurate quantitative analysis

  1. Quantitative proteomic analysis by accurate mass retention time pairs.

    PubMed

    Silva, Jeffrey C; Denny, Richard; Dorschel, Craig A; Gorenstein, Marc; Kass, Ignatius J; Li, Guo-Zhong; McKenna, Therese; Nold, Michael J; Richardson, Keith; Young, Phillip; Geromanos, Scott

    2005-04-01

    Current methodologies for protein quantitation include 2-dimensional gel electrophoresis techniques, metabolic labeling, and stable isotope labeling methods to name only a few. The current literature illustrates both pros and cons for each of the previously mentioned methodologies. Keeping with the teachings of William of Ockham, "with all things being equal the simplest solution tends to be correct", a simple LC/MS based methodology is presented that allows relative changes in abundance of proteins in highly complex mixtures to be determined. Utilizing a reproducible chromatographic separations system along with the high mass resolution and mass accuracy of an orthogonal time-of-flight mass spectrometer, the quantitative comparison of tens of thousands of ions emanating from identically prepared control and experimental samples can be made. Using this configuration, we can determine the change in relative abundance of a small number of ions between the two conditions solely by accurate mass and retention time. Employing standard operating procedures for both sample preparation and ESI-mass spectrometry, one typically obtains under 5 ppm mass precision and quantitative variations between 10 and 15%. The principal focus of this paper will demonstrate the quantitative aspects of the methodology and continue with a discussion of the associated, complementary qualitative capabilities.

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

    NASA Astrophysics Data System (ADS)

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

    2017-02-01

    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.

  3. 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.

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

    PubMed Central

    2010-01-01

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

  5. A Global Approach to Accurate and Automatic Quantitative Analysis of NMR Spectra by Complex Least-Squares Curve Fitting

    NASA Astrophysics Data System (ADS)

    Martin, Y. L.

    The performance of quantitative analysis of 1D NMR spectra depends greatly on the choice of the NMR signal model. Complex least-squares analysis is well suited for optimizing the quantitative determination of spectra containing a limited number of signals (<30) obtained under satisfactory conditions of signal-to-noise ratio (>20). From a general point of view it is concluded, on the basis of mathematical considerations and numerical simulations, that, in the absence of truncation of the free-induction decay, complex least-squares curve fitting either in the time or in the frequency domain and linear-prediction methods are in fact nearly equivalent and give identical results. However, in the situation considered, complex least-squares analysis in the frequency domain is more flexible since it enables the quality of convergence to be appraised at every resonance position. An efficient data-processing strategy has been developed which makes use of an approximate conjugate-gradient algorithm. All spectral parameters (frequency, damping factors, amplitudes, phases, initial delay associated with intensity, and phase parameters of a baseline correction) are simultaneously managed in an integrated approach which is fully automatable. The behavior of the error as a function of the signal-to-noise ratio is theoretically estimated, and the influence of apodization is discussed. The least-squares curve fitting is theoretically proved to be the most accurate approach for quantitative analysis of 1D NMR data acquired with reasonable signal-to-noise ratio. The method enables complex spectral residuals to be sorted out. These residuals, which can be cumulated thanks to the possibility of correcting for frequency shifts and phase errors, extract systematic components, such as isotopic satellite lines, and characterize the shape and the intensity of the spectral distortion with respect to the Lorentzian model. This distortion is shown to be nearly independent of the chemical species

  6. Simple, fast, and accurate methodology for quantitative analysis using Fourier transform infrared spectroscopy, with bio-hybrid fuel cell examples.

    PubMed

    Mackie, David M; Jahnke, Justin P; Benyamin, Marcus S; Sumner, James J

    2016-01-01

    The standard methodologies for quantitative analysis (QA) of mixtures using Fourier transform infrared (FTIR) instruments have evolved until they are now more complicated than necessary for many users' purposes. We present a simpler methodology, suitable for widespread adoption of FTIR QA as a standard laboratory technique across disciplines by occasional users.•Algorithm is straightforward and intuitive, yet it is also fast, accurate, and robust.•Relies on component spectra, minimization of errors, and local adaptive mesh refinement.•Tested successfully on real mixtures of up to nine components. We show that our methodology is robust to challenging experimental conditions such as similar substances, component percentages differing by three orders of magnitude, and imperfect (noisy) spectra. As examples, we analyze biological, chemical, and physical aspects of bio-hybrid fuel cells.

  7. 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

  8. Quantitative polymerase chain reaction analysis of DNA from noninvasive samples for accurate microsatellite genotyping of wild chimpanzees (Pan troglodytes verus).

    PubMed

    Morin, P A; Chambers, K E; Boesch, C; Vigilant, L

    2001-07-01

    Noninvasive samples are useful for molecular genetic analyses of wild animal populations. However, the low DNA content of such samples makes DNA amplification difficult, and there is the potential for erroneous results when one of two alleles at heterozygous microsatellite loci fails to be amplified. In this study we describe an assay designed to measure the amount of amplifiable nuclear DNA in low DNA concentration extracts from noninvasive samples. We describe the range of DNA amounts obtained from chimpanzee faeces and shed hair samples and formulate a new efficient approach for accurate microsatellite genotyping. Prescreening of extracts for DNA quantity is recommended for sorting of samples for likely success and reliability. Repetition of results remains extensive for analysis of microsatellite amplifications beginning from low starting amounts of DNA, but is reduced for those with higher DNA content.

  9. Groundtruth approach to accurate quantitation of fluorescence microarrays

    SciTech Connect

    Mascio-Kegelmeyer, L; Tomascik-Cheeseman, L; Burnett, M S; van Hummelen, P; Wyrobek, A J

    2000-12-01

    To more accurately measure fluorescent signals from microarrays, we calibrated our acquisition and analysis systems by using groundtruth samples comprised of known quantities of red and green gene-specific DNA probes hybridized to cDNA targets. We imaged the slides with a full-field, white light CCD imager and analyzed them with our custom analysis software. Here we compare, for multiple genes, results obtained with and without preprocessing (alignment, color crosstalk compensation, dark field subtraction, and integration time). We also evaluate the accuracy of various image processing and analysis techniques (background subtraction, segmentation, quantitation and normalization). This methodology calibrates and validates our system for accurate quantitative measurement of microarrays. Specifically, we show that preprocessing the images produces results significantly closer to the known ground-truth for these samples.

  10. Differential label-free quantitative proteomic analysis of Shewanella oneidensis cultured under aerobic and suboxic conditions by accurate mass and time tag approach.

    PubMed

    Fang, Ruihua; Elias, Dwayne A; Monroe, Matthew E; Shen, Yufeng; McIntosh, Martin; Wang, Pei; Goddard, Carrie D; Callister, Stephen J; Moore, Ronald J; Gorby, Yuri A; Adkins, Joshua N; Fredrickson, Jim K; Lipton, Mary S; Smith, Richard D

    2006-04-01

    We describe the application of LC-MS without the use of stable isotope labeling for differential quantitative proteomic analysis of whole cell lysates of Shewanella oneidensis MR-1 cultured under aerobic and suboxic conditions. LC-MS/MS was used to initially identify peptide sequences, and LC-FTICR was used to confirm these identifications as well as measure relative peptide abundances. 2343 peptides covering 668 proteins were identified with high confidence and quantified. Among these proteins, a subset of 56 changed significantly using statistical approaches such as statistical analysis of microarrays, whereas another subset of 56 that were annotated as performing housekeeping functions remained essentially unchanged in relative abundance. Numerous proteins involved in anaerobic energy metabolism exhibited up to a 10-fold increase in relative abundance when S. oneidensis was transitioned from aerobic to suboxic conditions.

  11. Differential Label-free Quantitative Proteomic Analysis of Shewanella oneidensis Cultured under Aerobic and Suboxic Conditions by Accurate Mass and Time Tag Approach

    SciTech Connect

    Fang, Ruihua; Elias, Dwayne A.; Monroe, Matthew E.; Shen, Yufeng; McIntosh, Martin; Wang, Pei; Goddard, Carrie D.; Callister, Stephen J.; Moore, Ronald J.; Gorby, Yuri A.; Adkins, Joshua N.; Fredrickson, Jim K.; Lipton, Mary S.; Smith, Richard D.

    2006-04-01

    We describe the application of liquid chromatography coupled to mass spectrometry (LC/MS) without the use of stable isotope labeling for differential quantitative proteomics analysis of whole cell lysates of Shewanella oneidensis MR-1 cultured under aerobic and sub-oxic conditions. Liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) was used to initially identify peptide sequences, and LC coupled to Fourier transform ion cyclotron resonance mass spectrometry (LC-FTICR) was used to confirm these identifications, as well as measure relative peptide abundances. 2343 peptides, covering 668 proteins were identified with high confidence and quantified. Among these proteins, a subset of 56 changed significantly using statistical approaches such as SAM, while another subset of 56 that were annotated as performing housekeeping functions remained essentially unchanged in relative abundance. Numerous proteins involved in anaerobic energy metabolism exhibited up to a 10-fold increase in relative abundance when S. oneidensis is transitioned from aerobic to sub-oxic conditions.

  12. Accurate Analysis of Array References

    DTIC Science & Technology

    1992-09-22

    This thesis addresses the problem of data dependence analysis, the base step in detecting loop level parallelism in scientific programs. Traditional...data dependence analysis research has concentrated on the simpler problem of affine memory disambiguation. Many algorithms have been developed that...can devise an experiment to test the effectiveness of affine memory disambiguation at approximating the full dependence problem. We discover that the

  13. FANSe: an accurate algorithm for quantitative mapping of large scale sequencing reads

    PubMed Central

    Zhang, Gong; Fedyunin, Ivan; Kirchner, Sebastian; Xiao, Chuanle; Valleriani, Angelo; Ignatova, Zoya

    2012-01-01

    The most crucial step in data processing from high-throughput sequencing applications is the accurate and sensitive alignment of the sequencing reads to reference genomes or transcriptomes. The accurate detection of insertions and deletions (indels) and errors introduced by the sequencing platform or by misreading of modified nucleotides is essential for the quantitative processing of the RNA-based sequencing (RNA-Seq) datasets and for the identification of genetic variations and modification patterns. We developed a new, fast and accurate algorithm for nucleic acid sequence analysis, FANSe, with adjustable mismatch allowance settings and ability to handle indels to accurately and quantitatively map millions of reads to small or large reference genomes. It is a seed-based algorithm which uses the whole read information for mapping and high sensitivity and low ambiguity are achieved by using short and non-overlapping reads. Furthermore, FANSe uses hotspot score to prioritize the processing of highly possible matches and implements modified Smith–Watermann refinement with reduced scoring matrix to accelerate the calculation without compromising its sensitivity. The FANSe algorithm stably processes datasets from various sequencing platforms, masked or unmasked and small or large genomes. It shows a remarkable coverage of low-abundance mRNAs which is important for quantitative processing of RNA-Seq datasets. PMID:22379138

  14. FANSe: an accurate algorithm for quantitative mapping of large scale sequencing reads.

    PubMed

    Zhang, Gong; Fedyunin, Ivan; Kirchner, Sebastian; Xiao, Chuanle; Valleriani, Angelo; Ignatova, Zoya

    2012-06-01

    The most crucial step in data processing from high-throughput sequencing applications is the accurate and sensitive alignment of the sequencing reads to reference genomes or transcriptomes. The accurate detection of insertions and deletions (indels) and errors introduced by the sequencing platform or by misreading of modified nucleotides is essential for the quantitative processing of the RNA-based sequencing (RNA-Seq) datasets and for the identification of genetic variations and modification patterns. We developed a new, fast and accurate algorithm for nucleic acid sequence analysis, FANSe, with adjustable mismatch allowance settings and ability to handle indels to accurately and quantitatively map millions of reads to small or large reference genomes. It is a seed-based algorithm which uses the whole read information for mapping and high sensitivity and low ambiguity are achieved by using short and non-overlapping reads. Furthermore, FANSe uses hotspot score to prioritize the processing of highly possible matches and implements modified Smith-Watermann refinement with reduced scoring matrix to accelerate the calculation without compromising its sensitivity. The FANSe algorithm stably processes datasets from various sequencing platforms, masked or unmasked and small or large genomes. It shows a remarkable coverage of low-abundance mRNAs which is important for quantitative processing of RNA-Seq datasets.

  15. Multivariate Quantitative Chemical Analysis

    NASA Technical Reports Server (NTRS)

    Kinchen, David G.; Capezza, Mary

    1995-01-01

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

  16. Quantitative Hydrocarbon Surface Analysis

    NASA Technical Reports Server (NTRS)

    Douglas, Vonnie M.

    2000-01-01

    The elimination of ozone depleting substances, such as carbon tetrachloride, has resulted in the use of new analytical techniques for cleanliness verification and contamination sampling. The last remaining application at Rocketdyne which required a replacement technique was the quantitative analysis of hydrocarbons by infrared spectrometry. This application, which previously utilized carbon tetrachloride, was successfully modified using the SOC-400, a compact portable FTIR manufactured by Surface Optics Corporation. This instrument can quantitatively measure and identify hydrocarbons from solvent flush of hardware as well as directly analyze the surface of metallic components without the use of ozone depleting chemicals. Several sampling accessories are utilized to perform analysis for various applications.

  17. Quantitative environmental risk analysis

    SciTech Connect

    Klovning, J.; Nilsen, E.F.

    1995-12-31

    According to regulations relating to implementation and rise of risk analysis in the petroleum activities issued by the Norwegian Petroleum Directorate, it is mandatory for an operator on the Norwegian Continental Shelf to establish acceptance criteria for environmental risk in the activities and carry out environmental risk analysis. This paper presents a {open_quotes}new{close_quotes} method for environmental risk analysis developed by the company. The objective has been to assist the company to meet rules and regulations and to assess and describe the environmental risk in a systematic manner. In the environmental risk analysis the most sensitive biological resource in the affected area is used to assess the environmental damage. The analytical method is based on the methodology for quantitative risk analysis related to loss of life. In addition it incorporates the effect of seasonal fluctuations in the environmental risk evaluations. The paper is describing the function of the main analytical sequences exemplified through an analysis of environmental risk related to exploration drilling in an environmental sensitive area on the Norwegian Continental Shelf.

  18. Quantitative Techniques in Volumetric Analysis

    NASA Astrophysics Data System (ADS)

    Zimmerman, John; Jacobsen, Jerrold J.

    1996-12-01

    Quantitative Techniques in Volumetric Analysis is a visual library of techniques used in making volumetric measurements. This 40-minute VHS videotape is designed as a resource for introducing students to proper volumetric methods and procedures. The entire tape, or relevant segments of the tape, can also be used to review procedures used in subsequent experiments that rely on the traditional art of quantitative analysis laboratory practice. The techniques included are: Quantitative transfer of a solid with a weighing spoon Quantitative transfer of a solid with a finger held weighing bottle Quantitative transfer of a solid with a paper strap held bottle Quantitative transfer of a solid with a spatula Examples of common quantitative weighing errors Quantitative transfer of a solid from dish to beaker to volumetric flask Quantitative transfer of a solid from dish to volumetric flask Volumetric transfer pipet A complete acid-base titration Hand technique variations The conventional view of contemporary quantitative chemical measurement tends to focus on instrumental systems, computers, and robotics. In this view, the analyst is relegated to placing standards and samples on a tray. A robotic arm delivers a sample to the analysis center, while a computer controls the analysis conditions and records the results. In spite of this, it is rare to find an analysis process that does not rely on some aspect of more traditional quantitative analysis techniques, such as careful dilution to the mark of a volumetric flask. Figure 2. Transfer of a solid with a spatula. Clearly, errors in a classical step will affect the quality of the final analysis. Because of this, it is still important for students to master the key elements of the traditional art of quantitative chemical analysis laboratory practice. Some aspects of chemical analysis, like careful rinsing to insure quantitative transfer, are often an automated part of an instrumental process that must be understood by the

  19. SILAC-Based Quantitative Strategies for Accurate Histone Posttranslational Modification Profiling Across Multiple Biological Samples.

    PubMed

    Cuomo, Alessandro; Soldi, Monica; Bonaldi, Tiziana

    2017-01-01

    Histone posttranslational modifications (hPTMs) play a key role in regulating chromatin dynamics and fine-tuning DNA-based processes. Mass spectrometry (MS) has emerged as a versatile technology for the analysis of histones, contributing to the dissection of hPTMs, with special strength in the identification of novel marks and in the assessment of modification cross talks. Stable isotope labeling by amino acid in cell culture (SILAC), when adapted to histones, permits the accurate quantification of PTM changes among distinct functional states; however, its application has been mainly confined to actively dividing cell lines. A spike-in strategy based on SILAC can be used to overcome this limitation and profile hPTMs across multiple samples. We describe here the adaptation of SILAC to the analysis of histones, in both standard and spike-in setups. We also illustrate its coupling to an implemented "shotgun" workflow, by which heavy arginine-labeled histone peptides, produced upon Arg-C digestion, are qualitatively and quantitatively analyzed in an LC-MS/MS system that combines ultrahigh-pressure liquid chromatography (UHPLC) with new-generation Orbitrap high-resolution instrument.

  20. Quantitative analysis of blood vessel geometry

    NASA Astrophysics Data System (ADS)

    Fuhrman, Michael G.; Abdul-Karim, Othman; Shah, Sujal; Gilbert, Steven G.; Van Bibber, Richard

    2001-07-01

    Re-narrowing or restenosis of a human coronary artery occurs within six months in one third of balloon angioplasty procedures. Accurate and repeatable quantitative analysis of vessel shape is important to characterize the progression and type of restenosis, and to evaluate effects new therapies might have. A combination of complicated geometry and image variability, and the need for high resolution and large image size makes visual/manual analysis slow, difficult, and prone to error. The image processing and analysis described here was developed to automate feature extraction of the lumen, internal elastic lamina, neointima, external elastic lamina, and tunica adventitia and to enable an objective, quantitative definition of blood vessel geometry. The quantitative geometrical analysis enables the measurement of several features including perimeter, area, and other metrics of vessel damage. Automation of feature extraction creates a high throughput capability that enables analysis of serial sections for more accurate measurement of restenosis dimensions. Measurement results are input into a relational database where they can be statistically analyzed compared across studies. As part of the integrated process, results are also imprinted on the images themselves to facilitate auditing of the results. The analysis is fast, repeatable and accurate while allowing the pathologist to control the measurement process.

  1. Quantitative analysis of endogenous compounds.

    PubMed

    Thakare, Rhishikesh; Chhonker, Yashpal S; Gautam, Nagsen; Alamoudi, Jawaher Abdullah; Alnouti, Yazen

    2016-09-05

    Accurate quantitative analysis of endogenous analytes is essential for several clinical and non-clinical applications. LC-MS/MS is the technique of choice for quantitative analyses. Absolute quantification by LC/MS requires preparing standard curves in the same matrix as the study samples so that the matrix effect and the extraction efficiency for analytes are the same in both the standard and study samples. However, by definition, analyte-free biological matrices do not exist for endogenous compounds. To address the lack of blank matrices for the quantification of endogenous compounds by LC-MS/MS, four approaches are used including the standard addition, the background subtraction, the surrogate matrix, and the surrogate analyte methods. This review article presents an overview these approaches, cite and summarize their applications, and compare their advantages and disadvantages. In addition, we discuss in details, validation requirements and compatibility with FDA guidelines to ensure method reliability in quantifying endogenous compounds. The standard addition, background subtraction, and the surrogate analyte approaches allow the use of the same matrix for the calibration curve as the one to be analyzed in the test samples. However, in the surrogate matrix approach, various matrices such as artificial, stripped, and neat matrices are used as surrogate matrices for the actual matrix of study samples. For the surrogate analyte approach, it is required to demonstrate similarity in matrix effect and recovery between surrogate and authentic endogenous analytes. Similarly, for the surrogate matrix approach, it is required to demonstrate similar matrix effect and extraction recovery in both the surrogate and original matrices. All these methods represent indirect approaches to quantify endogenous compounds and regardless of what approach is followed, it has to be shown that none of the validation criteria have been compromised due to the indirect analyses.

  2. Quantitative analysis of PET studies.

    PubMed

    Weber, Wolfgang A

    2010-09-01

    Quantitative analysis can be included relatively easily in clinical PET-imaging protocols, but in order to obtain meaningful quantitative results one needs to follow a standardized protocol for image acquisition and data analysis. Important factors to consider are the calibration of the PET scanner, the radiotracer uptake time and the approach for definition of regions of interests. Using such standardized acquisition protocols quantitative parameters of tumor metabolism or receptor status can be derived from tracer kinetic analysis and simplified approaches such as calculation of standardized uptake values (SUVs).

  3. Quantitative analysis in megageomorphology

    NASA Technical Reports Server (NTRS)

    Mayer, L.

    1985-01-01

    Megageomorphology is the study of regional topographic features and their relations to independent geomorphic variables that operate at the regional scale. These independent variables can be classified as either tectonic or climatic in nature. Quantitative megageomorphology stresses the causal relations between plate tectonic factors and landscape features or correlations between climatic factors and geomorphic processes. In addition, the cumulative effects of tectonics and climate on landscape evolution that simultaneously operate in a complex system of energy transfer is of interst. Regional topographic differentiation, say between continents and ocean floors, is largely the result of the different densities and density contrasts within the oceanic and continental lithosphere and their isostatic consequences. Regional tectonic processes that alter these lithospheric characteristics include rifting, collision, subduction, transpression and transtension.

  4. Mobile app-based quantitative scanometric analysis.

    PubMed

    Wong, Jessica X H; Liu, Frank S F; Yu, Hua-Zhong

    2014-12-16

    The feasibility of using smartphones and other mobile devices as the detection platform for quantitative scanometric assays is demonstrated. The different scanning modes (color, grayscale, black/white) and grayscale converting protocols (average, weighted average/luminosity, and software specific) have been compared in determining the optical darkness ratio (ODR) values, a conventional quantitation measure for scanometric assays. A mobile app was developed to image and analyze scanometric assays, as demonstrated by paper-printed tests and a biotin-streptavidin assay on a plastic substrate. Primarily for ODR analysis, the app has been shown to perform as well as a traditional desktop scanner, augmenting that smartphones (and other mobile devices) promise to be a practical platform for accurate, quantitative chemical analysis and medical diagnostics.

  5. Accurate Automated Apnea Analysis in Preterm Infants

    PubMed Central

    Vergales, Brooke D.; Paget-Brown, Alix O.; Lee, Hoshik; Guin, Lauren E.; Smoot, Terri J.; Rusin, Craig G.; Clark, Matthew T.; Delos, John B.; Fairchild, Karen D.; Lake, Douglas E.; Moorman, Randall; Kattwinkel, John

    2017-01-01

    Objective In 2006 the apnea of prematurity (AOP) consensus group identified inaccurate counting of apnea episodes as a major barrier to progress in AOP research. We compare nursing records of AOP to events detected by a clinically validated computer algorithm that detects apnea from standard bedside monitors. Study Design Waveform, vital sign, and alarm data were collected continuously from all very low-birth-weight infants admitted over a 25-month period, analyzed for central apnea, bradycardia, and desaturation (ABD) events, and compared with nursing documentation collected from charts. Our algorithm defined apnea as > 10 seconds if accompanied by bradycardia and desaturation. Results Of the 3,019 nurse-recorded events, only 68% had any algorithm-detected ABD event. Of the 5,275 algorithm-detected prolonged apnea events > 30 seconds, only 26% had nurse-recorded documentation within 1 hour. Monitor alarms sounded in only 74% of events of algorithm-detected prolonged apnea events > 10 seconds. There were 8,190,418 monitor alarms of any description throughout the neonatal intensive care unit during the 747 days analyzed, or one alarm every 2 to 3 minutes per nurse. Conclusion An automated computer algorithm for continuous ABD quantitation is a far more reliable tool than the medical record to address the important research questions identified by the 2006 AOP consensus group. PMID:23592319

  6. 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.

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

    PubMed Central

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

    2016-01-01

    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. PMID:27934889

  8. A fluorescence-based quantitative real-time PCR assay for accurate Pocillopora damicornis species identification

    NASA Astrophysics Data System (ADS)

    Thomas, Luke; Stat, Michael; Evans, Richard D.; Kennington, W. Jason

    2016-09-01

    Pocillopora damicornis is one of the most extensively studied coral species globally, but high levels of phenotypic plasticity within the genus make species identification based on morphology alone unreliable. As a result, there is a compelling need to develop cheap and time-effective molecular techniques capable of accurately distinguishing P. damicornis from other congeneric species. Here, we develop a fluorescence-based quantitative real-time PCR (qPCR) assay to genotype a single nucleotide polymorphism that accurately distinguishes P. damicornis from other morphologically similar Pocillopora species. We trial the assay across colonies representing multiple Pocillopora species and then apply the assay to screen samples of Pocillopora spp. collected at regional scales along the coastline of Western Australia. This assay offers a cheap and time-effective alternative to Sanger sequencing and has broad applications including studies on gene flow, dispersal, recruitment and physiological thresholds of P. damicornis.

  9. Quantitative proteomics using the high resolution accurate mass capabilities of the quadrupole-orbitrap mass spectrometer.

    PubMed

    Gallien, Sebastien; Domon, Bruno

    2014-08-01

    High resolution/accurate mass hybrid mass spectrometers have considerably advanced shotgun proteomics and the recent introduction of fast sequencing capabilities has expanded its use for targeted approaches. More specifically, the quadrupole-orbitrap instrument has a unique configuration and its new features enable a wide range of experiments. An overview of the analytical capabilities of this instrument is presented, with a focus on its application to quantitative analyses. The high resolution, the trapping capability and the versatility of the instrument have allowed quantitative proteomic workflows to be redefined and new data acquisition schemes to be developed. The initial proteomic applications have shown an improvement of the analytical performance. However, as quantification relies on ion trapping, instead of ion beam, further refinement of the technique can be expected.

  10. Highly sensitive capillary electrophoresis-mass spectrometry for rapid screening and accurate quantitation of drugs of abuse in urine.

    PubMed

    Kohler, Isabelle; Schappler, Julie; Rudaz, Serge

    2013-05-30

    The combination of capillary electrophoresis (CE) and mass spectrometry (MS) is particularly well adapted to bioanalysis due to its high separation efficiency, selectivity, and sensitivity; its short analytical time; and its low solvent and sample consumption. For clinical and forensic toxicology, a two-step analysis is usually performed: first, a screening step for compound identification, and second, confirmation and/or accurate quantitation in cases of presumed positive results. In this study, a fast and sensitive CE-MS workflow was developed for the screening and quantitation of drugs of abuse in urine samples. A CE with a time-of-flight MS (CE-TOF/MS) screening method was developed using a simple urine dilution and on-line sample preconcentration with pH-mediated stacking. The sample stacking allowed for a high loading capacity (20.5% of the capillary length), leading to limits of detection as low as 2 ng mL(-1) for drugs of abuse. Compound quantitation of positive samples was performed by CE-MS/MS with a triple quadrupole MS equipped with an adapted triple-tube sprayer and an electrospray ionization (ESI) source. The CE-ESI-MS/MS method was validated for two model compounds, cocaine (COC) and methadone (MTD), according to the Guidance of the Food and Drug Administration. The quantitative performance was evaluated for selectivity, response function, the lower limit of quantitation, trueness, precision, and accuracy. COC and MTD detection in urine samples was determined to be accurate over the range of 10-1000 ng mL(-1) and 21-1000 ng mL(-1), respectively.

  11. Quantitative spectroscopy of hot stars: accurate atomic data applied on a large scale as driver of recent breakthroughs

    NASA Astrophysics Data System (ADS)

    Przybilla, N.; Schaffenroth, V.; Nieva, M. F.; Butler, K.

    2016-10-01

    OB-type stars present hotbeds for non-LTE physics because of their strong radiation fields that drive the atmospheric plasma out of local thermodynamic equilibrium. We report on recent breakthroughs in the quantitative analysis of the optical and UV-spectra of OB-type stars that were facilitated by application of accurate and precise atomic data on a large scale. An astrophysicist's dream has come true, by bringing observed and model spectra into close match over wide parts of the observed wavelength ranges. This allows tight observational constraints to be derived from OB-type stars for a wide range of applications in astrophysics. However, despite the progress made, many details of the modelling may be improved further. We discuss atomic data needs in terms of laboratory measurements and also ab-initio calculations. Particular emphasis is given to quantitative spectroscopy in the near-IR, which will be the focus in the era of the upcoming extremely large telescopes.

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

  13. Software for quantitative trait analysis.

    PubMed

    Almasy, Laura; Warren, Diane M

    2005-09-01

    This paper provides a brief overview of software currently available for the genetic analysis of quantitative traits in humans. Programs that implement variance components, Markov Chain Monte Carlo (MCMC), Haseman-Elston (H-E) and penetrance model-based linkage analyses are discussed, as are programs for measured genotype association analyses and quantitative trait transmission disequilibrium tests. The software compared includes LINKAGE, FASTLINK, PAP, SOLAR, SEGPATH, ACT, Mx, MERLIN, GENEHUNTER, Loki, Mendel, SAGE, QTDT and FBAT. Where possible, the paper provides URLs for acquiring these programs through the internet, details of the platforms for which the software is available and the types of analyses performed.

  14. Optimization of sample preparation for accurate results in quantitative NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Yamazaki, Taichi; Nakamura, Satoe; Saito, Takeshi

    2017-04-01

    Quantitative nuclear magnetic resonance (qNMR) spectroscopy has received high marks as an excellent measurement tool that does not require the same reference standard as the analyte. Measurement parameters have been discussed in detail and high-resolution balances have been used for sample preparation. However, the high-resolution balances, such as an ultra-microbalance, are not general-purpose analytical tools and many analysts may find those balances difficult to use, thereby hindering accurate sample preparation for qNMR measurement. In this study, we examined the relationship between the resolution of the balance and the amount of sample weighed during sample preparation. We were able to confirm the accuracy of the assay results for samples weighed on a high-resolution balance, such as the ultra-microbalance. Furthermore, when an appropriate tare and amount of sample was weighed on a given balance, accurate assay results were obtained with another high-resolution balance. Although this is a fundamental result, it offers important evidence that would enhance the versatility of the qNMR method.

  15. 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.

  16. Quantitative analysis of glycated proteins.

    PubMed

    Priego-Capote, Feliciano; Ramírez-Boo, María; Finamore, Francesco; Gluck, Florent; Sanchez, Jean-Charles

    2014-02-07

    The proposed protocol presents a comprehensive approach for large-scale qualitative and quantitative analysis of glycated proteins (GP) in complex biological samples including biological fluids and cell lysates such as plasma and red blood cells. The method, named glycation isotopic labeling (GIL), is based on the differential labeling of proteins with isotopic [(13)C6]-glucose, which supports quantitation of the resulting glycated peptides after enzymatic digestion with endoproteinase Glu-C. The key principle of the GIL approach is the detection of doublet signals for each glycated peptide in MS precursor scanning (glycated peptide with in vivo [(12)C6]- and in vitro [(13)C6]-glucose). The mass shift of the doublet signals is +6, +3 or +2 Da depending on the peptide charge state and the number of glycation sites. The intensity ratio between doublet signals generates quantitative information of glycated proteins that can be related to the glycemic state of the studied samples. Tandem mass spectrometry with high-energy collisional dissociation (HCD-MS2) and data-dependent methods with collision-induced dissociation (CID-MS3 neutral loss scan) are used for qualitative analysis.

  17. Bioimaging for quantitative phenotype analysis.

    PubMed

    Chen, Weiyang; Xia, Xian; Huang, Yi; Chen, Xingwei; Han, Jing-Dong J

    2016-06-01

    With the development of bio-imaging techniques, an increasing number of studies apply these techniques to generate a myriad of image data. Its applications range from quantification of cellular, tissue, organismal and behavioral phenotypes of model organisms, to human facial phenotypes. The bio-imaging approaches to automatically detect, quantify, and profile phenotypic changes related to specific biological questions open new doors to studying phenotype-genotype associations and to precisely evaluating molecular changes associated with quantitative phenotypes. Here, we review major applications of bioimage-based quantitative phenotype analysis. Specifically, we describe the biological questions and experimental needs addressable by these analyses, computational techniques and tools that are available in these contexts, and the new perspectives on phenotype-genotype association uncovered by such analyses.

  18. Accurate detection and quantitation of heteroplasmic mitochondrial point mutations by pyrosequencing.

    PubMed

    White, Helen E; Durston, Victoria J; Seller, Anneke; Fratter, Carl; Harvey, John F; Cross, Nicholas C P

    2005-01-01

    Disease-causing mutations in mitochondrial DNA (mtDNA) are typically heteroplasmic and therefore interpretation of genetic tests for mitochondrial disorders can be problematic. Detection of low level heteroplasmy is technically demanding and it is often difficult to discriminate between the absence of a mutation or the failure of a technique to detect the mutation in a particular tissue. The reliable measurement of heteroplasmy in different tissues may help identify individuals who are at risk of developing specific complications and allow improved prognostic advice for patients and family members. We have evaluated Pyrosequencing technology for the detection and estimation of heteroplasmy for six mitochondrial point mutations associated with the following diseases: Leber's hereditary optical neuropathy (LHON), G3460A, G11778A, and T14484C; mitochondrial encephalopathy with lactic acidosis and stroke-like episodes (MELAS), A3243G; myoclonus epilepsy with ragged red fibers (MERRF), A8344G, and neurogenic muscle weakness, ataxia, and retinitis pigmentosa (NARP)/Leighs: T8993G/C. Results obtained from the Pyrosequencing assays for 50 patients with presumptive mitochondrial disease were compared to those obtained using the commonly used diagnostic technique of polymerase chain reaction (PCR) and restriction enzyme digestion. The Pyrosequencing assays provided accurate genotyping and quantitative determination of mutational load with a sensitivity and specificity of 100%. The MELAS A3243G mutation was detected reliably at a level of 1% heteroplasmy. We conclude that Pyrosequencing is a rapid and robust method for detecting heteroplasmic mitochondrial point mutations.

  19. 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

  20. Quantitative analysis of retinal OCT.

    PubMed

    Sonka, Milan; Abràmoff, Michael D

    2016-10-01

    Clinical acceptance of 3-D OCT retinal imaging brought rapid development of quantitative 3-D analysis of retinal layers, vasculature, retinal lesions as well as facilitated new research in retinal diseases. One of the cornerstones of many such analyses is segmentation and thickness quantification of retinal layers and the choroid, with an inherently 3-D simultaneous multi-layer LOGISMOS (Layered Optimal Graph Image Segmentation for Multiple Objects and Surfaces) segmentation approach being extremely well suited for the task. Once retinal layers are segmented, regional thickness, brightness, or texture-based indices of individual layers can be easily determined and thus contribute to our understanding of retinal or optic nerve head (ONH) disease processes and can be employed for determination of disease status, treatment responses, visual function, etc. Out of many applications, examples provided in this paper focus on image-guided therapy and outcome prediction in age-related macular degeneration and on assessing visual function from retinal layer structure in glaucoma.

  1. Progress toward accurate high spatial resolution actinide analysis by EPMA

    NASA Astrophysics Data System (ADS)

    Jercinovic, M. J.; Allaz, J. M.; Williams, M. L.

    2010-12-01

    High precision, high spatial resolution EPMA of actinides is a significant issue for geochronology, resource geochemistry, and studies involving the nuclear fuel cycle. Particular interest focuses on understanding of the behavior of Th and U in the growth and breakdown reactions relevant to actinide-bearing phases (monazite, zircon, thorite, allanite, etc.), and geochemical fractionation processes involving Th and U in fluid interactions. Unfortunately, the measurement of minor and trace concentrations of U in the presence of major concentrations of Th and/or REEs is particularly problematic, especially in complexly zoned phases with large compositional variation on the micro or nanoscale - spatial resolutions now accessible with modern instruments. Sub-micron, high precision compositional analysis of minor components is feasible in very high Z phases where scattering is limited at lower kV (15kV or less) and where the beam diameter can be kept below 400nm at high current (e.g. 200-500nA). High collection efficiency spectrometers and high performance electron optics in EPMA now allow the use of lower overvoltage through an exceptional range in beam current, facilitating higher spatial resolution quantitative analysis. The U LIII edge at 17.2 kV precludes L-series analysis at low kV (high spatial resolution), requiring careful measurements of the actinide M series. Also, U-La detection (wavelength = 0.9A) requires the use of LiF (220) or (420), not generally available on most instruments. Strong peak overlaps of Th on U make highly accurate interference correction mandatory, with problems compounded by the ThMIV and ThMV absorption edges affecting peak, background, and interference calibration measurements (especially the interference of the Th M line family on UMb). Complex REE bearing phases such as monazite, zircon, and allanite have particularly complex interference issues due to multiple peak and background overlaps from elements present in the activation

  2. Accurate stone analysis: the impact on disease diagnosis and treatment.

    PubMed

    Mandel, Neil S; Mandel, Ian C; Kolbach-Mandel, Ann M

    2017-02-01

    This manuscript reviews the requirements for acceptable compositional analysis of kidney stones using various biophysical methods. High-resolution X-ray powder diffraction crystallography and Fourier transform infrared spectroscopy (FTIR) are the only acceptable methods in our labs for kidney stone analysis. The use of well-constructed spectral reference libraries is the basis for accurate and complete stone analysis. The literature included in this manuscript identify errors in most commercial laboratories and in some academic centers. We provide personal comments on why such errors are occurring at such high rates, and although the work load is rather large, it is very worthwhile in providing accurate stone compositions. We also provide the results of our almost 90,000 stone analyses and a breakdown of the number of components we have observed in the various stones. We also offer advice on determining the method used by the various FTIR equipment manufacturers who also provide a stone analysis library so that the FTIR users can feel comfortable in the accuracy of their reported results. Such an analysis on the accuracy of the individual reference libraries could positively influence the reduction in their respective error rates.

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  4. Quantitative Analysis of Radar Returns from Insects

    NASA Technical Reports Server (NTRS)

    Riley, J. R.

    1979-01-01

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

  5. Accurate interlaminar stress recovery from finite element analysis

    NASA Technical Reports Server (NTRS)

    Tessler, Alexander; Riggs, H. Ronald

    1994-01-01

    The accuracy and robustness of a two-dimensional smoothing methodology is examined for the problem of recovering accurate interlaminar shear stress distributions in laminated composite and sandwich plates. The smoothing methodology is based on a variational formulation which combines discrete least-squares and penalty-constraint functionals in a single variational form. The smoothing analysis utilizes optimal strains computed at discrete locations in a finite element analysis. These discrete strain data are smoothed with a smoothing element discretization, producing superior accuracy strains and their first gradients. The approach enables the resulting smooth strain field to be practically C1-continuous throughout the domain of smoothing, exhibiting superconvergent properties of the smoothed quantity. The continuous strain gradients are also obtained directly from the solution. The recovered strain gradients are subsequently employed in the integration o equilibrium equations to obtain accurate interlaminar shear stresses. The problem is a simply-supported rectangular plate under a doubly sinusoidal load. The problem has an exact analytic solution which serves as a measure of goodness of the recovered interlaminar shear stresses. The method has the versatility of being applicable to the analysis of rather general and complex structures built of distinct components and materials, such as found in aircraft design. For these types of structures, the smoothing is achieved with 'patches', each patch covering the domain in which the smoothed quantity is physically continuous.

  6. How accurate is the Kubelka-Munk theory of diffuse reflection? A quantitative answer

    NASA Astrophysics Data System (ADS)

    Joseph, Richard I.; Thomas, Michael E.

    2012-10-01

    The (heuristic) Kubelka-Munk theory of diffuse reflectance and transmittance of a film on a substrate, which is widely used because it gives simple analytic results, is compared to the rigorous radiative transfer model of Chandrasekhar. The rigorous model has to be numerically solved, thus is less intuitive. The Kubelka-Munk theory uses an absorption coefficient and scatter coefficient as inputs, similar to the rigorous model of Chandrasekhar. The relationship between these two sets of coefficients is addressed. It is shown that the Kubelka-Munk theory is remarkably accurate if one uses the proper albedo parameter.

  7. Novel micelle PCR-based method for accurate, sensitive and quantitative microbiota profiling.

    PubMed

    Boers, Stefan A; Hays, John P; Jansen, Ruud

    2017-04-05

    In the last decade, many researchers have embraced 16S rRNA gene sequencing techniques, which has led to a wealth of publications and documented differences in the composition of microbial communities derived from many different ecosystems. However, comparison between different microbiota studies is currently very difficult due to the lack of a standardized 16S rRNA gene sequencing protocol. Here we report on a novel approach employing micelle PCR (micPCR) in combination with an internal calibrator that allows for standardization of microbiota profiles via their absolute abundances. The addition of an internal calibrator allows the researcher to express the resulting operational taxonomic units (OTUs) as a measure of 16S rRNA gene copies by correcting the number of sequences of each individual OTU in a sample for efficiency differences in the NGS process. Additionally, accurate quantification of OTUs obtained from negative extraction control samples allows for the subtraction of contaminating bacterial DNA derived from the laboratory environment or chemicals/reagents used. Using equimolar synthetic microbial community samples and low biomass clinical samples, we demonstrate that the calibrated micPCR/NGS methodology possess a much higher precision and a lower limit of detection compared with traditional PCR/NGS, resulting in more accurate microbiota profiles suitable for multi-study comparison.

  8. Novel micelle PCR-based method for accurate, sensitive and quantitative microbiota profiling

    PubMed Central

    Boers, Stefan A.; Hays, John P.; Jansen, Ruud

    2017-01-01

    In the last decade, many researchers have embraced 16S rRNA gene sequencing techniques, which has led to a wealth of publications and documented differences in the composition of microbial communities derived from many different ecosystems. However, comparison between different microbiota studies is currently very difficult due to the lack of a standardized 16S rRNA gene sequencing protocol. Here we report on a novel approach employing micelle PCR (micPCR) in combination with an internal calibrator that allows for standardization of microbiota profiles via their absolute abundances. The addition of an internal calibrator allows the researcher to express the resulting operational taxonomic units (OTUs) as a measure of 16S rRNA gene copies by correcting the number of sequences of each individual OTU in a sample for efficiency differences in the NGS process. Additionally, accurate quantification of OTUs obtained from negative extraction control samples allows for the subtraction of contaminating bacterial DNA derived from the laboratory environment or chemicals/reagents used. Using equimolar synthetic microbial community samples and low biomass clinical samples, we demonstrate that the calibrated micPCR/NGS methodology possess a much higher precision and a lower limit of detection compared with traditional PCR/NGS, resulting in more accurate microbiota profiles suitable for multi-study comparison. PMID:28378789

  9. Development and Validation of a Highly Accurate Quantitative Real-Time PCR Assay for Diagnosis of Bacterial Vaginosis

    PubMed Central

    Smith, William L.; Chadwick, Sean G.; Toner, Geoffrey; Mordechai, Eli; Adelson, Martin E.; Aguin, Tina J.; Sobel, Jack D.

    2016-01-01

    Bacterial vaginosis (BV) is the most common gynecological infection in the United States. Diagnosis based on Amsel's criteria can be challenging and can be aided by laboratory-based testing. A standard method for diagnosis in research studies is enumeration of bacterial morphotypes of a Gram-stained vaginal smear (i.e., Nugent scoring). However, this technique is subjective, requires specialized training, and is not widely available. Therefore, a highly accurate molecular assay for the diagnosis of BV would be of great utility. We analyzed 385 vaginal specimens collected prospectively from subjects who were evaluated for BV by clinical signs and Nugent scoring. We analyzed quantitative real-time PCR (qPCR) assays on DNA extracted from these specimens to quantify nine organisms associated with vaginal health or disease: Gardnerella vaginalis, Atopobium vaginae, BV-associated bacteria 2 (BVAB2, an uncultured member of the order Clostridiales), Megasphaera phylotype 1 or 2, Lactobacillus iners, Lactobacillus crispatus, Lactobacillus gasseri, and Lactobacillus jensenii. We generated a logistic regression model that identified G. vaginalis, A. vaginae, and Megasphaera phylotypes 1 and 2 as the organisms for which quantification provided the most accurate diagnosis of symptomatic BV, as defined by Amsel's criteria and Nugent scoring, with 92% sensitivity, 95% specificity, 94% positive predictive value, and 94% negative predictive value. The inclusion of Lactobacillus spp. did not contribute sufficiently to the quantitative model for symptomatic BV detection. This molecular assay is a highly accurate laboratory tool to assist in the diagnosis of symptomatic BV. PMID:26818677

  10. Quantitative analysis of glycoprotein glycans.

    PubMed

    Orlando, Ron

    2013-01-01

    The ability to quantitatively determine changes in the N- and O-linked glycans is an essential component of comparative glycomics. Multiple strategies are available to by which this can be accomplished, including; both label free approaches and isotopic labeling strategies. The focus of this chapter is to describe each of these approaches while providing insight into their strengths and weaknesses, so that glycomic investigators can make an educated choice of the strategy that is best suited for their particular application.

  11. Automated and quantitative headspace in-tube extraction for the accurate determination of highly volatile compounds from wines and beers.

    PubMed

    Zapata, Julián; Mateo-Vivaracho, Laura; Lopez, Ricardo; Ferreira, Vicente

    2012-03-23

    An automatic headspace in-tube extraction (ITEX) method for the accurate determination of acetaldehyde, ethyl acetate, diacetyl and other volatile compounds from wine and beer has been developed and validated. Method accuracy is based on the nearly quantitative transference of volatile compounds from the sample to the ITEX trap. For achieving that goal most methodological aspects and parameters have been carefully examined. The vial and sample sizes and the trapping materials were found to be critical due to the pernicious saturation effects of ethanol. Small 2 mL vials containing very small amounts of sample (20 μL of 1:10 diluted sample) and a trap filled with 22 mg of Bond Elut ENV resins could guarantee a complete trapping of sample vapors. The complete extraction requires 100 × 0.5 mL pumping strokes at 60 °C and takes 24 min. Analytes are further desorbed at 240 °C into the GC injector under a 1:5 split ratio. The proportion of analytes finally transferred to the trap ranged from 85 to 99%. The validation of the method showed satisfactory figures of merit. Determination coefficients were better than 0.995 in all cases and good repeatability was also obtained (better than 7% in all cases). Reproducibility was better than 8.3% except for acetaldehyde (13.1%). Detection limits were below the odor detection thresholds of these target compounds in wine and beer and well below the normal ranges of occurrence. Recoveries were not significantly different to 100%, except in the case of acetaldehyde. In such a case it could be determined that the method is not able to break some of the adducts that this compound forms with sulfites. However, such problem was avoided after incubating the sample with glyoxal. The method can constitute a general and reliable alternative for the analysis of very volatile compounds in other difficult matrixes.

  12. There's plenty of gloom at the bottom: the many challenges of accurate quantitation in size-based oligomeric separations.

    PubMed

    Striegel, André M

    2013-11-01

    There is a variety of small-molecule species (e.g., tackifiers, plasticizers, oligosaccharides) the size-based characterization of which is of considerable scientific and industrial importance. Likewise, quantitation of the amount of oligomers in a polymer sample is crucial for the import and export of substances into the USA and European Union (EU). While the characterization of ultra-high molar mass macromolecules by size-based separation techniques is generally considered a challenge, it is this author's contention that a greater challenge is encountered when trying to perform, for quantitation purposes, separations in and of the oligomeric region. The latter thesis is expounded herein, by detailing the various obstacles encountered en route to accurate, quantitative oligomeric separations by entropically dominated techniques such as size-exclusion chromatography, hydrodynamic chromatography, and asymmetric flow field-flow fractionation, as well as by methods which are, principally, enthalpically driven such as liquid adsorption and temperature gradient interaction chromatography. These obstacles include, among others, the diminished sensitivity of static light scattering (SLS) detection at low molar masses, the non-constancy of the response of SLS and of commonly employed concentration-sensitive detectors across the oligomeric region, and the loss of oligomers through the accumulation wall membrane in asymmetric flow field-flow fractionation. The battle is not lost, however, because, with some care and given a sufficient supply of sample, the quantitation of both individual oligomeric species and of the total oligomeric region is often possible.

  13. Quantitation of Insulin-Like Growth Factor 1 in Serum by Liquid Chromatography High Resolution Accurate-Mass Mass Spectrometry.

    PubMed

    Ketha, Hemamalini; Singh, Ravinder J

    2016-01-01

    Insulin-like growth factor 1 (IGF-1) is a 70 amino acid peptide hormone which acts as the principal mediator of the effects of growth hormone (GH). Due to a wide variability in circulating concentration of GH, IGF-1 quantitation is the first step in the diagnosis of GH excess or deficiency. Majority (>95 %) of IGF-1 circulates as a ternary complex along with its principle binding protein insulin-like growth factor 1 binding protein 3 (IGFBP-3) and acid labile subunit. The assay design approach for IGF-1 quantitation has to include a step to dissociate IGF-1 from its ternary complex. Several commercial assays employ a buffer containing acidified ethanol to achieve this. Despite several modifications, commercially available immunoassays have been shown to have challenges with interference from IGFBP-3. Additionally, inter-method comparison between IGF-1 immunoassays has been shown to be suboptimal. Mass spectrometry has been utilized for quantitation of IGF-1. In this chapter a liquid chromatography high resolution accurate-mass mass spectrometry (LC-HRAMS) based method for IGF-1 quantitation has been described.

  14. Electron Microprobe Analysis Techniques for Accurate Measurements of Apatite

    NASA Astrophysics Data System (ADS)

    Goldoff, B. A.; Webster, J. D.; Harlov, D. E.

    2010-12-01

    Apatite [Ca5(PO4)3(F, Cl, OH)] is a ubiquitous accessory mineral in igneous, metamorphic, and sedimentary rocks. The mineral contains halogens and hydroxyl ions, which can provide important constraints on fugacities of volatile components in fluids and other phases in igneous and metamorphic environments in which apatite has equilibrated. Accurate measurements of these components in apatite are therefore necessary. Analyzing apatite by electron microprobe (EMPA), which is a commonly used geochemical analytical technique, has often been found to be problematic and previous studies have identified sources of error. For example, Stormer et al. (1993) demonstrated that the orientation of an apatite grain relative to the incident electron beam could significantly affect the concentration results. In this study, a variety of alternative EMPA operating conditions for apatite analysis were investigated: a range of electron beam settings, count times, crystal grain orientations, and calibration standards were tested. Twenty synthetic anhydrous apatite samples that span the fluorapatite-chlorapatite solid solution series, and whose halogen concentrations were determined by wet chemistry, were analyzed. Accurate measurements of these samples were obtained with many EMPA techniques. One effective method includes setting a static electron beam to 10-15nA, 15kV, and 10 microns in diameter. Additionally, the apatite sample is oriented with the crystal’s c-axis parallel to the slide surface and the count times are moderate. Importantly, the F and Cl EMPA concentrations are in extremely good agreement with the wet-chemical data. We also present EMPA operating conditions and techniques that are problematic and should be avoided. J.C. Stormer, Jr. et al., Am. Mineral. 78 (1993) 641-648.

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

    SciTech Connect

    Pourmoghaddas, Amir Wells, R. Glenn

    2016-01-15

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

  16. Quantitative analysis of qualitative images

    NASA Astrophysics Data System (ADS)

    Hockney, David; Falco, Charles M.

    2005-03-01

    We show optical evidence that demonstrates artists as early as Jan van Eyck and Robert Campin (c1425) used optical projections as aids for producing their paintings. We also have found optical evidence within works by later artists, including Bermejo (c1475), Lotto (c1525), Caravaggio (c1600), de la Tour (c1650), Chardin (c1750) and Ingres (c1825), demonstrating a continuum in the use of optical projections by artists, along with an evolution in the sophistication of that use. However, even for paintings where we have been able to extract unambiguous, quantitative evidence of the direct use of optical projections for producing certain of the features, this does not mean that paintings are effectively photographs. Because the hand and mind of the artist are intimately involved in the creation process, understanding these complex images requires more than can be obtained from only applying the equations of geometrical optics.

  17. Development and Validation of a Highly Accurate Quantitative Real-Time PCR Assay for Diagnosis of Bacterial Vaginosis.

    PubMed

    Hilbert, David W; Smith, William L; Chadwick, Sean G; Toner, Geoffrey; Mordechai, Eli; Adelson, Martin E; Aguin, Tina J; Sobel, Jack D; Gygax, Scott E

    2016-04-01

    Bacterial vaginosis (BV) is the most common gynecological infection in the United States. Diagnosis based on Amsel's criteria can be challenging and can be aided by laboratory-based testing. A standard method for diagnosis in research studies is enumeration of bacterial morphotypes of a Gram-stained vaginal smear (i.e., Nugent scoring). However, this technique is subjective, requires specialized training, and is not widely available. Therefore, a highly accurate molecular assay for the diagnosis of BV would be of great utility. We analyzed 385 vaginal specimens collected prospectively from subjects who were evaluated for BV by clinical signs and Nugent scoring. We analyzed quantitative real-time PCR (qPCR) assays on DNA extracted from these specimens to quantify nine organisms associated with vaginal health or disease:Gardnerella vaginalis,Atopobium vaginae, BV-associated bacteria 2 (BVAB2, an uncultured member of the orderClostridiales),Megasphaeraphylotype 1 or 2,Lactobacillus iners,Lactobacillus crispatus,Lactobacillus gasseri, andLactobacillus jensenii We generated a logistic regression model that identifiedG. vaginalis,A. vaginae, andMegasphaeraphylotypes 1 and 2 as the organisms for which quantification provided the most accurate diagnosis of symptomatic BV, as defined by Amsel's criteria and Nugent scoring, with 92% sensitivity, 95% specificity, 94% positive predictive value, and 94% negative predictive value. The inclusion ofLactobacillusspp. did not contribute sufficiently to the quantitative model for symptomatic BV detection. This molecular assay is a highly accurate laboratory tool to assist in the diagnosis of symptomatic BV.

  18. Quantitative histogram analysis of images

    NASA Astrophysics Data System (ADS)

    Holub, Oliver; Ferreira, Sérgio T.

    2006-11-01

    A routine for histogram analysis of images has been written in the object-oriented, graphical development environment LabVIEW. The program converts an RGB bitmap image into an intensity-linear greyscale image according to selectable conversion coefficients. This greyscale image is subsequently analysed by plots of the intensity histogram and probability distribution of brightness, and by calculation of various parameters, including average brightness, standard deviation, variance, minimal and maximal brightness, mode, skewness and kurtosis of the histogram and the median of the probability distribution. The program allows interactive selection of specific regions of interest (ROI) in the image and definition of lower and upper threshold levels (e.g., to permit the removal of a constant background signal). The results of the analysis of multiple images can be conveniently saved and exported for plotting in other programs, which allows fast analysis of relatively large sets of image data. The program file accompanies this manuscript together with a detailed description of two application examples: The analysis of fluorescence microscopy images, specifically of tau-immunofluorescence in primary cultures of rat cortical and hippocampal neurons, and the quantification of protein bands by Western-blot. The possibilities and limitations of this kind of analysis are discussed. Program summaryTitle of program: HAWGC Catalogue identifier: ADXG_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADXG_v1_0 Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Computers: Mobile Intel Pentium III, AMD Duron Installations: No installation necessary—Executable file together with necessary files for LabVIEW Run-time engine Operating systems or monitors under which the program has been tested: WindowsME/2000/XP Programming language used: LabVIEW 7.0 Memory required to execute with typical data:˜16MB for starting and ˜160MB used for

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

    PubMed Central

    Jeffares, Daniel C.; Arzhaeva, Yulia; Bähler, Jürg

    2017-01-01

    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. PMID:27712582

  20. 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.

  1. Quantitative analysis of the heterogeneous population of endocytic vesicles.

    PubMed

    Kozlov, Konstantin; Kosheverova, Vera; Kamentseva, Rimma; Kharchenko, Marianna; Sokolkova, Alena; Kornilova, Elena; Samsonova, Maria

    2017-03-07

    The quantitative characterization of endocytic vesicles in images acquired with microscope is critically important for deciphering of endocytosis mechanisms. Image segmentation is the most important step of quantitative image analysis. In spite of availability of many segmentation methods, the accurate segmentation is challenging when the images are heterogeneous with respect to object shapes and signal intensities what is typical for images of endocytic vesicles. We present a Morphological reconstruction and Contrast mapping segmentation method (MrComas) for the segmentation of the endocytic vesicle population that copes with the heterogeneity in their shape and intensity. The method uses morphological opening and closing by reconstruction in the vicinity of local minima and maxima respectively thus creating the strong contrast between their basins of attraction. As a consequence, the intensity is flattened within the objects and their edges are enhanced. The method accurately recovered quantitative characteristics of synthetic images that preserve characteristic features of the endocytic vesicle population. In benchmarks and quantitative comparisons with two other popular segmentation methods, namely manual thresholding and Squash plugin, MrComas shows the best segmentation results on real biological images of EGFR (Epidermal Growth Factor Receptor) endocytosis. As a proof of feasibility, the method was applied to quantify the dynamical behavior of Early Endosomal Autoantigen 1 (EEA1)-positive endosome subpopulations during EGF-stimulated endocytosis.

  2. On the accurate molecular dynamics analysis of biological molecules

    NASA Astrophysics Data System (ADS)

    Yamashita, Takefumi

    2016-12-01

    As the evolution of computational technology has now enabled long molecular dynamics (MD) simulation, the evaluation of many physical properties shows improved convergence. Therefore, we can examine the detailed conditions of MD simulations and perform quantitative MD analyses. In this study, we address the quantitative and accuracy aspects of MD simulations using two example systems. First, it is found that several conditions of the MD simulations influence the area/lipid of the lipid bilayer. Second, we successfully detect the small but important differences in antibody motion between the antigen-bound and unbound states.

  3. Renal Cortical Lactate Dehydrogenase: A Useful, Accurate, Quantitative Marker of In Vivo Tubular Injury and Acute Renal Failure

    PubMed Central

    Zager, Richard A.; Johnson, Ali C. M.; Becker, Kirsten

    2013-01-01

    Studies of experimental acute kidney injury (AKI) are critically dependent on having precise methods for assessing the extent of tubular cell death. However, the most widely used techniques either provide indirect assessments (e.g., BUN, creatinine), suffer from the need for semi-quantitative grading (renal histology), or reflect the status of residual viable, not the number of lost, renal tubular cells (e.g., NGAL content). Lactate dehydrogenase (LDH) release is a highly reliable test for assessing degrees of in vitro cell death. However, its utility as an in vivo AKI marker has not been defined. Towards this end, CD-1 mice were subjected to graded renal ischemia (0, 15, 22, 30, 40, or 60 min) or to nephrotoxic (glycerol; maleate) AKI. Sham operated mice, or mice with AKI in the absence of acute tubular necrosis (ureteral obstruction; endotoxemia), served as negative controls. Renal cortical LDH or NGAL levels were assayed 2 or 24 hrs later. Ischemic, glycerol, and maleate-induced AKI were each associated with striking, steep, inverse correlations (r, −0.89) between renal injury severity and renal LDH content. With severe AKI, >65% LDH declines were observed. Corresponding prompt plasma and urinary LDH increases were observed. These observations, coupled with the maintenance of normal cortical LDH mRNA levels, indicated the renal LDH efflux, not decreased LDH synthesis, caused the falling cortical LDH levels. Renal LDH content was well maintained with sham surgery, ureteral obstruction or endotoxemic AKI. In contrast to LDH, renal cortical NGAL levels did not correlate with AKI severity. In sum, the above results indicate that renal cortical LDH assay is a highly accurate quantitative technique for gauging the extent of experimental acute ischemic and toxic renal injury. That it avoids the limitations of more traditional AKI markers implies great potential utility in experimental studies that require precise quantitation of tubule cell death. PMID:23825563

  4. Quantitative WDS analysis using electron probe microanalyzer

    SciTech Connect

    Ul-Hamid, Anwar . E-mail: anwar@kfupm.edu.sa; Tawancy, Hani M.; Mohammed, Abdul-Rashid I.; Al-Jaroudi, Said S.; Abbas, Nureddin M.

    2006-04-15

    In this paper, the procedure for conducting quantitative elemental analysis by ZAF correction method using wavelength dispersive X-ray spectroscopy (WDS) in an electron probe microanalyzer (EPMA) is elaborated. Analysis of a thermal barrier coating (TBC) system formed on a Ni-based single crystal superalloy is presented as an example to illustrate the analysis of samples consisting of a large number of major and minor elements. The analysis was performed by known standards and measured peak-to-background intensity ratios. The procedure for using separate set of acquisition conditions for major and minor element analysis is explained and its importance is stressed.

  5. Seniors' Online Communities: A Quantitative Content Analysis

    ERIC Educational Resources Information Center

    Nimrod, Galit

    2010-01-01

    Purpose: To examine the contents and characteristics of seniors' online communities and to explore their potential benefits to older adults. Design and Methods: Quantitative content analysis of a full year's data from 14 leading online communities using a novel computerized system. The overall database included 686,283 messages. Results: There was…

  6. A quantitative approach to scar analysis.

    PubMed

    Khorasani, Hooman; Zheng, Zhong; Nguyen, Calvin; Zara, Janette; Zhang, Xinli; Wang, Joyce; Ting, Kang; Soo, Chia

    2011-02-01

    Analysis of collagen architecture is essential to wound healing research. However, to date no consistent methodologies exist for quantitatively assessing dermal collagen architecture in scars. In this study, we developed a standardized approach for quantitative analysis of scar collagen morphology by confocal microscopy using fractal dimension and lacunarity analysis. Full-thickness wounds were created on adult mice, closed by primary intention, and harvested at 14 days after wounding for morphometrics and standard Fourier transform-based scar analysis as well as fractal dimension and lacunarity analysis. In addition, transmission electron microscopy was used to evaluate collagen ultrastructure. We demonstrated that fractal dimension and lacunarity analysis were superior to Fourier transform analysis in discriminating scar versus unwounded tissue in a wild-type mouse model. To fully test the robustness of this scar analysis approach, a fibromodulin-null mouse model that heals with increased scar was also used. Fractal dimension and lacunarity analysis effectively discriminated unwounded fibromodulin-null versus wild-type skin as well as healing fibromodulin-null versus wild-type wounds, whereas Fourier transform analysis failed to do so. Furthermore, fractal dimension and lacunarity data also correlated well with transmission electron microscopy collagen ultrastructure analysis, adding to their validity. These results demonstrate that fractal dimension and lacunarity are more sensitive than Fourier transform analysis for quantification of scar morphology.

  7. Quantitative ADF STEM: acquisition, analysis and interpretation

    NASA Astrophysics Data System (ADS)

    Jones, L.

    2016-01-01

    Quantitative annular dark-field in the scanning transmission electron microscope (ADF STEM), where image intensities are used to provide composition and thickness measurements, has enjoyed a renaissance during the last decade. Now in a post aberration-correction era many aspects of the technique are being revisited. Here the recent progress and emerging best-practice for such aberration corrected quantitative ADF STEM is discussed including issues relating to proper acquisition of experimental data and its calibration, approaches for data analysis, the utility of such data, its interpretation and limitations.

  8. Method and apparatus for chromatographic quantitative analysis

    DOEpatents

    Fritz, James S.; Gjerde, Douglas T.; Schmuckler, Gabriella

    1981-06-09

    An improved apparatus and method for the quantitative analysis of a solution containing a plurality of anion species by ion exchange chromatography which utilizes a single eluent and a single ion exchange bed which does not require periodic regeneration. The solution containing the anions is added to an anion exchange resin bed which is a low capacity macroreticular polystyrene-divinylbenzene resin containing quarternary ammonium functional groups, and is eluted therefrom with a dilute solution of a low electrical conductance organic acid salt. As each anion species is eluted from the bed, it is quantitatively sensed by conventional detection means such as a conductivity cell.

  9. Comprehensive quantitative analysis on privacy leak behavior.

    PubMed

    Fan, Lejun; Wang, Yuanzhuo; Jin, Xiaolong; Li, Jingyuan; Cheng, Xueqi; Jin, Shuyuan

    2013-01-01

    Privacy information is prone to be leaked by illegal software providers with various motivations. Privacy leak behavior has thus become an important research issue of cyber security. However, existing approaches can only qualitatively analyze privacy leak behavior of software applications. No quantitative approach, to the best of our knowledge, has been developed in the open literature. To fill this gap, in this paper we propose for the first time four quantitative metrics, namely, possibility, severity, crypticity, and manipulability, for privacy leak behavior analysis based on Privacy Petri Net (PPN). In order to compare the privacy leak behavior among different software, we further propose a comprehensive metric, namely, overall leak degree, based on these four metrics. Finally, we validate the effectiveness of the proposed approach using real-world software applications. The experimental results demonstrate that our approach can quantitatively analyze the privacy leak behaviors of various software types and reveal their characteristics from different aspects.

  10. Comprehensive Quantitative Analysis on Privacy Leak Behavior

    PubMed Central

    Fan, Lejun; Wang, Yuanzhuo; Jin, Xiaolong; Li, Jingyuan; Cheng, Xueqi; Jin, Shuyuan

    2013-01-01

    Privacy information is prone to be leaked by illegal software providers with various motivations. Privacy leak behavior has thus become an important research issue of cyber security. However, existing approaches can only qualitatively analyze privacy leak behavior of software applications. No quantitative approach, to the best of our knowledge, has been developed in the open literature. To fill this gap, in this paper we propose for the first time four quantitative metrics, namely, possibility, severity, crypticity, and manipulability, for privacy leak behavior analysis based on Privacy Petri Net (PPN). In order to compare the privacy leak behavior among different software, we further propose a comprehensive metric, namely, overall leak degree, based on these four metrics. Finally, we validate the effectiveness of the proposed approach using real-world software applications. The experimental results demonstrate that our approach can quantitatively analyze the privacy leak behaviors of various software types and reveal their characteristics from different aspects. PMID:24066046

  11. Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags

    PubMed Central

    Lipton, Mary S.; Paša-Tolić, Ljiljana; Anderson, Gordon A.; Anderson, David J.; Auberry, Deanna L.; Battista, John R.; Daly, Michael J.; Fredrickson, Jim; Hixson, Kim K.; Kostandarithes, Heather; Masselon, Christophe; Markillie, Lye Meng; Moore, Ronald J.; Romine, Margaret F.; Shen, Yufeng; Stritmatter, Eric; Tolić, Nikola; Udseth, Harold R.; Venkateswaran, Amudhan; Wong, Kwong-Kwok; Zhao, Rui; Smith, Richard D.

    2002-01-01

    Understanding biological systems and the roles of their constituents is facilitated by the ability to make quantitative, sensitive, and comprehensive measurements of how their proteome changes, e.g., in response to environmental perturbations. To this end, we have developed a high-throughput methodology to characterize an organism's dynamic proteome based on the combination of global enzymatic digestion, high-resolution liquid chromatographic separations, and analysis by Fourier transform ion cyclotron resonance mass spectrometry. The peptides produced serve as accurate mass tags for the proteins and have been used to identify with high confidence >61% of the predicted proteome for the ionizing radiation-resistant bacterium Deinococcus radiodurans. This fraction represents the broadest proteome coverage for any organism to date and includes 715 proteins previously annotated as either hypothetical or conserved hypothetical. PMID:12177431

  12. Accurate, fast and cost-effective diagnostic test for monosomy 1p36 using real-time quantitative PCR.

    PubMed

    Cunha, Pricila da Silva; Pena, Heloisa B; D'Angelo, Carla Sustek; Koiffmann, Celia P; Rosenfeld, Jill A; Shaffer, Lisa G; Stofanko, Martin; Gonçalves-Dornelas, Higgor; Pena, Sérgio Danilo Junho

    2014-01-01

    Monosomy 1p36 is considered the most common subtelomeric deletion syndrome in humans and it accounts for 0.5-0.7% of all the cases of idiopathic intellectual disability. The molecular diagnosis is often made by microarray-based comparative genomic hybridization (aCGH), which has the drawback of being a high-cost technique. However, patients with classic monosomy 1p36 share some typical clinical characteristics that, together with its common prevalence, justify the development of a less expensive, targeted diagnostic method. In this study, we developed a simple, rapid, and inexpensive real-time quantitative PCR (qPCR) assay for targeted diagnosis of monosomy 1p36, easily accessible for low-budget laboratories in developing countries. For this, we have chosen two target genes which are deleted in the majority of patients with monosomy 1p36: PRKCZ and SKI. In total, 39 patients previously diagnosed with monosomy 1p36 by aCGH, fluorescent in situ hybridization (FISH), and/or multiplex ligation-dependent probe amplification (MLPA) all tested positive on our qPCR assay. By simultaneously using these two genes we have been able to detect 1p36 deletions with 100% sensitivity and 100% specificity. We conclude that qPCR of PRKCZ and SKI is a fast and accurate diagnostic test for monosomy 1p36, costing less than 10 US dollars in reagent costs.

  13. Accurate, Fast and Cost-Effective Diagnostic Test for Monosomy 1p36 Using Real-Time Quantitative PCR

    PubMed Central

    Cunha, Pricila da Silva; Pena, Heloisa B.; D'Angelo, Carla Sustek; Koiffmann, Celia P.; Rosenfeld, Jill A.; Shaffer, Lisa G.; Stofanko, Martin; Gonçalves-Dornelas, Higgor; Pena, Sérgio Danilo Junho

    2014-01-01

    Monosomy 1p36 is considered the most common subtelomeric deletion syndrome in humans and it accounts for 0.5–0.7% of all the cases of idiopathic intellectual disability. The molecular diagnosis is often made by microarray-based comparative genomic hybridization (aCGH), which has the drawback of being a high-cost technique. However, patients with classic monosomy 1p36 share some typical clinical characteristics that, together with its common prevalence, justify the development of a less expensive, targeted diagnostic method. In this study, we developed a simple, rapid, and inexpensive real-time quantitative PCR (qPCR) assay for targeted diagnosis of monosomy 1p36, easily accessible for low-budget laboratories in developing countries. For this, we have chosen two target genes which are deleted in the majority of patients with monosomy 1p36: PRKCZ and SKI. In total, 39 patients previously diagnosed with monosomy 1p36 by aCGH, fluorescent in situ hybridization (FISH), and/or multiplex ligation-dependent probe amplification (MLPA) all tested positive on our qPCR assay. By simultaneously using these two genes we have been able to detect 1p36 deletions with 100% sensitivity and 100% specificity. We conclude that qPCR of PRKCZ and SKI is a fast and accurate diagnostic test for monosomy 1p36, costing less than 10 US dollars in reagent costs. PMID:24839341

  14. Good practices for quantitative bias analysis.

    PubMed

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

    2014-12-01

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

  15. Quantitative image analysis of celiac disease.

    PubMed

    Ciaccio, Edward J; Bhagat, Govind; Lewis, Suzanne K; Green, Peter H

    2015-03-07

    We outline the use of quantitative techniques that are currently used for analysis of celiac disease. Image processing techniques can be useful to statistically analyze the pixular data of endoscopic images that is acquired with standard or videocapsule endoscopy. It is shown how current techniques have evolved to become more useful for gastroenterologists who seek to understand celiac disease and to screen for it in suspected patients. New directions for focus in the development of methodology for diagnosis and treatment of this disease are suggested. It is evident that there are yet broad areas where there is potential to expand the use of quantitative techniques for improved analysis in suspected or known celiac disease patients.

  16. Quantitative analysis to guide orphan drug development.

    PubMed

    Lesko, L J

    2012-08-01

    The development of orphan drugs for rare diseases has made impressive strides in the past 10 years. There has been a surge in orphan drug designations, but new drug approvals have not kept up. This article presents a three-pronged hierarchical strategy for quantitative analysis of data at the descriptive, mechanistic, and systems levels of the biological system that could represent a standardized and rational approach to orphan drug development. Examples are provided to illustrate the concept.

  17. Using Qualitative Hazard Analysis to Guide Quantitative Safety Analysis

    NASA Technical Reports Server (NTRS)

    Shortle, J. F.; Allocco, M.

    2005-01-01

    Quantitative methods can be beneficial in many types of safety investigations. However, there are many difficulties in using quantitative m ethods. Far example, there may be little relevant data available. This paper proposes a framework for using quantitative hazard analysis to prioritize hazard scenarios most suitable for quantitative mziysis. The framework first categorizes hazard scenarios by severity and likelihood. We then propose another metric "modeling difficulty" that desc ribes the complexity in modeling a given hazard scenario quantitatively. The combined metrics of severity, likelihood, and modeling difficu lty help to prioritize hazard scenarios for which quantitative analys is should be applied. We have applied this methodology to proposed concepts of operations for reduced wake separation for airplane operatio ns at closely spaced parallel runways.

  18. Influence analysis in quantitative trait loci detection

    PubMed Central

    Dou, Xiaoling; Kuriki, Satoshi; Maeno, Akiteru; Takada, Toyoyuki; Shiroishi, Toshihiko

    2014-01-01

    This paper presents systematic methods for the detection of influential individuals that affect the log odds (LOD) score curve. We derive general formulas of influence functions for profile likelihoods and introduce them into two standard quantitative trait locus detection methods—the interval mapping method and single marker analysis. Besides influence analysis on specific LOD scores, we also develop influence analysis methods on the shape of the LOD score curves. A simulation-based method is proposed to assess the significance of the influence of the individuals. These methods are shown useful in the influence analysis of a real dataset of an experimental population from an F2 mouse cross. By receiver operating characteristic analysis, we confirm that the proposed methods show better performance than existing diagnostics. PMID:24740424

  19. Flow quantitation by radio frequency analysis of contrast echocardiography.

    PubMed

    Rovai, D; Lombardi, M; Mazzarisi, A; Landini, L; Taddei, L; Distante, A; Benassi, A; L'Abbate, A

    1993-03-01

    Contrast echocardiography has the potential for measuring cardiac output and regional blood flow. However, accurate quantitation is limited both by the use of non-standard contrast agents and by the electronic signal distortion inherent to the echocardiographic instruments. Thus, the aim of this study is to quantify flow by combining a stable contrast agent and a modified echo equipment, able to sample the radio frequency (RF) signal from a region of interest (ROI) in the echo image. The contrast agent SHU-454 (0.8 ml) was bolus injected into an in vitro calf vein, at 23 flow rates (ranging from 376 to 3620 ml/min) but constant volume and pressure. The ROI was placed in the centre of the vein, the RF signal was processed in real time and transferred to a personal computer to generate time-intensity curves. In the absence of recirculation, contrast washout slope and mean transit time (MTT) of curves (1.11-8.52 seconds) yielded excellent correlations with flow: r = 0.93 and 0.95, respectively. To compare the accuracy of RF analysis with that of conventional image processing as to flow quantitation, conventional images were collected in the same flow model by two different scanners: a) the mechanical sector scanner used for RF analysis, and b) a conventional electronic sector scanner. These images were digitized off-line, mean videodensity inside an identical ROI was measured and time-intensity curves were built. MTT by RF was shorter than by videodensitometric analysis of the images generated by the same scanner (p < 0.001). In contrast, MTT by RF was longer than by the conventional scanner (p < 0.001). Significant differences in MTT were also found with changes in the gain setting controls of the conventional scanner. To study the stability of the contrast effect, 6 contrast injections (20 ml) were performed at a constant flow rate during recirculation: the spontaneous decay in RF signal intensity (t1/2 = 64 +/- 8 seconds) was too long to affect MTT significantly

  20. Quantitative resilience analysis through control design.

    SciTech Connect

    Sunderland, Daniel; Vugrin, Eric D.; Camphouse, Russell Chris

    2009-09-01

    Critical infrastructure resilience has become a national priority for the U. S. Department of Homeland Security. System resilience has been studied for several decades in many different disciplines, but no standards or unifying methods exist for critical infrastructure resilience analysis. Few quantitative resilience methods exist, and those existing approaches tend to be rather simplistic and, hence, not capable of sufficiently assessing all aspects of critical infrastructure resilience. This report documents the results of a late-start Laboratory Directed Research and Development (LDRD) project that investigated the development of quantitative resilience through application of control design methods. Specifically, we conducted a survey of infrastructure models to assess what types of control design might be applicable for critical infrastructure resilience assessment. As a result of this survey, we developed a decision process that directs the resilience analyst to the control method that is most likely applicable to the system under consideration. Furthermore, we developed optimal control strategies for two sets of representative infrastructure systems to demonstrate how control methods could be used to assess the resilience of the systems to catastrophic disruptions. We present recommendations for future work to continue the development of quantitative resilience analysis methods.

  1. Infectious titres of sheep scrapie and bovine spongiform encephalopathy agents cannot be accurately predicted from quantitative laboratory test results.

    PubMed

    González, Lorenzo; Thorne, Leigh; Jeffrey, Martin; Martin, Stuart; Spiropoulos, John; Beck, Katy E; Lockey, Richard W; Vickery, Christopher M; Holder, Thomas; Terry, Linda

    2012-11-01

    It is widely accepted that abnormal forms of the prion protein (PrP) are the best surrogate marker for the infectious agent of prion diseases and, in practice, the detection of such disease-associated (PrP(d)) and/or protease-resistant (PrP(res)) forms of PrP is the cornerstone of diagnosis and surveillance of the transmissible spongiform encephalopathies (TSEs). Nevertheless, some studies question the consistent association between infectivity and abnormal PrP detection. To address this discrepancy, 11 brain samples of sheep affected with natural scrapie or experimental bovine spongiform encephalopathy were selected on the basis of the magnitude and predominant types of PrP(d) accumulation, as shown by immunohistochemical (IHC) examination; contra-lateral hemi-brain samples were inoculated at three different dilutions into transgenic mice overexpressing ovine PrP and were also subjected to quantitative analysis by three biochemical tests (BCTs). Six samples gave 'low' infectious titres (10⁶·⁵ to 10⁶·⁷ LD₅₀ g⁻¹) and five gave 'high titres' (10⁸·¹ to ≥ 10⁸·⁷ LD₅₀ g⁻¹) and, with the exception of the Western blot analysis, those two groups tended to correspond with samples with lower PrP(d)/PrP(res) results by IHC/BCTs. However, no statistical association could be confirmed due to high individual sample variability. It is concluded that although detection of abnormal forms of PrP by laboratory methods remains useful to confirm TSE infection, infectivity titres cannot be predicted from quantitative test results, at least for the TSE sources and host PRNP genotypes used in this study. Furthermore, the near inverse correlation between infectious titres and Western blot results (high protease pre-treatment) argues for a dissociation between infectivity and PrP(res).

  2. Accurate feature detection and estimation using nonlinear and multiresolution analysis

    NASA Astrophysics Data System (ADS)

    Rudin, Leonid; Osher, Stanley

    1994-11-01

    A program for feature detection and estimation using nonlinear and multiscale analysis was completed. The state-of-the-art edge detection was combined with multiscale restoration (as suggested by the first author) and robust results in the presence of noise were obtained. Successful applications to numerous images of interest to DOD were made. Also, a new market in the criminal justice field was developed, based in part, on this work.

  3. Toward Sensitive and Accurate Analysis of Antibody Biotherapeutics by Liquid Chromatography Coupled with Mass Spectrometry

    PubMed Central

    An, Bo; Zhang, Ming

    2014-01-01

    Remarkable methodological advances in the past decade have expanded the application of liquid chromatography coupled with mass spectrometry (LC/MS) analysis of biotherapeutics. Currently, LC/MS represents a promising alternative or supplement to the traditional ligand binding assay (LBA) in the pharmacokinetic, pharmacodynamic, and toxicokinetic studies of protein drugs, owing to the rapid and cost-effective method development, high specificity and reproducibility, low sample consumption, the capacity of analyzing multiple targets in one analysis, and the fact that a validated method can be readily adapted across various matrices and species. While promising, technical challenges associated with sensitivity, sample preparation, method development, and quantitative accuracy need to be addressed to enable full utilization of LC/MS. This article introduces the rationale and technical challenges of LC/MS techniques in biotherapeutics analysis and summarizes recently developed strategies to alleviate these challenges. Applications of LC/MS techniques on quantification and characterization of antibody biotherapeutics are also discussed. We speculate that despite the highly attractive features of LC/MS, it will not fully replace traditional assays such as LBA in the foreseeable future; instead, the forthcoming trend is likely the conjunction of biochemical techniques with versatile LC/MS approaches to achieve accurate, sensitive, and unbiased characterization of biotherapeutics in highly complex pharmaceutical/biologic matrices. Such combinations will constitute powerful tools to tackle the challenges posed by the rapidly growing needs for biotherapeutics development. PMID:25185260

  4. Reduction procedures for accurate analysis of MSX surveillance experiment data

    NASA Technical Reports Server (NTRS)

    Gaposchkin, E. Mike; Lane, Mark T.; Abbot, Rick I.

    1994-01-01

    Technical challenges of the Midcourse Space Experiment (MSX) science instruments require careful characterization and calibration of these sensors for analysis of surveillance experiment data. Procedures for reduction of Resident Space Object (RSO) detections will be presented which include refinement and calibration of the metric and radiometric (and photometric) data and calculation of a precise MSX ephemeris. Examples will be given which support the reduction, and these are taken from ground-test data similar in characteristics to the MSX sensors and from the IRAS satellite RSO detections. Examples to demonstrate the calculation of a precise ephemeris will be provided from satellites in similar orbits which are equipped with S-band transponders.

  5. Digitally Enhanced Thin-Layer Chromatography: An Inexpensive, New Technique for Qualitative and Quantitative Analysis

    ERIC Educational Resources Information Center

    Hess, Amber Victoria Irish

    2007-01-01

    A study conducted shows that if digital photography is combined with regular thin-layer chromatography (TLC), it could perform highly improved qualitative analysis as well as make accurate quantitative analysis possible for a much lower cost than commercial equipment. The findings suggest that digitally enhanced TLC (DE-TLC) is low-cost and easy…

  6. Quantitative analysis of non-Hodgkin's lymphoma.

    PubMed Central

    Abbott, C R; Blewitt, R W; Bird, C C

    1982-01-01

    A preliminary attempt has been made to characterise a small series of non-Hodgkin's lymphomas (NHL) by morphometric means using the Quantimet 720 Kontron MOP/AMO3 image analysis systems. In most cases it was found that the distribution of nuclear area and correlation between mean nuclear area and frequency per unit field, corresponded closely with tumour classification determined by light microscopy. These results suggest that it may be possible to devise an objective and reproducible grading system for NHL using quantitative morphometric techniques. PMID:7040479

  7. Quantitative NIR Raman analysis in liquid mixtures.

    PubMed

    Sato-Berrú, R Ysacc; Medina-Valtierra, Jorge; Medina-Gutiérrez, Cirilo; Frausto-Reyes, Claudio

    2004-08-01

    The capability to obtain quantitative information of a simple way from Raman spectra is a subject of considerable interest. In this work, this is demonstrated for mixtures of ethanol with water and rhodamine-6G (R-6G) with methanol, which were analyzed directly in glass vessel. The Raman intensities and a simple mathematical model have been used and applied for the analysis of liquid samples. It is starting point to generate a general expression, from the experimental spectra, as the sum of the particular expression for each pure compound allow us to obtain an expression for the mixtures which can be used for determining concentrations, from the Raman spectrum, of the mixture.

  8. Quantitative analysis of retinal changes in hypertension

    NASA Astrophysics Data System (ADS)

    Giansanti, Roberto; Boemi, Massimo; Fumelli, Paolo; Passerini, Giorgio; Zingaretti, Primo

    1995-05-01

    Arterial hypertension is a high prevalence disease in Western countries and it is associated with increased risk for cardiovascular accidents. Retinal vessel changes are common findings in patients suffering from long-standing hypertensive disease. Morphological evaluations of the fundus oculi represent a fundamental tool for the clinical approach to the patient with hypertension. A qualitative analysis of the retinal lesions is usually performed and this implies severe limitations both in the classification of the different degrees of the pathology and in the follow-up of the disease. A diagnostic system based on a quantitative analysis of the retinal changes could overcome these problems. Our computerized approach was intended for this scope. The paper concentrates on the results and the implications of a computerized approach to the automatic extraction of numerical indexes describing morphological details of the fundus oculi. A previously developed image processing and recognition system, documented elsewhere and briefly described here, was successfully tested in pre-clinical experiments and applied in the evaluation of normal as well as of pathological fundus. The software system was developed to extract indexes such as caliber and path of vessels, local tortuosity of arteries and arterioles, positions and angles of crossings between two vessels. The reliability of the results, justified by their low variability, makes feasible the standardization of quantitative parameters to be used both in the diagnosis and in the prognosis of hypertension, and also allows prospective studies based upon them.

  9. Quantitative interactome analysis reveals a chemoresistant edgotype

    PubMed Central

    Chavez, Juan D.; Schweppe, Devin K.; Eng, Jimmy K.; Zheng, Chunxiang; Taipale, Alex; Zhang, Yiyi; Takara, Kohji; Bruce, James E.

    2015-01-01

    Chemoresistance is a common mode of therapy failure for many cancers. Tumours develop resistance to chemotherapeutics through a variety of mechanisms, with proteins serving pivotal roles. Changes in protein conformations and interactions affect the cellular response to environmental conditions contributing to the development of new phenotypes. The ability to understand how protein interaction networks adapt to yield new function or alter phenotype is limited by the inability to determine structural and protein interaction changes on a proteomic scale. Here, chemical crosslinking and mass spectrometry were employed to quantify changes in protein structures and interactions in multidrug-resistant human carcinoma cells. Quantitative analysis of the largest crosslinking-derived, protein interaction network comprising 1,391 crosslinked peptides allows for ‘edgotype' analysis in a cell model of chemoresistance. We detect consistent changes to protein interactions and structures, including those involving cytokeratins, topoisomerase-2-alpha, and post-translationally modified histones, which correlate with a chemoresistant phenotype. PMID:26235782

  10. Automated quantitative image analysis of nanoparticle assembly

    NASA Astrophysics Data System (ADS)

    Murthy, Chaitanya R.; Gao, Bo; Tao, Andrea R.; Arya, Gaurav

    2015-05-01

    The ability to characterize higher-order structures formed by nanoparticle (NP) assembly is critical for predicting and engineering the properties of advanced nanocomposite materials. Here we develop a quantitative image analysis software to characterize key structural properties of NP clusters from experimental images of nanocomposites. This analysis can be carried out on images captured at intermittent times during assembly to monitor the time evolution of NP clusters in a highly automated manner. The software outputs averages and distributions in the size, radius of gyration, fractal dimension, backbone length, end-to-end distance, anisotropic ratio, and aspect ratio of NP clusters as a function of time along with bootstrapped error bounds for all calculated properties. The polydispersity in the NP building blocks and biases in the sampling of NP clusters are accounted for through the use of probabilistic weights. This software, named Particle Image Characterization Tool (PICT), has been made publicly available and could be an invaluable resource for researchers studying NP assembly. To demonstrate its practical utility, we used PICT to analyze scanning electron microscopy images taken during the assembly of surface-functionalized metal NPs of differing shapes and sizes within a polymer matrix. PICT is used to characterize and analyze the morphology of NP clusters, providing quantitative information that can be used to elucidate the physical mechanisms governing NP assembly.The ability to characterize higher-order structures formed by nanoparticle (NP) assembly is critical for predicting and engineering the properties of advanced nanocomposite materials. Here we develop a quantitative image analysis software to characterize key structural properties of NP clusters from experimental images of nanocomposites. This analysis can be carried out on images captured at intermittent times during assembly to monitor the time evolution of NP clusters in a highly automated

  11. Materials characterization through quantitative digital image analysis

    SciTech Connect

    J. Philliber; B. Antoun; B. Somerday; N. Yang

    2000-07-01

    A digital image analysis system has been developed to allow advanced quantitative measurement of microstructural features. This capability is maintained as part of the microscopy facility at Sandia, Livermore. The system records images digitally, eliminating the use of film. Images obtained from other sources may also be imported into the system. Subsequent digital image processing enhances image appearance through the contrast and brightness adjustments. The system measures a variety of user-defined microstructural features--including area fraction, particle size and spatial distributions, grain sizes and orientations of elongated particles. These measurements are made in a semi-automatic mode through the use of macro programs and a computer controlled translation stage. A routine has been developed to create large montages of 50+ separate images. Individual image frames are matched to the nearest pixel to create seamless montages. Results from three different studies are presented to illustrate the capabilities of the system.

  12. Near Real Time Quantitative Gas Analysis Techniques

    NASA Astrophysics Data System (ADS)

    Herget, William F.; Tromp, Marianne L.; Anderson, Charles R.

    1985-12-01

    A Fourier transform infrared (FT-IR) - based system has been developed and is undergoing evaluation for near real time multicomponent quantitative analysis of undiluted gaseous automotive exhaust emissions. The total system includes: (1) a gas conditioning system (GCS) for tracer gas injection, gas mixing, and temperature stabilization; and (2) an exhaust gas analyzer (EGA) consisting of a sample cell, an FT-IR system, and a computerized data processing system. Tests have shown that the system can monitor about 20 individual species (concentrations down to the 1-20 ppm range) with a time resolution of one second. Tests have been conducted on a chassis dynamometer system utilizing different autos, different fuels, and different driving cycles. Results were compared with those obtained using a standard constant volume sampling (CVS) system.

  13. Nonlinear dynamics and quantitative EEG analysis.

    PubMed

    Jansen, B H

    1996-01-01

    Quantitative, computerized electroencephalogram (EEG) analysis appears to be based on a phenomenological approach to EEG interpretation, and is primarily rooted in linear systems theory. A fundamentally different approach to computerized EEG analysis, however, is making its way into the laboratories. The basic idea, inspired by recent advances in the area of nonlinear dynamics and chaos theory, is to view an EEG as the output of a deterministic system of relatively simple complexity, but containing nonlinearities. This suggests that studying the geometrical dynamics of EEGs, and the development of neurophysiologically realistic models of EEG generation may produce more successful automated EEG analysis techniques than the classical, stochastic methods. A review of the fundamentals of chaos theory is provided. Evidence supporting the nonlinear dynamics paradigm to EEG interpretation is presented, and the kind of new information that can be extracted from the EEG is discussed. A case is made that a nonlinear dynamic systems viewpoint to EEG generation will profoundly affect the way EEG interpretation is currently done.

  14. Quantitative analysis in outcome assessment of instrumented lumbosacral arthrodesis.

    PubMed

    Champain, Sabina; Mazel, Christian; Mitulescu, Anca; Skalli, Wafa

    2007-08-01

    The outcome assessment in instrumented lumbosacral fusion mostly focuses on clinical criteria, complications and scores, with a high variability of imaging means, methods of fusion grading and parameters describing degenerative changes, making comparisons between studies difficult. The aim of this retrospective evaluation was to evaluate the interest of quantified radiographic analysis of lumbar spine in global outcome assessment and to highlight the key biomechanical factors involved. Clinical data and Beaujon-Lassale scores were collected for 49 patients who underwent lumbosacral arthrodesis after prior lumbar discectomy (mean follow-up: 5 years). Sagittal standing and lumbar flexion-extension X-ray films allowed quantifying vertebral, lumbar, pelvic and kinematic parameters of the lumbar spine, which were compared to reference values. Statistics were performed to assess evolution for all variables. At long-term follow-up, 90% of patients presented satisfactory clinical outcomes, associated to normal sagittal alignment; vertebral parameters objectified adjacent level degeneration in four cases (8%). Clinical outcome was correlated (r = 0.8) with fusion that was confirmed in 80% of cases, doubtful in 16% and pseudarthrosis seemed to occur in 4% (2) of cases. In addition to clinical data (outcomes comparable to the literature), quantitative analysis accurately described lumbar spine geometry and kinematics, highlighting parameters related to adjacent level's degeneration and a significant correlation between clinical outcome and fusion. Furthermore, criteria proposed to quantitatively evaluate fusion from lumbar dynamic radiographs seem to be appropriate and in agreement with surgeon's qualitative grading in 87% of cases.

  15. In vivo osteogenesis assay: a rapid method for quantitative analysis.

    PubMed

    Dennis, J E; Konstantakos, E K; Arm, D; Caplan, A I

    1998-08-01

    A quantitative in vivo osteogenesis assay is a useful tool for the analysis of cells and bioactive factors that affect the amount or rate of bone formation. There are currently two assays in general use for the in vivo assessment of osteogenesis by isolated cells: diffusion chambers and porous calcium phosphate ceramics. Due to the relative ease of specimen preparation and reproducibility of results, the porous ceramic assay was chosen for the development of a rapid method for quantitating in vivo bone formation. The ceramic cube implantation technique consists of combining osteogenic cells with 27-mm3 porous calcium phosphate ceramics, implanting the cell-ceramic composites subcutaneously into an immuno-tolerant host, and, after 2-6 weeks, harvesting and preparing the ceramic implants for histologic analysis. A drawback to the analysis of bone formation within these porous ceramics is that the entire cube must be examined to find small foci of bone present in some samples; a single cross-sectional area is not representative. For this reason, image analysis of serial sections from ceramics is often prohibitively time-consuming. Two alternative scoring methodologies were tested and compared to bone volume measurements obtained by image analysis. The two subjective scoring methods were: (1) Bone Scale: the amount of bone within pores of the ceramic implant is estimated on a scale of 0-4 based on the degree of bone fill (0=no bone, 1=up to 25%, 2=25 to 75%, 4=75 to 100% fill); and (2) Percentage Bone: the amount of bone is estimated by determining the percentage of ceramic pores which contain bone. Every tenth section of serially sectioned cubes was scored by each of these methods under double-blind conditions, and the Bone Scale and Percentage Bone results were directly compared to image analysis measurements from identical samples. Correlation coefficients indicate that the Percentage Bone method was more accurate than the Bone Scale scoring method. The Bone Scale

  16. Quantitative analysis of protein turnover in plants.

    PubMed

    Nelson, Clark J; Li, Lei; Millar, A Harvey

    2014-03-01

    Proteins are constantly being synthesised and degraded as plant cells age and as plants grow, develop and adapt the proteome. Given that plants develop through a series of events from germination to fruiting and even undertake whole organ senescence, an understanding of protein turnover as a fundamental part of this process in plants is essential. Both synthesis and degradation processes are spatially separated in a cell across its compartmented structure. The majority of protein synthesis occurs in the cytosol, while synthesis of specific components occurs inside plastids and mitochondria. Degradation of proteins occurs in both the cytosol, through the action of the plant proteasome, and in organelles and lytic structures through different protease classes. Tracking the specific synthesis and degradation rate of individual proteins can be undertaken using stable isotope feeding and the ability of peptide MS to track labelled peptide fractions over time. Mathematical modelling can be used to follow the isotope signature of newly synthesised protein as it accumulates and natural abundance proteins as they are lost through degradation. Different technical and biological constraints govern the potential for the use of (13)C, (15)N, (2)H and (18)O for these experiments in complete labelling and partial labelling strategies. Future development of quantitative protein turnover analysis will involve analysis of protein populations in complexes and subcellular compartments, assessing the effect of PTMs and integrating turnover studies into wider system biology study of plants.

  17. Quantitative Analysis of Triple Mutant Genetic Interactions

    PubMed Central

    Braberg, Hannes; Alexander, Richard; Shales, Michael; Xu, Jiewei; Franks-Skiba, Kathleen E.; Wu, Qiuqin; Haber, James E.; Krogan, Nevan J.

    2014-01-01

    The quantitative analysis of genetic interactions between pairs of gene mutations has proven effective for characterizing cellular functions but can miss important interactions for functionally redundant genes. To address this limitation, we have developed an approach termed Triple Mutant Analysis (TMA). The procedure relies on a query strain that contains two deletions in a pair of redundant or otherwise related genes, that is crossed against a panel of candidate deletion strains to isolate triple mutants and measure their growth. A central feature of TMA is to interrogate mutants that are synthetically sick when two other genes are deleted but interact minimally with either single deletion. This approach has been valuable for discovering genes that restore critical functions when the principle actors are deleted. TMA has also uncovered double mutant combinations that produce severe defects because a third protein becomes deregulated and acts in a deleterious fashion, and it has revealed functional differences between proteins presumed to act together. The protocol is optimized for Singer ROTOR pinning robots, takes 3 weeks to complete, and measures interactions for up to 30 double mutants against a library of 1536 single mutants. PMID:25010907

  18. Quantitative analysis of tumor burden in mouse lung via MRI.

    PubMed

    Tidwell, Vanessa K; Garbow, Joel R; Krupnick, Alexander S; Engelbach, John A; Nehorai, Arye

    2012-02-01

    Lung cancer is the leading cause of cancer death in the United States. Despite recent advances in screening protocols, the majority of patients still present with advanced or disseminated disease. Preclinical rodent models provide a unique opportunity to test novel therapeutic drugs for targeting lung cancer. Respiratory-gated MRI is a key tool for quantitatively measuring lung-tumor burden and monitoring the time-course progression of individual tumors in mouse models of primary and metastatic lung cancer. However, quantitative analysis of lung-tumor burden in mice by MRI presents significant challenges. Herein, a method for measuring tumor burden based upon average lung-image intensity is described and validated. The method requires accurate lung segmentation; its efficiency and throughput would be greatly aided by the ability to automatically segment the lungs. A technique for automated lung segmentation in the presence of varying tumor burden levels is presented. The method includes development of a new, two-dimensional parametric model of the mouse lungs and a multi-faceted cost function to optimally fit the model parameters to each image. Results demonstrate a strong correlation (0.93), comparable with that of fully manual expert segmentation, between the automated method's tumor-burden metric and the tumor burden measured by lung weight.

  19. Quantitative Analysis of Peripheral Tissue Perfusion Using Spatiotemporal Molecular Dynamics

    PubMed Central

    Lee, Jungsul; Koh, Gou Young; Kwon, Kihwan; Choi, Chulhee

    2009-01-01

    Background Accurate measurement of peripheral tissue perfusion is challenging but necessary to diagnose peripheral vascular insufficiency. Because near infrared (NIR) radiation can penetrate relatively deep into tissue, significant attention has been given to intravital NIR fluorescence imaging. Methodology/Principal Findings We developed a new optical imaging-based strategy for quantitative measurement of peripheral tissue perfusion by time-series analysis of local pharmacokinetics of the NIR fluorophore, indocyanine green (ICG). Time-series NIR fluorescence images were obtained after injecting ICG intravenously in a murine hindlimb ischemia model. Mathematical modeling and computational simulations were used for translating time-series ICG images into quantitative pixel perfusion rates and a perfusion map. We could successfully predict the prognosis of ischemic hindlimbs based on the perfusion profiles obtained immediately after surgery, which were dependent on the preexisting collaterals. This method also reflected increases in perfusion and improvements in prognosis of ischemic hindlimbs induced by treatment with vascular endothelial growth factor and COMP-angiopoietin-1. Conclusions/Significance We propose that this novel NIR-imaging-based strategy is a powerful tool for biomedical studies related to the evaluation of therapeutic interventions directed at stimulating angiogenesis. PMID:19169354

  20. Applying Knowledge of Quantitative Design and Analysis

    ERIC Educational Resources Information Center

    Baskas, Richard S.

    2011-01-01

    This study compared and contrasted two quantitative scholarly articles in relation to their research designs. Their designs were analyzed by the comparison of research references and research specific vocabulary to describe how various research methods were used. When researching and analyzing quantitative scholarly articles, it is imperative to…

  1. Can a quantitative simulation of an Otto engine be accurately rendered by a simple Novikov model with heat leak?

    NASA Astrophysics Data System (ADS)

    Fischer, A.; Hoffmann, K.-H.

    2004-03-01

    In this case study a complex Otto engine simulation provides data including, but not limited to, effects from losses due to heat conduction, exhaust losses and frictional losses. This data is used as a benchmark to test whether the Novikov engine with heat leak, a simple endoreversible model, can reproduce the complex engine behavior quantitatively by an appropriate choice of model parameters. The reproduction obtained proves to be of high quality.

  2. EBprot: Statistical analysis of labeling-based quantitative proteomics data.

    PubMed

    Koh, Hiromi W L; Swa, Hannah L F; Fermin, Damian; Ler, Siok Ghee; Gunaratne, Jayantha; Choi, Hyungwon

    2015-08-01

    Labeling-based proteomics is a powerful method for detection of differentially expressed proteins (DEPs). The current data analysis platform typically relies on protein-level ratios, which is obtained by summarizing peptide-level ratios for each protein. In shotgun proteomics, however, some proteins are quantified with more peptides than others, and this reproducibility information is not incorporated into the differential expression (DE) analysis. Here, we propose a novel probabilistic framework EBprot that directly models the peptide-protein hierarchy and rewards the proteins with reproducible evidence of DE over multiple peptides. To evaluate its performance with known DE states, we conducted a simulation study to show that the peptide-level analysis of EBprot provides better receiver-operating characteristic and more accurate estimation of the false discovery rates than the methods based on protein-level ratios. We also demonstrate superior classification performance of peptide-level EBprot analysis in a spike-in dataset. To illustrate the wide applicability of EBprot in different experimental designs, we applied EBprot to a dataset for lung cancer subtype analysis with biological replicates and another dataset for time course phosphoproteome analysis of EGF-stimulated HeLa cells with multiplexed labeling. Through these examples, we show that the peptide-level analysis of EBprot is a robust alternative to the existing statistical methods for the DE analysis of labeling-based quantitative datasets. The software suite is freely available on the Sourceforge website http://ebprot.sourceforge.net/. All MS data have been deposited in the ProteomeXchange with identifier PXD001426 (http://proteomecentral.proteomexchange.org/dataset/PXD001426/).

  3. Functional Linear Models for Association Analysis of Quantitative Traits

    PubMed Central

    Fan, Ruzong; Wang, Yifan; Mills, James L.; Wilson, Alexander F.; Bailey-Wilson, Joan E.; Xiong, Momiao

    2014-01-01

    Functional linear models are developed in this paper for testing associations between quantitative traits and genetic variants, which can be rare variants or common variants or the combination of the two. By treating multiple genetic variants of an individual in a human population as a realization of a stochastic process, the genome of an individual in a chromosome region is a continuum of sequence data rather than discrete observations. The genome of an individual is viewed as a stochastic function that contains both linkage and linkage disequilibrium (LD) information of the genetic markers. By using techniques of functional data analysis, both fixed and mixed effect functional linear models are built to test the association between quantitative traits and genetic variants adjusting for covariates. After extensive simulation analysis, it is shown that the F-distributed tests of the proposed fixed effect functional linear models have higher power than that of sequence kernel association test (SKAT) and its optimal unified test (SKAT-O) for three scenarios in most cases: (1) the causal variants are all rare, (2) the causal variants are both rare and common, and (3) the causal variants are common. The superior performance of the fixed effect functional linear models is most likely due to its optimal utilization of both genetic linkage and LD information of multiple genetic variants in a genome and similarity among different individuals, while SKAT and SKAT-O only model the similarities and pairwise LD but do not model linkage and higher order LD information sufficiently. In addition, the proposed fixed effect models generate accurate type I error rates in simulation studies. We also show that the functional kernel score tests of the proposed mixed effect functional linear models are preferable in candidate gene analysis and small sample problems. The methods are applied to analyze three biochemical traits in data from the Trinity Students Study. PMID:24130119

  4. Functional linear models for association analysis of quantitative traits.

    PubMed

    Fan, Ruzong; Wang, Yifan; Mills, James L; Wilson, Alexander F; Bailey-Wilson, Joan E; Xiong, Momiao

    2013-11-01

    Functional linear models are developed in this paper for testing associations between quantitative traits and genetic variants, which can be rare variants or common variants or the combination of the two. By treating multiple genetic variants of an individual in a human population as a realization of a stochastic process, the genome of an individual in a chromosome region is a continuum of sequence data rather than discrete observations. The genome of an individual is viewed as a stochastic function that contains both linkage and linkage disequilibrium (LD) information of the genetic markers. By using techniques of functional data analysis, both fixed and mixed effect functional linear models are built to test the association between quantitative traits and genetic variants adjusting for covariates. After extensive simulation analysis, it is shown that the F-distributed tests of the proposed fixed effect functional linear models have higher power than that of sequence kernel association test (SKAT) and its optimal unified test (SKAT-O) for three scenarios in most cases: (1) the causal variants are all rare, (2) the causal variants are both rare and common, and (3) the causal variants are common. The superior performance of the fixed effect functional linear models is most likely due to its optimal utilization of both genetic linkage and LD information of multiple genetic variants in a genome and similarity among different individuals, while SKAT and SKAT-O only model the similarities and pairwise LD but do not model linkage and higher order LD information sufficiently. In addition, the proposed fixed effect models generate accurate type I error rates in simulation studies. We also show that the functional kernel score tests of the proposed mixed effect functional linear models are preferable in candidate gene analysis and small sample problems. The methods are applied to analyze three biochemical traits in data from the Trinity Students Study.

  5. Automatic quantitative analysis of cardiac MR perfusion images

    NASA Astrophysics Data System (ADS)

    Breeuwer, Marcel M.; Spreeuwers, Luuk J.; Quist, Marcel J.

    2001-07-01

    Magnetic Resonance Imaging (MRI) is a powerful technique for imaging cardiovascular diseases. The introduction of cardiovascular MRI into clinical practice is however hampered by the lack of efficient and accurate image analysis methods. This paper focuses on the evaluation of blood perfusion in the myocardium (the heart muscle) from MR images, using contrast-enhanced ECG-triggered MRI. We have developed an automatic quantitative analysis method, which works as follows. First, image registration is used to compensate for translation and rotation of the myocardium over time. Next, the boundaries of the myocardium are detected and for each position within the myocardium a time-intensity profile is constructed. The time interval during which the contrast agent passes for the first time through the left ventricle and the myocardium is detected and various parameters are measured from the time-intensity profiles in this interval. The measured parameters are visualized as color overlays on the original images. Analysis results are stored, so that they can later on be compared for different stress levels of the heart. The method is described in detail in this paper and preliminary validation results are presented.

  6. Quantitative Analysis of Hypoperfusion in Acute Stroke

    PubMed Central

    Nael, Kambiz; Meshksar, Arash; Liebeskind, David S.; Coull, Bruce M.; Krupinski, Elizabeth A.; Villablanca, J. Pablo

    2014-01-01

    Background and Purpose This study compares the concordance between arterial spin labeling (ASL) and dynamic susceptibility contrast (DSC) for the identification of regional hypoperfusion and diffusion-perfusion mismatch tissue classification using a quantitative method. Methods The inclusion criteria for this retrospective study were as follows: patients with acute ischemic syndrome with symptom onset <24 hours and acquisition of both ASL and DSC MR perfusion. The volumes of infarction and hypoperfused lesions were calculated on ASL and DSC multi-parametric maps. Patients were classified into reperfused, matched, or mismatch groups using time to maximum >6 sec as the reference. In a subset of patients who were successfully recanalized, the identical analysis was performed and the infarction and hypoperfused lesion volumes were used for paired pre- and posttreatment comparisons. Results Forty-one patients met our inclusion criteria. Twenty patients underwent successful endovascular revascularization (TICI>2a), resulting in a total of 61 ASL-DSC data pairs for comparison. The hypoperfusion volume on ASL-cerebral blood flow best approximated the DSC-time to peak volume (r=0.83) in pretreatment group and time to maximum (r=0.46) after recanalization. Both ASL-cerebral blood flow and DSC-TTP overestimated the hypoperfusion volume compared with time to maximum volume in pretreatment (F=27.41, P<0.0001) and recanalized patients (F=8.78, P<0.0001). Conclusions ASL-cerebral blood flow overestimates the DSC time to maximum hypoperfusion volume and mismatch classification in patients with acute ischemic syndrome. Continued overestimation of hypoperfused volume after recanalization suggests flow pattern and velocity changes in addition to arterial transit delay can affects the performance of ASL. PMID:23988646

  7. Quantitative Auger analysis of Nb-Ge superconducting alloys

    SciTech Connect

    Buitrago, R.H.

    1980-01-01

    The feasibility of using Auger electron analysis for quantitative analysis was investigated by studying Nb/sub 3/Ge thin-film Auger data with different approaches. A method base on elemental standards gave consistent quantitative values with reported Nb-Ge data. Alloy sputter yields were also calculated and results were consistent with those for pure elements.

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

    PubMed Central

    2010-01-01

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

  9. Quantitative image analysis in the assessment of diffuse large B-cell lymphoma.

    PubMed

    Chabot-Richards, Devon S; Martin, David R; Myers, Orrin B; Czuchlewski, David R; Hunt, Kristin E

    2011-12-01

    Proliferation rates in diffuse large B-cell lymphoma have been associated with conflicting outcomes in the literature, more often with high proliferation associated with poor prognosis. In most studies, the proliferation rate was estimated by a pathologist using an immunohistochemical stain for the monoclonal antibody Ki-67. We hypothesized that a quantitative image analysis algorithm would give a more accurate estimate of the proliferation rate, leading to better associations with survival. In all, 84 cases of diffuse large B-cell lymphoma were selected according to the World Health Organization criteria. Ki-67 percentage positivity estimated by the pathologist was recorded from the original report. The same slides were then scanned using an Aperio ImageScope, and Ki-67 percentage positivity was calculated using a computer-based quantitative immunohistochemistry nuclear algorithm. In addition, chart review was performed and survival time was recorded. The Ki-67 percentage estimated by the pathologist from the original report versus quantitative image analysis was significantly correlated (P<0.001), but pathologist Ki-67 percentages were significantly higher than quantitative image analysis (P=0.021). There was less agreement at lower Ki-67 percentages. Comparison of Ki-67 percentage positivity versus survival did not show significant association either with pathologist estimate or quantitative image analysis. However, although not significant, there was a trend of worse survival at higher proliferation rates detected by the pathologist but not by quantitative image analysis. Interestingly, our data suggest that the Ki-67 percentage positivity as assessed by the pathologist may be more closely associated with survival outcome than that identified by quantitative image analysis. This may indicate that pathologists are better at selecting appropriate areas of the slide. More cases are needed to assess whether this finding would be statistically significant. Due to

  10. Quantitative analysis in outcome assessment of instrumented lumbosacral arthrodesis

    PubMed Central

    Mazel, Christian; Mitulescu, Anca

    2007-01-01

    The outcome assessment in instrumented lumbosacral fusion mostly focuses on clinical criteria, complications and scores, with a high variability of imaging means, methods of fusion grading and parameters describing degenerative changes, making comparisons between studies difficult. The aim of this retrospective evaluation was to evaluate the interest of quantified radiographic analysis of lumbar spine in global outcome assessment and to highlight the key biomechanical factors involved. Clinical data and Beaujon–Lassale scores were collected for 49 patients who underwent lumbosacral arthrodesis after prior lumbar discectomy (mean follow-up: 5 years). Sagittal standing and lumbar flexion-extension X-ray films allowed quantifying vertebral, lumbar, pelvic and kinematic parameters of the lumbar spine, which were compared to reference values. Statistics were performed to assess evolution for all variables. At long-term follow-up, 90% of patients presented satisfactory clinical outcomes, associated to normal sagittal alignment; vertebral parameters objectified adjacent level degeneration in four cases (8%). Clinical outcome was correlated (r = 0.8) with fusion that was confirmed in 80% of cases, doubtful in 16% and pseudarthrosis seemed to occur in 4% (2) of cases. In addition to clinical data (outcomes comparable to the literature), quantitative analysis accurately described lumbar spine geometry and kinematics, highlighting parameters related to adjacent level’s degeneration and a significant correlation between clinical outcome and fusion. Furthermore, criteria proposed to quantitatively evaluate fusion from lumbar dynamic radiographs seem to be appropriate and in agreement with surgeon’s qualitative grading in 87% of cases. PMID:17216227

  11. Identification and quantitative analysis of chemical compounds based on multiscale linear fitting of terahertz spectra

    NASA Astrophysics Data System (ADS)

    Qiao, Lingbo; Wang, Yingxin; Zhao, Ziran; Chen, Zhiqiang

    2014-07-01

    Terahertz (THz) time-domain spectroscopy is considered as an attractive tool for the analysis of chemical composition. The traditional methods for identification and quantitative analysis of chemical compounds by THz spectroscopy are all based on full-spectrum data. However, intrinsic features of the THz spectrum only lie in absorption peaks due to existence of disturbances, such as unexpected components, scattering effects, and barrier materials. We propose a strategy that utilizes Lorentzian parameters of THz absorption peaks, extracted by a multiscale linear fitting method, for both identification of pure chemicals and quantitative analysis of mixtures. The multiscale linear fitting method can automatically remove background content and accurately determine Lorentzian parameters of the absorption peaks. The high recognition rate for 16 pure chemical compounds and the accurate predicted concentrations for theophylline-lactose mixtures demonstrate the practicability of our approach.

  12. Application of an Effective Statistical Technique for an Accurate and Powerful Mining of Quantitative Trait Loci for Rice Aroma Trait

    PubMed Central

    Golestan Hashemi, Farahnaz Sadat; Rafii, Mohd Y.; Ismail, Mohd Razi; Mohamed, Mahmud Tengku Muda; Rahim, Harun A.; Latif, Mohammad Abdul; Aslani, Farzad

    2015-01-01

    When a phenotype of interest is associated with an external/internal covariate, covariate inclusion in quantitative trait loci (QTL) analyses can diminish residual variation and subsequently enhance the ability of QTL detection. In the in vitro synthesis of 2-acetyl-1-pyrroline (2AP), the main fragrance compound in rice, the thermal processing during the Maillard-type reaction between proline and carbohydrate reduction produces a roasted, popcorn-like aroma. Hence, for the first time, we included the proline amino acid, an important precursor of 2AP, as a covariate in our QTL mapping analyses to precisely explore the genetic factors affecting natural variation for rice scent. Consequently, two QTLs were traced on chromosomes 4 and 8. They explained from 20% to 49% of the total aroma phenotypic variance. Additionally, by saturating the interval harboring the major QTL using gene-based primers, a putative allele of fgr (major genetic determinant of fragrance) was mapped in the QTL on the 8th chromosome in the interval RM223-SCU015RM (1.63 cM). These loci supported previous studies of different accessions. Such QTLs can be widely used by breeders in crop improvement programs and for further fine mapping. Moreover, no previous studies and findings were found on simultaneous assessment of the relationship among 2AP, proline and fragrance QTLs. Therefore, our findings can help further our understanding of the metabolomic and genetic basis of 2AP biosynthesis in aromatic rice. PMID:26061689

  13. Some Epistemological Considerations Concerning Quantitative Analysis

    ERIC Educational Resources Information Center

    Dobrescu, Emilian

    2008-01-01

    This article presents the author's address at the 2007 "Journal of Applied Quantitative Methods" ("JAQM") prize awarding festivity. The festivity was included in the opening of the 4th International Conference on Applied Statistics, November 22, 2008, Bucharest, Romania. In the address, the author reflects on three theses that…

  14. Quantitative analysis of planetary reflectance spectra with principal components analysis

    NASA Technical Reports Server (NTRS)

    Johnson, P. E.; Smith, M. O.; Adams, J. B.

    1985-01-01

    A technique is presented for quantitative analysis of planetary reflectance spectra as mixtures of particles on microscopic and macroscopic scales using principal components analysis. This technique allows for determination of the endmembers being mixed, their abundance, and the scale of mixing, as well as other physical parameters. Eighteen lunar telescopic reflectance spectra of the Copernicus crater region, from 600 nm to 1800 nm in wavelength, are modeled in terms of five likely endmembers: mare basalt, mature mare soil, anorthosite, mature highland soil, and clinopyroxene. These endmembers were chosen from a similar analysis of 92 lunar soil and rock samples. The models fit the data to within 2 percent rms. It is found that the goodness of fit is marginally better for intimate mixing over macroscopic mixing.

  15. Towards quantitative analysis of retinal features in optical coherence tomography.

    PubMed

    Baroni, Maurizio; Fortunato, Pina; La Torre, Agostino

    2007-05-01

    The purpose of this paper was to propose a new computer method for quantitative evaluation of representative features of the retina using optical coherence tomography (OCT). A multi-step approach was devised and positively tested for segmentation of the three main retinal layers: the vitreo-retinal interface and the inner and outer retina. Following a preprocessing step, three regions of interest were delimited. Significant peaks corresponding to high and low intensity strips were located along the OCT A-scan lines and accurate boundaries between different layers were obtained by maximizing an edge likelihood function. For a quantitative description, thickness measurement, densitometry, texture and curvature analyses were performed. As a first application, the effect of intravitreal injection of triamcinolone acetonide (IVTA) for the treatment of vitreo-retinal interface syndrome was evaluated. Almost all the parameters, measured on a set of 16 pathologic OCT images, were statistically different before and after IVTA injection (p<0.05). Shape analysis of the internal limiting membrane confirmed the reduction of the pathological traction state. Other significant parameters, such as reflectivity and texture contrast, exhibited relevant changes both at the vitreo-retinal interface and in the inner retinal layers. Texture parameters in the inner and outer retinal layers significantly correlated with the visual acuity restoration. According to these findings an IVTA injection might be considered a possible alternative to surgery for selected patients. In conclusion, the proposed approach appeared to be a promising tool for the investigation of tissue changes produced by pathology and/or therapy.

  16. Quantitative analysis and parametric display of regional myocardial mechanics

    NASA Astrophysics Data System (ADS)

    Eusemann, Christian D.; Bellemann, Matthias E.; Robb, Richard A.

    2000-04-01

    Quantitative assessment of regional heart motion has significant potential for more accurate diagnosis of heart disease and/or cardiac irregularities. Local heart motion may be studied from medical imaging sequences. Using functional parametric mapping, regional myocardial motion during a cardiac cycle can be color mapped onto a deformable heart model to obtain better understanding of the structure- to-function relationships in the myocardium, including regional patterns of akinesis or diskinesis associated with ischemia or infarction. In this study, 3D reconstructions were obtained from the Dynamic Spatial Reconstructor at 15 time points throughout one cardiac cycle of pre-infarct and post-infarct hearts. Deformable models were created from the 3D images for each time point of the cardiac cycles. Form these polygonal models, regional excursions and velocities of each vertex representing a unit of myocardium were calculated for successive time-intervals. The calculated results were visualized through model animations and/or specially formatted static images. The time point of regional maximum velocity and excursion of myocardium through the cardiac cycle was displayed using color mapping. The absolute value of regional maximum velocity and maximum excursion were displayed in a similar manner. Using animations, the local myocardial velocity changes were visualized as color changes on the cardiac surface during the cardiac cycle. Moreover, the magnitude and direction of motion for individual segments of myocardium could be displayed. Comparison of these dynamic parametric displays suggest that the ability to encode quantitative functional information on dynamic cardiac anatomy enhances the diagnostic value of 4D images of the heart. Myocardial mechanics quantified this way adds a new dimension to the analysis of cardiac functional disease, including regional patterns of akinesis and diskinesis associated with ischemia and infarction. Similarly, disturbances in

  17. Toward Quantitatively Accurate Calculation of the Redox-Associated Acid–Base and Ligand Binding Equilibria of Aquacobalamin

    SciTech Connect

    Johnston, Ryne C.; Zhou, Jing; Smith, Jeremy C.; Parks, Jerry M.

    2016-07-08

    In redox processes in complex transition metal-containing species are often intimately associated with changes in ligand protonation states and metal coordination number. Moreover, a major challenge is therefore to develop consistent computational approaches for computing pH-dependent redox and ligand dissociation properties of organometallic species. Reduction of the Co center in the vitamin B12 derivative aquacobalamin can be accompanied by ligand dissociation, protonation, or both, making these properties difficult to compute accurately. We examine this challenge here by using density functional theory and continuum solvation to compute Co ligand binding equilibrium constants (Kon/off), pKas and reduction potentials for models of aquacobalamin in aqueous solution. We consider two models for cobalamin ligand coordination: the first follows the hexa, penta, tetra coordination scheme for CoIII, CoII, and CoI species, respectively, and the second model features saturation of each vacant axial coordination site on CoII and CoI species with a single, explicit water molecule to maintain six directly interacting ligands or water molecules in each oxidation state. Comparing these two coordination schemes in combination with five dispersion-corrected density functionals, we find that the accuracy of the computed properties is largely independent of the scheme used, but including only a continuum representation of the solvent yields marginally better results than saturating the first solvation shell around Co throughout. PBE performs best, displaying balanced accuracy and superior performance overall, with RMS errors of 80 mV for seven reduction potentials, 2.0 log units for five pKas and 2.3 log units for two log Kon/off values for the aquacobalamin system. Furthermore, we find that the BP86 functional commonly used in corrinoid studies suffers from erratic behavior and inaccurate descriptions of

  18. Toward Quantitatively Accurate Calculation of the Redox-Associated Acid–Base and Ligand Binding Equilibria of Aquacobalamin

    DOE PAGES

    Johnston, Ryne C.; Zhou, Jing; Smith, Jeremy C.; ...

    2016-07-08

    In redox processes in complex transition metal-containing species are often intimately associated with changes in ligand protonation states and metal coordination number. Moreover, a major challenge is therefore to develop consistent computational approaches for computing pH-dependent redox and ligand dissociation properties of organometallic species. Reduction of the Co center in the vitamin B12 derivative aquacobalamin can be accompanied by ligand dissociation, protonation, or both, making these properties difficult to compute accurately. We examine this challenge here by using density functional theory and continuum solvation to compute Co ligand binding equilibrium constants (Kon/off), pKas and reduction potentials for models of aquacobalaminmore » in aqueous solution. We consider two models for cobalamin ligand coordination: the first follows the hexa, penta, tetra coordination scheme for CoIII, CoII, and CoI species, respectively, and the second model features saturation of each vacant axial coordination site on CoII and CoI species with a single, explicit water molecule to maintain six directly interacting ligands or water molecules in each oxidation state. Comparing these two coordination schemes in combination with five dispersion-corrected density functionals, we find that the accuracy of the computed properties is largely independent of the scheme used, but including only a continuum representation of the solvent yields marginally better results than saturating the first solvation shell around Co throughout. PBE performs best, displaying balanced accuracy and superior performance overall, with RMS errors of 80 mV for seven reduction potentials, 2.0 log units for five pKas and 2.3 log units for two log Kon/off values for the aquacobalamin system. Furthermore, we find that the BP86 functional commonly used in corrinoid studies suffers from erratic behavior and inaccurate descriptions of Co axial ligand binding, leading to substantial errors in predicted

  19. Toward Quantitatively Accurate Calculation of the Redox-Associated Acid-Base and Ligand Binding Equilibria of Aquacobalamin.

    PubMed

    Johnston, Ryne C; Zhou, Jing; Smith, Jeremy C; Parks, Jerry M

    2016-08-04

    Redox processes in complex transition metal-containing species are often intimately associated with changes in ligand protonation states and metal coordination number. A major challenge is therefore to develop consistent computational approaches for computing pH-dependent redox and ligand dissociation properties of organometallic species. Reduction of the Co center in the vitamin B12 derivative aquacobalamin can be accompanied by ligand dissociation, protonation, or both, making these properties difficult to compute accurately. We examine this challenge here by using density functional theory and continuum solvation to compute Co-ligand binding equilibrium constants (Kon/off), pKas, and reduction potentials for models of aquacobalamin in aqueous solution. We consider two models for cobalamin ligand coordination: the first follows the hexa, penta, tetra coordination scheme for Co(III), Co(II), and Co(I) species, respectively, and the second model features saturation of each vacant axial coordination site on Co(II) and Co(I) species with a single, explicit water molecule to maintain six directly interacting ligands or water molecules in each oxidation state. Comparing these two coordination schemes in combination with five dispersion-corrected density functionals, we find that the accuracy of the computed properties is largely independent of the scheme used, but including only a continuum representation of the solvent yields marginally better results than saturating the first solvation shell around Co throughout. PBE performs best, displaying balanced accuracy and superior performance overall, with RMS errors of 80 mV for seven reduction potentials, 2.0 log units for five pKas and 2.3 log units for two log Kon/off values for the aquacobalamin system. Furthermore, we find that the BP86 functional commonly used in corrinoid studies suffers from erratic behavior and inaccurate descriptions of Co-axial ligand binding, leading to substantial errors in predicted pKas and

  20. Quantitative gas chromatographic analysis of volatile fatty acids in spent culture media and body fluids.

    PubMed Central

    van den Bogaard, A E; Hazen, M J; Van Boven, C P

    1986-01-01

    Gas chromatographic analysis of volatile fatty acids for identification of obligately anaerobic bacteria and for presumptive diagnosis of anaerobic infections is now widely practiced. However, it is difficult to compare data because only a qualitative analysis is done or only chromatograms are presented instead of quantitative data on volatile fatty acid production. We compared three stationary phases for volatile fatty acid analysis of aqueous solutions and four methods of pretreating samples for gas chromatography. Quantitative analysis could be done accurately by using Carbowax as the stationary phase after pretreatment of spent culture media with Dowex columns. If only qualitative analysis is required (e.g., for presumptive diagnosis of anaerobic infections), ether extraction and headspace analysis are equally suitable. The overall variation coefficient for volatile fatty acid production by four reference strains of obligately anaerobic bacteria after 24 h of incubation was approximately 10%. PMID:3958144

  1. Functionalized Magnetic Nanoparticles for the Detection and Quantitative Analysis of Cell Surface Antigen

    PubMed Central

    Shahbazi-Gahrouei, Daryoush; Abdolahi, Mohammad; Zarkesh-Esfahani, Sayyed Hamid; Laurent, Sophie; Sermeus, Corine; Gruettner, Cordula

    2013-01-01

    Cell surface antigens as biomarkers offer tremendous potential for early diagnosis, prognosis, and therapeutic response in a variety of diseases such as cancers. In this research, a simple, rapid, accurate, inexpensive, and easily available in vitro assay based on magnetic nanoparticles and magnetic cell separation principle was applied to identify and quantitatively analyze the cell surface antigen expression in the case of prostate cancer cells. Comparing the capability of the assay with flow cytometry as a gold standard method showed similar results. The results showed that the antigen-specific magnetic cell separation with antibody-coated magnetic nanoparticles has high potential for quantitative cell surface antigen detection and analysis. PMID:23484112

  2. Energy Dispersive Spectrometry and Quantitative Analysis Short Course. Introduction to X-ray Energy Dispersive Spectrometry and Quantitative Analysis

    NASA Technical Reports Server (NTRS)

    Carpenter, Paul; Curreri, Peter A. (Technical Monitor)

    2002-01-01

    This course will cover practical applications of the energy-dispersive spectrometer (EDS) to x-ray microanalysis. Topics covered will include detector technology, advances in pulse processing, resolution and performance monitoring, detector modeling, peak deconvolution and fitting, qualitative and quantitative analysis, compositional mapping, and standards. An emphasis will be placed on use of the EDS for quantitative analysis, with discussion of typical problems encountered in the analysis of a wide range of materials and sample geometries.

  3. Can MRI accurately detect pilon articular malreduction? A quantitative comparison between CT and 3T MRI bone models

    PubMed Central

    Radzi, Shairah; Dlaska, Constantin Edmond; Cowin, Gary; Robinson, Mark; Pratap, Jit; Schuetz, Michael Andreas; Mishra, Sanjay

    2016-01-01

    Background Pilon fracture reduction is a challenging surgery. Radiographs are commonly used to assess the quality of reduction, but are limited in revealing the remaining bone incongruities. The study aimed to develop a method in quantifying articular malreductions using 3D computed tomography (CT) and magnetic resonance imaging (MRI) models. Methods CT and MRI data were acquired using three pairs of human cadaveric ankle specimens. Common tibial pilon fractures were simulated by performing osteotomies to the ankle specimens. Five of the created fractures [three AO type-B (43-B1), and two AO type-C (43-C1) fractures] were then reduced and stabilised using titanium implants, then rescanned. All datasets were reconstructed into CT and MRI models, and were analysed in regards to intra-articular steps and gaps, surface deviations, malrotations and maltranslations of the bone fragments. Results Initial results reveal that type B fracture CT and MRI models differed by ~0.2 (step), ~0.18 (surface deviations), ~0.56° (rotation) and ~0.4 mm (translation). Type C fracture MRI models showed metal artefacts extending to the articular surface, thus unsuitable for analysis. Type C fracture CT models differed from their CT and MRI contralateral models by ~0.15 (surface deviation), ~1.63° (rotation) and ~0.4 mm (translation). Conclusions Type B fracture MRI models were comparable to CT and may potentially be used for the postoperative assessment of articular reduction on a case-to-case basis. PMID:28090442

  4. Tools for Accurate and Efficient Analysis of Complex Evolutionary Mechanisms in Microbial Genomes. Final Report

    SciTech Connect

    Nakhleh, Luay

    2014-03-12

    I proposed to develop computationally efficient tools for accurate detection and reconstruction of microbes' complex evolutionary mechanisms, thus enabling rapid and accurate annotation, analysis and understanding of their genomes. To achieve this goal, I proposed to address three aspects. (1) Mathematical modeling. A major challenge facing the accurate detection of HGT is that of distinguishing between these two events on the one hand and other events that have similar "effects." I proposed to develop a novel mathematical approach for distinguishing among these events. Further, I proposed to develop a set of novel optimization criteria for the evolutionary analysis of microbial genomes in the presence of these complex evolutionary events. (2) Algorithm design. In this aspect of the project, I proposed to develop an array of e cient and accurate algorithms for analyzing microbial genomes based on the formulated optimization criteria. Further, I proposed to test the viability of the criteria and the accuracy of the algorithms in an experimental setting using both synthetic as well as biological data. (3) Software development. I proposed the nal outcome to be a suite of software tools which implements the mathematical models as well as the algorithms developed.

  5. Structural and quantitative analysis of Equisetum alkaloids.

    PubMed

    Cramer, Luise; Ernst, Ludger; Lubienski, Marcus; Papke, Uli; Schiebel, Hans-Martin; Jerz, Gerold; Beuerle, Till

    2015-08-01

    Equisetum palustre L. is known for its toxicity for livestock. Several studies in the past addressed the isolation and identification of the responsible alkaloids. So far, palustrine (1) and N(5)-formylpalustrine (2) are known alkaloids of E. palustre. A HPLC-ESI-MS/MS method in combination with simple sample work-up was developed to identify and quantitate Equisetum alkaloids. Besides the two known alkaloids six related alkaloids were detected in different Equisetum samples. The structure of the alkaloid palustridiene (3) was derived by comprehensive 1D and 2D NMR experiments. N(5)-Acetylpalustrine (4) was also thoroughly characterized by NMR for the first time. The structure of N(5)-formylpalustridiene (5) is proposed based on mass spectrometry results. Twenty-two E. palustre samples were screened by a HPLC-ESI-MS/MS method after development of a simple sample work-up and in most cases the set of all eight alkaloids were detected in all parts of the plant. A high variability of the alkaloid content and distribution was found depending on plant organ, plant origin and season ranging from 88 to 597mg/kg dried weight. However, palustrine (1) and the alkaloid palustridiene (3) always represented the main alkaloids. For the first time, a comprehensive identification, quantitation and distribution of Equisetum alkaloids was achieved.

  6. Identification and validation of reference genes for accurate normalization of real-time quantitative PCR data in kiwifruit.

    PubMed

    Ferradás, Yolanda; Rey, Laura; Martínez, Óscar; Rey, Manuel; González, Ma Victoria

    2016-05-01

    Identification and validation of reference genes are required for the normalization of qPCR data. We studied the expression stability produced by eight primer pairs amplifying four common genes used as references for normalization. Samples representing different tissues, organs and developmental stages in kiwifruit (Actinidia chinensis var. deliciosa (A. Chev.) A. Chev.) were used. A total of 117 kiwifruit samples were divided into five sample sets (mature leaves, axillary buds, stigmatic arms, fruit flesh and seeds). All samples were also analysed as a single set. The expression stability of the candidate primer pairs was tested using three algorithms (geNorm, NormFinder and BestKeeper). The minimum number of reference genes necessary for normalization was also determined. A unique primer pair was selected for amplifying the 18S rRNA gene. The primer pair selected for amplifying the ACTIN gene was different depending on the sample set. 18S 2 and ACT 2 were the candidate primer pairs selected for normalization in the three sample sets (mature leaves, fruit flesh and stigmatic arms). 18S 2 and ACT 3 were the primer pairs selected for normalization in axillary buds. No primer pair could be selected for use as the reference for the seed sample set. The analysis of all samples in a single set did not produce the selection of any stably expressing primer pair. Considering data previously reported in the literature, we validated the selected primer pairs amplifying the FLOWERING LOCUS T gene for use in the normalization of gene expression in kiwifruit.

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

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

  8. Joint association analysis of bivariate quantitative and qualitative traits.

    PubMed

    Yuan, Mengdie; Diao, Guoqing

    2011-11-29

    Univariate genome-wide association analysis of quantitative and qualitative traits has been investigated extensively in the literature. In the presence of correlated phenotypes, it is more intuitive to analyze all phenotypes simultaneously. We describe an efficient likelihood-based approach for the joint association analysis of quantitative and qualitative traits in unrelated individuals. We assume a probit model for the qualitative trait, under which an unobserved latent variable and a prespecified threshold determine the value of the qualitative trait. To jointly model the quantitative and qualitative traits, we assume that the quantitative trait and the latent variable follow a bivariate normal distribution. The latent variable is allowed to be correlated with the quantitative phenotype. Simultaneous modeling of the quantitative and qualitative traits allows us to make more precise inference on the pleiotropic genetic effects. We derive likelihood ratio tests for the testing of genetic effects. An application to the Genetic Analysis Workshop 17 data is provided. The new method yields reasonable power and meaningful results for the joint association analysis of the quantitative trait Q1 and the qualitative trait disease status at SNPs with not too small MAF.

  9. Qualitative and quantitative analysis of endocytic recycling.

    PubMed

    Reineke, James B; Xie, Shuwei; Naslavsky, Naava; Caplan, Steve

    2015-01-01

    Endocytosis, which encompasses the internalization and sorting of plasma membrane (PM) lipids and proteins to distinct membrane-bound intracellular compartments, is a highly regulated and fundamental cellular process by which eukaryotic cells dynamically regulate their PM composition. Indeed, endocytosis is implicated in crucial cellular processes that include proliferation, migration, and cell division as well as maintenance of tissue homeostasis such as apical-basal polarity. Once PM constituents have been taken up into the cell, either via clathrin-dependent endocytosis (CDE) or clathrin-independent endocytosis (CIE), they typically have two fates: degradation through the late-endosomal/lysosomal pathway or returning to the PM via endocytic recycling pathways. In this review, we will detail experimental procedures that allow for both qualitative and quantitative assessment of endocytic recycling of transmembrane proteins internalized by CDE and CIE, using the HeLa cervical cancer cell line as a model system.

  10. Lipid biomarker analysis for the quantitative analysis of airborne microorganisms

    SciTech Connect

    Macnaughton, S.J.; Jenkins, T.L.; Cormier, M.R.

    1997-08-01

    There is an ever increasing concern regarding the presence of airborne microbial contaminants within indoor air environments. Exposure to such biocontaminants can give rise to large numbers of different health effects including infectious diseases, allergenic responses and respiratory problems, Biocontaminants typically round in indoor air environments include bacteria, fungi, algae, protozoa and dust mites. Mycotoxins, endotoxins, pollens and residues of organisms are also known to cause adverse health effects. A quantitative detection/identification technique independent of culturability that assays both culturable and non culturable biomass including endotoxin is critical in defining risks from indoor air biocontamination. Traditionally, methods employed for the monitoring of microorganism numbers in indoor air environments involve classical culture based techniques and/or direct microscopic counting. It has been repeatedly documented that viable microorganism counts only account for between 0.1-10% of the total community detectable by direct counting. The classic viable microbiologic approach doe`s not provide accurate estimates of microbial fragments or other indoor air components that can act as antigens and induce or potentiate allergic responses. Although bioaerosol samplers are designed to damage the microbes as little as possible, microbial stress has been shown to result from air sampling, aerosolization and microbial collection. Higher collection efficiency results in greater cell damage while less cell damage often results in lower collection efficiency. Filtration can collect particulates at almost 100% efficiency, but captured microorganisms may become dehydrated and damaged resulting in non-culturability, however, the lipid biomarker assays described herein do not rely on cell culture. Lipids are components that are universally distributed throughout cells providing a means to assess independent of culturability.

  11. Evaluating the Quantitative Capabilities of Metagenomic Analysis Software.

    PubMed

    Kerepesi, Csaba; Grolmusz, Vince

    2016-05-01

    DNA sequencing technologies are applied widely and frequently today to describe metagenomes, i.e., microbial communities in environmental or clinical samples, without the need for culturing them. These technologies usually return short (100-300 base-pairs long) DNA reads, and these reads are processed by metagenomic analysis software that assign phylogenetic composition-information to the dataset. Here we evaluate three metagenomic analysis software (AmphoraNet--a webserver implementation of AMPHORA2--, MG-RAST, and MEGAN5) for their capabilities of assigning quantitative phylogenetic information for the data, describing the frequency of appearance of the microorganisms of the same taxa in the sample. The difficulties of the task arise from the fact that longer genomes produce more reads from the same organism than shorter genomes, and some software assign higher frequencies to species with longer genomes than to those with shorter ones. This phenomenon is called the "genome length bias." Dozens of complex artificial metagenome benchmarks can be found in the literature. Because of the complexity of those benchmarks, it is usually difficult to judge the resistance of a metagenomic software to this "genome length bias." Therefore, we have made a simple benchmark for the evaluation of the "taxon-counting" in a metagenomic sample: we have taken the same number of copies of three full bacterial genomes of different lengths, break them up randomly to short reads of average length of 150 bp, and mixed the reads, creating our simple benchmark. Because of its simplicity, the benchmark is not supposed to serve as a mock metagenome, but if a software fails on that simple task, it will surely fail on most real metagenomes. We applied three software for the benchmark. The ideal quantitative solution would assign the same proportion to the three bacterial taxa. We have found that AMPHORA2/AmphoraNet gave the most accurate results and the other two software were under

  12. Quantitative analysis of Euclidean distance to complement qualitative analysis of facial expression during deception

    PubMed Central

    Mondal, Ananya; Mukhopadhyay, Pritha; Basu, Nabanita; Bandyopadhyay, Samir Kumar; Chatterjee, Tanima

    2016-01-01

    Background: Accurate evaluation of an individuals' veracity is a fundamental aspect of social functioning that allows individuals to act in adaptive ways. The domain of deception detection ability is still young, and many components in this field are yet to be touched which demands more research in this field. Aims: The present study aims at deciphering the structural composition of face during felt, posed, and deceived emotions in facial expression unique to Indian culture, using Facial Action Coding System (FACS). Quantitative analysis of Euclidean distance has been done to complement qualitative FACS analysis. Methods: In this study, thirty female, young adults with age range of 23–27 years were chosen randomly for portraying their (felt, posed, and deceived) facial expression. All facial expressions were captured through instruction, and videos were converted into static images. The static images were coded on the basis of FACS to decipher the felt, posed, and deceived expressions. Quantitative analysis of the data has been done using MATLAB to meet the objectives of the study and to complement the qualitative analysis. Results: Felt and posed emotions differ in terms of intensity of the expression and subjective experience. Posed emotional and deceived expressions differ in intent. Facial asymmetry is an important indicator for detecting deception. PMID:28163412

  13. Quantitative analysis of airway abnormalities in CT

    NASA Astrophysics Data System (ADS)

    Petersen, Jens; Lo, Pechin; Nielsen, Mads; Edula, Goutham; Ashraf, Haseem; Dirksen, Asger; de Bruijne, Marleen

    2010-03-01

    A coupled surface graph cut algorithm for airway wall segmentation from Computed Tomography (CT) images is presented. Using cost functions that highlight both inner and outer wall borders, the method combines the search for both borders into one graph cut. The proposed method is evaluated on 173 manually segmented images extracted from 15 different subjects and shown to give accurate results, with 37% less errors than the Full Width at Half Maximum (FWHM) algorithm and 62% less than a similar graph cut method without coupled surfaces. Common measures of airway wall thickness such as the Interior Area (IA) and Wall Area percentage (WA%) was measured by the proposed method on a total of 723 CT scans from a lung cancer screening study. These measures were significantly different for participants with Chronic Obstructive Pulmonary Disease (COPD) compared to asymptomatic participants. Furthermore, reproducibility was good as confirmed by repeat scans and the measures correlated well with the outcomes of pulmonary function tests, demonstrating the use of the algorithm as a COPD diagnostic tool. Additionally, a new measure of airway wall thickness is proposed, Normalized Wall Intensity Sum (NWIS). NWIS is shown to correlate better with lung function test values and to be more reproducible than previous measures IA, WA% and airway wall thickness at a lumen perimeter of 10 mm (PI10).

  14. Quantitative infrared analysis of hydrogen fluoride

    SciTech Connect

    Manuta, D.M.

    1997-04-01

    This work was performed at the Portsmouth Gaseous Diffusion Plant where hydrogen fluoride is produced upon the hydrolysis of UF{sub 6}. This poses a problem for in this setting and a method for determining the mole percent concentration was desired. HF has been considered to be a non-ideal gas for many years. D. F. Smith utilized complex equations in his HF studies in the 1950s. We have evaluated HF behavior as a function of pressure from three different perspectives. (1) Absorbance at 3877 cm{sup -1} as a function of pressure for 100% HF. (2) Absorbance at 3877 cm{sup -1} as a function of increasing partial pressure HF. Total pressure = 300 mm HgA maintained with nitrogen. (3) Absorbance at 3877 cm{sup -1} for constant partial pressure HF. Total pressure is increased to greater than 800 mm HgA with nitrogen. These experiments have shown that at partial pressures up to 35mm HgA, HIF follows the ideal gas law. The absorbance at 3877 cm{sup -1} can be quantitatively analyzed via infrared methods.

  15. Quantitative Analysis of HIV-1 Preintegration Complexes

    PubMed Central

    Engelman, Alan; Oztop, Ilker; Vandegraaff, Nick; Raghavendra, Nidhanapati K.

    2009-01-01

    Retroviral replication proceeds through the formation of a provirus, an integrated DNA copy of the viral RNA genome. The linear cDNA product of reverse transcription is the integration substrate and two different integrase activities, 3′ processing and DNA strand transfer, are required for provirus formation. Integrase nicks the cDNA ends adjacent to phylogenetically-conserved CA dinucleotides during 3′ processing. After nuclear entry and locating a suitable chromatin acceptor site, integrase joins the recessed 3′-OHs to the 5′-phosphates of a double-stranded staggered cut in the DNA target. Integrase functions in the context of a large nucleoprotein complex, called the preintegration complex (PIC), and PICs are analyzed to determine levels of integrase 3′ processing and DNA strand transfer activities that occur during acute virus infection. Denatured cDNA end regions are monitored by indirect end-labeling to measure the extent of 3′ processing. Native PICs can efficiently integrate their viral cDNA into exogenously added target DNA in vitro, and Southern blotting or nested PCR assays are used to quantify the resultant DNA strand transfer activity. This study details HIV-1 infection, PIC extraction, partial purification, and quantitative analyses of integrase 3′ processing and DNA strand transfer activities. PMID:19233280

  16. Quantitative multi-modal NDT data analysis

    SciTech Connect

    Heideklang, René; Shokouhi, Parisa

    2014-02-18

    A single NDT technique is often not adequate to provide assessments about the integrity of test objects with the required coverage or accuracy. In such situations, it is often resorted to multi-modal testing, where complementary and overlapping information from different NDT techniques are combined for a more comprehensive evaluation. Multi-modal material and defect characterization is an interesting task which involves several diverse fields of research, including signal and image processing, statistics and data mining. The fusion of different modalities may improve quantitative nondestructive evaluation by effectively exploiting the augmented set of multi-sensor information about the material. It is the redundant information in particular, whose quantification is expected to lead to increased reliability and robustness of the inspection results. There are different systematic approaches to data fusion, each with its specific advantages and drawbacks. In our contribution, these will be discussed in the context of nondestructive materials testing. A practical study adopting a high-level scheme for the fusion of Eddy Current, GMR and Thermography measurements on a reference metallic specimen with built-in grooves will be presented. Results show that fusion is able to outperform the best single sensor regarding detection specificity, while retaining the same level of sensitivity.

  17. Accurate analysis of planar optical waveguide devices using higher-order FDTD scheme.

    PubMed

    Kong, Fanmin; Li, Kang; Liu, Xin

    2006-11-27

    A higher-order finite-difference time-domain (HO-FDTD) numerical method is proposed for the time-domain analysis of planar optical waveguide devices. The anisotropic perfectly matched layer (APML) absorbing boundary condition for the HO-FDTD scheme is implemented and the numerical dispersion of this scheme is studied. The numerical simulations for the parallel-slab directional coupler are presented and the computing results using this scheme are in highly accordance with analytical solutions. Compared with conventional FDTD method, this scheme can save considerable computational resource without sacrificing solution accuracy and especially could be applied in the accurate analysis of optical devices.

  18. Fast and accurate focusing analysis of large photon sieve using pinhole ring diffraction model.

    PubMed

    Liu, Tao; Zhang, Xin; Wang, Lingjie; Wu, Yanxiong; Zhang, Jizhen; Qu, Hemeng

    2015-06-10

    In this paper, we developed a pinhole ring diffraction model for the focusing analysis of a large photon sieve. Instead of analyzing individual pinholes, we discuss the focusing of all of the pinholes in a single ring. An explicit equation for the diffracted field of individual pinhole ring has been proposed. We investigated the validity range of this generalized model and analytically describe the sufficient conditions for the validity of this pinhole ring diffraction model. A practical example and investigation reveals the high accuracy of the pinhole ring diffraction model. This simulation method could be used for fast and accurate focusing analysis of a large photon sieve.

  19. The quantitative failure of human reliability analysis

    SciTech Connect

    Bennett, C.T.

    1995-07-01

    This philosophical treatise argues the merits of Human Reliability Analysis (HRA) in the context of the nuclear power industry. Actually, the author attacks historic and current HRA as having failed in informing policy makers who make decisions based on risk that humans contribute to systems performance. He argues for an HRA based on Bayesian (fact-based) inferential statistics, which advocates a systems analysis process that employs cogent heuristics when using opinion, and tempers itself with a rational debate over the weight given subjective and empirical probabilities.

  20. Quantitive and Sociological Analysis of Blog Networks

    NASA Astrophysics Data System (ADS)

    Bachnik, W.; Szymczyk, S.; Leszczynski, S.; Podsiadlo, R.; Rymszewicz, E.; Kurylo, L.; Makowiec, D.; Bykowska, B.

    2005-10-01

    This paper examines the emerging phenomenon of blogging, using three different Polish blogging services as the base of the research. Authors show that blog networks are sharing their characteristics with complex networks (gamma coefficients, small worlds, cliques, etc.). Elements of sociometric analysis were used to prove existence of some social structures in the blog networks.

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

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

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

  2. A Comparative Assessment of Greek Universities' Efficiency Using Quantitative Analysis

    ERIC Educational Resources Information Center

    Katharaki, Maria; Katharakis, George

    2010-01-01

    In part due to the increased demand for higher education, typical evaluation frameworks for universities often address the key issue of available resource utilisation. This study seeks to estimate the efficiency of 20 public universities in Greece through quantitative analysis (including performance indicators, data envelopment analysis (DEA) and…

  3. Influence of corrosion layers on quantitative analysis

    NASA Astrophysics Data System (ADS)

    Denker, A.; Bohne, W.; Opitz-Coutureau, J.; Rauschenberg, J.; Röhrich, J.; Strub, E.

    2005-09-01

    Art historians and restorers in charge of ancient metal objects are often reluctant to remove the corrosion layer evolved over time, as this would change the appearance of the artefact dramatically. Therefore, when an elemental analysis of the objects is required, this has to be done by penetrating the corrosion layer. In this work the influence of corrosion was studied on Chinese and Roman coins, where removal of oxidized material was possible. Measurements on spots with and without corrosion are presented and the results discussed.

  4. Segmentation and Quantitative Analysis of Epithelial Tissues.

    PubMed

    Aigouy, Benoit; Umetsu, Daiki; Eaton, Suzanne

    2016-01-01

    Epithelia are tissues that regulate exchanges with the environment. They are very dynamic and can acquire virtually any shape; at the cellular level, they are composed of cells tightly connected by junctions. Most often epithelia are amenable to live imaging; however, the large number of cells composing an epithelium and the absence of informatics tools dedicated to epithelial analysis largely prevented tissue scale studies. Here we present Tissue Analyzer, a free tool that can be used to segment and analyze epithelial cells and monitor tissue dynamics.

  5. Analysis of Artifacts Suggests DGGE Should Not Be Used For Quantitative Diversity Analysis

    PubMed Central

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

    2014-01-01

    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. PMID:23313091

  6. Phenotypic analysis of Arabidopsis mutants: quantitative analysis of root growth.

    PubMed

    Doerner, Peter

    2008-03-01

    INTRODUCTIONThe growth of plant roots is very easy to measure and is particularly straightforward in Arabidopsis thaliana, because the increase in organ size is essentially restricted to one dimension. The precise measurement of root apical growth can be used to accurately determine growth activity (the rate of growth at a given time) during development in mutants, transgenic backgrounds, or in response to experimental treatments. Root growth is measured in a number of ways, the simplest of which is to grow the seedlings in a Petri dish and record the position of the advancing root tip at appropriate time points. The increase in root length is measured with a ruler and the data are entered into Microsoft Excel for analysis. When dealing with large numbers of seedlings, however, this procedure can be tedious, as well as inaccurate. An alternative approach, described in this protocol, uses "snapshots" of the growing plants, which are taken using gel-documentation equipment (i.e., a video camera with a frame-grabber unit, now commonly used to capture images from ethidium-bromide-stained electrophoresis gels). The images are analyzed using publicly available software (NIH-Image), which allows the user simply to cut and paste data into Microsoft Excel.

  7. Quantitative Analysis of Seismicity in Iran

    NASA Astrophysics Data System (ADS)

    Raeesi, Mohammad; Zarifi, Zoya; Nilfouroushan, Faramarz; Boroujeni, Samar Amini; Tiampo, Kristy

    2017-03-01

    We use historical and recent major earthquakes and GPS geodetic data to compute seismic strain rate, geodetic slip deficit, static stress drop, the parameters of the magnitude-frequency distribution and geodetic strain rate in the Iranian Plateau to identify seismically mature fault segments and regions. Our analysis suggests that 11 fault segments are in the mature stage of the earthquake cycle, with the possibility of generating major earthquakes. These faults primarily are located in the north and the east of Iran. Four seismically mature regions in southern Iran with the potential for damaging strong earthquakes are also identified. We also delineate four additional fault segments in Iran that can generate major earthquakes without robust clues to their maturity.The most important fault segment in this study is the strike-slip system near the capital city of Tehran, with the potential to cause more than one million fatalities.

  8. Quantitative Analysis of Seismicity in Iran

    NASA Astrophysics Data System (ADS)

    Raeesi, Mohammad; Zarifi, Zoya; Nilfouroushan, Faramarz; Boroujeni, Samar Amini; Tiampo, Kristy

    2016-12-01

    We use historical and recent major earthquakes and GPS geodetic data to compute seismic strain rate, geodetic slip deficit, static stress drop, the parameters of the magnitude-frequency distribution and geodetic strain rate in the Iranian Plateau to identify seismically mature fault segments and regions. Our analysis suggests that 11 fault segments are in the mature stage of the earthquake cycle, with the possibility of generating major earthquakes. These faults primarily are located in the north and the east of Iran. Four seismically mature regions in southern Iran with the potential for damaging strong earthquakes are also identified. We also delineate four additional fault segments in Iran that can generate major earthquakes without robust clues to their maturity.The most important fault segment in this study is the strike-slip system near the capital city of Tehran, with the potential to cause more than one million fatalities.

  9. Qualitative and Quantitative Proteome Analysis of Oral Fluids in Health and Periodontal Disease by Mass Spectrometry.

    PubMed

    Salih, Erdjan

    2017-01-01

    The significance of protein identification and characterization by classical protein chemistry approaches is clearly highlighted by our detailed understanding of the biological systems assembled over a time period of almost a century. The advent of state-of-the-art mass spectrometry (MS) with sensitivity, speed, and global protein analysis capacity without individual protein purification has transformed the classical protein chemistry with premise to accelerate discovery. These combined with the ability of the oral fluids such as whole saliva (WS) and gingival crevicular fluid (GCF) to reflect both systemic and locally derived proteins have generated significant interest to characterize these fluids more extensively by MS technology. This chapter deals with the experimental details of preanalytical steps using multidimensional protein separation combined with MS analysis of WS and GCF to achieve detailed protein composition at qualitative and quantitative levels. These approaches are interfaced with gold standard "stable-isotope" labeling technologies for large-scale quantitative MS analysis which is a prerequisite to determine accurate alterations in protein levels as a function of disease progression. The latter incorporates two stable-isotope chemistries one specific for cysteine containing proteins and the other universal amine-specific reagent in conjunction with oral fluids in health and periodontal disease to perform quantitative MS analysis. In addition, specific preanalytical steps demanded by the oral fluids such as GCF and WS for sample preparations to overcome limitations and uncertainties are elaborated for reliable large-scale quantitative MS analysis.

  10. Nonlinear Aeroelastic Analysis Using a Time-Accurate Navier-Stokes Equations Solver

    NASA Technical Reports Server (NTRS)

    Kuruvila, Geojoe; Bartels, Robert E.; Hong, Moeljo S.; Bhatia, G.

    2007-01-01

    A method to simulate limit cycle oscillation (LCO) due to control surface freeplay using a modified CFL3D, a time-accurate Navier-Stokes computational fluid dynamics (CFD) analysis code with structural modeling capability, is presented. This approach can be used to analyze aeroelastic response of aircraft with structural behavior characterized by nonlinearity in the force verses displacement curve. A limited validation of the method, using very low Mach number experimental data for a three-degrees-of-freedom (pitch/plunge/flap deflection) airfoil model with flap freeplay, is also presented.

  11. Uncertainty of quantitative microbiological methods of pharmaceutical analysis.

    PubMed

    Gunar, O V; Sakhno, N G

    2015-12-30

    The total uncertainty of quantitative microbiological methods, used in pharmaceutical analysis, consists of several components. The analysis of the most important sources of the quantitative microbiological methods variability demonstrated no effect of culture media and plate-count techniques in the estimation of microbial count while the highly significant effect of other factors (type of microorganism, pharmaceutical product and individual reading and interpreting errors) was established. The most appropriate method of statistical analysis of such data was ANOVA which enabled not only the effect of individual factors to be estimated but also their interactions. Considering all the elements of uncertainty and combining them mathematically the combined relative uncertainty of the test results was estimated both for method of quantitative examination of non-sterile pharmaceuticals and microbial count technique without any product. These data did not exceed 35%, appropriated for a traditional plate count methods.

  12. A rapid and accurate method for the quantitative estimation of natural polysaccharides and their fractions using high performance size exclusion chromatography coupled with multi-angle laser light scattering and refractive index detector.

    PubMed

    Cheong, Kit-Leong; Wu, Ding-Tao; Zhao, Jing; Li, Shao-Ping

    2015-06-26

    In this study, a rapid and accurate method for quantitative analysis of natural polysaccharides and their different fractions was developed. Firstly, high performance size exclusion chromatography (HPSEC) was utilized to separate natural polysaccharides. And then the molecular masses of their fractions were determined by multi-angle laser light scattering (MALLS). Finally, quantification of polysaccharides or their fractions was performed based on their response to refractive index detector (RID) and their universal refractive index increment (dn/dc). Accuracy of the developed method for the quantification of individual and mixed polysaccharide standards, including konjac glucomannan, CM-arabinan, xyloglucan, larch arabinogalactan, oat β-glucan, dextran (410, 270, and 25 kDa), mixed xyloglucan and CM-arabinan, and mixed dextran 270 K and CM-arabinan was determined, and their average recoveries were between 90.6% and 98.3%. The limits of detection (LOD) and quantification (LOQ) were ranging from 10.68 to 20.25 μg/mL, and 42.70 to 68.85 μg/mL, respectively. Comparing to the conventional phenol sulfuric acid assay and HPSEC coupled with evaporative light scattering detection (HPSEC-ELSD) analysis, the developed HPSEC-MALLS-RID method based on universal dn/dc for the quantification of polysaccharides and their fractions is much more simple, rapid, and accurate with no need of individual polysaccharide standard, as well as free of calibration curve. The developed method was also successfully utilized for quantitative analysis of polysaccharides and their different fractions from three medicinal plants of Panax genus, Panax ginseng, Panax notoginseng and Panax quinquefolius. The results suggested that the HPSEC-MALLS-RID method based on universal dn/dc could be used as a routine technique for the quantification of polysaccharides and their fractions in natural resources.

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

    PubMed Central

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

    2008-01-01

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

  14. Quantitative flow cytometric analysis of membrane antigen expression.

    PubMed

    D'hautcourt, Jean-Luc

    2002-11-01

    Immunological analysis for cell antigens has been performed by flow cytometry in a qualitative fashion for over thirty years. During that time it has become increasingly apparent that quantitative measurements such as number of antigens per cell provide unique and useful information. This unit on quantitative flow cytometry (QFCM) describes the most commonly used protocols, both direct and indirect, and the major methods of analysis for the number of antibody binding sites on a cell or particle. Practical applications include detection of antigen under- or overexpression in hematological malignancies, distinguishing between B cell lymphoproliferative disorders, and precise diagnosis of certain rare diseases.

  15. Control of separation and quantitative analysis by GC-FTIR

    NASA Astrophysics Data System (ADS)

    Semmoud, A.; Huvenne, Jean P.; Legrand, P.

    1992-03-01

    Software for 3-D representations of the 'Absorbance-Wavenumber-Retention time' is used to control the quality of the GC separation. Spectral information given by the FTIR detection allows the user to be sure that a chromatographic peak is 'pure.' The analysis of peppermint essential oil is presented as an example. This assurance is absolutely required for quantitative applications. In these conditions, we have worked out a quantitative analysis of caffeine. Correlation coefficients between integrated absorbance measurements and concentration of caffeine are discussed at two steps of the data treatment.

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

    SciTech Connect

    Malik, Afshan N.; Shahni, Rojeen; Rodriguez-de-Ledesma, Ana; Laftah, Abas; Cunningham, Phil

    2011-08-19

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

  17. Accurate, quantitative assays for the hydrolysis of soluble type I, II, and III /sup 3/H-acetylated collagens by bacterial and tissue collagenases

    SciTech Connect

    Mallya, S.K.; Mookhtiar, K.A.; Van Wart, H.E.

    1986-11-01

    Accurate and quantitative assays for the hydrolysis of soluble /sup 3/H-acetylated rat tendon type I, bovine cartilage type II, and human amnion type III collagens by both bacterial and tissue collagenases have been developed. The assays are carried out at any temperature in the 1-30/sup 0/C range in a single reaction tube and the progress of the reaction is monitored by withdrawing aliquots as a function of time, quenching with 1,10-phenanthroline, and quantitation of the concentration of hydrolysis fragments. The latter is achieved by selective denaturation of these fragments by incubation under conditions described in the previous paper of this issue. The assays give percentages of hydrolysis of all three collagen types by neutrophil collagenase that agree well with the results of gel electrophoresis experiments. The initial rates of hydrolysis of all three collagens are proportional to the concentration of both neutrophil or Clostridial collagenases over a 10-fold range of enzyme concentrations. All three assays can be carried out at collagen concentrations that range from 0.06 to 2 mg/ml and give linear double reciprocal plots for both tissue and bacterial collagenases that can be used to evaluate the kinetic parameters K/sub m/ and k/sub cat/ or V/sub max/. The assay developed for the hydrolysis of rat type I collagen by neutrophil collagenase is shown to be more sensitive by at least one order of magnitude than comparable assays that use rat type I collagen fibrils or gels as substrate.

  18. Accurate and unambiguous tag-to-gene mapping in serial analysis of gene expression

    PubMed Central

    Malig, Rodrigo; Varela, Cristian; Agosin, Eduardo; Melo, Francisco

    2006-01-01

    Background In this study, we present a robust and reliable computational method for tag-to-gene assignment in serial analysis of gene expression (SAGE). The method relies on current genome information and annotation, incorporation of several new features, and key improvements over alternative methods, all of which are important to determine gene expression levels more accurately. The method provides a complete annotation of potential virtual SAGE tags within a genome, along with an estimation of their confidence for experimental observation that ranks tags that present multiple matches in the genome. Results We applied this method to the Saccharomyces cerevisiae genome, producing the most thorough and accurate annotation of potential virtual SAGE tags that is available today for this organism. The usefulness of this method is exemplified by the significant reduction of ambiguous cases in existing experimental SAGE data. In addition, we report new insights from the analysis of existing SAGE data. First, we found that experimental SAGE tags mapping onto introns, intron-exon boundaries, and non-coding RNA elements are observed in all available SAGE data. Second, a significant fraction of experimental SAGE tags was found to map onto genomic regions currently annotated as intergenic. Third, a significant number of existing experimental SAGE tags for yeast has been derived from truncated cDNAs, which are synthesized through oligo-d(T) priming to internal poly-(A) regions during reverse transcription. Conclusion We conclude that an accurate and unambiguous tag mapping process is essential to increase the quality and the amount of information that can be extracted from SAGE experiments. This is supported by the results obtained here and also by the large impact that the erroneous interpretation of these data could have on downstream applications. PMID:17083742

  19. Continuous digital ECG analysis over accurate R-peak detection using adaptive wavelet technique.

    PubMed

    Gopalakrishnan Nair, T R; Geetha, A P; Asharani, M

    2013-10-01

    Worldwide, health care segment is under a severe challenge to achieve more accurate and intelligent biomedical systems in order to assist healthcare professionals with more accurate and consistent data as well as reliability. The role of ECG in healthcare is one of the paramount importances and it has got a multitude of abnormal relations and anomalies which characterizes intricate cardiovascular performance image. Until the recent past, ECG instruments and analysis played the role of providing the PQRST signal as raw observational output either on paper or on a console or in a file having many diagnostic clues embedded in the signal left to the expert cardiologist to look out for characteristic intervals and to detect the cardiovascular abnormality. Methods and practises are required more and more, to automate this process of cardiac expertise using knowledge engineering and an intelligent systems approach. This paper presents one of the challenging R-peak detections to classify diagnosis and estimate cardio disorders in a fully automated signal processing sequence. This study used an adaptive wavelet approach to generate an appropriate wavelet for R-signal identification under noise, baseband wandering and temporal variations of R-positions. This study designed an adaptive wavelet and successfully detected R- peak variations under various ECG signal conditions. The result and analysis of this method and the ways to use it for further purposes are presented here.

  20. Quantitative analysis of urinary stone composition with micro-Raman spectroscopy

    NASA Astrophysics Data System (ADS)

    Huang, Yi-Yu; Chiu, Yi-Chun; Chiang, Huihua Kenny; Chou, Y. H. Jet; Lu, Shing-Hwa; Chiu, Allen W.

    2010-02-01

    Urolithiasis is a common, disturbing disease with high recurrent rate (60% in five years). Accurate identification of urinary stone composition is important for treatment and prevention purpose. Our previous studies have demonstrated that micro-Raman spectroscopy (MRS)-based approach successfully detects the composition of tiny stone powders after minimal invasive urological surgery. But quantitative analysis of urinary stones was not established yet. In this study, human urinary stone mixed with two compositions of COM, HAP, COD, and uric acid, were analyzed quantitatively by using a 632.98 nm Raman spectrometric system. This quantitative analysis was based on the construction of calibration curves of known mixtures of synthetically prepared pure COM, HAP, COD and uric acid. First, the various concentration (mole fraction) ratio of binary mixtures including COM and HAP, COM and COD, or COM and uric acid, were produced. Second, the intensities of the characteristic bands at 1462cm -1(IRCOM), 1477cm-1(IRCOD), 961cm-1(IRHAP) and 1402cm-1(IRuric acid), for COD, COM, HAP and uric acid were used respectively for intensity calculation. Various binary mixtures of known concentration ratio were recorded as the basis for the quantitative analysis. The ratios of the relative intensities of the Raman bands corresponding to binary mixtures of known composition on the inverse of the COM concentration yielded a linear dependence. Third, urinary stone fragments collected from patients after management were analyzed with the use of the calibration curve and the quantitative analysis of unknown samples was made by the interpolation analysis. We successfully developed a MRS-based quantitative analytical method for measuring two composition.

  1. A quantitative analysis of the F18 flight control system

    NASA Technical Reports Server (NTRS)

    Doyle, Stacy A.; Dugan, Joanne B.; Patterson-Hine, Ann

    1993-01-01

    This paper presents an informal quantitative analysis of the F18 flight control system (FCS). The analysis technique combines a coverage model with a fault tree model. To demonstrate the method's extensive capabilities, we replace the fault tree with a digraph model of the F18 FCS, the only model available to us. The substitution shows that while digraphs have primarily been used for qualitative analysis, they can also be used for quantitative analysis. Based on our assumptions and the particular failure rates assigned to the F18 FCS components, we show that coverage does have a significant effect on the system's reliability and thus it is important to include coverage in the reliability analysis.

  2. Issues in Quantitative Analysis of Ultraviolet Imager (UV) Data: Airglow

    NASA Technical Reports Server (NTRS)

    Germany, G. A.; Richards, P. G.; Spann, J. F.; Brittnacher, M. J.; Parks, G. K.

    1999-01-01

    The GGS Ultraviolet Imager (UVI) has proven to be especially valuable in correlative substorm, auroral morphology, and extended statistical studies of the auroral regions. Such studies are based on knowledge of the location, spatial, and temporal behavior of auroral emissions. More quantitative studies, based on absolute radiometric intensities from UVI images, require a more intimate knowledge of the instrument behavior and data processing requirements and are inherently more difficult than studies based on relative knowledge of the oval location. In this study, UVI airglow observations are analyzed and compared with model predictions to illustrate issues that arise in quantitative analysis of UVI images. These issues include instrument calibration, long term changes in sensitivity, and imager flat field response as well as proper background correction. Airglow emissions are chosen for this study because of their relatively straightforward modeling requirements and because of their implications for thermospheric compositional studies. The analysis issues discussed here, however, are identical to those faced in quantitative auroral studies.

  3. EXPLoRA-web: linkage analysis of quantitative trait loci using bulk segregant analysis

    PubMed Central

    Pulido-Tamayo, Sergio; Duitama, Jorge; Marchal, Kathleen

    2016-01-01

    Identification of genomic regions associated with a phenotype of interest is a fundamental step toward solving questions in biology and improving industrial research. Bulk segregant analysis (BSA) combined with high-throughput sequencing is a technique to efficiently identify these genomic regions associated with a trait of interest. However, distinguishing true from spuriously linked genomic regions and accurately delineating the genomic positions of these truly linked regions requires the use of complex statistical models currently implemented in software tools that are generally difficult to operate for non-expert users. To facilitate the exploration and analysis of data generated by bulked segregant analysis, we present EXPLoRA-web, a web service wrapped around our previously published algorithm EXPLoRA, which exploits linkage disequilibrium to increase the power and accuracy of quantitative trait loci identification in BSA analysis. EXPLoRA-web provides a user friendly interface that enables easy data upload and parallel processing of different parameter configurations. Results are provided graphically and as BED file and/or text file and the input is expected in widely used formats, enabling straightforward BSA data analysis. The web server is available at http://bioinformatics.intec.ugent.be/explora-web/. PMID:27105844

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

    PubMed

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

    2013-01-01

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

  5. Allele Specific Locked Nucleic Acid Quantitative PCR (ASLNAqPCR): An Accurate and Cost-Effective Assay to Diagnose and Quantify KRAS and BRAF Mutation

    PubMed Central

    Morandi, Luca; de Biase, Dario; Visani, Michela; Cesari, Valentina; De Maglio, Giovanna; Pizzolitto, Stefano; Pession, Annalisa; Tallini, Giovanni

    2012-01-01

    The use of tyrosine kinase inhibitors (TKIs) requires the testing for hot spot mutations of the molecular effectors downstream the membrane-bound tyrosine kinases since their wild type status is expected for response to TKI therapy. We report a novel assay that we have called Allele Specific Locked Nucleic Acid quantitative PCR (ASLNAqPCR). The assay uses LNA-modified allele specific primers and LNA-modified beacon probes to increase sensitivity, specificity and to accurately quantify mutations. We designed primers specific for codon 12/13 KRAS mutations and BRAF V600E, and validated the assay with 300 routine samples from a variety of sources, including cytology specimens. All were analyzed by ASLNAqPCR and Sanger sequencing. Discordant cases were pyrosequenced. ASLNAqPCR correctly identified BRAF and KRAS mutations in all discordant cases and all had a mutated/wild type DNA ratio below the analytical sensitivity of the Sanger method. ASLNAqPCR was 100% specific with greater accuracy, positive and negative predictive values compared with Sanger sequencing. The analytical sensitivity of ASLNAqPCR is 0.1%, allowing quantification of mutated DNA in small neoplastic cell clones. ASLNAqPCR can be performed in any laboratory with real-time PCR equipment, is very cost-effective and can easily be adapted to detect hot spot mutations in other oncogenes. PMID:22558339

  6. 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.

  7. An efficient approach to the quantitative analysis of humic acid in water.

    PubMed

    Wang, Xue; Li, Bao Qiong; Zhai, Hong Lin; Xiong, Meng Yi; Liu, Ying

    2016-01-01

    Rayleigh and Raman scatterings inevitably appear in fluorescence measurements, which make the quantitative analysis more difficult, especially in the overlap of target signals and scattering signals. Based on the grayscale images of three-dimensional fluorescence spectra, the linear model with two selected Zernike moments was established for the determination of humic acid, and applied to the quantitative analysis of the real sample taken from the Yellow River. The correlation coefficient (R(2)) and leave-one-out cross validation correlation coefficient (R(2)cv) were up to 0.9994 and 0.9987, respectively. The average recoveries were reached 96.28%. Compared with N-way partial least square and alternating trilinear decomposition methods, our approach was immune from the scattering and noise signals owing to its powerful multi-resolution characteristic and the obtained results were more reliable and accurate, which could be applied in food analyses.

  8. CUMULATIVE RISK ASSESSMENT: GETTING FROM TOXICOLOGY TO QUANTITATIVE ANALYSIS

    EPA Science Inventory

    INTRODUCTION: GETTING FROM TOXICOLOGY TO QUANTITATIVE ANALYSIS FOR CUMULATIVE RISK

    Hugh A. Barton1 and Carey N. Pope2
    1US EPA, Office of Research and Development, National Health and Environmental Effects Research Laboratory, Research Triangle Park, NC
    2Department of...

  9. Quantitating the subtleties of microglial morphology with fractal analysis

    PubMed Central

    Karperien, Audrey; Ahammer, Helmut; Jelinek, Herbert F.

    2013-01-01

    It is well established that microglial form and function are inextricably linked. In recent years, the traditional view that microglial form ranges between “ramified resting” and “activated amoeboid” has been emphasized through advancing imaging techniques that point to microglial form being highly dynamic even within the currently accepted morphological categories. Moreover, microglia adopt meaningful intermediate forms between categories, with considerable crossover in function and varying morphologies as they cycle, migrate, wave, phagocytose, and extend and retract fine and gross processes. From a quantitative perspective, it is problematic to measure such variability using traditional methods, but one way of quantitating such detail is through fractal analysis. The techniques of fractal analysis have been used for quantitating microglial morphology, to categorize gross differences but also to differentiate subtle differences (e.g., amongst ramified cells). Multifractal analysis in particular is one technique of fractal analysis that may be useful for identifying intermediate forms. Here we review current trends and methods of fractal analysis, focusing on box counting analysis, including lacunarity and multifractal analysis, as applied to microglial morphology. PMID:23386810

  10. 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

  11. Advances in liquid chromatography-high-resolution mass spectrometry for quantitative and qualitative environmental analysis.

    PubMed

    Aceña, Jaume; Stampachiacchiere, Serena; Pérez, Sandra; Barceló, Damià

    2015-08-01

    This review summarizes the advances in environmental analysis by liquid chromatography-high-resolution mass spectrometry (LC-HRMS) during the last decade and discusses different aspects of their application. LC-HRMS has become a powerful tool for simultaneous quantitative and qualitative analysis of organic pollutants, enabling their quantitation and the search for metabolites and transformation products or the detection of unknown compounds. LC-HRMS provides more information than low-resolution (LR) MS for each sample because it can accurately determine the mass of the molecular ion and its fragment ions if it can be used for MS-MS. Another advantage is that the data can be processed using either target analysis, suspect screening, retrospective analysis, or non-target screening. With the growing popularity and acceptance of HRMS analysis, current guidelines for compound confirmation need to be revised for quantitative and qualitative purposes. Furthermore, new commercial software and user-built libraries are required to mine data in an efficient and comprehensive way. The scope of this critical review is not to provide a comprehensive overview of the many studies performed with LC-HRMS in the field of environmental analysis, but to reveal its advantages and limitations using different workflows.

  12. Fast and accurate sensitivity analysis of IMPT treatment plans using Polynomial Chaos Expansion

    NASA Astrophysics Data System (ADS)

    Perkó, Zoltán; van der Voort, Sebastian R.; van de Water, Steven; Hartman, Charlotte M. H.; Hoogeman, Mischa; Lathouwers, Danny

    2016-06-01

    The highly conformal planned dose distribution achievable in intensity modulated proton therapy (IMPT) can severely be compromised by uncertainties in patient setup and proton range. While several robust optimization approaches have been presented to address this issue, appropriate methods to accurately estimate the robustness of treatment plans are still lacking. To fill this gap we present Polynomial Chaos Expansion (PCE) techniques which are easily applicable and create a meta-model of the dose engine by approximating the dose in every voxel with multidimensional polynomials. This Polynomial Chaos (PC) model can be built in an automated fashion relatively cheaply and subsequently it can be used to perform comprehensive robustness analysis. We adapted PC to provide among others the expected dose, the dose variance, accurate probability distribution of dose-volume histogram (DVH) metrics (e.g. minimum tumor or maximum organ dose), exact bandwidths of DVHs, and to separate the effects of random and systematic errors. We present the outcome of our verification experiments based on 6 head-and-neck (HN) patients, and exemplify the usefulness of PCE by comparing a robust and a non-robust treatment plan for a selected HN case. The results suggest that PCE is highly valuable for both research and clinical applications.

  13. Fast and accurate sensitivity analysis of IMPT treatment plans using Polynomial Chaos Expansion.

    PubMed

    Perkó, Zoltán; van der Voort, Sebastian R; van de Water, Steven; Hartman, Charlotte M H; Hoogeman, Mischa; Lathouwers, Danny

    2016-06-21

    The highly conformal planned dose distribution achievable in intensity modulated proton therapy (IMPT) can severely be compromised by uncertainties in patient setup and proton range. While several robust optimization approaches have been presented to address this issue, appropriate methods to accurately estimate the robustness of treatment plans are still lacking. To fill this gap we present Polynomial Chaos Expansion (PCE) techniques which are easily applicable and create a meta-model of the dose engine by approximating the dose in every voxel with multidimensional polynomials. This Polynomial Chaos (PC) model can be built in an automated fashion relatively cheaply and subsequently it can be used to perform comprehensive robustness analysis. We adapted PC to provide among others the expected dose, the dose variance, accurate probability distribution of dose-volume histogram (DVH) metrics (e.g. minimum tumor or maximum organ dose), exact bandwidths of DVHs, and to separate the effects of random and systematic errors. We present the outcome of our verification experiments based on 6 head-and-neck (HN) patients, and exemplify the usefulness of PCE by comparing a robust and a non-robust treatment plan for a selected HN case. The results suggest that PCE is highly valuable for both research and clinical applications.

  14. Accurate palm vein recognition based on wavelet scattering and spectral regression kernel discriminant analysis

    NASA Astrophysics Data System (ADS)

    Elnasir, Selma; Shamsuddin, Siti Mariyam; Farokhi, Sajad

    2015-01-01

    Palm vein recognition (PVR) is a promising new biometric that has been applied successfully as a method of access control by many organizations, which has even further potential in the field of forensics. The palm vein pattern has highly discriminative features that are difficult to forge because of its subcutaneous position in the palm. Despite considerable progress and a few practical issues, providing accurate palm vein readings has remained an unsolved issue in biometrics. We propose a robust and more accurate PVR method based on the combination of wavelet scattering (WS) with spectral regression kernel discriminant analysis (SRKDA). As the dimension of WS generated features is quite large, SRKDA is required to reduce the extracted features to enhance the discrimination. The results based on two public databases-PolyU Hyper Spectral Palmprint public database and PolyU Multi Spectral Palmprint-show the high performance of the proposed scheme in comparison with state-of-the-art methods. The proposed approach scored a 99.44% identification rate and a 99.90% verification rate [equal error rate (EER)=0.1%] for the hyperspectral database and a 99.97% identification rate and a 99.98% verification rate (EER=0.019%) for the multispectral database.

  15. Accurate and flexible calibration technique for fringe projection profilometry by using encoded points and Fourier analysis

    NASA Astrophysics Data System (ADS)

    González, Andrés. L.; Contreras, Carlos R.; Meneses, Jaime E.

    2014-05-01

    In order to get measures with a high accurate, three-dimensional reconstruction systems are implemented in industrial, medical, and investigative fields. To obtain high accurate is necessary to carry out an appropriate calibration procedure. In fringe projection profilometry, this procedure allows obtaining a relation between absolute phase and three-dimensional (3D) information of the object in study; however, to execute such procedure a precise movement stage is required. A fringe projection system is formed by a projector, a digital camera and a control unit, called like a projection-acquisition unit in this paper. The calibration of the projection-acquisition unit consists in to establish the parameters that are required to transform the phase of the projected fringes to metric coordinates of the object surface. These parameters are a function of the intrinsic and extrinsic parameters of both camera and projector, due to the projector is modeled as an inverse camera. For this purpose, in this paper a novel and flexible calibration method that allows calibrating any device that works with fringe projection profilometry is proposed. In this method is used a reference plane placed in random positions and the projection of an encoded pattern of control points. The camera parameters are computed using Zhang's calibration method; and the projector parameters are computed from the camera parameters and the phase of the pattern of control points, which is determined by using Fourier analysis. Experimental results are presented to demonstrate the performance of the calibration method.

  16. Quantitative analysis of regional myocardial performance in coronary artery disease

    NASA Technical Reports Server (NTRS)

    Stewart, D. K.; Dodge, H. T.; Frimer, M.

    1975-01-01

    Findings from a group of subjects with significant coronary artery stenosis are given. A group of controls determined by use of a quantitative method for the study of regional myocardial performance based on the frame-by-frame analysis of biplane left ventricular angiograms are presented. Particular emphasis was placed upon the analysis of wall motion in terms of normalized segment dimensions, timing and velocity of contraction. The results were compared with the method of subjective assessment used clinically.

  17. Quantitative analysis of culture using millions of digitized books.

    PubMed

    Michel, Jean-Baptiste; Shen, Yuan Kui; Aiden, Aviva Presser; Veres, Adrian; Gray, Matthew K; Pickett, Joseph P; Hoiberg, Dale; Clancy, Dan; Norvig, Peter; Orwant, Jon; Pinker, Steven; Nowak, Martin A; Aiden, Erez Lieberman

    2011-01-14

    We constructed a corpus of digitized texts containing about 4% of all books ever printed. Analysis of this corpus enables us to investigate cultural trends quantitatively. We survey the vast terrain of 'culturomics,' focusing on linguistic and cultural phenomena that were reflected in the English language between 1800 and 2000. We show how this approach can provide insights about fields as diverse as lexicography, the evolution of grammar, collective memory, the adoption of technology, the pursuit of fame, censorship, and historical epidemiology. Culturomics extends the boundaries of rigorous quantitative inquiry to a wide array of new phenomena spanning the social sciences and the humanities.

  18. Quantitative analysis of culture using millions of digitized books

    PubMed Central

    Michel, Jean-Baptiste; Shen, Yuan Kui; Aiden, Aviva P.; Veres, Adrian; Gray, Matthew K.; Pickett, Joseph P.; Hoiberg, Dale; Clancy, Dan; Norvig, Peter; Orwant, Jon; Pinker, Steven; Nowak, Martin A.; Aiden, Erez Lieberman

    2011-01-01

    We constructed a corpus of digitized texts containing about 4% of all books ever printed. Analysis of this corpus enables us to investigate cultural trends quantitatively. We survey the vast terrain of ‘culturomics’, focusing on linguistic and cultural phenomena that were reflected in the English language between 1800 and 2000. We show how this approach can provide insights about fields as diverse as lexicography, the evolution of grammar, collective memory, the adoption of technology, the pursuit of fame, censorship, and historical epidemiology. ‘Culturomics’ extends the boundaries of rigorous quantitative inquiry to a wide array of new phenomena spanning the social sciences and the humanities. PMID:21163965

  19. Quantitative numerical analysis of transient IR-experiments on buildings

    NASA Astrophysics Data System (ADS)

    Maierhofer, Ch.; Wiggenhauser, H.; Brink, A.; Röllig, M.

    2004-12-01

    Impulse-thermography has been established as a fast and reliable tool in many areas of non-destructive testing. In recent years several investigations have been done to apply active thermography to civil engineering. For quantitative investigations in this area of application, finite difference calculations have been performed for systematic studies on the influence of environmental conditions, heating power and time, defect depth and size and thermal properties of the bulk material (concrete). The comparison of simulated and experimental data enables the quantitative analysis of defects.

  20. Improved method and apparatus for chromatographic quantitative analysis

    DOEpatents

    Fritz, J.S.; Gjerde, D.T.; Schmuckler, G.

    An improved apparatus and method are described for the quantitative analysis of a solution containing a plurality of anion species by ion exchange chromatography which utilizes a single element and a single ion exchange bed which does not require periodic regeneration. The solution containing the anions is added to an anion exchange resin bed which is a low capacity macroreticular polystyrene-divinylbenzene resin containing quarternary ammonium functional groups, and is eluted therefrom with a dilute solution of a low electrical conductance organic acid salt. As each anion species is eluted from the bed, it is quantitatively sensed by conventional detection means such as a conductivity cell.

  1. Quantitative analysis of autophagy using advanced 3D fluorescence microscopy.

    PubMed

    Changou, Chun A; Wolfson, Deanna L; Ahluwalia, Balpreet Singh; Bold, Richard J; Kung, Hsing-Jien; Chuang, Frank Y S

    2013-05-03

    Prostate cancer is the leading form of malignancies among men in the U.S. While surgery carries a significant risk of impotence and incontinence, traditional chemotherapeutic approaches have been largely unsuccessful. Hormone therapy is effective at early stage, but often fails with the eventual development of hormone-refractory tumors. We have been interested in developing therapeutics targeting specific metabolic deficiency of tumor cells. We recently showed that prostate tumor cells specifically lack an enzyme (argininosuccinate synthase, or ASS) involved in the synthesis of the amino acid arginine(1). This condition causes the tumor cells to become dependent on exogenous arginine, and they undergo metabolic stress when free arginine is depleted by arginine deiminase (ADI)(1,10). Indeed, we have shown that human prostate cancer cells CWR22Rv1 are effectively killed by ADI with caspase-independent apoptosis and aggressive autophagy (or macroautophagy)(1,2,3). Autophagy is an evolutionarily-conserved process that allows cells to metabolize unwanted proteins by lysosomal breakdown during nutritional starvation(4,5). Although the essential components of this pathway are well-characterized(6,7,8,9), many aspects of the molecular mechanism are still unclear - in particular, what is the role of autophagy in the death-response of prostate cancer cells after ADI treatment? In order to address this question, we required an experimental method to measure the level and extent of autophagic response in cells - and since there are no known molecular markers that can accurately track this process, we chose to develop an imaging-based approach, using quantitative 3D fluorescence microscopy(11,12). Using CWR22Rv1 cells specifically-labeled with fluorescent probes for autophagosomes and lysosomes, we show that 3D image stacks acquired with either widefield deconvolution microscopy (and later, with super-resolution, structured-illumination microscopy) can clearly capture the early

  2. Markov chain Monte Carlo linkage analysis of complex quantitative phenotypes.

    PubMed

    Hinrichs, A; Reich, T

    2001-01-01

    We report a Markov chain Monte Carlo analysis of the five simulated quantitative traits in Genetic Analysis Workshop 12 using the Loki software. Our objectives were to determine the efficacy of the Markov chain Monte Carlo method and to test a new scoring technique. Our initial blind analysis, on replicate 42 (the "best replicate") successfully detected four out of the five disease loci and found no false positives. A power analysis shows that the software could usually detect 4 of the 10 trait/gene combinations at an empirical point-wise p-value of 1.5 x 10(-4).

  3. Time-Accurate Simulations and Acoustic Analysis of Slat Free-Shear Layer

    NASA Technical Reports Server (NTRS)

    Khorrami, Mehdi R.; Singer, Bart A.; Berkman, Mert E.

    2001-01-01

    A detailed computational aeroacoustic analysis of a high-lift flow field is performed. Time-accurate Reynolds Averaged Navier-Stokes (RANS) computations simulate the free shear layer that originates from the slat cusp. Both unforced and forced cases are studied. Preliminary results show that the shear layer is a good amplifier of disturbances in the low to mid-frequency range. The Ffowcs-Williams and Hawkings equation is solved to determine the acoustic field using the unsteady flow data from the RANS calculations. The noise radiated from the excited shear layer has a spectral shape qualitatively similar to that obtained from measurements in a corresponding experimental study of the high-lift system.

  4. An algorithm for selecting the most accurate protocol for contact angle measurement by drop shape analysis.

    PubMed

    Xu, Z N

    2014-12-01

    In this study, an error analysis is performed to study real water drop images and the corresponding numerically generated water drop profiles for three widely used static contact angle algorithms: the circle- and ellipse-fitting algorithms and the axisymmetric drop shape analysis-profile (ADSA-P) algorithm. The results demonstrate the accuracy of the numerically generated drop profiles based on the Laplace equation. A significant number of water drop profiles with different volumes, contact angles, and noise levels are generated, and the influences of the three factors on the accuracies of the three algorithms are systematically investigated. The results reveal that the above-mentioned three algorithms are complementary. In fact, the circle- and ellipse-fitting algorithms show low errors and are highly resistant to noise for water drops with small/medium volumes and contact angles, while for water drop with large volumes and contact angles just the ADSA-P algorithm can meet accuracy requirement. However, this algorithm introduces significant errors in the case of small volumes and contact angles because of its high sensitivity to noise. The critical water drop volumes of the circle- and ellipse-fitting algorithms corresponding to a certain contact angle error are obtained through a significant amount of computation. To improve the precision of the static contact angle measurement, a more accurate algorithm based on a combination of the three algorithms is proposed. Following a systematic investigation, the algorithm selection rule is described in detail, while maintaining the advantages of the three algorithms and overcoming their deficiencies. In general, static contact angles over the entire hydrophobicity range can be accurately evaluated using the proposed algorithm. The ease of erroneous judgment in static contact angle measurements is avoided. The proposed algorithm is validated by a static contact angle evaluation of real and numerically generated water drop

  5. An algorithm for selecting the most accurate protocol for contact angle measurement by drop shape analysis

    NASA Astrophysics Data System (ADS)

    Xu, Z. N.

    2014-12-01

    In this study, an error analysis is performed to study real water drop images and the corresponding numerically generated water drop profiles for three widely used static contact angle algorithms: the circle- and ellipse-fitting algorithms and the axisymmetric drop shape analysis-profile (ADSA-P) algorithm. The results demonstrate the accuracy of the numerically generated drop profiles based on the Laplace equation. A significant number of water drop profiles with different volumes, contact angles, and noise levels are generated, and the influences of the three factors on the accuracies of the three algorithms are systematically investigated. The results reveal that the above-mentioned three algorithms are complementary. In fact, the circle- and ellipse-fitting algorithms show low errors and are highly resistant to noise for water drops with small/medium volumes and contact angles, while for water drop with large volumes and contact angles just the ADSA-P algorithm can meet accuracy requirement. However, this algorithm introduces significant errors in the case of small volumes and contact angles because of its high sensitivity to noise. The critical water drop volumes of the circle- and ellipse-fitting algorithms corresponding to a certain contact angle error are obtained through a significant amount of computation. To improve the precision of the static contact angle measurement, a more accurate algorithm based on a combination of the three algorithms is proposed. Following a systematic investigation, the algorithm selection rule is described in detail, while maintaining the advantages of the three algorithms and overcoming their deficiencies. In general, static contact angles over the entire hydrophobicity range can be accurately evaluated using the proposed algorithm. The ease of erroneous judgment in static contact angle measurements is avoided. The proposed algorithm is validated by a static contact angle evaluation of real and numerically generated water drop

  6. Experimental and theoretical oscillator strengths of Mg i for accurate abundance analysis

    NASA Astrophysics Data System (ADS)

    Pehlivan Rhodin, A.; Hartman, H.; Nilsson, H.; Jönsson, P.

    2017-02-01

    Context. With the aid of stellar abundance analysis, it is possible to study the galactic formation and evolution. Magnesium is an important element to trace the α-element evolution in our Galaxy. For chemical abundance analysis, such as magnesium abundance, accurate and complete atomic data are essential. Inaccurate atomic data lead to uncertain abundances and prevent discrimination between different evolution models. Aims: We study the spectrum of neutral magnesium from laboratory measurements and theoretical calculations. Our aim is to improve the oscillator strengths (f-values) of Mg i lines and to create a complete set of accurate atomic data, particularly for the near-IR region. Methods: We derived oscillator strengths by combining the experimental branching fractions with radiative lifetimes reported in the literature and computed in this work. A hollow cathode discharge lamp was used to produce free atoms in the plasma and a Fourier transform spectrometer recorded the intensity-calibrated high-resolution spectra. In addition, we performed theoretical calculations using the multiconfiguration Hartree-Fock program ATSP2K. Results: This project provides a set of experimental and theoretical oscillator strengths. We derived 34 experimental oscillator strengths. Except from the Mg i optical triplet lines (3p 3P°0,1,2-4s 3S1), these oscillator strengths are measured for the first time. The theoretical oscillator strengths are in very good agreement with the experimental data and complement the missing transitions of the experimental data up to n = 7 from even and odd parity terms. We present an evaluated set of oscillator strengths, gf, with uncertainties as small as 5%. The new values of the Mg i optical triplet line (3p 3P°0,1,2-4s 3S1) oscillator strength values are 0.08 dex larger than the previous measurements.

  7. 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.

  8. Quantitative mass spectrometric analysis of glycoproteins combined with enrichment methods.

    PubMed

    Ahn, Yeong Hee; Kim, Jin Young; Yoo, Jong Shin

    2015-01-01

    Mass spectrometry (MS) has been a core technology for high sensitive and high-throughput analysis of the enriched glycoproteome in aspects of quantitative assays as well as qualitative profiling of glycoproteins. Because it has been widely recognized that aberrant glycosylation in a glycoprotein may involve in progression of a certain disease, the development of efficient analysis tool for the aberrant glycoproteins is very important for deep understanding about pathological function of the glycoprotein and new biomarker development. This review first describes the protein glycosylation-targeting enrichment technologies mainly employing solid-phase extraction methods such as hydrizide-capturing, lectin-specific capturing, and affinity separation techniques based on porous graphitized carbon, hydrophilic interaction chromatography, or immobilized boronic acid. Second, MS-based quantitative analysis strategies coupled with the protein glycosylation-targeting enrichment technologies, by using a label-free MS, stable isotope-labeling, or targeted multiple reaction monitoring (MRM) MS, are summarized with recent published studies.

  9. Simultaneous qualitative and quantitative analysis of the Escherichia coli proteome: a sweet tale.

    PubMed

    Silva, Jeffrey C; Denny, Richard; Dorschel, Craig; Gorenstein, Marc V; Li, Guo-Zhong; Richardson, Keith; Wall, Daniel; Geromanos, Scott J

    2006-04-01

    We describe a novel LCMS approach to the relative quantitation and simultaneous identification of proteins within the complex milieu of unfractionated Escherichia coli. This label-free, LCMS acquisition method observes all detectable, eluting peptides and their corresponding fragment ions. Postacquisition data analysis methods extract both the chromatographic and the mass spectrometric information on the tryptic peptides to provide time-resolved, accurate mass measurements, which are subsequently used for quantitation and identification of constituent proteins. The response of E. coli to carbon source variation is well understood, and it is thus commonly used as a model biological system when validating an analytical method. Using this LCMS approach, we characterized proteins isolated from E. coli grown in glucose, lactose, and acetate. The change in relative abundance of the corresponding proteins was measured from peptides common to both conditions. Protein identities were also determined for those peptides that were unique to each condition, and these identities were found to be consistent with the underlying biochemical restrictions imposed by the growth conditions. The relative change in abundance of the characterized proteins ranged from 0.1- to 90-fold among the three binary comparisons. The overall coverage of the characterized proteins ranged from 10 to 80%, consisting of one to 34 peptides per protein. The quantitative results obtained from our study were comparable to other existing proteomic and transcriptional profiling approaches. This study illustrates the robustness of this novel LCMS approach for the simultaneous quantitative and comprehensive qualitative analysis of proteins in complex mixtures.

  10. Sources of Technical Variability in Quantitative LC-MS Proteomics: Human Brain Tissue Sample Analysis.

    SciTech Connect

    Piehowski, Paul D.; Petyuk, Vladislav A.; Orton, Daniel J.; Xie, Fang; Moore, Ronald J.; Ramirez Restrepo, Manuel; Engel, Anzhelika; Lieberman, Andrew P.; Albin, Roger L.; Camp, David G.; Smith, Richard D.; Myers, Amanda J.

    2013-05-03

    To design a robust quantitative proteomics study, an understanding of both the inherent heterogeneity of the biological samples being studied as well as the technical variability of the proteomics methods and platform is needed. Additionally, accurately identifying the technical steps associated with the largest variability would provide valuable information for the improvement and design of future processing pipelines. We present an experimental strategy that allows for a detailed examination of the variability of the quantitative LC-MS proteomics measurements. By replicating analyses at different stages of processing, various technical components can be estimated and their individual contribution to technical variability can be dissected. This design can be easily adapted to other quantitative proteomics pipelines. Herein, we applied this methodology to our label-free workflow for the processing of human brain tissue. For this application, the pipeline was divided into four critical components: Tissue dissection and homogenization (extraction), protein denaturation followed by trypsin digestion and SPE clean-up (digestion), short-term run-to-run instrumental response fluctuation (instrumental variance), and long-term drift of the quantitative response of the LC-MS/MS platform over the 2 week period of continuous analysis (instrumental stability). From this analysis, we found the following contributions to variability: extraction (72%) >> instrumental variance (16%) > instrumental stability (8.4%) > digestion (3.1%). Furthermore, the stability of the platform and its’ suitability for discovery proteomics studies is demonstrated.

  11. Some selected quantitative methods of thermal image analysis in Matlab.

    PubMed

    Koprowski, Robert

    2016-05-01

    The paper presents a new algorithm based on some selected automatic quantitative methods for analysing thermal images. It shows the practical implementation of these image analysis methods in Matlab. It enables to perform fully automated and reproducible measurements of selected parameters in thermal images. The paper also shows two examples of the use of the proposed image analysis methods for the area of ​​the skin of a human foot and face. The full source code of the developed application is also provided as an attachment. The main window of the program during dynamic analysis of the foot thermal image.

  12. Quantitative risk analysis of oil storage facilities in seismic areas.

    PubMed

    Fabbrocino, Giovanni; Iervolino, Iunio; Orlando, Francesca; Salzano, Ernesto

    2005-08-31

    Quantitative risk analysis (QRA) of industrial facilities has to take into account multiple hazards threatening critical equipment. Nevertheless, engineering procedures able to evaluate quantitatively the effect of seismic action are not well established. Indeed, relevant industrial accidents may be triggered by loss of containment following ground shaking or other relevant natural hazards, either directly or through cascade effects ('domino effects'). The issue of integrating structural seismic risk into quantitative probabilistic seismic risk analysis (QpsRA) is addressed in this paper by a representative study case regarding an oil storage plant with a number of atmospheric steel tanks containing flammable substances. Empirical seismic fragility curves and probit functions, properly defined both for building-like and non building-like industrial components, have been crossed with outcomes of probabilistic seismic hazard analysis (PSHA) for a test site located in south Italy. Once the seismic failure probabilities have been quantified, consequence analysis has been performed for those events which may be triggered by the loss of containment following seismic action. Results are combined by means of a specific developed code in terms of local risk contour plots, i.e. the contour line for the probability of fatal injures at any point (x, y) in the analysed area. Finally, a comparison with QRA obtained by considering only process-related top events is reported for reference.

  13. An improved quantitative analysis method for plant cortical microtubules.

    PubMed

    Lu, Yi; Huang, Chenyang; Wang, Jia; Shang, Peng

    2014-01-01

    The arrangement of plant cortical microtubules can reflect the physiological state of cells. However, little attention has been paid to the image quantitative analysis of plant cortical microtubules so far. In this paper, Bidimensional Empirical Mode Decomposition (BEMD) algorithm was applied in the image preprocessing of the original microtubule image. And then Intrinsic Mode Function 1 (IMF1) image obtained by decomposition was selected to do the texture analysis based on Grey-Level Cooccurrence Matrix (GLCM) algorithm. Meanwhile, in order to further verify its reliability, the proposed texture analysis method was utilized to distinguish different images of Arabidopsis microtubules. The results showed that the effect of BEMD algorithm on edge preserving accompanied with noise reduction was positive, and the geometrical characteristic of the texture was obvious. Four texture parameters extracted by GLCM perfectly reflected the different arrangements between the two images of cortical microtubules. In summary, the results indicate that this method is feasible and effective for the image quantitative analysis of plant cortical microtubules. It not only provides a new quantitative approach for the comprehensive study of the role played by microtubules in cell life activities but also supplies references for other similar studies.

  14. Data from quantitative label free proteomics analysis of rat spleen.

    PubMed

    Dudekula, Khadar; Le Bihan, Thierry

    2016-09-01

    The dataset presented in this work has been obtained using a label-free quantitative proteomic analysis of rat spleen. A robust method for extraction of proteins from rat spleen tissue and LC-MS-MS analysis was developed using a urea and SDS-based buffer. Different fractionation methods were compared. A total of 3484 different proteins were identified from the pool of all experiments run in this study (a total of 2460 proteins with at least two peptides). A total of 1822 proteins were identified from nine non-fractionated pulse gels, 2288 proteins and 2864 proteins were identified by SDS-PAGE fractionation into three and five fractions respectively. The proteomics data are deposited in ProteomeXchange Consortium via PRIDE PXD003520, Progenesis and Maxquant output are presented in the supported information. The generated list of proteins under different regimes of fractionation allow assessing the nature of the identified proteins; variability in the quantitative analysis associated with the different sampling strategy and allow defining a proper number of replicates for future quantitative analysis.

  15. Comparative analysis of quantitative methodologies for Vibrionaceae biofilms

    PubMed Central

    Chavez-Dozal, Alba A.; Nourabadi, Neda; Erken, Martina; McDougald, Diane; Nishiguchi, Michele K.

    2016-01-01

    Multiple symbiotic and free living Vibrio sp. grow as a form of microbial community known as 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. PMID:27009592

  16. Quantitative Analysis of Matrine in Liquid Crystalline Nanoparticles by HPLC

    PubMed Central

    Peng, Xinsheng; 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 μg/mL. The regression equation is y = 10706x − 2959 (R2 = 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. PMID:24834359

  17. Accurate determination of succinimide degradation products using high fidelity trypsin digestion peptide map analysis.

    PubMed

    Yu, X Christopher; Joe, Koman; Zhang, Yu; Adriano, Andrea; Wang, Yaning; Gazzano-Santoro, Helene; Keck, Rodney G; Deperalta, Galahad; Ling, Victor

    2011-08-01

    We report an efficient, high fidelity trypsin digestion method for peptide map analysis. This method minimizes artifacts caused by the sample preparation process, and we show its utility for the accurate determination of succinimide formation in a degraded monoclonal antibody product. A basic charge variant was detected by imaged capillary isoelectric focusing and was shown with reduced antigen binding and biological activity. Samples were reduced under denaturing conditions at pH 5.0, and digestion of the reduced protein with porcine trypsin was performed at pH 7.0 for 1 h. Following reversed phase high-performance liquid chromatography and online mass spectrometric analysis, succinimide formation was identified at Asp30 in the light chain. This result contrasts with the observation of only iso-Asp and Asp residues under conventional sample preparation conditions, which are therefore concluded to be artificially generated. The Asp30 residue is seen in the cocrystal structure model to participate in favorable charge interaction with an antigen molecule. Formation of succinimide and the resulting loss of negative charge are therefore hypothesized to be the degradation mechanism. After treatment of the degraded antibody sample to mildly alkaline pH conditions, we observed only Asp residue as the succinimide hydrolysis product and concurrent recovery of biological activity.

  18. Enantiomeric separation in comprehensive two-dimensional gas chromatography with accurate mass analysis.

    PubMed

    Chin, Sung-Tong; Nolvachai, Yada; Marriott, Philip J

    2014-11-01

    Chiral comprehensive two-dimensional gas chromatography (eGC×GC) coupled to quadrupole-accurate mass time-of-flight mass spectrometry (QTOFMS) was evaluated for its capability to report the chiral composition of several monoterpenes, namely, α-pinene, β-pinene, and limonene in cardamom oil. Enantiomers in a standard mixture were fully resolved by direct enantiomeric-GC analysis with a 2,3-di-O-methyl-6-t-butylsilyl derivatized β-cyclodextrin phase; however, the (+)-(R)-limonene enantiomer in cardamom oil was overlapped with other background components including cymene and cineole. Verification of (+)-(R)-limonene components based on characteristic ions at m/z 136, 121, and 107 acquired by chiral single-dimension GC-QTOFMS in the alternate MS/MSMS mode of operation was unsuccessful due to similar parent/daughter ions generated by interfering or co-eluting cymene and cineole. Column phases SUPELCOWAX, SLB-IL111, HP-88, and SLB-IL59, were incorporated as the second dimension column ((2)D) in chiral GC×GC analysis; the SLB-IL59 offered the best resolution for the tested monoterpene enantiomers from the matrix background. Enantiomeric ratios for α-pinene, β-pinene, and limonene were determined to be 1.325, 2.703, and 1.040, respectively, in the cardamom oil sample based on relative peak area data.

  19. Accurate airway segmentation based on intensity structure analysis and graph-cut

    NASA Astrophysics Data System (ADS)

    Meng, Qier; Kitsaka, Takayuki; Nimura, Yukitaka; Oda, Masahiro; Mori, Kensaku

    2016-03-01

    This paper presents a novel airway segmentation method based on intensity structure analysis and graph-cut. Airway segmentation is an important step in analyzing chest CT volumes for computerized lung cancer detection, emphysema diagnosis, asthma diagnosis, and pre- and intra-operative bronchoscope navigation. However, obtaining a complete 3-D airway tree structure from a CT volume is quite challenging. Several researchers have proposed automated algorithms basically based on region growing and machine learning techniques. However these methods failed to detect the peripheral bronchi branches. They caused a large amount of leakage. This paper presents a novel approach that permits more accurate extraction of complex bronchial airway region. Our method are composed of three steps. First, the Hessian analysis is utilized for enhancing the line-like structure in CT volumes, then a multiscale cavity-enhancement filter is employed to detect the cavity-like structure from the previous enhanced result. In the second step, we utilize the support vector machine (SVM) to construct a classifier for removing the FP regions generated. Finally, the graph-cut algorithm is utilized to connect all of the candidate voxels to form an integrated airway tree. We applied this method to sixteen cases of 3D chest CT volumes. The results showed that the branch detection rate of this method can reach about 77.7% without leaking into the lung parenchyma areas.

  20. Quantitative quenching evaluation and direct intracellular metabolite analysis in Penicillium chrysogenum.

    PubMed

    Meinert, Sabine; Rapp, Sina; Schmitz, Katja; Noack, Stephan; Kornfeld, Georg; Hardiman, Timo

    2013-07-01

    Sustained progress in metabolic engineering methodologies has stimulated new efforts toward optimizing fungal production strains such as through metabolite analysis of Penicillium chrysogenum industrial-scale processes. Accurate intracellular metabolite quantification requires sampling procedures that rapidly stop metabolism (quenching) and avoid metabolite loss via the cell membrane (leakage). When sampling protocols are validated, the quenching efficiency is generally not quantitatively assessed. For fungal metabolomics, quantitative biomass separation using centrifugation is a further challenge. In this study, P. chrysogenum intracellular metabolites were quantified directly from biomass extracts using automated sampling and fast filtration. A master/slave bioreactor concept was applied to provide industrial production conditions. Metabolic activity during sampling was monitored by 13C tracing. Enzyme activities were efficiently stopped and metabolite leakage was absent. This work provides a reliable method for P. chrysogenum metabolomics and will be an essential base for metabolic engineering of industrial processes.

  1. Tritium speciation in nuclear reactor bioshield concrete and its impact on accurate analysis.

    PubMed

    Kim, Dae Ji; E Warwick, Phillip; Croudace, Ian W

    2008-07-15

    Tritium ((3)H) is produced in nuclear reactors via several neutron-induced reactions [(2)H(n, gamma)(3)H, (6)Li(n, alpha)(3)H, (10)B(n, 2alpha)(3)H, (14)N(n, (3)H)(12)C, and ternary fission (fission yield <0.01%)]. Typically, (3)H is present as tritiated water (HTO) and can become adsorbed into structural concrete from the surface inward where it will be held in a weakly bound form. However, a systematic analysis of a sequence of subsamples taken from a reactor bioshield using combustion and liquid scintillation analysis has identified two forms of (3)H, one weakly bound and one strongly bound. The strongly bound tritium, which originates from neutron capture on trace lithium ((6)Li) within mineral phases, requires temperatures in excess of 350 degrees C to achieve quantitative recovery. The weakly bound form of tritium can be liberated at significantly lower temperatures (100 degrees C) as HTO and is associated with dehydration of hydrous mineral components. Without an appreciation that two forms of tritium can exist in reactor bioshields, the (3)H content of samples may be severely underestimated using conventional analytical approaches. These findings exemplify the need to develop robust radioactive waste characterization procedures in support of nuclear decommissioning programs.

  2. Smartphone-Based Accurate Analysis of Retinal Vasculature towards Point-of-Care Diagnostics

    PubMed Central

    Xu, Xiayu; Ding, Wenxiang; Wang, Xuemin; Cao, Ruofan; Zhang, Maiye; Lv, Peilin; Xu, Feng

    2016-01-01

    Retinal vasculature analysis is important for the early diagnostics of various eye and systemic diseases, making it a potentially useful biomarker, especially for resource-limited regions and countries. Here we developed a smartphone-based retinal image analysis system for point-of-care diagnostics that is able to load a fundus image, segment retinal vessels, analyze individual vessel width, and store or uplink results. The proposed system was not only evaluated on widely used public databases and compared with the state-of-the-art methods, but also validated on clinical images directly acquired with a smartphone. An Android app is also developed to facilitate on-site application of the proposed methods. Both visual assessment and quantitative assessment showed that the proposed methods achieved comparable results to the state-of-the-art methods that require high-standard workstations. The proposed system holds great potential for the early diagnostics of various diseases, such as diabetic retinopathy, for resource-limited regions and countries. PMID:27698369

  3. Qualitative and quantitative stability analysis of penta-rhythmic circuits

    NASA Astrophysics Data System (ADS)

    Schwabedal, Justus T. C.; Knapper, Drake E.; Shilnikov, Andrey L.

    2016-12-01

    Inhibitory circuits of relaxation oscillators are often-used models for dynamics of biological networks. We present a qualitative and quantitative stability analysis of such a circuit constituted by three generic oscillators (of a Fitzhugh-Nagumo type) as its nodes coupled reciprocally. Depending on inhibitory strengths, and parameters of individual oscillators, the circuit exhibits polyrhythmicity of up to five simultaneously stable rhythms. With methods of bifurcation analysis and phase reduction, we investigate qualitative changes in stability of these circuit rhythms for a wide range of parameters. Furthermore, we quantify robustness of the rhythms maintained under random perturbations by monitoring phase diffusion in the circuit. Our findings allow us to describe how circuit dynamics relate to dynamics of individual nodes. We also find that quantitative and qualitative stability properties of polyrhythmicity do not always align.

  4. Implementing a Quantitative Analysis Design Tool for Future Generation Interfaces

    DTIC Science & Technology

    2012-03-01

    future MAC-enabled systems. A human-computer interaction ( HCI ) Index, originally applied to multi-function displays was applied to the prototype Vigilant...Spirit interface. A modified version of the HCI Index was successfully applied to perform a quantitative analysis of the baseline VSCS interface and...two modified interface designs. The modified HCI Index incorporates the Hick-Hyman decision time, Fitts’ Law time, and the physical actions

  5. Quantitative NMR Analysis of Partially Substituted Biodiesel Glycerols

    SciTech Connect

    Nagy, M.; Alleman, T. L.; Dyer, T.; Ragauskas, A. J.

    2009-01-01

    Phosphitylation of hydroxyl groups in biodiesel samples with 2-chloro-4,4,5,5-tetramethyl-1,3,2-dioxaphospholane followed by 31P-NMR analysis provides a rapid quantitative analytical technique for the determination of substitution patterns on partially esterified glycerols. The unique 31P-NMR chemical shift data was established with a series mono and di-substituted fatty acid esters of glycerol and then utilized to characterize an industrial sample of partially processed biodiesel.

  6. Comprehensive Quantitative Analysis of SQ Injection Using Multiple Chromatographic Technologies.

    PubMed

    Chau, Siu-Leung; Huang, Zhi-Bing; Song, Yan-Gang; Yue, Rui-Qi; Ho, Alan; Lin, Chao-Zhan; Huang, Wen-Hua; Han, Quan-Bin

    2016-08-19

    Quality control of Chinese medicine injections remains a challenge due to our poor knowledge of their complex chemical profile. This study aims to investigate the chemical composition of one of the best-selling injections, Shenqi Fuzheng (SQ) injection (SQI), via a full component quantitative analysis. A total of 15 representative small molecular components of SQI were simultaneously determined using ultra-high performance liquid chromatography (UHPLC) coupled with quadrupole tandem time-of-flight mass spectrometry (Q-TOF-MS); saccharide composition of SQI was also quantitatively determined by high performance liquid chromatography (HPLC) with evaporative light scattering detector (ELSD) on an amino column before and after acid hydrolysis. The existence of polysaccharides was also examined on a gel permeation chromatography column. The method was well validated in terms of linearity, sensitivity, precision, accuracy and stability, and was successfully applied to analyze 13 SQI samples. The results demonstrate that up to 94.69% (w/w) of this injection product are quantitatively determined, in which small molecules and monosaccharide/sucrose account for 0.18%-0.21%, and 53.49%-58.2%, respectively. The quantitative information contributes to accumulating scientific evidence to better understand the therapy efficacy and safety of complex Chinese medicine injections.

  7. Quantitative Proteomic Approaches for Analysis of Protein S-Nitrosylation.

    PubMed

    Qu, Zhe; Greenlief, C Michael; Gu, Zezong

    2016-01-04

    S-Nitrosylation is a redox-based post-translational modification of a protein in response to nitric oxide (NO) signaling, and it participates in a variety of processes in diverse biological systems. The significance of this type of protein modification in health and diseases is increasingly recognized. In the central nervous system, aberrant S-nitrosylation, due to excessive NO production, is known to cause protein misfolding, mitochondrial dysfunction, transcriptional dysregulation, and neuronal death. This leads to an altered physiological state and consequently contributes to pathogenesis of neurodegenerative disorders. To date, much effort has been made to understand the mechanisms underlying protein S-nitrosylation, and several approaches have been developed to unveil S-nitrosylated proteins from different organisms. Interest in determining the dynamic changes of protein S-nitrosylation under different physiological and pathophysiological conditions has underscored the need for the development of quantitative proteomic approaches. Currently, both gel-based and gel-free mass spectrometry-based quantitative methods are widely used, and they each have advantages and disadvantages but may also be used together to produce complementary data. This review evaluates current available quantitative proteomic techniques for the analysis of protein S-nitrosylation and highlights recent advances, with emphasis on applications in neurodegenerative diseases. An important goal is to provide a comprehensive guide of feasible quantitative proteomic methodologies for examining protein S-nitrosylation in research to yield insights into disease mechanisms, diagnostic biomarkers, and drug discovery.

  8. The accurate use of impedance analysis for the study of microbial electrochemical systems.

    PubMed

    Dominguez-Benetton, Xochitl; Sevda, Surajbhan; Vanbroekhoven, Karolien; Pant, Deepak

    2012-11-07

    The present critical review aims to portray the principles and theoretical foundations that have been used for the application of electrochemical impedance spectroscopy (EIS) to study electron-transfer mechanisms, mass transfer phenomena and distribution of the heterogeneous properties of microbial electrochemical systems (MXCs). Over the past eight years, the application of this method has allowed major breakthroughs, especially in the field of microbial fuel cells (MFCs); however, it is still most widely extended only to the calculation of internal resistances. The use and interpretation of EIS should greatly improve since the intrinsic knowledge of this field, and efforts and current trends in this field have already allowed its understanding based on rather meaningful physical properties and not only on fitting electrical analogues. From this perspective, the use, analysis and interpretation of EIS applied to the study of MXCs are critically examined. Together with the revision of more than 150 articles directly devoted to this topic, two examples of the correct and improved analysis of EIS data are extensively presented. The first one focuses on the use of graphical methods for improving EIS analysis and the other one concentrates on the elucidation of the constant phase element (CPE) parameters. CPEs have been introduced in equivalent circuit models, sometimes without solid justification or analysis; the effective capacitance has been obtained from CPE parameters, following an unsuitable theory for the case of microbial-electrochemical interfaces. The use of CPE is reviewed in terms of meaningful physical parameters, such as biofilm thickness. The use of a finite-diffusion element is reviewed throughout estimation of accurate values for obtaining the dimensionless numbers, Schmidt and Sherwood, in the context of a dioxygen-reducing-biocathode, under different flow-rate conditions. The use and analysis of EIS in this context are still emerging, but because of

  9. 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

  10. Spectral neighbor analysis method for automated generation of quantum-accurate interatomic potentials

    SciTech Connect

    Thompson, A.P.; Swiler, L.P.; Trott, C.R.; Foiles, S.M.; Tucker, G.J.

    2015-03-15

    We present a new interatomic potential for solids and liquids called Spectral Neighbor Analysis Potential (SNAP). The SNAP potential has a very general form and uses machine-learning techniques to reproduce the energies, forces, and stress tensors of a large set of small configurations of atoms, which are obtained using high-accuracy quantum electronic structure (QM) calculations. The local environment of each atom is characterized by a set of bispectrum components of the local neighbor density projected onto a basis of hyperspherical harmonics in four dimensions. The bispectrum components are the same bond-orientational order parameters employed by the GAP potential [1]. The SNAP potential, unlike GAP, assumes a linear relationship between atom energy and bispectrum components. The linear SNAP coefficients are determined using weighted least-squares linear regression against the full QM training set. This allows the SNAP potential to be fit in a robust, automated manner to large QM data sets using many bispectrum components. The calculation of the bispectrum components and the SNAP potential are implemented in the LAMMPS parallel molecular dynamics code. We demonstrate that a previously unnoticed symmetry property can be exploited to reduce the computational cost of the force calculations by more than one order of magnitude. We present results for a SNAP potential for tantalum, showing that it accurately reproduces a range of commonly calculated properties of both the crystalline solid and the liquid phases. In addition, unlike simpler existing potentials, SNAP correctly predicts the energy barrier for screw dislocation migration in BCC tantalum.

  11. Spectral neighbor analysis method for automated generation of quantum-accurate interatomic potentials

    NASA Astrophysics Data System (ADS)

    Thompson, A. P.; Swiler, L. P.; Trott, C. R.; Foiles, S. M.; Tucker, G. J.

    2015-03-01

    We present a new interatomic potential for solids and liquids called Spectral Neighbor Analysis Potential (SNAP). The SNAP potential has a very general form and uses machine-learning techniques to reproduce the energies, forces, and stress tensors of a large set of small configurations of atoms, which are obtained using high-accuracy quantum electronic structure (QM) calculations. The local environment of each atom is characterized by a set of bispectrum components of the local neighbor density projected onto a basis of hyperspherical harmonics in four dimensions. The bispectrum components are the same bond-orientational order parameters employed by the GAP potential [1]. The SNAP potential, unlike GAP, assumes a linear relationship between atom energy and bispectrum components. The linear SNAP coefficients are determined using weighted least-squares linear regression against the full QM training set. This allows the SNAP potential to be fit in a robust, automated manner to large QM data sets using many bispectrum components. The calculation of the bispectrum components and the SNAP potential are implemented in the LAMMPS parallel molecular dynamics code. We demonstrate that a previously unnoticed symmetry property can be exploited to reduce the computational cost of the force calculations by more than one order of magnitude. We present results for a SNAP potential for tantalum, showing that it accurately reproduces a range of commonly calculated properties of both the crystalline solid and the liquid phases. In addition, unlike simpler existing potentials, SNAP correctly predicts the energy barrier for screw dislocation migration in BCC tantalum.

  12. Fully Automatic System for Accurate Localisation and Analysis of Cephalometric Landmarks in Lateral Cephalograms

    PubMed Central

    Lindner, Claudia; Wang, Ching-Wei; Huang, Cheng-Ta; Li, Chung-Hsing; Chang, Sheng-Wei; Cootes, Tim F.

    2016-01-01

    Cephalometric tracing is a standard analysis tool for orthodontic diagnosis and treatment planning. The aim of this study was to develop and validate a fully automatic landmark annotation (FALA) system for finding cephalometric landmarks in lateral cephalograms and its application to the classification of skeletal malformations. Digital cephalograms of 400 subjects (age range: 7–76 years) were available. All cephalograms had been manually traced by two experienced orthodontists with 19 cephalometric landmarks, and eight clinical parameters had been calculated for each subject. A FALA system to locate the 19 landmarks in lateral cephalograms was developed. The system was evaluated via comparison to the manual tracings, and the automatically located landmarks were used for classification of the clinical parameters. The system achieved an average point-to-point error of 1.2 mm, and 84.7% of landmarks were located within the clinically accepted precision range of 2.0 mm. The automatic landmark localisation performance was within the inter-observer variability between two clinical experts. The automatic classification achieved an average classification accuracy of 83.4% which was comparable to an experienced orthodontist. The FALA system rapidly and accurately locates and analyses cephalometric landmarks in lateral cephalograms, and has the potential to significantly improve the clinical work flow in orthodontic treatment. PMID:27645567

  13. Mini-Column Ion-Exchange Separation and Atomic Absorption Quantitation of Nickel, Cobalt, and Iron: An Undergraduate Quantitative Analysis Experiment.

    ERIC Educational Resources Information Center

    Anderson, James L.; And Others

    1980-01-01

    Presents an undergraduate quantitative analysis experiment, describing an atomic absorption quantitation scheme that is fast, sensitive and comparatively simple relative to other titration experiments. (CS)

  14. Quantitative analysis of rib kinematics based on dynamic chest bone images: preliminary results.

    PubMed

    Tanaka, Rie; Sanada, Shigeru; Sakuta, Keita; Kawashima, Hiroki

    2015-04-01

    An image-processing technique for separating bones from soft tissue in static chest radiographs has been developed. The present study was performed to evaluate the usefulness of dynamic bone images in quantitative analysis of rib movement. Dynamic chest radiographs of 16 patients were obtained using a dynamic flat-panel detector and processed to create bone images by using commercial software (Clear Read BS, Riverain Technologies). Velocity vectors were measured in local areas on the dynamic images, which formed a map. The velocity maps obtained with bone and original images for scoliosis and normal cases were compared to assess the advantages of bone images. With dynamic bone images, we were able to quantify and distinguish movements of ribs from those of other lung structures accurately. Limited rib movements of scoliosis patients appeared as a reduced rib velocity field, resulting in an asymmetrical distribution of rib movement. Vector maps in all normal cases exhibited left/right symmetric distributions of the velocity field, whereas those in abnormal cases showed asymmetric distributions because of locally limited rib movements. Dynamic bone images were useful for accurate quantitative analysis of rib movements. The present method has a potential for an additional functional examination in chest radiography.

  15. Quantitative Phosphoproteomic Analysis of T-Cell Receptor Signaling.

    PubMed

    Ahsan, Nagib; Salomon, Arthur R

    2017-01-01

    TCR signaling critically depends on protein phosphorylation across many proteins. Localization of each phosphorylation event relative to the T-cell receptor (TCR) and canonical T-cell signaling proteins will provide clues about the structure of TCR signaling networks. Quantitative phosphoproteomic analysis by mass spectrometry provides a wide-scale view of cellular phosphorylation networks. However, analysis of phosphorylation by mass spectrometry is still challenging due to the relative low abundance of phosphorylated proteins relative to all proteins and the extraordinary diversity of phosphorylation sites across the proteome. Highly selective enrichment of phosphorylated peptides is essential to provide the most comprehensive view of the phosphoproteome. Optimization of phosphopeptide enrichment methods coupled with highly sensitive mass spectrometry workflows significantly improves the sequencing depth of the phosphoproteome to over 10,000 unique phosphorylation sites from complex cell lysates. Here we describe a step-by-step method for phosphoproteomic analysis that has achieved widespread success for identification of serine, threonine, and tyrosine phosphorylation. Reproducible quantification of relative phosphopeptide abundance is provided by intensity-based label-free quantitation. An ideal set of mass spectrometry analysis parameters is also provided that optimize the yield of identified sites. We also provide guidelines for the bioinformatic analysis of this type of data to assess the quality of the data and to comply with proteomic data reporting requirements.

  16. A Quantitative Method for Microtubule Analysis in Fluorescence Images.

    PubMed

    Lan, Xiaodong; Li, Lingfei; Hu, Jiongyu; Zhang, Qiong; Dang, Yongming; Huang, Yuesheng

    2015-12-01

    Microtubule analysis is of significant value for a better understanding of normal and pathological cellular processes. Although immunofluorescence microscopic techniques have proven useful in the study of microtubules, comparative results commonly rely on a descriptive and subjective visual analysis. We developed an objective and quantitative method based on image processing and analysis of fluorescently labeled microtubular patterns in cultured cells. We used a multi-parameter approach by analyzing four quantifiable characteristics to compose our quantitative feature set. Then we interpreted specific changes in the parameters and revealed the contribution of each feature set using principal component analysis. In addition, we verified that different treatment groups could be clearly discriminated using principal components of the multi-parameter model. High predictive accuracy of four commonly used multi-classification methods confirmed our method. These results demonstrated the effectiveness and efficiency of our method in the analysis of microtubules in fluorescence images. Application of the analytical methods presented here provides information concerning the organization and modification of microtubules, and could aid in the further understanding of structural and functional aspects of microtubules under normal and pathological conditions.

  17. Methods for Applying Accurate Digital PCR Analysis on Low Copy DNA Samples

    PubMed Central

    Whale, Alexandra S.; Cowen, Simon; Foy, Carole A.; Huggett, Jim F.

    2013-01-01

    Digital PCR (dPCR) is a highly accurate molecular approach, capable of precise measurements, offering a number of unique opportunities. However, in its current format dPCR can be limited by the amount of sample that can be analysed and consequently additional considerations such as performing multiplex reactions or pre-amplification can be considered. This study investigated the impact of duplexing and pre-amplification on dPCR analysis by using three different assays targeting a model template (a portion of the Arabidopsis thaliana alcohol dehydrogenase gene). We also investigated the impact of different template types (linearised plasmid clone and more complex genomic DNA) on measurement precision using dPCR. We were able to demonstrate that duplex dPCR can provide a more precise measurement than uniplex dPCR, while applying pre-amplification or varying template type can significantly decrease the precision of dPCR. Furthermore, we also demonstrate that the pre-amplification step can introduce measurement bias that is not consistent between experiments for a sample or assay and so could not be compensated for during the analysis of this data set. We also describe a model for estimating the prevalence of molecular dropout and identify this as a source of dPCR imprecision. Our data have demonstrated that the precision afforded by dPCR at low sample concentration can exceed that of the same template post pre-amplification thereby negating the need for this additional step. Our findings also highlight the technical differences between different templates types containing the same sequence that must be considered if plasmid DNA is to be used to assess or control for more complex templates like genomic DNA. PMID:23472156

  18. Accurate means of detecting and characterizing abnormal patterns of ventricular activation by phase image analysis

    SciTech Connect

    Botvinick, E.H.; Frais, M.A.; Shosa, D.W.; O'Connell, J.W.; Pacheco-Alvarez, J.A.; Scheinman, M.; Hattner, R.S.; Morady, F.; Faulkner, D.B.

    1982-08-01

    The ability of scintigraphic phase image analysis to characterize patterns of abnormal ventricular activation was investigated. The pattern of phase distribution and sequential phase changes over both right and left ventricular regions of interest were evaluated in 16 patients with normal electrical activation and wall motion and compared with those in 8 patients with an artificial pacemaker and 4 patients with sinus rhythm with the Wolff-Parkinson-White syndrome and delta waves. Normally, the site of earliest phase angle was seen at the base of the interventricular septum, with sequential change affecting the body of the septum and the cardiac apex and then spreading laterally to involve the body of both ventricles. The site of earliest phase angle was located at the apex of the right ventricle in seven patients with a right ventricular endocardial pacemaker and on the lateral left ventricular wall in one patient with a left ventricular epicardial pacemaker. In each case the site corresponded exactly to the position of the pacing electrode as seen on posteroanterior and left lateral chest X-ray films, and sequential phase changes spread from the initial focus to affect both ventricles. In each of the patients with the Wolff-Parkinson-White syndrome, the site of earliest ventricular phase angle was located, and it corresponded exactly to the site of the bypass tract as determined by endocardial mapping. In this way, four bypass pathways, two posterior left paraseptal, one left lateral and one right lateral, were correctly localized scintigraphically. On the basis of the sequence of mechanical contraction, phase image analysis provides an accurate noninvasive method of detecting abnormal foci of ventricular activation.

  19. Fast and Accurate Radiative Transfer Calculations Using Principal Component Analysis for (Exo-)Planetary Retrieval Models

    NASA Astrophysics Data System (ADS)

    Kopparla, P.; Natraj, V.; Shia, R. L.; Spurr, R. J. D.; Crisp, D.; Yung, Y. L.

    2015-12-01

    Radiative transfer (RT) computations form the engine of atmospheric retrieval codes. However, full treatment of RT processes is computationally expensive, prompting usage of two-stream approximations in current exoplanetary atmospheric retrieval codes [Line et al., 2013]. Natraj et al. [2005, 2010] and Spurr and Natraj [2013] demonstrated the ability of a technique using principal component analysis (PCA) to speed up RT computations. In the PCA method for RT performance enhancement, empirical orthogonal functions are developed for binned sets of inherent optical properties that possess some redundancy; costly multiple-scattering RT calculations are only done for those few optical states corresponding to the most important principal components, and correction factors are applied to approximate radiation fields. Kopparla et al. [2015, in preparation] extended the PCA method to a broadband spectral region from the ultraviolet to the shortwave infrared (0.3-3 micron), accounting for major gas absorptions in this region. Here, we apply the PCA method to a some typical (exo-)planetary retrieval problems. Comparisons between the new model, called Universal Principal Component Analysis Radiative Transfer (UPCART) model, two-stream models and line-by-line RT models are performed, for spectral radiances, spectral fluxes and broadband fluxes. Each of these are calculated at the top of the atmosphere for several scenarios with varying aerosol types, extinction and scattering optical depth profiles, and stellar and viewing geometries. We demonstrate that very accurate radiance and flux estimates can be obtained, with better than 1% accuracy in all spectral regions and better than 0.1% in most cases, as compared to a numerically exact line-by-line RT model. The accuracy is enhanced when the results are convolved to typical instrument resolutions. The operational speed and accuracy of UPCART can be further improved by optimizing binning schemes and parallelizing the codes, work

  20. Cell poking: quantitative analysis of indentation of thick viscoelastic layers.

    PubMed

    Duszyk, M; Schwab, B; Zahalak, G I; Qian, H; Elson, E L

    1989-04-01

    A recently introduced device, the cell poker, measures the force required to indent the exposed surface of a cell adherent to a rigid substratum. The cell poker has provided phenomenological information about the viscoelastic properties of several different types of cells, about mechanical changes triggered by external stimuli, and about the role of the cytoskeleton in these mechanical functions. Except in special cases, however, it has not been possible to extract quantitative estimates of viscosity and elasticity moduli from cell poker measurements. This paper presents cell poker measurements of well characterized viscoelastic polymeric materials, polydimethylsiloxanes of different degrees of polymerization, in a simple shape, a flat, thick layer, which for our purposes can be treated as a half space. Analysis of the measurements in terms of a linear viscoelasticity theory yields viscosity values for three polymer samples in agreement with those determined by measurements on a macroscopic scale. Theoretical analysis further indicates that the measured limiting static elasticity of the layers may result from the tension generated at the interface between the polymer and water. This work demonstrates the possibility of obtaining quantitative viscoelastic material properties from cell poker measurements and represents the first step in extending these quantitative studies to more complicated structures including cells.

  1. Cell poking: quantitative analysis of indentation of thick viscoelastic layers.

    PubMed Central

    Duszyk, M; Schwab, B; Zahalak, G I; Qian, H; Elson, E L

    1989-01-01

    A recently introduced device, the cell poker, measures the force required to indent the exposed surface of a cell adherent to a rigid substratum. The cell poker has provided phenomenological information about the viscoelastic properties of several different types of cells, about mechanical changes triggered by external stimuli, and about the role of the cytoskeleton in these mechanical functions. Except in special cases, however, it has not been possible to extract quantitative estimates of viscosity and elasticity moduli from cell poker measurements. This paper presents cell poker measurements of well characterized viscoelastic polymeric materials, polydimethylsiloxanes of different degrees of polymerization, in a simple shape, a flat, thick layer, which for our purposes can be treated as a half space. Analysis of the measurements in terms of a linear viscoelasticity theory yields viscosity values for three polymer samples in agreement with those determined by measurements on a macroscopic scale. Theoretical analysis further indicates that the measured limiting static elasticity of the layers may result from the tension generated at the interface between the polymer and water. This work demonstrates the possibility of obtaining quantitative viscoelastic material properties from cell poker measurements and represents the first step in extending these quantitative studies to more complicated structures including cells. PMID:2720066

  2. Quantitative multivariate analysis of dynamic multicellular morphogenic trajectories.

    PubMed

    White, Douglas E; Sylvester, Jonathan B; Levario, Thomas J; Lu, Hang; Streelman, J Todd; McDevitt, Todd C; Kemp, Melissa L

    2015-07-01

    Interrogating fundamental cell biology principles that govern tissue morphogenesis is critical to better understanding of developmental biology and engineering novel multicellular systems. Recently, functional micro-tissues derived from pluripotent embryonic stem cell (ESC) aggregates have provided novel platforms for experimental investigation; however elucidating the factors directing emergent spatial phenotypic patterns remains a significant challenge. Computational modelling techniques offer a unique complementary approach to probe mechanisms regulating morphogenic processes and provide a wealth of spatio-temporal data, but quantitative analysis of simulations and comparison to experimental data is extremely difficult. Quantitative descriptions of spatial phenomena across multiple systems and scales would enable unprecedented comparisons of computational simulations with experimental systems, thereby leveraging the inherent power of computational methods to interrogate the mechanisms governing emergent properties of multicellular biology. To address these challenges, we developed a portable pattern recognition pipeline consisting of: the conversion of cellular images into networks, extraction of novel features via network analysis, and generation of morphogenic trajectories. This novel methodology enabled the quantitative description of morphogenic pattern trajectories that could be compared across diverse systems: computational modelling of multicellular structures, differentiation of stem cell aggregates, and gastrulation of cichlid fish. Moreover, this method identified novel spatio-temporal features associated with different stages of embryo gastrulation, and elucidated a complex paracrine mechanism capable of explaining spatiotemporal pattern kinetic differences in ESC aggregates of different sizes.

  3. Quantitative analysis of endocytosis with cytoplasmic pHluorin chimeras.

    PubMed

    Prosser, Derek C; Whitworth, Karen; Wendland, Beverly

    2010-09-01

    The pH-sensitive green fluorescent protein (GFP) variant pHluorin is typically fused to the extracellular domain of transmembrane proteins to monitor endocytosis. Here, we have turned pHluorin inside-out, and show that cytoplasmic fusions of pHluorin are effective quantitative reporters for endocytosis and multivesicular body (MVB) sorting. In yeast in particular, fusion of GFP and its variants on the extracellular side of transmembrane proteins can result in perturbed trafficking. In contrast, cytoplasmic fusions are well tolerated, allowing for the quantitative assessment of trafficking of virtually any transmembrane protein. Quenching of degradation-resistant pHluorin in the acidic vacuole permits quantification of extravacuolar cargo proteins at steady-state levels and is compatible with kinetic analysis of endocytosis in live cells.

  4. Quantitative analysis of virus-like particle size and distribution by field-flow fractionation.

    PubMed

    Chuan, Yap P; Fan, Yuan Y; Lua, Linda; Middelberg, Anton P J

    2008-04-15

    Asymmetric flow field-flow fractionation (AFFFF) coupled with multiple-angle light scattering (MALS) is a powerful technique showing potential for the analysis of pharmaceutically-relevant virus-like particles (VLPs). A lack of published methods, and concerns that membrane adsorption during sample fractionation may cause sample aggregation, have limited widespread acceptance. Here we report a reliable optimized method for VLP analysis using AFFFF-MALS, and benchmark it against dynamic light scattering (DLS) and transmission electron microscopy (TEM). By comparing chemically identical VLPs having very different quaternary structure, sourced from both bacteria and insect cells, we show that optimized AFFFF analysis does not cause significant aggregation, and that accurate size and distribution information can be obtained for heterogeneous samples in a way not possible with TEM and DLS. Optimized AFFFF thus provides a quantitative way to monitor batch consistency for new vaccine products, and rapidly provides unique information on the whole population of particles within a sample.

  5. [Simultaneous quantitative analysis of four lignanoids in Schisandra chinensis by quantitative analysis of multi-components by single marker].

    PubMed

    He, Feng-Cheng; Li, Shou-Xin; Zhao, Zhi-Quan; Dong, Jin-Ping; Liu, Wu-Zhan; Su, Rui-Qiang

    2012-07-01

    The aim of the study is to establish a new method of quality evaluation and validate its feasibilities by the simultaneous quantitative assay of four lignanoids in Schisandra chinensis. A new quality evaluation method, quantitative analysis of multi-components by single marker (QAMS), was established and validated with Schisandra chinensis. Four main lignanoids, schisandrin, schisantherin A, deoxyschizandrin and gamma-schizandrin, were selected as analytes and schisandrin as internal reference substance to evaluate the quality. Their contents in 13 different batches of samples, collected from different bathes, were determined by both external standard method and QAMS. The method was evaluated by comparison of the quantitative results between external standard method and QAMS. No significant differences were found in the quantitative results of four lignanoids in 13 batches of S. chinensis determined by external standard method and QAMS. QAMS is feasible for determination of four lignanoids simultaneously when some authentic standard substances were unavailable, and the developed method can be used for quality control of S. chinensis.

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

    EPA Science Inventory

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

  7. Quantitative analysis of in vivo confocal microscopy images: a review.

    PubMed

    Patel, Dipika V; McGhee, Charles N

    2013-01-01

    In vivo confocal microscopy (IVCM) is a non-invasive method of examining the living human cornea. The recent trend towards quantitative studies using IVCM has led to the development of a variety of methods for quantifying image parameters. When selecting IVCM images for quantitative analysis, it is important to be consistent regarding the location, depth, and quality of images. All images should be de-identified, randomized, and calibrated prior to analysis. Numerous image analysis software are available, each with their own advantages and disadvantages. Criteria for analyzing corneal epithelium, sub-basal nerves, keratocytes, endothelium, and immune/inflammatory cells have been developed, although there is inconsistency among research groups regarding parameter definition. The quantification of stromal nerve parameters, however, remains a challenge. Most studies report lower inter-observer repeatability compared with intra-observer repeatability, and observer experience is known to be an important factor. Standardization of IVCM image analysis through the use of a reading center would be crucial for any future large, multi-centre clinical trials using IVCM.

  8. Anatomy-Correlated Breast Imaging and Visual Grading Analysis Using Quantitative Transmission Ultrasound™

    PubMed Central

    Iuanow, Elaine; Malik, Bilal; Obuchowski, Nancy A.; Wiskin, James

    2016-01-01

    Objectives. This study presents correlations between cross-sectional anatomy of human female breasts and Quantitative Transmission (QT) Ultrasound, does discriminate classifier analysis to validate the speed of sound correlations, and does a visual grading analysis comparing QT Ultrasound with mammography. Materials and Methods. Human cadaver breasts were imaged using QT Ultrasound, sectioned, and photographed. Biopsies confirmed microanatomy and areas were correlated with QT Ultrasound images. Measurements were taken in live subjects from QT Ultrasound images and values of speed of sound for each identified anatomical structure were plotted. Finally, a visual grading analysis was performed on images to determine whether radiologists' confidence in identifying breast structures with mammography (XRM) is comparable to QT Ultrasound. Results. QT Ultrasound identified all major anatomical features of the breast, and speed of sound calculations showed specific values for different breast tissues. Using linear discriminant analysis overall accuracy is 91.4%. Using visual grading analysis readers scored the image quality on QT Ultrasound as better than on XRM in 69%–90% of breasts for specific tissues. Conclusions. QT Ultrasound provides accurate anatomic information and high tissue specificity using speed of sound information. Quantitative Transmission Ultrasound can distinguish different types of breast tissue with high resolution and accuracy. PMID:27752261

  9. Anatomy-Correlated Breast Imaging and Visual Grading Analysis Using Quantitative Transmission Ultrasound™.

    PubMed

    Klock, John C; Iuanow, Elaine; Malik, Bilal; Obuchowski, Nancy A; Wiskin, James; Lenox, Mark

    2016-01-01

    Objectives. This study presents correlations between cross-sectional anatomy of human female breasts and Quantitative Transmission (QT) Ultrasound, does discriminate classifier analysis to validate the speed of sound correlations, and does a visual grading analysis comparing QT Ultrasound with mammography. Materials and Methods. Human cadaver breasts were imaged using QT Ultrasound, sectioned, and photographed. Biopsies confirmed microanatomy and areas were correlated with QT Ultrasound images. Measurements were taken in live subjects from QT Ultrasound images and values of speed of sound for each identified anatomical structure were plotted. Finally, a visual grading analysis was performed on images to determine whether radiologists' confidence in identifying breast structures with mammography (XRM) is comparable to QT Ultrasound. Results. QT Ultrasound identified all major anatomical features of the breast, and speed of sound calculations showed specific values for different breast tissues. Using linear discriminant analysis overall accuracy is 91.4%. Using visual grading analysis readers scored the image quality on QT Ultrasound as better than on XRM in 69%-90% of breasts for specific tissues. Conclusions. QT Ultrasound provides accurate anatomic information and high tissue specificity using speed of sound information. Quantitative Transmission Ultrasound can distinguish different types of breast tissue with high resolution and accuracy.

  10. Quantitative analysis of volatiles in edible oils following accelerated oxidation using broad spectrum isotope standards

    PubMed Central

    Gómez-Cortés, Pilar; Sacks, Gavin L.; Brenna, J. Thomas

    2014-01-01

    Analysis of food volatiles generated by processing are widely reported but comparisons across studies is challenging in part because most reports are inherently semi-quantitative for most analytes due to limited availability of chemical standards. We recently introduced a novel strategy for creation of broad spectrum isotopic standards for accurate quantitative food chemical analysis. Here we apply the principle to quantification of 25 volatiles in seven thermally oxidized edible oils. After extended oxidation, total volatiles of high n-3 oils (flax, fish, cod liver) were 120-170 mg/kg while low n-3 vegetable oils were <50 mg/kg. Separate experiments on thermal degradation of d5-ethyl linolenate indicate that off-aroma volatiles originate throughout the n-3 molecule and not solely the n-3 terminal end. These data represent the first report using broad-spectrum isotopically labeled standards for quantitative characterization of processing-induced volatile generation across related foodstuffs, and verify the origin of specific volatiles from parent n-3 fatty acids. PMID:25529686

  11. Quantitative analysis of volatiles in edible oils following accelerated oxidation using broad spectrum isotope standards.

    PubMed

    Gómez-Cortés, Pilar; Sacks, Gavin L; Brenna, J Thomas

    2015-05-01

    Analysis of food volatiles generated by processing are widely reported but comparisons across studies is challenging in part because most reports are inherently semi-quantitative for most analytes due to limited availability of chemical standards. We recently introduced a novel strategy for creation of broad spectrum isotopic standards for accurate quantitative food chemical analysis. Here we apply the principle to quantification of 25 volatiles in seven thermally oxidised edible oils. After extended oxidation, total volatiles of high n-3 oils (flax, fish, cod liver) were 120-170 mg/kg while low n-3 vegetable oils were <50mg/kg. Separate experiments on thermal degradation of d5-ethyl linolenate indicate that off-aroma volatiles originate throughout the n-3 molecule and not solely the n-3 terminal end. These data represent the first report using broad-spectrum isotopically labelled standards for quantitative characterisation of processing-induced volatile generation across related foodstuffs, and verify the origin of specific volatiles from parent n-3 fatty acids.

  12. 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.

  13. Using multiple PCR and CE with chemiluminescence detection for simultaneous qualitative and quantitative analysis of genetically modified organism.

    PubMed

    Guo, Longhua; Qiu, Bin; Chi, Yuwu; Chen, Guonan

    2008-09-01

    In this paper, an ultrasensitive CE-CL detection system coupled with a novel double-on-column coaxial flow detection interface was developed for the detection of PCR products. A reliable procedure based on this system had been demonstrated for qualitative and quantitative analysis of genetically modified organism-the detection of Roundup Ready Soy (RRS) samples was presented as an example. The promoter, terminator, function and two reference genes of RRS were amplified with multiplex PCR simultaneously. After that, the multiplex PCR products were labeled with acridinium ester at the 5'-terminal through an amino modification and then analyzed by the proposed CE-CL system. Reproducibility of analysis times and peak heights for the CE-CL analysis were determined to be better than 0.91 and 3.07% (RSD, n=15), respectively, for three consecutive days. It was shown that this method could accurately and qualitatively detect RRS standards and the simulative samples. The evaluation in terms of quantitative analysis of RRS provided by this new method was confirmed by comparing our assay results with those of the standard real-time quantitative PCR (RT-QPCR) using SYBR Green I dyes. The results showed a good coherence between the two methods. This approach demonstrated the possibility for accurate qualitative and quantitative detection of GM plants in a single run.

  14. A quantitative analysis of IRAS maps of molecular clouds

    NASA Technical Reports Server (NTRS)

    Wiseman, Jennifer J.; Adams, Fred C.

    1994-01-01

    We present an analysis of IRAS maps of five molecular clouds: Orion, Ophiuchus, Perseus, Taurus, and Lupus. For the classification and description of these astrophysical maps, we use a newly developed technique which considers all maps of a given type to be elements of a pseudometric space. For each physical characteristic of interest, this formal system assigns a distance function (a pseudometric) to the space of all maps: this procedure allows us to measure quantitatively the difference between any two maps and to order the space of all maps. We thus obtain a quantitative classification scheme for molecular clouds. In this present study we use the IRAS continuum maps at 100 and 60 micrometer(s) to produce column density (or optical depth) maps for the five molecular cloud regions given above. For this sample of clouds, we compute the 'output' functions which measure the distribution of density, the distribution of topological components, the self-gravity, and the filamentary nature of the clouds. The results of this work provide a quantitative description of the structure in these molecular cloud regions. We then order the clouds according to the overall environmental 'complexity' of these star-forming regions. Finally, we compare our results with the observed populations of young stellar objects in these clouds and discuss the possible environmental effects on the star-formation process. Our results are consistent with the recently stated conjecture that more massive stars tend to form in more 'complex' environments.

  15. Simulating realistic predator signatures in quantitative fatty acid signature analysis

    USGS Publications Warehouse

    Bromaghin, Jeffrey F.

    2015-01-01

    Diet estimation is an important field within quantitative ecology, providing critical insights into many aspects of ecology and community dynamics. Quantitative fatty acid signature analysis (QFASA) is a prominent method of diet estimation, particularly for marine mammal and bird species. Investigators using QFASA commonly use computer simulation to evaluate statistical characteristics of diet estimators for the populations they study. Similar computer simulations have been used to explore and compare the performance of different variations of the original QFASA diet estimator. In both cases, computer simulations involve bootstrap sampling prey signature data to construct pseudo-predator signatures with known properties. However, bootstrap sample sizes have been selected arbitrarily and pseudo-predator signatures therefore may not have realistic properties. I develop an algorithm to objectively establish bootstrap sample sizes that generates pseudo-predator signatures with realistic properties, thereby enhancing the utility of computer simulation for assessing QFASA estimator performance. The algorithm also appears to be computationally efficient, resulting in bootstrap sample sizes that are smaller than those commonly used. I illustrate the algorithm with an example using data from Chukchi Sea polar bears (Ursus maritimus) and their marine mammal prey. The concepts underlying the approach may have value in other areas of quantitative ecology in which bootstrap samples are post-processed prior to their use.

  16. Quantitative analysis of motion control in long term microgravity.

    PubMed

    Baroni, G; Ferrigno, G; Anolli, A; Andreoni, G; Pedotti, A

    1998-01-01

    In the frame of the 179-days EUROMIR '95 space mission, two in-flight experiments have foreseen quantitative three-dimensional human movement analysis in microgravity. For this aim, a space qualified opto-electronic motion analyser based on passive markers has been installed onboard the Russian Space Station MIR and 8 in flight sessions have been performed. Techhology and method for the collection of kinematics data are described, evaluating the accuracy in three-dimensional marker localisation. Results confirm the suitability of opto-electronic technology for quantitative human motion analysis on orbital modules and raise a set of "lessons learned", leading to the improvement of motion analyser performance with a contemporary swiftness of the on-board operations. Among the experimental program of T4, results of three voluntary posture perturbation protocols are described. The analysis suggests that a short term reinterpretation of proprioceptive information and re-calibration of sensorimotor mechanisms seem to end within the first weeks of flight, while a continuous long term adaptation process allows the refinement of motor performance, in the frame of never abandoned terrestrial strategies.

  17. QUANTITATIVE MASS SPECTROMETRIC ANALYSIS OF GLYCOPROTEINS COMBINED WITH ENRICHMENT METHODS

    PubMed Central

    Ahn, Yeong Hee; Kim, Jin Young; Yoo, Jong Shin

    2015-01-01

    Mass spectrometry (MS) has been a core technology for high sensitive and high-throughput analysis of the enriched glycoproteome in aspects of quantitative assays as well as qualitative profiling of glycoproteins. Because it has been widely recognized that aberrant glycosylation in a glycoprotein may involve in progression of a certain disease, the development of efficient analysis tool for the aberrant glycoproteins is very important for deep understanding about pathological function of the glycoprotein and new biomarker development. This review first describes the protein glycosylation-targeting enrichment technologies mainly employing solid-phase extraction methods such as hydrizide-capturing, lectin-specific capturing, and affinity separation techniques based on porous graphitized carbon, hydrophilic interaction chromatography, or immobilized boronic acid. Second, MS-based quantitative analysis strategies coupled with the protein glycosylation-targeting enrichment technologies, by using a label-free MS, stable isotope-labeling, or targeted multiple reaction monitoring (MRM) MS, are summarized with recent published studies. © 2014 The Authors. Mass Spectrometry Reviews Published by Wiley Periodicals, Inc. Rapid Commun. Mass Spec Rev 34:148–165, 2015. PMID:24889823

  18. Computer compensation for NMR quantitative analysis of trace components

    SciTech Connect

    Nakayama, T.; Fujiwara, Y.

    1981-07-22

    A computer program has been written that determines trace components and separates overlapping components in multicomponent NMR spectra. This program uses the Lorentzian curve as a theoretical curve of NMR spectra. The coefficients of the Lorentzian are determined by the method of least squares. Systematic errors such as baseline/phase distortion are compensated and random errors are smoothed by taking moving averages, so that there processes contribute substantially to decreasing the accumulation time of spectral data. The accuracy of quantitative analysis of trace components has been improved by two significant figures. This program was applied to determining the abundance of 13C and the saponification degree of PVA.

  19. Quantitative analysis of sideband coupling in photoinduced force microscopy

    NASA Astrophysics Data System (ADS)

    Jahng, Junghoon; Kim, Bongsu; Lee, Eun Seong; Potma, Eric Olaf

    2016-11-01

    We present a theoretical and experimental analysis of the cantilever motions detected in photoinduced force microscopy (PiFM) using the sideband coupling detection scheme. In sideband coupling, the cantilever dynamics are probed at a combination frequency of a fundamental mechanical eigenmode and the modulation frequency of the laser beam. Using this detection mode, we develop a method for reconstructing the modulated photoinduced force gradient from experimental parameters in a quantitative manner. We show evidence, both theoretically and experimentally, that the sideband coupling detection mode provides PiFM images with superior contrast compared to images obtained when detecting the cantilever motions directly at the laser modulation frequency.

  20. 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

  1. Quantitative paleobathymetric analysis from subsidence data: example from middle Ordovician of Michigan basin

    SciTech Connect

    Howell, P.D.; Budai, J.M.

    1989-03-01

    Quantitative paleobathymetry is difficult to determine for any rock sequence with a significant subtidal component. Water depth estimates are traditionally obtained from detailed sedimentology and paleontology, but this type of data is seldom available in subsurface work. Further, a good geological data base may be inconclusive for paleobathymetry in subtidal or substorm-wave base environments. More accurate facies prediction would be possible if paleobathymetry could be determined from the conventional subsurface data normally available to explorationists. Subsidence analysis of sedimentary basins has the potential to provide precise paleobathymetric estimates for a variety of depositional settings. This technique is illustrated using the Middle Ordovician carbonates of the Michigan basin. Tectonic subsidence patterns established from stratigraphic and subsidence modeling of the Lower-Middle Ordovician Prairie du Chien Group in Michigan are projected forward through the Middle Ordovician. Isopach thicknesses of the Black River and Trenton carbonates are superimposed on the tectonic subsidence patterns to provide a quantitative basin-fill model. The model paleobathymetry is then compared with core data from exploration wells to evaluate the model facies interpretation. An excellent fit is achieved for the shallow to deep subtidal platform and basinal Trenton carbonates. This technique allows paleobathymetry to be calculated in many basins where tectonic subsidence patterns can be accurately modeled.

  2. Functional Regression Models for Epistasis Analysis of Multiple Quantitative Traits.

    PubMed

    Zhang, Futao; Xie, Dan; Liang, Meimei; Xiong, Momiao

    2016-04-01

    To date, most genetic analyses of phenotypes have focused on analyzing single traits or analyzing each phenotype independently. However, joint epistasis analysis of multiple complementary traits will increase statistical power and improve our understanding of the complicated genetic structure of the complex diseases. Despite their importance in uncovering the genetic structure of complex traits, the statistical methods for identifying epistasis in multiple phenotypes remains fundamentally unexplored. To fill this gap, we formulate a test for interaction between two genes in multiple quantitative trait analysis as a multiple functional regression (MFRG) in which the genotype functions (genetic variant profiles) are defined as a function of the genomic position of the genetic variants. We use large-scale simulations to calculate Type I error rates for testing interaction between two genes with multiple phenotypes and to compare the power with multivariate pairwise interaction analysis and single trait interaction analysis by a single variate functional regression model. To further evaluate performance, the MFRG for epistasis analysis is applied to five phenotypes of exome sequence data from the NHLBI's Exome Sequencing Project (ESP) to detect pleiotropic epistasis. A total of 267 pairs of genes that formed a genetic interaction network showed significant evidence of epistasis influencing five traits. The results demonstrate that the joint interaction analysis of multiple phenotypes has a much higher power to detect interaction than the interaction analysis of a single trait and may open a new direction to fully uncovering the genetic structure of multiple phenotypes.

  3. Quantitative Analysis of Intra-chromosomal Contacts: The 3C-qPCR Method.

    PubMed

    Ea, Vuthy; Court, Franck; Forné, Thierry

    2017-01-01

    The chromosome conformation capture (3C) technique is fundamental to many population-based methods investigating chromatin dynamics and organization in eukaryotes. Here, we provide a modified quantitative 3C (3C-qPCR) protocol for improved quantitative analyses of intra-chromosomal contacts. We also describe an algorithm for data normalization which allows more accurate comparisons between contact profiles.

  4. Digital photogrammetry for quantitative wear analysis of retrieved TKA components.

    PubMed

    Grochowsky, J C; Alaways, L W; Siskey, R; Most, E; Kurtz, S M

    2006-11-01

    The use of new materials in knee arthroplasty demands a way in which to accurately quantify wear in retrieved components. Methods such as damage scoring, coordinate measurement, and in vivo wear analysis have been used in the past. The limitations in these methods illustrate a need for a different methodology that can accurately quantify wear, which is relatively easy to perform and uses a minimal amount of expensive equipment. Off-the-shelf digital photogrammetry represents a potentially quick and easy alternative to what is readily available. Eighty tibial inserts were visually examined for front and backside wear and digitally photographed in the presence of two calibrated reference fields. All images were segmented (via manual and automated algorithms) using Adobe Photoshop and National Institute of Health ImageJ. Finally, wear was determined using ImageJ and Rhinoceros software. The absolute accuracy of the method and repeatability/reproducibility by different observers were measured in order to determine the uncertainty of wear measurements. To determine if variation in wear measurements was due to implant design, 35 implants of the three most prevalent designs were subjected to retrieval analysis. The overall accuracy of area measurements was 97.8%. The error in automated segmentation was found to be significantly lower than that of manual segmentation. The photogrammetry method was found to be reasonably accurate and repeatable in measuring 2-D areas and applicable to determining wear. There was no significant variation in uncertainty detected among different implant designs. Photogrammetry has a broad range of applicability since it is size- and design-independent. A minimal amount of off-the-shelf equipment is needed for the procedure and no proprietary knowledge of the implant is needed.

  5. Quantitative analysis of fitness and genetic interactions in yeast on a genome scale.

    PubMed

    Baryshnikova, Anastasia; Costanzo, Michael; Kim, Yungil; Ding, Huiming; Koh, Judice; Toufighi, Kiana; Youn, Ji-Young; Ou, Jiongwen; San Luis, Bryan-Joseph; Bandyopadhyay, Sunayan; Hibbs, Matthew; Hess, David; Gingras, Anne-Claude; Bader, Gary D; Troyanskaya, Olga G; Brown, Grant W; Andrews, Brenda; Boone, Charles; Myers, Chad L

    2010-12-01

    Global quantitative analysis of genetic interactions is a powerful approach for deciphering the roles of genes and mapping functional relationships among pathways. Using colony size as a proxy for fitness, we developed a method for measuring fitness-based genetic interactions from high-density arrays of yeast double mutants generated by synthetic genetic array (SGA) analysis. We identified several experimental sources of systematic variation and developed normalization strategies to obtain accurate single- and double-mutant fitness measurements, which rival the accuracy of other high-resolution studies. We applied the SGA score to examine the relationship between physical and genetic interaction networks, and we found that positive genetic interactions connect across functionally distinct protein complexes revealing a network of genetic suppression among loss-of-function alleles.

  6. Systematic and quantitative analysis of G protein-coupled receptor trafficking motifs.

    PubMed

    Hurt, Carl M; Ho, Vincent K; Angelotti, Timothy

    2013-01-01

    Plasma membrane expression of G protein-coupled receptors (GPCRs) is a dynamic process balancing anterograde and retrograde trafficking. Multiple interrelated cellular processes determine the final level of cell surface expression, including endoplasmic reticulum (ER) export/retention, receptor internalization, recycling, and degradation. These processes are highly regulated to achieve specific localization to subcellular domains (e.g., dendrites or basolateral membranes) and to affect receptor signaling. Analysis of potential ER trafficking motifs within GPCRs requires careful consideration of intracellular dynamics, such as protein folding, ER export and retention, and glycosylation. This chapter presents an approach and methods for qualitative and quantitative assessment of these processes to aid in accurate identification of GPCR trafficking motifs, utilizing the analysis of a hydrophobic extracellular trafficking motif in α2C adrenergic receptors as a model system.

  7. Quantitative chemical analysis of ocular melanosomes in the TEM.

    PubMed

    Eibl, O; Schultheiss, S; Blitgen-Heinecke, P; Schraermeyer, U

    2006-01-01

    Melanosomes in retinal tissues of a human, monkey and rat were analyzed by EDX in the TEM. Samples were prepared by ultramicrotomy at different thicknesses. The material was mounted on Al grids and samples were analyzed in a Zeiss 912 TEM equipped with an Omega filter and EDX detector with ultrathin window. Melanosomes consist of C and O as main components, mole fractions are about 90 and 3-10 at.%, respectively, and small mole fraction ratios, between 2 and 0.1 at.%, of Na, Mg, K, Si, P, S, Cl, Ca. All elements were measured quantitatively by standardless EDX with high precision. Mole fractions of transition metals Fe, Cu and Zn were also measured. For Fe a mole fraction ratio of less than 0.1at.% was found and gives the melanin its paramagnetic properties. Its mole fraction is however close to or below the minimum detectable mass fraction of the used equipment. Only in the human eye and only in the retinal pigment epitelium (rpe) the mole fractions of Zn (0.1 at.% or 5000 microg/g) and Cu were clearly beyond the minimum detectable mass fraction. In the rat and monkey eye the mole fraction of Zn was at or below the minimum detectable mass fraction and could not be measured quantitatively. The obtained results yielded the chemical composition of the melanosomes in the choroidal tissue and the retinal pigment epitelium (rpe) of the three different species. The results of the chemical analysis are discussed by mole fraction correlation diagrams. Similarities and differences between the different species are outlined. Correlation behavior was found to hold over species, e.g. the Ca-O correlation. It indicates that Ca is bound to oxygen rich sites in the melanin. These are the first quantitative analyses of melanosomes by EDX reported so far. The quantitative chemical analysis should open a deeper understanding of the metabolic processes in the eye that are of central importance for the understanding of a large number of eye-related diseases. The chemical analysis also

  8. Evaluation of reference genes for accurate normalization of gene expression for real time-quantitative PCR in Pyrus pyrifolia using different tissue samples and seasonal conditions.

    PubMed

    Imai, Tsuyoshi; Ubi, Benjamin E; Saito, Takanori; Moriguchi, Takaya

    2014-01-01

    We have evaluated suitable reference genes for real time (RT)-quantitative PCR (qPCR) analysis in Japanese pear (Pyrus pyrifolia). We tested most frequently used genes in the literature such as β-Tubulin, Histone H3, Actin, Elongation factor-1α, Glyceraldehyde-3-phosphate dehydrogenase, together with newly added genes Annexin, SAND and TIP41. A total of 17 primer combinations for these eight genes were evaluated using cDNAs synthesized from 16 tissue samples from four groups, namely: flower bud, flower organ, fruit flesh and fruit skin. Gene expression stabilities were analyzed using geNorm and NormFinder software packages or by ΔCt method. geNorm analysis indicated three best performing genes as being sufficient for reliable normalization of RT-qPCR data. Suitable reference genes were different among sample groups, suggesting the importance of validation of gene expression stability of reference genes in the samples of interest. Ranking of stability was basically similar between geNorm and NormFinder, suggesting usefulness of these programs based on different algorithms. ΔCt method suggested somewhat different results in some groups such as flower organ or fruit skin; though the overall results were in good correlation with geNorm or NormFinder. Gene expression of two cold-inducible genes PpCBF2 and PpCBF4 were quantified using the three most and the three least stable reference genes suggested by geNorm. Although normalized quantities were different between them, the relative quantities within a group of samples were similar even when the least stable reference genes were used. Our data suggested that using the geometric mean value of three reference genes for normalization is quite a reliable approach to evaluating gene expression by RT-qPCR. We propose that the initial evaluation of gene expression stability by ΔCt method, and subsequent evaluation by geNorm or NormFinder for limited number of superior gene candidates will be a practical way of finding out

  9. Quantitative Proteomic and Phosphoproteomic Analysis of Trypanosoma cruzi Amastigogenesis*

    PubMed Central

    Queiroz, Rayner M. L.; Charneau, Sébastien; Mandacaru, Samuel C.; Schwämmle, Veit; Lima, Beatriz D.; Roepstorff, Peter; Ricart, Carlos A. O.

    2014-01-01

    Chagas disease is a tropical neglected disease endemic in Latin America caused by the protozoan Trypanosoma cruzi. The parasite has four major life stages: epimastigote, metacyclic trypomastigote, bloodstream trypomastigote, and amastigote. The differentiation from infective trypomastigotes into replicative amastigotes, called amastigogenesis, takes place in vivo inside mammalian host cells after a period of incubation in an acidic phagolysosome. This differentiation process can be mimicked in vitro by incubating tissue-culture-derived trypomastigotes in acidic DMEM. Here we used this well-established differentiation protocol to perform a comprehensive quantitative proteomic and phosphoproteomic analysis of T. cruzi amastigogenesis. Samples from fully differentiated forms and two biologically relevant intermediate time points were Lys-C/trypsin digested, iTRAQ-labeled, and multiplexed. Subsequently, phosphopeptides were enriched using a TiO2 matrix. Non-phosphorylated peptides were fractionated via hydrophilic interaction liquid chromatography prior to LC-MS/MS analysis. LC-MS/MS and bioinformatics procedures were used for protein and phosphopeptide quantitation, identification, and phosphorylation site assignment. We were able to identify regulated proteins and pathways involved in coordinating amastigogenesis. We also observed that a significant proportion of the regulated proteins were membrane proteins. Modulated phosphorylation events coordinated by protein kinases and phosphatases that are part of the signaling cascade induced by incubation in acidic medium were also evinced. To our knowledge, this work is the most comprehensive quantitative proteomics study of T. cruzi amastigogenesis, and these data will serve as a trustworthy basis for future studies, and possibly for new potential drug targets. PMID:25225356

  10. Quantitative and chemical fingerprint analysis for quality control of rhizoma Coptidischinensis based on UPLC-PAD combined with chemometrics methods.

    PubMed

    Kong, Wei-Jun; Zhao, Yan-Ling; Xiao, Xiao-He; Jin, Cheng; Li, Zu-Lun

    2009-10-01

    To control the quality of rhizoma Coptidis, a method based on ultra performance liquid chromatography with photodiode array detector (UPLC-PAD) was developed for quantitative analysis of five active alkaloids and chemical fingerprint analysis. In quantitative analysis, the five alkaloids showed good regression (R > 0.9992) within test ranges and the recovery of the method was in the range of 98.4-100.8%. The limit of detections and quantifications for five alkaloids in PAD were less than 0.07 and 0.22 microg/ml, respectively. In order to compare the UPLC fingerprints between rhizoma Coptidis from different origins, the chemometrics procedures, including similarity analysis (SA), hierarchical clustering analysis (HCA), principal component analysis (PCA) were applied to classify the rhizoma Coptidis samples according to their cultivated origins. Consistent results were obtained to show that rhizoma Coptidis samples could be successfully grouped in accordance with the province of origin. Furthermore, five marker constituents were screened out to be the main chemical marker, which could be applied to accurate discrimination and quality control for rhizoma Coptidis by quantitative analysis. This study revealed that UPLC-PAD method was simple, sensitive and reliable for quantitative and chemical fingerprint analysis, moreover, for the quality evaluation and control of rhizoma Coptidis.

  11. Quantitative analysis of intermolecular interactions in orthorhombic rubrene

    SciTech Connect

    Hathwar, Venkatesha R.; Sist, Mattia; Jørgensen, Mads R. V.; Mamakhel, Aref H.; Wang, Xiaoping; Hoffmann, Christina M.; Sugimoto, Kunihisa; Overgaard, Jacob; Iversen, Bo Brummerstedt

    2015-08-14

    Rubrene is one of the most studied organic semiconductors to date due to its high charge carrier mobility which makes it a potentially applicable compound in modern electronic devices. Previous electronic device characterizations and first principles theoretical calculations assigned the semiconducting properties of rubrene to the presence of a large overlap of the extended π-conjugated core between molecules. We present here the electron density distribution in rubrene at 20 K and at 100 K obtained using a combination of high-resolution X-ray and neutron diffraction data. The topology of the electron density and energies of intermolecular interactions are studied quantitatively. Specifically, the presence of Cπ...Cπinteractions between neighbouring tetracene backbones of the rubrene molecules is experimentally confirmed from a topological analysis of the electron density, Non-Covalent Interaction (NCI) analysis and the calculated interaction energy of molecular dimers. A significant contribution to the lattice energy of the crystal is provided by H—H interactions. The electron density features of H—H bonding, and the interaction energy of molecular dimers connected by H—H interaction clearly demonstrate an importance of these weak interactions in the stabilization of the crystal structure. Finally, the quantitative nature of the intermolecular interactions is virtually unchanged between 20 K and 100 K suggesting that any changes in carrier transport at these low temperatures would have a different origin. The obtained experimental results are further supported by theoretical calculations.

  12. Quantitative analysis of Caenorhabditis elegans chemotaxis using a microfluidic device.

    PubMed

    Hu, Liang; Ye, Jinjuan; Tan, Haowei; Ge, Anle; Tang, Lichun; Feng, Xiaojun; Du, Wei; Liu, Bi-Feng

    2015-08-05

    Caenorhabditis elegans, one of the widely studied model organisms, sense external chemical cues and perform relative chemotaxis behaviors through its simple chemosensory neuronal system. To study the mechanism underlying chemosensory behavior, a rapid and reliable method for quantitatively analyzing the worms' behaviors is essential. In this work, we demonstrated a microfluidic approach for investigating chemotaxis responses of worms to chemical gradients. The flow-based microfluidic chip was consisted of circular tree-like microchannels, which was able to generate eight flow streams containing stepwise chemical concentrations without the difference in flow velocity. Worms' upstream swimming into microchannels with various concentrations was monitored for quantitative analysis of the chemotaxis behavior. By using this microfluidic chip, the attractive and repellent responses of C. elegans to NaCl were successfully quantified within several minutes. The results demonstrated the wild type-like repellent responses and severely impaired attractive responses in grk-2 mutant animals with defects in calcium influx. In addition, the chemotaxis analysis of the third stage larvae revealed that its gustatory response was different from that in the adult stage. Thus, our microfluidic method provided a useful platform for studying the chemosensory behaviors of C. elegans and screening of chemosensation-related chemical drugs.

  13. Multivariate calibration applied to the quantitative analysis of infrared spectra

    SciTech Connect

    Haaland, D.M.

    1991-01-01

    Multivariate calibration methods are very useful for improving the precision, accuracy, and reliability of quantitative spectral analyses. Spectroscopists can more effectively use these sophisticated statistical tools if they have a qualitative understanding of the techniques involved. A qualitative picture of the factor analysis multivariate calibration methods of partial least squares (PLS) and principal component regression (PCR) is presented using infrared calibrations based upon spectra of phosphosilicate glass thin films on silicon wafers. Comparisons of the relative prediction abilities of four different multivariate calibration methods are given based on Monte Carlo simulations of spectral calibration and prediction data. The success of multivariate spectral calibrations is demonstrated for several quantitative infrared studies. The infrared absorption and emission spectra of thin-film dielectrics used in the manufacture of microelectronic devices demonstrate rapid, nondestructive at-line and in-situ analyses using PLS calibrations. Finally, the application of multivariate spectral calibrations to reagentless analysis of blood is presented. We have found that the determination of glucose in whole blood taken from diabetics can be precisely monitored from the PLS calibration of either mind- or near-infrared spectra of the blood. Progress toward the non-invasive determination of glucose levels in diabetics is an ultimate goal of this research. 13 refs., 4 figs.

  14. Quantitative analysis of live cells using digital holographic microscopy

    NASA Astrophysics Data System (ADS)

    Lewis, Tan Rongwei; Qu, Weijuan; Chee, Oi Choo; Singh, Vijay Raj; Asundi, Anand

    2010-03-01

    During the life time of a cell, it goes through changes to the plasma membrane as well as its internal structures especially distinctive during processes like cell division and death. Different types of microscope are used to fulfill the observation of the cell's variation. In our experiment, Vero cells have been investigated by using phase contrast microscopy and digital holographic microscopy (DHM). A comparison of the images obtained for cell division is presented here. The conventional phase contrast microscope provided a good imaging method in the real time analysis of cell division. The off-axis digital hologram recorded by the DHM system can be reconstructed to obtain both the intensity image and phase contrast image of the test object. These can be used for live cell imaging to provide multiple results from a single equipment setup. The DHM system, besides being a qualitative tool, is able to provide quantitative results and 3D images of the cell division process. The ability of DHM to provide quantitative analysis makes it an ideal tool for life science applications.

  15. Quantitative analysis of live cells using digital holographic microscopy

    NASA Astrophysics Data System (ADS)

    Lewis, Tan Rongwei; Qu, Weijuan; Chee, Oi Choo; Singh, Vijay Raj; Asundi, Anand

    2009-12-01

    During the life time of a cell, it goes through changes to the plasma membrane as well as its internal structures especially distinctive during processes like cell division and death. Different types of microscope are used to fulfill the observation of the cell's variation. In our experiment, Vero cells have been investigated by using phase contrast microscopy and digital holographic microscopy (DHM). A comparison of the images obtained for cell division is presented here. The conventional phase contrast microscope provided a good imaging method in the real time analysis of cell division. The off-axis digital hologram recorded by the DHM system can be reconstructed to obtain both the intensity image and phase contrast image of the test object. These can be used for live cell imaging to provide multiple results from a single equipment setup. The DHM system, besides being a qualitative tool, is able to provide quantitative results and 3D images of the cell division process. The ability of DHM to provide quantitative analysis makes it an ideal tool for life science applications.

  16. Quantitative analysis of intermolecular interactions in orthorhombic rubrene

    PubMed Central

    Hathwar, Venkatesha R.; Sist, Mattia; Jørgensen, Mads R. V.; Mamakhel, Aref H.; Wang, Xiaoping; Hoffmann, Christina M.; Sugimoto, Kunihisa; Overgaard, Jacob; Iversen, Bo Brummerstedt

    2015-01-01

    Rubrene is one of the most studied organic semiconductors to date due to its high charge carrier mobility which makes it a potentially applicable compound in modern electronic devices. Previous electronic device characterizations and first principles theoretical calculations assigned the semiconducting properties of rubrene to the presence of a large overlap of the extended π-conjugated core between molecules. We present here the electron density distribution in rubrene at 20 K and at 100 K obtained using a combination of high-resolution X-ray and neutron diffraction data. The topology of the electron density and energies of intermolecular interactions are studied quantitatively. Specifically, the presence of Cπ⋯Cπ interactions between neighbouring tetracene backbones of the rubrene molecules is experimentally confirmed from a topological analysis of the electron density, Non-Covalent Interaction (NCI) analysis and the calculated interaction energy of molecular dimers. A significant contribution to the lattice energy of the crystal is provided by H—H interactions. The electron density features of H—H bonding, and the interaction energy of molecular dimers connected by H—H interaction clearly demonstrate an importance of these weak interactions in the stabilization of the crystal structure. The quantitative nature of the intermolecular interactions is virtually unchanged between 20 K and 100 K suggesting that any changes in carrier transport at these low temperatures would have a different origin. The obtained experimental results are further supported by theoretical calculations. PMID:26306198

  17. Quantitative analysis of intermolecular interactions in orthorhombic rubrene

    DOE PAGES

    Hathwar, Venkatesha R.; Sist, Mattia; Jørgensen, Mads R. V.; ...

    2015-08-14

    Rubrene is one of the most studied organic semiconductors to date due to its high charge carrier mobility which makes it a potentially applicable compound in modern electronic devices. Previous electronic device characterizations and first principles theoretical calculations assigned the semiconducting properties of rubrene to the presence of a large overlap of the extended π-conjugated core between molecules. We present here the electron density distribution in rubrene at 20 K and at 100 K obtained using a combination of high-resolution X-ray and neutron diffraction data. The topology of the electron density and energies of intermolecular interactions are studied quantitatively. Specifically,more » the presence of Cπ...Cπinteractions between neighbouring tetracene backbones of the rubrene molecules is experimentally confirmed from a topological analysis of the electron density, Non-Covalent Interaction (NCI) analysis and the calculated interaction energy of molecular dimers. A significant contribution to the lattice energy of the crystal is provided by H—H interactions. The electron density features of H—H bonding, and the interaction energy of molecular dimers connected by H—H interaction clearly demonstrate an importance of these weak interactions in the stabilization of the crystal structure. Finally, the quantitative nature of the intermolecular interactions is virtually unchanged between 20 K and 100 K suggesting that any changes in carrier transport at these low temperatures would have a different origin. The obtained experimental results are further supported by theoretical calculations.« less

  18. Quantitative Analysis of the Interdisciplinarity of Applied Mathematics.

    PubMed

    Xie, Zheng; Duan, Xiaojun; Ouyang, Zhenzheng; Zhang, Pengyuan

    2015-01-01

    The increasing use of mathematical techniques in scientific research leads to the interdisciplinarity of applied mathematics. This viewpoint is validated quantitatively here by statistical and network analysis on the corpus PNAS 1999-2013. A network describing the interdisciplinary relationships between disciplines in a panoramic view is built based on the corpus. Specific network indicators show the hub role of applied mathematics in interdisciplinary research. The statistical analysis on the corpus content finds that algorithms, a primary topic of applied mathematics, positively correlates, increasingly co-occurs, and has an equilibrium relationship in the long-run with certain typical research paradigms and methodologies. The finding can be understood as an intrinsic cause of the interdisciplinarity of applied mathematics.

  19. [Quantitative analysis of transformer oil dissolved gases using FTIR].

    PubMed

    Zhao, An-xin; Tang, Xiao-jun; Wang, Er-zhen; Zhang, Zhong-hua; Liu, Jun-hua

    2013-09-01

    For the defects of requiring carrier gas and regular calibration, and low safety using chromatography to on line monitor transformer dissolved gases, it was attempted to establish a dissolved gas analysis system based on Fourier transform infrared spectroscopy. Taking into account the small amount of characteristic gases, many components, detection limit and safety requirements and the difficulty of degasser to put an end to the presence of interference gas, the quantitative analysis model was established based on sparse partial least squares, piecewise section correction and feature variable extraction algorithm using improvement TR regularization. With the characteristic gas of CH4, C2H6, C2H6, and CO2, the results show that using FTIR meets DGA requirements with the spectrum wave number resolution of 1 cm(-1) and optical path of 10 cm.

  20. Quantitative Analysis of the Interdisciplinarity of Applied Mathematics

    PubMed Central

    Zhang, Pengyuan

    2015-01-01

    The increasing use of mathematical techniques in scientific research leads to the interdisciplinarity of applied mathematics. This viewpoint is validated quantitatively here by statistical and network analysis on the corpus PNAS 1999–2013. A network describing the interdisciplinary relationships between disciplines in a panoramic view is built based on the corpus. Specific network indicators show the hub role of applied mathematics in interdisciplinary research. The statistical analysis on the corpus content finds that algorithms, a primary topic of applied mathematics, positively correlates, increasingly co-occurs, and has an equilibrium relationship in the long-run with certain typical research paradigms and methodologies. The finding can be understood as an intrinsic cause of the interdisciplinarity of applied mathematics. PMID:26352604

  1. Fusing Quantitative Requirements Analysis with Model-based Systems Engineering

    NASA Technical Reports Server (NTRS)

    Cornford, Steven L.; Feather, Martin S.; Heron, Vance A.; Jenkins, J. Steven

    2006-01-01

    A vision is presented for fusing quantitative requirements analysis with model-based systems engineering. This vision draws upon and combines emergent themes in the engineering milieu. "Requirements engineering" provides means to explicitly represent requirements (both functional and non-functional) as constraints and preferences on acceptable solutions, and emphasizes early-lifecycle review, analysis and verification of design and development plans. "Design by shopping" emphasizes revealing the space of options available from which to choose (without presuming that all selection criteria have previously been elicited), and provides means to make understandable the range of choices and their ramifications. "Model-based engineering" emphasizes the goal of utilizing a formal representation of all aspects of system design, from development through operations, and provides powerful tool suites that support the practical application of these principles. A first step prototype towards this vision is described, embodying the key capabilities. Illustrations, implications, further challenges and opportunities are outlined.

  2. Quantitative Phase Analysis by the Rietveld Method for Forensic Science.

    PubMed

    Deng, Fei; Lin, Xiaodong; He, Yonghong; Li, Shu; Zi, Run; Lai, Shijun

    2015-07-01

    Quantitative phase analysis (QPA) is helpful to determine the type attribute of the object because it could present the content of the constituents. QPA by Rietveld method requires neither measurement of calibration data nor the use of an internal standard; however, the approximate crystal structure of each phase in a mixture is necessary. In this study, 8 synthetic mixtures composed of potassium nitrate and sulfur were analyzed by Rietveld QPA method. The Rietveld refinement was accomplished with a material analysis using diffraction program and evaluated by three agreement indices. Results showed that Rietveld QPA yielded precise results, with errors generally less than 2.0% absolute. In addition, a criminal case which was broken successfully with the help of Rietveld QPA method was also introduced. This method will allow forensic investigators to acquire detailed information of the material evidence, which could point out the direction for case detection and court proceedings.

  3. 3D quantitative analysis of brain SPECT images

    NASA Astrophysics Data System (ADS)

    Loncaric, Sven; Ceskovic, Ivan; Petrovic, Ratimir; Loncaric, Srecko

    2001-07-01

    The main purpose of this work is to develop a computer-based technique for quantitative analysis of 3-D brain images obtained by single photon emission computed tomography (SPECT). In particular, the volume and location of ischemic lesion and penumbra is important for early diagnosis and treatment of infracted regions of the brain. SPECT imaging is typically used as diagnostic tool to assess the size and location of the ischemic lesion. The segmentation method presented in this paper utilizes a 3-D deformable model in order to determine size and location of the regions of interest. The evolution of the model is computed using a level-set implementation of the algorithm. In addition to 3-D deformable model the method utilizes edge detection and region growing for realization of a pre-processing. Initial experimental results have shown that the method is useful for SPECT image analysis.

  4. Quantitative morphometric analysis for the tectonic characterisation of northern Tunisia.

    NASA Astrophysics Data System (ADS)

    Camafort, Miquel; Pérez-Peña, José Vicente; Booth-Rea, Guillermo; Ranero, César R.; Gràcia, Eulàlia; Azañón, José Miguel; Melki, Fetheddine; Ouadday, Mohamed

    2016-04-01

    Northern Tunisia is characterized by low deformation rates and low to moderate seismicity. Although instrumental seismicity reaches maximum magnitudes of Mw 5.5, some historical earthquakes have occurred with catastrophic consequences in this region. Aiming to improve our knowledge of active tectonics in Tunisia, we carried out both a quantitative morphometric analysis and field study in the north-western region. We applied different morphometric tools, like river profiles, knickpoint analysis, hypsometric curves and integrals and drainage pattern anomalies in order to differentiate between zones with high or low recent tectonic activity. This analysis helps identifying uplift and subsidence zones, which we relate to fault activity. Several active faults in a sparse distribution were identified. A selected sector was studied with a field campaign to test the results obtained with the quantitative analysis. During the fieldwork we identified geological evidence of recent activity and a considerable seismogenic potential along El Alia-Teboursouk (ETF) and Dkhila (DF) faults. The ETF fault could be responsible of one of the most devastating historical earthquakes in northern Tunisia that destroyed Utique in 412 A.D. Geological evidence include fluvial terraces folded by faults, striated and cracked pebbles, clastic dikes, sand volcanoes, coseismic cracks, etc. Although not reflected in the instrumental seismicity, our results support an important seismic hazard, evidenced by the several active tectonic structures identified and the two seismogenic faults described. After obtaining the current active tectonic framework of Tunisia we discuss our results within the western Mediterranean trying to contribute to the understanding of the western Mediterranean tectonic context. With our results, we suggest that the main reason explaining the sparse and scarce seismicity of the area in contrast with the adjacent parts of the Nubia-Eurasia boundary is due to its extended

  5. Quantitative analysis of gene expression by reverse transcription polymerase chain reaction and capillary electrophoresis with laser-induced fluorescence detection.

    PubMed

    Richards, Mark P; Poch, Stephen M

    2002-05-01

    There has been a dramatic expansion of DNA sequence information compiled over the past several years for a variety of eukaryotic and prokaryotic genomes. Accompanying this increase in knowledge of genomic structure and organization has been a growing interest in studying the function of individual genes including regulation of their expression. A number of methods such as Northern blotting, ribonuclease protection assay, and hybridization arrays have been developed to analyze gene expression at the transcriptional (mRNA) level. Although quantitative estimates of mRNA transcripts can be obtained from each of these methods, oftentimes they lack sufficient sensitivity or the methodology is too costly or too labor-intensive to be applied to the analysis of a large number of samples. The most sensitive method for analyzing gene expression at the mRNA level involves the combination of reverse transcription and polymerase chain reaction (RT-PCR). However, in order to provide accurate quantitative estimates of gene expression, a rapid and efficient method is required for separation and detection of the double-stranded DNA (dsDNA) products of RT-PCR. Recent advances in capillary electrophoresis with laser-induced fluorescence detection (CE/LIF) have made this method suitable for the automated analysis of large numbers of RT-PCR samples. An overview of the application of CE/LIF to quantitative analysis of gene expression by RT-PCR is presented along with selected protocols and examples. Both relative-quantitative (RQ) and quantitative-competitive (QC) approaches to RT-PCR are discussed in conjunction with the use of CE/LIF for rapid and accurate quantitative analysis of PCR products.

  6. 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

  7. Trophic relationships in an estuarine environment: A quantitative fatty acid analysis signature approach

    NASA Astrophysics Data System (ADS)

    Magnone, Larisa; Bessonart, Martin; Gadea, Juan; Salhi, María

    2015-12-01

    In order to better understand the functioning of aquatic environments, it is necessary to obtain accurate diet estimations in food webs. Their description should incorporate information about energy flow and the relative importance of trophic pathways. Fatty acids have been extensively used in qualitative studies on trophic relationships in food webs. Recently a new method to estimate quantitatively single predator diet has been developed. In this study, a model of aquatic food web through quantitative fatty acid signature analysis was generated to identify the trophic interactions among the species in the Rocha Lagoon. The biological sampling over two consecutive annual periods was comprehensive enough to identify all functional groups in the aquatic food web (except birds and mammals). Heleobia australis seemed to play a central role in this estuarine ecosystem. As both, a grazer and a prey to several other species, probably H. australis is transferring a great amount of energy to upper trophic levels. Most of the species at Rocha Lagoon have a wide range of prey items in their diet reflecting a complex food web, which is characteristic of extremely dynamic environment as estuarine ecosystems. QFASA is a model in tracing and quantitative estimate trophic pathways among species in an estuarine food web. The results obtained in the present work are a valuable contribution in the understanding of trophic relationships in Rocha Lagoon.

  8. Quantitative analysis of cyclic beta-turn models.

    PubMed Central

    Perczel, A.; Fasman, G. D.

    1992-01-01

    The beta-turn is a frequently found structural unit in the conformation of globular proteins. Although the circular dichroism (CD) spectra of the alpha-helix and beta-pleated sheet are well defined, there remains some ambiguity concerning the pure component CD spectra of the different types of beta-turns. Recently, it has been reported (Hollósi, M., Kövér, K.E., Holly, S., Radics, L., & Fasman, G.D., 1987, Biopolymers 26, 1527-1572; Perczel, A., Hollósi, M., Foxman, B.M., & Fasman, G.D., 1991a, J. Am. Chem. Soc. 113, 9772-9784) that some pseudohexapeptides (e.g., the cyclo[(delta)Ava-Gly-Pro-Aaa-Gly] where Aaa = Ser, Ser(OtBu), or Gly) in many solvents adopt a conformational mixture of type I and the type II beta-turns, although the X-ray-determined conformation was an ideal type I beta-turn. In addition to these pseudohexapeptides, conformational analysis was also carried out on three pseudotetrapeptides and three pseudooctapeptides. The target of the conformation analysis reported herein was to determine whether the ring stress of the above beta-turn models has an influence on their conformational properties. Quantitative nuclear Overhauser effect (NOE) measurements yielded interproton distances. The conformational average distances so obtained were interpreted utilizing molecular dynamics (MD) simulations to yield the conformational percentages. These conformational ratios were correlated with the conformational weights obtained by quantitative CD analysis of the same compounds. The pure component CD curves of type I and type II beta-turns were also obtained, using a recently developed algorithm (Perczel, A., Tusnády, G., Hollósi, M., & Fasman, G.D., 1991b, Protein Eng. 4(6), 669-679). For the first time the results of a CD deconvolution, based on the CD spectra of 14 beta-turn models, were assigned by quantitative NOE results. The NOE experiments confirmed the ratios of the component curves found for the two major beta-turns by CD analysis. These results

  9. Quantitative image analysis in sonograms of the thyroid gland

    NASA Astrophysics Data System (ADS)

    Catherine, Skouroliakou; Maria, Lyra; Aristides, Antoniou; Lambros, Vlahos

    2006-12-01

    High-resolution, real-time ultrasound is a routine examination for assessing the disorders of the thyroid gland. However, the current diagnosis practice is based mainly on qualitative evaluation of the resulting sonograms, therefore depending on the physician's experience. Computerized texture analysis is widely employed in sonographic images of various organs (liver, breast), and it has been proven to increase the sensitivity of diagnosis by providing a better tissue characterization. The present study attempts to characterize thyroid tissue by automatic texture analysis. The texture features that are calculated are based on co-occurrence matrices as they have been proposed by Haralick. The sample consists of 40 patients. For each patient two sonographic images (one for each lobe) are recorded in DICOM format. The lobe is manually delineated in each sonogram, and the co-occurrence matrices for 52 separation vectors are calculated. The texture features extracted from each one of these matrices are: contrast, correlation, energy and homogeneity. Primary component analysis is used to select the optimal set of features. The statistical analysis resulted in the extraction of 21 optimal descriptors. The optimal descriptors are all co-occurrence parameters as the first-order statistics did not prove to be representative of the images characteristics. The bigger number of components depends mainly on correlation for very close or very far distances. The results indicate that quantitative analysis of thyroid sonograms can provide an objective characterization of thyroid tissue.

  10. Quantitative Analysis of Single-Molecule RNA-Protein Interaction

    PubMed Central

    Fuhrmann, Alexander; Schoening, Jan C.; Anselmetti, Dario; Staiger, Dorothee; Ros, Robert

    2009-01-01

    Abstract RNA-binding proteins impact gene expression at the posttranscriptional level by interacting with cognate cis elements within the transcripts. Here, we apply dynamic single-molecule force spectroscopy to study the interaction of the Arabidopsis glycine-rich RNA-binding protein AtGRP8 with its RNA target. A dwell-time-dependent analysis of the single-molecule data in combination with competition assays and site-directed mutagenesis of both the RNA target and the RNA-binding domain of the protein allowed us to distinguish and quantify two different binding modes. For dwell times <0.21 s an unspecific complex with a lifetime of 0.56 s is observed, whereas dwell times >0.33 s result in a specific interaction with a lifetime of 208 s. The corresponding reaction lengths are 0.28 nm for the unspecific and 0.55 nm for the specific AtGRP8-RNA interactions, indicating formation of a tighter complex with increasing dwell time. These two binding modes cannot be dissected in ensemble experiments. Quantitative titration in RNA bandshift experiments yields an ensemble-averaged equilibrium constant of dissociation of KD = 2 × 10−7 M. Assuming comparable on-rates for the specific and nonspecific binding modes allows us to estimate their free energies as ΔG0 = −42 kJ/mol and ΔG0 = −28 kJ/mol for the specific and nonspecific binding modes, respectively. Thus, we show that single-molecule force spectroscopy with a refined statistical analysis is a potent tool for the analysis of protein-RNA interactions without the drawback of ensemble averaging. This makes it possible to discriminate between different binding modes or sites and to analyze them quantitatively. We propose that this method could be applied to complex interactions of biomolecules in general, and be of particular interest for the investigation of multivalent binding reactions. PMID:19527663

  11. The Quantitative Analysis of Chennai Automotive Industry Cluster

    NASA Astrophysics Data System (ADS)

    Bhaskaran, Ethirajan

    2016-07-01

    Chennai, also called as Detroit of India due to presence of Automotive Industry producing over 40 % of the India's vehicle and components. During 2001-2002, the Automotive Component Industries (ACI) in Ambattur, Thirumalizai and Thirumudivakkam Industrial Estate, Chennai has faced problems on infrastructure, technology, procurement, production and marketing. The objective is to study the Quantitative Performance of Chennai Automotive Industry Cluster before (2001-2002) and after the CDA (2008-2009). The methodology adopted is collection of primary data from 100 ACI using quantitative questionnaire and analyzing using Correlation Analysis (CA), Regression Analysis (RA), Friedman Test (FMT), and Kruskall Wallis Test (KWT).The CA computed for the different set of variables reveals that there is high degree of relationship between the variables studied. The RA models constructed establish the strong relationship between the dependent variable and a host of independent variables. The models proposed here reveal the approximate relationship in a closer form. KWT proves, there is no significant difference between three locations clusters with respect to: Net Profit, Production Cost, Marketing Costs, Procurement Costs and Gross Output. This supports that each location has contributed for development of automobile component cluster uniformly. The FMT proves, there is no significant difference between industrial units in respect of cost like Production, Infrastructure, Technology, Marketing and Net Profit. To conclude, the Automotive Industries have fully utilized the Physical Infrastructure and Centralised Facilities by adopting CDA and now exporting their products to North America, South America, Europe, Australia, Africa and Asia. The value chain analysis models have been implemented in all the cluster units. This Cluster Development Approach (CDA) model can be implemented in industries of under developed and developing countries for cost reduction and productivity

  12. Revisit to three-dimensional percolation theory: Accurate analysis for highly stretchable conductive composite materials

    PubMed Central

    Kim, Sangwoo; Choi, Seongdae; Oh, Eunho; Byun, Junghwan; Kim, Hyunjong; Lee, Byeongmoon; Lee, Seunghwan; Hong, Yongtaek

    2016-01-01

    A percolation theory based on variation of conductive filler fraction has been widely used to explain the behavior of conductive composite materials under both small and large deformation conditions. However, it typically fails in properly analyzing the materials under the large deformation since the assumption may not be valid in such a case. Therefore, we proposed a new three-dimensional percolation theory by considering three key factors: nonlinear elasticity, precisely measured strain-dependent Poisson’s ratio, and strain-dependent percolation threshold. Digital image correlation (DIC) method was used to determine actual Poisson’s ratios at various strain levels, which were used to accurately estimate variation of conductive filler volume fraction under deformation. We also adopted strain-dependent percolation threshold caused by the filler re-location with deformation. When three key factors were considered, electrical performance change was accurately analyzed for composite materials with both isotropic and anisotropic mechanical properties. PMID:27694856

  13. Revisit to three-dimensional percolation theory: Accurate analysis for highly stretchable conductive composite materials

    NASA Astrophysics Data System (ADS)

    Kim, Sangwoo; Choi, Seongdae; Oh, Eunho; Byun, Junghwan; Kim, Hyunjong; Lee, Byeongmoon; Lee, Seunghwan; Hong, Yongtaek

    2016-10-01

    A percolation theory based on variation of conductive filler fraction has been widely used to explain the behavior of conductive composite materials under both small and large deformation conditions. However, it typically fails in properly analyzing the materials under the large deformation since the assumption may not be valid in such a case. Therefore, we proposed a new three-dimensional percolation theory by considering three key factors: nonlinear elasticity, precisely measured strain-dependent Poisson’s ratio, and strain-dependent percolation threshold. Digital image correlation (DIC) method was used to determine actual Poisson’s ratios at various strain levels, which were used to accurately estimate variation of conductive filler volume fraction under deformation. We also adopted strain-dependent percolation threshold caused by the filler re-location with deformation. When three key factors were considered, electrical performance change was accurately analyzed for composite materials with both isotropic and anisotropic mechanical properties.

  14. Advance in orientation microscopy: quantitative analysis of nanocrystalline structures.

    PubMed

    Seyring, Martin; Song, Xiaoyan; Rettenmayr, Markus

    2011-04-26

    The special properties of nanocrystalline materials are generally accepted to be a consequence of the high density of planar defects (grain and twin boundaries) and their characteristics. However, until now, nanograin structures have not been characterized with similar detail and statistical relevance as coarse-grained materials, due to the lack of an appropriate method. In the present paper, a novel method based on quantitative nanobeam diffraction in transmission electron microscopy (TEM) is presented to determine the misorientation of adjacent nanograins and subgrains. Spatial resolution of <5 nm can be achieved. This method is applicable to characterize orientation relationships in wire, film, and bulk materials with nanocrystalline structures. As a model material, nanocrystalline Cu is used. Several important features of the nanograin structure are discovered utilizing quantitative analysis: the fraction of twin boundaries is substantially higher than that observed in bright-field images in the TEM; small angle grain boundaries are prominent; there is an obvious dependence of the grain boundary characteristics on grain size distribution and mean grain size.

  15. Quantitative analysis of incipient mineral loss in hard tissues

    NASA Astrophysics Data System (ADS)

    Matvienko, Anna; Mandelis, Andreas; Hellen, Adam; Jeon, Raymond; Abrams, Stephen; Amaechi, Bennett

    2009-02-01

    A coupled diffuse-photon-density-wave and thermal-wave theoretical model was developed to describe the biothermophotonic phenomena in multi-layered hard tissue structures. Photothermal Radiometry was applied as a safe, non-destructive, and highly sensitive tool for the detection of early tooth enamel demineralization to test the theory. Extracted human tooth was treated sequentially with an artificial demineralization gel to simulate controlled mineral loss in the enamel. The experimental setup included a semiconductor laser (659 nm, 120 mW) as the source of the photothermal signal. Modulated laser light generated infrared blackbody radiation from teeth upon absorption and nonradiative energy conversion. The infrared flux emitted by the treated region of the tooth surface and sub-surface was monitored with an infrared detector, both before and after treatment. Frequency scans with a laser beam size of 3 mm were performed in order to guarantee one-dimensionality of the photothermal field. TMR images showed clear differences between sound and demineralized enamel, however this technique is destructive. Dental radiographs did not indicate any changes. The photothermal signal showed clear change even after 1 min of gel treatment. As a result of the fittings, thermal and optical properties of sound and demineralized enamel were obtained, which allowed for quantitative differentiation of healthy and non-healthy regions. In conclusion, the developed model was shown to be a promising tool for non-invasive quantitative analysis of early demineralization of hard tissues.

  16. A Technique Using Calibrated Photography and Photoshop for Accurate Shade Analysis and Communication.

    PubMed

    McLaren, Edward A; Figueira, Johan; Goldstein, Ronald E

    2017-02-01

    This article reviews the critical aspects of controlling the shade-taking environment and discusses various modalities introduced throughout the years to acquire and communicate shade information. Demonstrating a highly calibrated digital photographic technique for capturing shade information, this article shows how to use Photoshop® to standardize images and extract color information from the tooth and shade tab for use by a ceramist for an accurate shade-matching restoration.

  17. The utility of accurate mass and LC elution time information in the analysis of complex proteomes

    SciTech Connect

    Norbeck, Angela D.; Monroe, Matthew E.; Adkins, Joshua N.; Anderson, Kevin K.; Daly, Don S.; Smith, Richard D.

    2005-08-01

    Theoretical tryptic digests of all predicted proteins from the genomes of three organisms of varying complexity were evaluated for specificity and possible utility of combined peptide accurate mass and predicted LC normalized elution time (NET) information. The uniqueness of each peptide was evaluated using its combined mass (+/- 5 ppm and 1 ppm) and NET value (no constraint, +/- 0.05 and 0.01 on a 0-1 NET scale). The set of peptides both underestimates actual biological complexity due to the lack of specific modifications, and overestimates the expected complexity since many proteins will not be present in the sample or observable on the mass spectrometer because of dynamic range limitations. Once a peptide is identified from an LCMS/MS experiment, its mass and elution time is representative of a unique fingerprint for that peptide. The uniqueness of that fingerprint in comparison to that for the other peptides present is indicative of the ability to confidently identify that peptide based on accurate mass and NET measurements. These measurements can be made using HPLC coupled with high resolution MS in a high-throughput manner. Results show that for organisms with comparatively small proteomes, such as Deinococcus radiodurans, modest mass and elution time accuracies are generally adequate for peptide identifications. For more complex proteomes, increasingly accurate easurements are required. However, the majority of proteins should be uniquely identifiable by using LC-MS with mass accuracies within +/- 1 ppm and elution time easurements within +/- 0.01 NET.

  18. Liver steatosis in pre-transplant liver biopsies can be quantified rapidly and accurately by nuclear magnetic resonance analysis.

    PubMed

    Bertram, Stefanie; Myland, Cathrin; Swoboda, Sandra; Gallinat, Anja; Minor, Thomas; Lehmann, Nils; Thie, Michael; Kälsch, Julia; Pott, Leona; Canbay, Ali; Bajanowski, Thomas; Reis, Henning; Paul, Andreas; Baba, Hideo A

    2017-02-01

    Donor livers marginally acceptable or acceptable according to extended criteria are more frequently transplanted due to the growing discrepancy between demand and availability of donor organs. One type of marginally acceptable graft is a steatotic donor liver, because it is more sensitive to ischemia-reperfusion injury. Thus, quantitative assessment of steatosis is crucial prior to liver transplantation. Extent of steatosis of 49 pre-reperfusion liver biopsies from patients who received orthotopic liver transplantation was assessed by three techniques: semi-quantitative histological evaluation, computerized histomorphometry, and NMR-based estimation of fat content. The findings were correlated to clinical data and to histological examination of corresponding post-reperfusion biopsies for quantification of ischemia-reperfusion injury. We found that values obtained through all three assessment methods were positively correlated. None of the values obtained by the three applied methods correlated with clinical outcome or extent of ischemia-reperfusion injury. Quantitative evaluation of steatosis by NMR yields results comparable to histological and morphometrical assessment. This technique is rapid (<5 min), accurately quantifies fat in donor livers, and provides results that can be used when evaluation by a pathologist is not available.

  19. Quantitative multi-image analysis for biomedical Raman spectroscopic imaging.

    PubMed

    Hedegaard, Martin A B; Bergholt, Mads S; Stevens, Molly M

    2016-05-01

    Imaging by Raman spectroscopy enables unparalleled label-free insights into cell and tissue composition at the molecular level. With established approaches limited to single image analysis, there are currently no general guidelines or consensus on how to quantify biochemical components across multiple Raman images. Here, we describe a broadly applicable methodology for the combination of multiple Raman images into a single image for analysis. This is achieved by removing image specific background interference, unfolding the series of Raman images into a single dataset, and normalisation of each Raman spectrum to render comparable Raman images. Multivariate image analysis is finally applied to derive the contributing 'pure' biochemical spectra for relative quantification. We present our methodology using four independently measured Raman images of control cells and four images of cells treated with strontium ions from substituted bioactive glass. We show that the relative biochemical distribution per area of the cells can be quantified. In addition, using k-means clustering, we are able to discriminate between the two cell types over multiple Raman images. This study shows a streamlined quantitative multi-image analysis tool for improving cell/tissue characterisation and opens new avenues in biomedical Raman spectroscopic imaging.

  20. Quantitative three-dimensional holographic interferometry for flow field analysis

    NASA Astrophysics Data System (ADS)

    Holden, C. M. E.; Parker, S. C. J.; Bryanston-Cross, P. J.

    Holographic interferometry offers the potential for quantitative, wholefield analysis of three-dimensional compressible flows. The technique is non-intrusive, does not require the introduction of seeding particles, and records the entire flow information within the pulse duration of a Q-switched ruby laser (~30ns). At present, however, holographic interferometry is mainly used qualitatively due to the practical restrictions of data recording, acquisition and processing. To address the potential of holographic flow analysis a prototype multi-channel interferometer has been designed and preliminary wind tunnel results have been obtained. The proposed configuration uses specular illumination which, unlike comparable diffuse systems, does not suffer from fringe localisation and speckle noise. Beam collimation and steering through the flow field is achieved in a single operation by the use of holographic optical elements (HOEs). The resulting design is compact, light efficient, has aberration compensation, and the recorded data are conducive to both tomographic analysis and direct comparison to computational fluid dynamics (CFD) predictions. Holograms have been recorded of simple two-dimensional and axisymmetric compressible flows, to compare the accuracy of holographic density measurements with data from conventional pressure sensors and CFD codes. Data extraction from the holograms, and the elimination of rigid body motion, was achieved using digital Fourier transform fringe analysis. The introduction of phase errors by image processing has been investigated by analysing simulated fringe patterns generated from a combination of experimental amplitude information and computer generated phase data.

  1. Multipoint quantitative-trait linkage analysis in general pedigrees.

    PubMed Central

    Almasy, L; Blangero, J

    1998-01-01

    Multipoint linkage analysis of quantitative-trait loci (QTLs) has previously been restricted to sibships and small pedigrees. In this article, we show how variance-component linkage methods can be used in pedigrees of arbitrary size and complexity, and we develop a general framework for multipoint identity-by-descent (IBD) probability calculations. We extend the sib-pair multipoint mapping approach of Fulker et al. to general relative pairs. This multipoint IBD method uses the proportion of alleles shared identical by descent at genotyped loci to estimate IBD sharing at arbitrary points along a chromosome for each relative pair. We have derived correlations in IBD sharing as a function of chromosomal distance for relative pairs in general pedigrees and provide a simple framework whereby these correlations can be easily obtained for any relative pair related by a single line of descent or by multiple independent lines of descent. Once calculated, the multipoint relative-pair IBDs can be utilized in variance-component linkage analysis, which considers the likelihood of the entire pedigree jointly. Examples are given that use simulated data, demonstrating both the accuracy of QTL localization and the increase in power provided by multipoint analysis with 5-, 10-, and 20-cM marker maps. The general pedigree variance component and IBD estimation methods have been implemented in the SOLAR (Sequential Oligogenic Linkage Analysis Routines) computer package. PMID:9545414

  2. Quantitative analysis of the reconstruction performance of interpolants

    NASA Technical Reports Server (NTRS)

    Lansing, Donald L.; Park, Stephen K.

    1987-01-01

    The analysis presented provides a quantitative measure of the reconstruction or interpolation performance of linear, shift-invariant interpolants. The performance criterion is the mean square error of the difference between the sampled and reconstructed functions. The analysis is applicable to reconstruction algorithms used in image processing and to many types of splines used in numerical analysis and computer graphics. When formulated in the frequency domain, the mean square error clearly separates the contribution of the interpolation method from the contribution of the sampled data. The equations provide a rational basis for selecting an optimal interpolant; that is, one which minimizes the mean square error. The analysis has been applied to a selection of frequently used data splines and reconstruction algorithms: parametric cubic and quintic Hermite splines, exponential and nu splines (including the special case of the cubic spline), parametric cubic convolution, Keys' fourth-order cubic, and a cubic with a discontinuous first derivative. The emphasis in this paper is on the image-dependent case in which no a priori knowledge of the frequency spectrum of the sampled function is assumed.

  3. Quantitative multielement analysis using high energy particle bombardment

    NASA Technical Reports Server (NTRS)

    Clark, P. J.; Neal, G. F.; Allen, R. O.

    1974-01-01

    Charged particles ranging in energy from 0.8 to 4.0 MeV are used to induce resonant nuclear reactions, Coulomb excitation (gamma X-rays), and X-ray emission in both thick and thin targets. Quantitative analysis is possible for elements from Li to Pb in complex environmental samples, although the matrix can severely reduce the sensitivity. It is necessary to use a comparator technique for the gamma-rays, while for X-rays an internal standard can be used. A USGS standard rock is analyzed for a total of 28 elements. Water samples can be analyzed either by nebulizing the sample doped with Cs or Y onto a thin formvar film or by extracting the sample (with or without an internal standard) onto ion exchange resin which is pressed into a pellet.

  4. Large-Scale Quantitative Analysis of Painting Arts

    PubMed Central

    Kim, Daniel; Son, Seung-Woo; Jeong, Hawoong

    2014-01-01

    Scientists have made efforts to understand the beauty of painting art in their own languages. As digital image acquisition of painting arts has made rapid progress, researchers have come to a point where it is possible to perform statistical analysis of a large-scale database of artistic paints to make a bridge between art and science. Using digital image processing techniques, we investigate three quantitative measures of images – the usage of individual colors, the variety of colors, and the roughness of the brightness. We found a difference in color usage between classical paintings and photographs, and a significantly low color variety of the medieval period. Interestingly, moreover, the increment of roughness exponent as painting techniques such as chiaroscuro and sfumato have advanced is consistent with historical circumstances. PMID:25501877

  5. Quantitative genetic analysis of injury liability in infants and toddlers

    SciTech Connect

    Phillips, K.; Matheny, A.P. Jr.

    1995-02-27

    A threshold model of latent liability was applied to infant and toddler twin data on total count of injuries sustained during the interval from birth to 36 months of age. A quantitative genetic analysis of estimated twin correlations in injury liability indicated strong genetic dominance effects, but no additive genetic variance was detected. Because interpretations involving overdominance have little research support, the results may be due to low order epistasis or other interaction effects. Boys had more injuries than girls, but this effect was found only for groups whose parents were prompted and questioned in detail about their children`s injuries. Activity and impulsivity are two behavioral predictors of childhood injury, and the results are discussed in relation to animal research on infant and adult activity levels, and impulsivity in adult humans. Genetic epidemiological approaches to childhood injury should aid in targeting higher risk children for preventive intervention. 30 refs., 4 figs., 3 tabs.

  6. Quantitative multielement analysis using high energy particle bombardment

    NASA Technical Reports Server (NTRS)

    Clark, P. J.; Neal, G. F.; Allen, R. O.

    1975-01-01

    Charged particles ranging in energy from 0.8 to 4.0 MeV are used to induce resonant nuclear reactions, Coulomb excitation (gamma-rays), and X-ray emission in both thick and thin targets. Quantitative analysis is possible for elements from Li to Pb in complex environmental samples, although the matrix can severely reduce the sensitivity. It is necessary to use a comparator technique for the gamma-rays while for X-rays an internal standard can be used. A USGS standard rock is analyzed for a total of 28 elements. Water samples can be analyzed either by nebulizing the sample doped with Cs or Y a thin Formvar film or by extracting the sample onto ion exchange resin which is pressed into a pellet.

  7. Large-Scale Quantitative Analysis of Painting Arts

    NASA Astrophysics Data System (ADS)

    Kim, Daniel; Son, Seung-Woo; Jeong, Hawoong

    2014-12-01

    Scientists have made efforts to understand the beauty of painting art in their own languages. As digital image acquisition of painting arts has made rapid progress, researchers have come to a point where it is possible to perform statistical analysis of a large-scale database of artistic paints to make a bridge between art and science. Using digital image processing techniques, we investigate three quantitative measures of images - the usage of individual colors, the variety of colors, and the roughness of the brightness. We found a difference in color usage between classical paintings and photographs, and a significantly low color variety of the medieval period. Interestingly, moreover, the increment of roughness exponent as painting techniques such as chiaroscuro and sfumato have advanced is consistent with historical circumstances.

  8. Quantitative image analysis of WE43-T6 cracking behavior

    NASA Astrophysics Data System (ADS)

    Ahmad, A.; Yahya, Z.

    2013-06-01

    Environment-assisted cracking of WE43 cast magnesium (4.2 wt.% Yt, 2.3 wt.% Nd, 0.7% Zr, 0.8% HRE) in the T6 peak-aged condition was induced in ambient air in notched specimens. The mechanism of fracture was studied using electron backscatter diffraction, serial sectioning and in situ observations of crack propagation. The intermetallic (rare earthed-enriched divorced intermetallic retained at grain boundaries and predominantly at triple points) material was found to play a significant role in initiating cracks which leads to failure of this material. Quantitative measurements were required for this project. The populations of the intermetallic and clusters of intermetallic particles were analyzed using image analysis of metallographic images. This is part of the work to generate a theoretical model of the effect of notch geometry on the static fatigue strength of this material.

  9. Quantitative analysis of gallstones using laser-induced breakdown spectroscopy

    SciTech Connect

    Singh, Vivek K.; Singh, Vinita; Rai, Awadhesh K.; Thakur, Surya N.; Rai, Pradeep K.; Singh, Jagdish P

    2008-11-01

    The utility of laser-induced breakdown spectroscopy (LIBS) for categorizing different types of gallbladder stone has been demonstrated by analyzing their major and minor constituents. LIBS spectra of three types of gallstone have been recorded in the 200-900 nm spectral region. Calcium is found to be the major element in all types of gallbladder stone. The spectrophotometric method has been used to classify the stones. A calibration-free LIBS method has been used for the quantitative analysis of metal elements, and the results have been compared with those obtained from inductively coupled plasma atomic emission spectroscopy (ICP-AES) measurements. The single-shot LIBS spectra from different points on the cross section (in steps of 0.5 mm from one end to the other) of gallstones have also been recorded to study the variation of constituents from the center to the surface. The presence of different metal elements and their possible role in gallstone formation is discussed.

  10. Automatic analysis of quantitative NMR data of pharmaceutical compound libraries.

    PubMed

    Liu, Xuejun; Kolpak, Michael X; Wu, Jiejun; Leo, Gregory C

    2012-08-07

    In drug discovery, chemical library compounds are usually dissolved in DMSO at a certain concentration and then distributed to biologists for target screening. Quantitative (1)H NMR (qNMR) is the preferred method for the determination of the actual concentrations of compounds because the relative single proton peak areas of two chemical species represent the relative molar concentrations of the two compounds, that is, the compound of interest and a calibrant. Thus, an analyte concentration can be determined using a calibration compound at a known concentration. One particularly time-consuming step in the qNMR analysis of compound libraries is the manual integration of peaks. In this report is presented an automated method for performing this task without prior knowledge of compound structures and by using an external calibration spectrum. The script for automated integration is fast and adaptable to large-scale data sets, eliminating the need for manual integration in ~80% of the cases.

  11. Quantitative analysis of forest island pattern in selected Ohio landscapes

    SciTech Connect

    Bowen, G.W.; Burgess, R.L.

    1981-07-01

    The purpose of this study was to quantitatively describe the various aspects of regional distribution patterns of forest islands and relate those patterns to other landscape features. Several maps showing the forest cover of various counties in Ohio were selected as representative examples of forest patterns to be quantified. Ten thousand hectare study areas (landscapes) were delineated on each map. A total of 15 landscapes representing a wide variety of forest island patterns was chosen. Data were converted into a series of continuous variables which contained information pertinent to the sizes, shape, numbers, and spacing of woodlots within a landscape. The continuous variables were used in a factor analysis to describe the variation among landscapes in terms of forest island pattern. The results showed that forest island patterns are related to topography and other environmental features correlated with topography.

  12. Quantitative microstructure analysis of polymer-modified mortars.

    PubMed

    Jenni, A; Herwegh, M; Zurbriggen, R; Aberle, T; Holzer, L

    2003-11-01

    Digital light, fluorescence and electron microscopy in combination with wavelength-dispersive spectroscopy were used to visualize individual polymers, air voids, cement phases and filler minerals in a polymer-modified cementitious tile adhesive. In order to investigate the evolution and processes involved in formation of the mortar microstructure, quantifications of the phase distribution in the mortar were performed including phase-specific imaging and digital image analysis. The required sample preparation techniques and imaging related topics are discussed. As a form of case study, the different techniques were applied to obtain a quantitative characterization of a specific mortar mixture. The results indicate that the mortar fractionates during different stages ranging from the early fresh mortar until the final hardened mortar stage. This induces process-dependent enrichments of the phases at specific locations in the mortar. The approach presented provides important information for a comprehensive understanding of the functionality of polymer-modified mortars.

  13. Quantitative analysis of protein-ligand interactions by NMR.

    PubMed

    Furukawa, Ayako; Konuma, Tsuyoshi; Yanaka, Saeko; Sugase, Kenji

    2016-08-01

    Protein-ligand interactions have been commonly studied through static structures of the protein-ligand complex. Recently, however, there has been increasing interest in investigating the dynamics of protein-ligand interactions both for fundamental understanding of the underlying mechanisms and for drug development. NMR is a versatile and powerful tool, especially because it provides site-specific quantitative information. NMR has widely been used to determine the dissociation constant (KD), in particular, for relatively weak interactions. The simplest NMR method is a chemical-shift titration experiment, in which the chemical-shift changes of a protein in response to ligand titration are measured. There are other quantitative NMR methods, but they mostly apply only to interactions in the fast-exchange regime. These methods derive the dissociation constant from population-averaged NMR quantities of the free and bound states of a protein or ligand. In contrast, the recent advent of new relaxation-based experiments, including R2 relaxation dispersion and ZZ-exchange, has enabled us to obtain kinetic information on protein-ligand interactions in the intermediate- and slow-exchange regimes. Based on R2 dispersion or ZZ-exchange, methods that can determine the association rate, kon, dissociation rate, koff, and KD have been developed. In these approaches, R2 dispersion or ZZ-exchange curves are measured for multiple samples with different protein and/or ligand concentration ratios, and the relaxation data are fitted to theoretical kinetic models. It is critical to choose an appropriate kinetic model, such as the two- or three-state exchange model, to derive the correct kinetic information. The R2 dispersion and ZZ-exchange methods are suitable for the analysis of protein-ligand interactions with a micromolar or sub-micromolar dissociation constant but not for very weak interactions, which are typical in very fast exchange. This contrasts with the NMR methods that are used

  14. Laser-dephosphorylation of phosphogelatin and its indirect quantitative analysis using FT-IR

    NASA Astrophysics Data System (ADS)

    Ishii, Katsunori; Ninomiya, Yoshihisa; Takegoshi, Minori; Kushibiki, Toshihiro; Yoshihashi-Suzuki, Sachiko; Yamamoto, Masaya; Tabata, Yasuhiko; Awazu, Kunio

    2006-02-01

    Phosphorylation and dephosphorylation are considered to be important reactions that control the active and inactive factors of proteins. In regenerative medicine of the osteoconnective tissue (a tendon, a ligament), it has been reported that the biomaterial possessing phosphate groups promote formation of HAP, the main component of hard tissues. The noncontact measurement of phosphate groups and low-destructive controlling of phosphate groups allow for the accurate regeneration of the osteoconnective tissue, and the validation. Our objective is to propose the nondestructive controlling and measuring method of phosphorylation for regenerative medicine. In this study, as the indirect quantitative analysis of phosphate groups, we examine the correlation between the mid-infrared absorbance ratio and the ratio of phosphate groups introduction theoretically calculated from a colorimetric determination method. And the noncontact controlling method of the quantities of phosphate groups, we examine the selective and low-destructive bond cutting of phosphate groups in the phosphogelatin using a mid-infrared laser.

  15. Visualization of moving fluid: quantitative analysis of blood flow velocity using MR imaging.

    PubMed

    Shimizu, K; Matsuda, T; Sakurai, T; Fujita, A; Ohara, H; Okamura, S; Hashimoto, S; Mano, H; Kawai, C; Kiri, M

    1986-04-01

    A new method for the measurement of blood flow using magnetic resonance imaging has been developed. The flow velocities are calculated from the distances that the fluid has moved. The distances are directly visualized by a new pulse sequence. In a phantom study, the measured flow rates showed very good correlation with actual flow rates of up to 20 l/min (3 m/sec). In a volunteer study, pulsatile flow velocities of a large artery were measured with electrocardiographic gating. The flow pattern of a cardiac cycle at the abdominal aorta is similar to that revealed by other methods of measurement, such as Doppler ultrasound. This method allows reasonably accurate quantitative analysis of blood flow in the large arteries.

  16. The utility of accurate mass and LC elution time information in the analysis of complex proteomes

    PubMed Central

    Norbeck, Angela D.; Monroe, Matthew E.; Adkins, Joshua N.; Smith, Richard D.

    2007-01-01

    Theoretical tryptic digests of all predicted proteins from the genomes of three organisms of varying complexity were evaluated for specificity and possible utility of combined peptide accurate mass and predicted LC normalized elution time (NET) information. The uniqueness of each peptide was evaluated using its combined mass (+/− 5 ppm and 1 ppm) and NET value (no constraint, +/− 0.05 and 0.01 on a 0–1 NET scale). The set of peptides both underestimates actual biological complexity due to the lack of specific modifications, and overestimates the expected complexity since many proteins will not be present in the sample or observable on the mass spectrometer because of dynamic range limitations. Once a peptide is identified from an LC-MS/MS experiment, its mass and elution time is representative of a unique fingerprint for that peptide. The uniqueness of that fingerprint in comparison to that for the other peptides present is indicative of the ability to confidently identify that peptide based on accurate mass and NET measurements. These measurements can be made using HPLC coupled with high resolution MS in a high-throughput manner. Results show that for organisms with comparatively small proteomes, such as Deinococcus radiodurans, modest mass and elution time accuracies are generally adequate for peptide identifications. For more complex proteomes, increasingly accurate measurements are required. However, the majority of proteins should be uniquely identifiable by using LC-MS with mass accuracies within +/− 1 ppm and elution time measurements within +/− 0.01 NET. PMID:15979333

  17. QTL analysis for some quantitative traits in bread wheat*

    PubMed Central

    Pushpendra, Kumar Gupta; Harindra, Singh Balyan; Pawan, Laxminarayan Kulwal; Neeraj, Kumar; Ajay, Kumar; Reyazul, Rouf Mir; Amita, Mohan; Jitendra, Kumar

    2007-01-01

    Quantitative trait loci (QTL) analysis was conducted in bread wheat for 14 important traits utilizing data from four different mapping populations involving different approaches of QTL analysis. Analysis for grain protein content (GPC) suggested that the major part of genetic variation for this trait is due to environmental interactions. In contrast, pre-harvest sprouting tolerance (PHST) was controlled mainly by main effect QTL (M-QTL) with very little genetic variation due to environmental interactions; a major QTL for PHST was detected on chromosome arm 3AL. For grain weight, one QTL each was detected on chromosome arms 1AS, 2BS and 7AS. QTL for 4 growth related traits taken together detected by different methods ranged from 37 to 40; nine QTL that were detected by single-locus as well as two-locus analyses were all M-QTL. Similarly, single-locus and two-locus QTL analyses for seven yield and yield contributing traits in two populations respectively allowed detection of 25 and 50 QTL by composite interval mapping (CIM), 16 and 25 QTL by multiple-trait composite interval mapping (MCIM) and 38 and 37 QTL by two-locus analyses. These studies should prove useful in QTL cloning and wheat improvement through marker aided selection. PMID:17973342

  18. A Quantitative Analysis of the Solar Composition Problem

    NASA Astrophysics Data System (ADS)

    Villante, F. L.; Serenelli, A. M.

    We perform a quantitative analysis of the solar composition problem by using a statistical approach that allows us to combine the information provided by helioseismic and solar neutrino data in an effective way. We show that the opacity profile of the Sun is well constrained by the solar observational properties. In the context of a two parameter analysis in which elements are grouped as volatiles (i.e. C, N, O and Ne) and refractories (i.e. Mg, Si, S, Fe), the optimal surface composition is found by increasing the abundance of volatiles by (45 ± 4) % and that of refractories by (19 ± 3) % with respect to the values provided by Asplund et al., 2009. As an additional result of our analysis, we show that the best fit to the observational data is obtained with values of input parameters of the standard solar models (radiative opacities, gravitational settling rate, the astrophysical factors S 34 and S 17) that differ at the ∼ 1σ level from those presently adopted.

  19. A new method for quantitative real-time polymerase chain reaction data analysis.

    PubMed

    Rao, Xiayu; Lai, Dejian; Huang, Xuelin

    2013-09-01

    Quantitative real-time polymerase chain reaction (qPCR) is a sensitive gene quantification method that has been extensively used in biological and biomedical fields. The currently used methods for PCR data analysis, including the threshold cycle method and linear and nonlinear model-fitting methods, all require subtracting background fluorescence. However, the removal of background fluorescence can hardly be accurate and therefore can distort results. We propose a new method, the taking-difference linear regression method, to overcome this limitation. Briefly, for each two consecutive PCR cycles, we subtract the fluorescence in the former cycle from that in the latter cycle, transforming the n cycle raw data into n-1 cycle data. Then, linear regression is applied to the natural logarithm of the transformed data. Finally, PCR amplification efficiencies and the initial DNA molecular numbers are calculated for each reaction. This taking-difference method avoids the error in subtracting an unknown background, and thus it is more accurate and reliable. This method is easy to perform, and this strategy can be extended to all current methods for PCR data analysis.

  20. 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).

  1. An approach for quantitative image quality analysis for CT

    NASA Astrophysics Data System (ADS)

    Rahimi, Amir; Cochran, Joe; Mooney, Doug; Regensburger, Joe

    2016-03-01

    An objective and standardized approach to assess image quality of Compute Tomography (CT) systems is required in a wide variety of imaging processes to identify CT systems appropriate for a given application. We present an overview of the framework we have developed to help standardize and to objectively assess CT image quality for different models of CT scanners used for security applications. Within this framework, we have developed methods to quantitatively measure metrics that should correlate with feature identification, detection accuracy and precision, and image registration capabilities of CT machines and to identify strengths and weaknesses in different CT imaging technologies in transportation security. To that end we have designed, developed and constructed phantoms that allow for systematic and repeatable measurements of roughly 88 image quality metrics, representing modulation transfer function, noise equivalent quanta, noise power spectra, slice sensitivity profiles, streak artifacts, CT number uniformity, CT number consistency, object length accuracy, CT number path length consistency, and object registration. Furthermore, we have developed a sophisticated MATLAB based image analysis tool kit to analyze CT generated images of phantoms and report these metrics in a format that is standardized across the considered models of CT scanners, allowing for comparative image quality analysis within a CT model or between different CT models. In addition, we have developed a modified sparse principal component analysis (SPCA) method to generate a modified set of PCA components as compared to the standard principal component analysis (PCA) with sparse loadings in conjunction with Hotelling T2 statistical analysis method to compare, qualify, and detect faults in the tested systems.

  2. Time-Accurate Simulations and Acoustic Analysis of Slat Free-Shear-Layer. Part 2

    NASA Technical Reports Server (NTRS)

    Khorrami, Mehdi R.; Singer, Bart A.; Lockard, David P.

    2002-01-01

    Unsteady computational simulations of a multi-element, high-lift configuration are performed. Emphasis is placed on accurate spatiotemporal resolution of the free shear layer in the slat-cove region. The excessive dissipative effects of the turbulence model, so prevalent in previous simulations, are circumvented by switching off the turbulence-production term in the slat cove region. The justifications and physical arguments for taking such a step are explained in detail. The removal of this excess damping allows the shear layer to amplify large-scale structures, to achieve a proper non-linear saturation state, and to permit vortex merging. The large-scale disturbances are self-excited, and unlike our prior fully turbulent simulations, no external forcing of the shear layer is required. To obtain the farfield acoustics, the Ffowcs Williams and Hawkings equation is evaluated numerically using the simulated time-accurate flow data. The present comparison between the computed and measured farfield acoustic spectra shows much better agreement for the amplitude and frequency content than past calculations. The effect of the angle-of-attack on the slat's flow features radiated acoustic field are also simulated presented.

  3. Analysis of hydraulic fracturing flowback and produced waters using accurate mass: identification of ethoxylated surfactants.

    PubMed

    Thurman, E Michael; Ferrer, Imma; Blotevogel, Jens; Borch, Thomas

    2014-10-07

    Two series of ethylene oxide (EO) surfactants, polyethylene glycols (PEGs from EO3 to EO33) and linear alkyl ethoxylates (LAEs C-9 to C-15 with EO3-EO28), were identified in hydraulic fracturing flowback and produced water using a new application of the Kendrick mass defect and liquid chromatography/quadrupole-time-of-flight mass spectrometry. The Kendrick mass defect differentiates the proton, ammonium, and sodium adducts in both singly and doubly charged forms. A structural model of adduct formation is presented, and binding constants are calculated, which is based on a spherical cagelike conformation, where the central cation (NH4(+) or Na(+)) is coordinated with ether oxygens. A major purpose of the study was the identification of the ethylene oxide (EO) surfactants and the construction of a database with accurate masses and retention times in order to unravel the mass spectral complexity of surfactant mixtures used in hydraulic fracturing fluids. For example, over 500 accurate mass assignments are made in a few seconds of computer time, which then is used as a fingerprint chromatogram of the water samples. This technique is applied to a series of flowback and produced water samples to illustrate the usefulness of ethoxylate "fingerprinting", in a first application to monitor water quality that results from fluids used in hydraulic fracturing.

  4. The workflow for quantitative proteome analysis of chloroplast development and differentiation, chloroplast mutants, and protein interactions by spectral counting.

    PubMed

    Friso, Giulia; Olinares, Paul Dominic B; van Wijk, Klaas J

    2011-01-01

    This chapter outlines a quantitative proteomics workflow using a label-free spectral counting technique. The workflow has been tested on different aspects of chloroplast biology in maize and Arabidopsis, including chloroplast mutant analysis, cell-type specific chloroplast differentiation, and the proplastid-to-chloroplast transition. The workflow involves one-dimensional SDS-PAGE of the proteomes of leaves or chloroplast subfractions, tryptic digestions, online LC-MS/MS using a mass spectrometer with high mass accuracy and duty cycle, followed by semiautomatic data processing. The bioinformatics analysis can effectively select best gene models and deals with quantification of closely related proteins; the workflow avoids overidentification of proteins and results in more accurate protein quantification. The final output includes pairwise comparative quantitative analysis, as well as hierarchical clustering for discovery of temporal and spatial patterns of protein accumulation. A brief discussion about potential pitfalls, as well as the advantages and disadvantages of spectral counting, is provided.

  5. Quantitative analysis of drug-induced tremor in mice.

    PubMed

    Shinozaki, H

    1984-12-01

    A method of analyzing tremor in mice was developed using a power spectral analysis of the random current induced by the movement of a magnet attached to a mouse, on a wire coil. The power spectral density function defined the frequency composition of the tremor, and the mean square value of the data in any frequency range of concern was determined. It was possible to determine qualitative differences in the tremor caused by various tremorgenic agents, and to differentiate the drug-induced tremor from spontaneous motor activity. The power spectral densities of the tremorine- and oxotremorine-induced tremors were tentatively expressed as the sum of 3 main components (Cauchy distribution) with different peak frequencies, consisting of the spontaneous motor activity component and two tremor components. On the other hand, the power spectral densities of the harmaline-induced tremor were expressed as the sum of two components with two peak frequencies, and the plots of the power spectral densities versus frequency, consisting of the spontaneous motor activity component and a tremor component. The frequency of the peak spectral density was almost independent of the dose of tremorgenic agents, but changed slightly with the lapse of time after their injection. The severity of the tremor was determined quantitatively in terms of the sum of the mean square value. The sum of the mean square value for a period of 45 min after the injection of tremorine, changed in a dose-dependent manner. The severity of the tremor was different for each of the mouse strains. The method studied in the present paper is expected to be utilized for the quantitative examination of the fine motor movement of the experimental animal, particularly, for the screening test of new anti-tremor drugs.

  6. Quantitative DNA Methylation Analysis of Candidate Genes in Cervical Cancer

    PubMed Central

    Siegel, Erin M.; Riggs, Bridget M.; Delmas, Amber L.; Koch, Abby; Hakam, Ardeshir; Brown, Kevin D.

    2015-01-01

    Aberrant DNA methylation has been observed in cervical cancer; however, most studies have used non-quantitative approaches to measure DNA methylation. The objective of this study was to quantify methylation within a select panel of genes previously identified as targets for epigenetic silencing in cervical cancer and to identify genes with elevated methylation that can distinguish cancer from normal cervical tissues. We identified 49 women with invasive squamous cell cancer of the cervix and 22 women with normal cytology specimens. Bisulfite-modified genomic DNA was amplified and quantitative pyrosequencing completed for 10 genes (APC, CCNA, CDH1, CDH13, WIF1, TIMP3, DAPK1, RARB, FHIT, and SLIT2). A Methylation Index was calculated as the mean percent methylation across all CpG sites analyzed per gene (~4-9 CpG site) per sequence. A binary cut-point was defined at >15% methylation. Sensitivity, specificity and area under ROC curve (AUC) of methylation in individual genes or a panel was examined. The median methylation index was significantly higher in cases compared to controls in 8 genes, whereas there was no difference in median methylation for 2 genes. Compared to HPV and age, the combination of DNA methylation level of DAPK1, SLIT2, WIF1 and RARB with HPV and age significantly improved the AUC from 0.79 to 0.99 (95% CI: 0.97–1.00, p-value = 0.003). Pyrosequencing analysis confirmed that several genes are common targets for aberrant methylation in cervical cancer and DNA methylation level of four genes appears to increase specificity to identify cancer compared to HPV detection alone. Alterations in DNA methylation of specific genes in cervical cancers, such as DAPK1, RARB, WIF1, and SLIT2, may also occur early in cervical carcinogenesis and should be evaluated. PMID:25826459

  7. Quantitative Analysis Of Acoustic Emission From Rock Fracture Experiments

    NASA Astrophysics Data System (ADS)

    Goodfellow, Sebastian David

    This thesis aims to advance the methods of quantitative acoustic emission (AE) analysis by calibrating sensors, characterizing sources, and applying the results to solve engi- neering problems. In the first part of this thesis, we built a calibration apparatus and successfully calibrated two commercial AE sensors. The ErgoTech sensor was found to have broadband velocity sensitivity and the Panametrics V103 was sensitive to surface normal displacement. These calibration results were applied to two AE data sets from rock fracture experiments in order to characterize the sources of AE events. The first data set was from an in situ rock fracture experiment conducted at the Underground Research Laboratory (URL). The Mine-By experiment was a large scale excavation response test where both AE (10 kHz - 1 MHz) and microseismicity (MS) (1 Hz - 10 kHz) were monitored. Using the calibration information, magnitude, stress drop, dimension and energy were successfully estimated for 21 AE events recorded in the tensile region of the tunnel wall. Magnitudes were in the range -7.5 < Mw < -6.8, which is consistent with other laboratory AE results, and stress drops were within the range commonly observed for induced seismicity in the field (0.1 - 10 MPa). The second data set was AE collected during a true-triaxial deformation experiment, where the objectives were to characterize laboratory AE sources and identify issues related to moving the analysis from ideal in situ conditions to more complex laboratory conditions in terms of the ability to conduct quantitative AE analysis. We found AE magnitudes in the range -7.8 < Mw < -6.7 and as with the in situ data, stress release was within the expected range of 0.1 - 10 MPa. We identified four major challenges to quantitative analysis in the laboratory, which in- hibited our ability to study parameter scaling (M0 ∝ fc -3 scaling). These challenges were 0c (1) limited knowledge of attenuation which we proved was continuously evolving, (2

  8. Quantitative assessment of human body shape using Fourier analysis

    NASA Astrophysics Data System (ADS)

    Friess, Martin; Rohlf, F. J.; Hsiao, Hongwei

    2004-04-01

    Fall protection harnesses are commonly used to reduce the number and severity of injuries. Increasing the efficiency of harness design requires the size and shape variation of the user population to be assessed as detailed and as accurately as possible. In light of the unsatisfactory performance of traditional anthropometry with respect to such assessments, we propose the use of 3D laser surface scans of whole bodies and the statistical analysis of elliptic Fourier coefficients. Ninety-eight male and female adults were scanned. Key features of each torso were extracted as a 3D curve along front, back and the thighs. A 3D extension of Elliptic Fourier analysis4 was used to quantify their shape through multivariate statistics. Shape change as a function of size (allometry) was predicted by regressing the coefficients onto stature, weight and hip circumference. Upper and lower limits of torso shape variation were determined and can be used to redefine the design of the harness that will fit most individual body shapes. Observed allometric changes are used for adjustments to the harness shape in each size. Finally, the estimated outline data were used as templates for a free-form deformation of the complete torso surface using NURBS models (non-uniform rational B-splines).

  9. Quantitative Phosphoproteomics Analysis of ERBB3/ERBB4 Signaling

    PubMed Central

    Jacobs, Kris; Klammer, Martin; Jordan, Nicole; Elschenbroich, Sarah; Parade, Marc; Jacoby, Edgar; Linders, Joannes T. M.; Brehmer, Dirk; Cools, Jan; Daub, Henrik

    2016-01-01

    The four members of the epidermal growth factor receptor (EGFR/ERBB) family form homo- and heterodimers which mediate ligand-specific regulation of many key cellular processes in normal and cancer tissues. While signaling through the EGFR has been extensively studied on the molecular level, signal transduction through ERBB3/ERBB4 heterodimers is less well understood. Here, we generated isogenic mouse Ba/F3 cells that express full-length and functional membrane-integrated ERBB3 and ERBB4 or ERBB4 alone, to serve as a defined cellular model for biological and phosphoproteomics analysis of ERBB3/ERBB4 signaling. ERBB3 co-expression significantly enhanced Ba/F3 cell proliferation upon neuregulin-1 (NRG1) treatment. For comprehensive signaling studies we performed quantitative mass spectrometry (MS) experiments to compare the basal ERBB3/ERBB4 cell phosphoproteome to NRG1 treatment of ERBB3/ERBB4 and ERBB4 cells. We employed a workflow comprising differential isotope labeling with mTRAQ reagents followed by chromatographic peptide separation and final phosphopeptide enrichment prior to MS analysis. Overall, we identified 9686 phosphorylation sites which could be confidently localized to specific residues. Statistical analysis of three replicate experiments revealed 492 phosphorylation sites which were significantly changed in NRG1-treated ERBB3/ERBB4 cells. Bioinformatics data analysis recapitulated regulation of mitogen-activated protein kinase and Akt pathways, but also indicated signaling links to cytoskeletal functions and nuclear biology. Comparative assessment of NRG1-stimulated ERBB4 Ba/F3 cells revealed that ERBB3 did not trigger defined signaling pathways but more broadly enhanced phosphoproteome regulation in cells expressing both receptors. In conclusion, our data provide the first global picture of ERBB3/ERBB4 signaling and provide numerous potential starting points for further mechanistic studies. PMID:26745281

  10. 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.

  11. Quantitative evaluation of midpalatal suture maturation via fractal analysis

    PubMed Central

    Kwak, Kyoung Ho; Kim, Yong-Il; Kim, Yong-Deok

    2016-01-01

    Objective The purpose of this study was to determine whether the results of fractal analysis can be used as criteria for midpalatal suture maturation evaluation. Methods The study included 131 subjects aged over 18 years of age (range 18.1–53.4 years) who underwent cone-beam computed tomography. Skeletonized images of the midpalatal suture were obtained via image processing software and used to calculate fractal dimensions. Correlations between maturation stage and fractal dimensions were calculated using Spearman's correlation coefficient. Optimal fractal dimension cut-off values were determined using a receiver operating characteristic curve. Results The distribution of maturation stages of the midpalatal suture according to the cervical vertebrae maturation index was highly variable, and there was a strong negative correlation between maturation stage and fractal dimension (−0.623, p < 0.001). Fractal dimension was a statistically significant indicator of dichotomous results with regard to maturation stage (area under curve = 0.794, p < 0.001). A test in which fractal dimension was used to predict the resulting variable that splits maturation stages into ABC and D or E yielded an optimal fractal dimension cut-off value of 1.0235. Conclusions There was a strong negative correlation between fractal dimension and midpalatal suture maturation. Fractal analysis is an objective quantitative method, and therefore we suggest that it may be useful for the evaluation of midpalatal suture maturation. PMID:27668195

  12. A quantitative risk analysis approach to port hydrocarbon logistics.

    PubMed

    Ronza, A; Carol, S; Espejo, V; Vílchez, J A; Arnaldos, J

    2006-01-16

    A method is presented that allows quantitative risk analysis to be performed on marine hydrocarbon terminals sited in ports. A significant gap was identified in the technical literature on QRA for the handling of hazardous materials in harbours published prior to this work. The analysis is extended to tanker navigation through port waters and loading and unloading facilities. The steps of the method are discussed, beginning with data collecting. As to accident scenario identification, an approach is proposed that takes into account minor and massive spills due to loading arm failures and tank rupture. Frequency estimation is thoroughly reviewed and a shortcut approach is proposed for frequency calculation. This allows for the two-fold possibility of a tanker colliding/grounding at/near the berth or while navigating to/from the berth. A number of probability data defining the possibility of a cargo spill after an external impact on a tanker are discussed. As to consequence and vulnerability estimates, a scheme is proposed for the use of ratios between the numbers of fatal victims, injured and evacuated people. Finally, an example application is given, based on a pilot study conducted in the Port of Barcelona, where the method was tested.

  13. Inside Single Cells: Quantitative Analysis with Advanced Optics and Nanomaterials

    PubMed Central

    Cui, Yi; Irudayaraj, Joseph

    2014-01-01

    Single cell explorations offer a unique window to inspect molecules and events relevant to mechanisms and heterogeneity constituting the central dogma of biology. A large number of nucleic acids, proteins, metabolites and small molecules are involved in determining and fine-tuning the state and function of a single cell at a given time point. Advanced optical platforms and nanotools provide tremendous opportunities to probe intracellular components with single-molecule accuracy, as well as promising tools to adjust single cell activity. In order to obtain quantitative information (e.g. molecular quantity, kinetics and stoichiometry) within an intact cell, achieving the observation with comparable spatiotemporal resolution is a challenge. For single cell studies both the method of detection and the biocompatibility are critical factors as they determine the feasibility, especially when considering live cell analysis. Although a considerable proportion of single cell methodologies depend on specialized expertise and expensive instruments, it is our expectation that the information content and implication will outweigh the costs given the impact on life science enabled by single cell analysis. PMID:25430077

  14. Therapeutic electrical stimulation for spasticity: quantitative gait analysis.

    PubMed

    Pease, W S

    1998-01-01

    Improvement in motor function following electrical stimulation is related to strengthening of the stimulated spastic muscle and inhibition of the antagonist. A 26-year-old man with familial spastic paraparesis presented with gait dysfunction and bilateral lower limb spastic muscle tone. Clinically, muscle strength and sensation were normal. He was considered appropriate for a trial of therapeutic electrical stimulation following failed trials of physical therapy and baclofen. No other treatment was used concurrent with the electrical stimulation. Before treatment, quantitative gait analysis revealed 63% of normal velocity and a crouched gait pattern, associated with excessive electromyographic activity in the hamstrings and gastrocnemius muscles. Based on these findings, bilateral stimulation of the quadriceps and anterior compartment musculature was performed two to three times per week for three months. Repeat gait analysis was conducted three weeks after the cessation of stimulation treatment. A 27% increase in velocity was noted associated with an increase in both cadence and right step length. Right hip and bilateral knee stance motion returned to normal (rather than "crouched"). No change in the timing of dynamic electromyographic activity was seen. These findings suggest a role for the use of electrical stimulation for rehabilitation of spasticity. The specific mechanism of this improvement remains uncertain.

  15. Comprehensive Quantitative Analysis of Ovarian and Breast Cancer Tumor Peptidomes

    SciTech Connect

    Xu, Zhe; Wu, Chaochao; Xie, Fang; Slysz, Gordon W.; Tolic, Nikola; Monroe, Matthew E.; Petyuk, Vladislav A.; Payne, Samuel H.; Fujimoto, Grant M.; Moore, Ronald J.; Fillmore, Thomas L.; Schepmoes, Athena A.; Levine, Douglas; Townsend, Reid; Davies, Sherri; Li, Shunqiang; Ellis, Matthew; Boja, Emily; Rivers, Robert; Rodriguez, Henry; Rodland, Karin D.; Liu, Tao; Smith, Richard D.

    2015-01-02

    Aberrant degradation of proteins is associated with many pathological states, including cancers. Mass spectrometric analysis of tumor peptidomes, the intracellular and intercellular products of protein degradation, has the potential to provide biological insights on proteolytic processing in cancer. However, attempts to use the information on these smaller protein degradation products from tumors for biomarker discovery and cancer biology studies have been fairly limited to date, largely due to the lack of effective approaches for robust peptidomics identification and quantification, and the prevalence of confounding factors and biases associated with sample handling and processing. Herein, we have developed an effective and robust analytical platform for comprehensive analyses of tissue peptidomes, which is suitable for high throughput quantitative studies. The reproducibility and coverage of the platform, as well as the suitability of clinical ovarian tumor and patient-derived breast tumor xenograft samples with post-excision delay of up to 60 min before freezing for peptidomics analysis, have been demonstrated. Moreover, our data also show that the peptidomics profiles can effectively separate breast cancer subtypes, reflecting tumor-associated protease activities. Peptidomics complements results obtainable from conventional bottom-up proteomics, and provides insights not readily obtainable from such approaches.

  16. A Computational Tool for Quantitative Analysis of Vascular Networks

    PubMed Central

    Zudaire, Enrique; Gambardella, Laure; Kurcz, Christopher; Vermeren, Sonja

    2011-01-01

    Angiogenesis is the generation of mature vascular networks from pre-existing vessels. Angiogenesis is crucial during the organism' development, for wound healing and for the female reproductive cycle. Several murine experimental systems are well suited for studying developmental and pathological angiogenesis. They include the embryonic hindbrain, the post-natal retina and allantois explants. In these systems vascular networks are visualised by appropriate staining procedures followed by microscopical analysis. Nevertheless, quantitative assessment of angiogenesis is hampered by the lack of readily available, standardized metrics and software analysis tools. Non-automated protocols are being used widely and they are, in general, time - and labour intensive, prone to human error and do not permit computation of complex spatial metrics. We have developed a light-weight, user friendly software, AngioTool, which allows for quick, hands-off and reproducible quantification of vascular networks in microscopic images. AngioTool computes several morphological and spatial parameters including the area covered by a vascular network, the number of vessels, vessel length, vascular density and lacunarity. In addition, AngioTool calculates the so-called “branching index” (branch points / unit area), providing a measurement of the sprouting activity of a specimen of interest. We have validated AngioTool using images of embryonic murine hindbrains, post-natal retinas and allantois explants. AngioTool is open source and can be downloaded free of charge. PMID:22110636

  17. Quantitative analysis of triple-mutant genetic interactions.

    PubMed

    Braberg, Hannes; Alexander, Richard; Shales, Michael; Xu, Jiewei; Franks-Skiba, Kathleen E; Wu, Qiuqin; Haber, James E; Krogan, Nevan J

    2014-08-01

    The quantitative analysis of genetic interactions between pairs of gene mutations has proven to be effective for characterizing cellular functions, but it can miss important interactions for functionally redundant genes. To address this limitation, we have developed an approach termed triple-mutant analysis (TMA). The procedure relies on a query strain that contains two deletions in a pair of redundant or otherwise related genes, which is crossed against a panel of candidate deletion strains to isolate triple mutants and measure their growth. A central feature of TMA is to interrogate mutants that are synthetically sick when two other genes are deleted but interact minimally with either single deletion. This approach has been valuable for discovering genes that restore critical functions when the principal actors are deleted. TMA has also uncovered double-mutant combinations that produce severe defects because a third protein becomes deregulated and acts in a deleterious fashion, and it has revealed functional differences between proteins presumed to act together. The protocol is optimized for Singer ROTOR pinning robots, takes 3 weeks to complete and measures interactions for up to 30 double mutants against a library of 1,536 single mutants.

  18. Colocalization analysis in fluorescence micrographs: verification of a more accurate calculation of pearson's correlation coefficient.

    PubMed

    Barlow, Andrew L; Macleod, Alasdair; Noppen, Samuel; Sanderson, Jeremy; Guérin, Christopher J

    2010-12-01

    One of the most routine uses of fluorescence microscopy is colocalization, i.e., the demonstration of a relationship between pairs of biological molecules. Frequently this is presented simplistically by the use of overlays of red and green images, with areas of yellow indicating colocalization of the molecules. Colocalization data are rarely quantified and can be misleading. Our results from both synthetic and biological datasets demonstrate that the generation of Pearson's correlation coefficient between pairs of images can overestimate positive correlation and fail to demonstrate negative correlation. We have demonstrated that the calculation of a thresholded Pearson's correlation coefficient using only intensity values over a determined threshold in both channels produces numerical values that more accurately describe both synthetic datasets and biological examples. Its use will bring clarity and accuracy to colocalization studies using fluorescent microscopy.

  19. Easy Leaf Area: Automated digital image analysis for rapid and accurate measurement of leaf area1

    PubMed Central

    Easlon, Hsien Ming; Bloom, Arnold J.

    2014-01-01

    • Premise of the study: Measurement of leaf areas from digital photographs has traditionally required significant user input unless backgrounds are carefully masked. Easy Leaf Area was developed to batch process hundreds of Arabidopsis rosette images in minutes, removing background artifacts and saving results to a spreadsheet-ready CSV file. • Methods and Results: Easy Leaf Area uses the color ratios of each pixel to distinguish leaves and calibration areas from their background and compares leaf pixel counts to a red calibration area to eliminate the need for camera distance calculations or manual ruler scale measurement that other software methods typically require. Leaf areas estimated by this software from images taken with a camera phone were more accurate than ImageJ estimates from flatbed scanner images. • Conclusions: Easy Leaf Area provides an easy-to-use method for rapid measurement of leaf area and nondestructive estimation of canopy area from digital images. PMID:25202639

  20. Accurate size measurement of monosize calibration spheres by differential mobility analysis

    SciTech Connect

    Mulholland, George W.; Fernandez, Marco

    1998-11-24

    A differential mobility analyzer was used to measure the mean particle size of three monosize suspensions of polystyrene spheres in water. Key features of the experiment to minimize the uncertainty in the results include developing a recirculating flow to ensure equal flows into and out of the classifier, an accurate divider circuit for calibrating the electrode voltage, and use of the 100.7 nm NIST SRM for calibrating the flow of the classifier. The measured average sizes and expanded uncertainties with a coverage factor of 2 are 92.4 nm{+-}1.1 nm, 126.9 nm{+-}1.4 nm, and 217.7 nm{+-}3.4 nm. These calibration sizes were characterized by NIST to improve the calibration of scanning surface inspection systems.

  1. Importance of accurate spectral simulations for the analysis of terahertz spectra: citric acid anhydrate and monohydrate.

    PubMed

    King, Matthew D; Davis, Eric A; Smith, Tiffany M; Korter, Timothy M

    2011-10-13

    The terahertz (THz) spectra of crystalline solids are typically uniquely sensitive to the molecular packing configurations, allowing for the detection of polymorphs and hydrates by THz spectroscopic techniques. It is possible, however, that coincident absorptions may be observed between related crystal forms, in which case careful assessment of the lattice vibrations of each system must be performed. Presented here is a THz spectroscopic investigation of citric acid in its anhydrous and monohydrate phases. Remarkably similar features were observed in the THz spectra of both systems, requiring the accurate calculation of the low-frequency vibrational modes by solid-state density functional theory to determine the origins of these spectral features. The results of the simulations demonstrate the necessity of reliable and rigorous methods for THz vibrational modes to ensure the proper evaluation of the THz spectra of molecular solids.

  2. Methods for accurate analysis of galaxy clustering on non-linear scales

    NASA Astrophysics Data System (ADS)

    Vakili, Mohammadjavad

    2017-01-01

    Measurements of galaxy clustering with the low-redshift galaxy surveys provide sensitive probe of cosmology and growth of structure. Parameter inference with galaxy clustering relies on computation of likelihood functions which requires estimation of the covariance matrix of the observables used in our analyses. Therefore, accurate estimation of the covariance matrices serves as one of the key ingredients in precise cosmological parameter inference. This requires generation of a large number of independent galaxy mock catalogs that accurately describe the statistical distribution of galaxies in a wide range of physical scales. We present a fast method based on low-resolution N-body simulations and approximate galaxy biasing technique for generating mock catalogs. Using a reference catalog that was created using the high resolution Big-MultiDark N-body simulation, we show that our method is able to produce catalogs that describe galaxy clustering at a percentage-level accuracy down to highly non-linear scales in both real-space and redshift-space.In most large-scale structure analyses, modeling of galaxy bias on non-linear scales is performed assuming a halo model. Clustering of dark matter halos has been shown to depend on halo properties beyond mass such as halo concentration, a phenomenon referred to as assembly bias. Standard large-scale structure studies assume that halo mass alone is sufficient in characterizing the connection between galaxies and halos. However, modeling of galaxy bias can face systematic effects if the number of galaxies are correlated with other halo properties. Using the Small MultiDark-Planck high resolution N-body simulation and the clustering measurements of Sloan Digital Sky Survey DR7 main galaxy sample, we investigate the extent to which the dependence of galaxy bias on halo concentration can improve our modeling of galaxy clustering.

  3. Applying Qualitative Hazard Analysis to Support Quantitative Safety Analysis for Proposed Reduced Wake Separation Conops

    NASA Technical Reports Server (NTRS)

    Shortle, John F.; Allocco, Michael

    2005-01-01

    This paper describes a scenario-driven hazard analysis process to identify, eliminate, and control safety-related risks. Within this process, we develop selective criteria to determine the applicability of applying engineering modeling to hypothesized hazard scenarios. This provides a basis for evaluating and prioritizing the scenarios as candidates for further quantitative analysis. We have applied this methodology to proposed concepts of operations for reduced wake separation for closely spaced parallel runways. For arrivals, the process identified 43 core hazard scenarios. Of these, we classified 12 as appropriate for further quantitative modeling, 24 that should be mitigated through controls, recommendations, and / or procedures (that is, scenarios not appropriate for quantitative modeling), and 7 that have the lowest priority for further analysis.

  4. Qualitative and quantitative analysis of atmospheric organosulfates in Centreville, Alabama

    NASA Astrophysics Data System (ADS)

    Hettiyadura, Anusha P. S.; Jayarathne, Thilina; Baumann, Karsten; Goldstein, Allen H.; de Gouw, Joost A.; Koss, Abigail; Keutsch, Frank N.; Skog, Kate; Stone, Elizabeth A.

    2017-01-01

    Organosulfates are components of secondary organic aerosols (SOA) that form from oxidation of volatile organic compounds (VOCs) in the presence of sulfate. In this study, the composition and abundance of organosulfates were determined in fine particulate matter (PM2.5) collected from Centreville, AL, during the Southern Oxidant and Aerosol Study (SOAS) in summer 2013. Six organosulfates were quantified using hydrophilic interaction liquid chromatography (HILIC) with triple quadrupole mass spectrometry (TQD) against authentic standards. Among these, the three most abundant species were glycolic acid sulfate (0.5-52.5 ng m-3), lactic acid sulfate (0.5-36.7 ng m-3), and hydroxyacetone sulfate (0.5-14.3 ng m-3). These three species were strongly inter-correlated, suggesting similar precursors and/or formation pathways. Further correlations with sulfate, isoprene, and isoprene oxidation products indicate important roles for these precursors in organosulfate formation in Centreville. Positive filter sampling artifacts associated with these organosulfates due to gas adsorption or reaction of gas phase precursors of organosulfates with sulfuric acid were assessed for a subset of samples and were less than 7.8 % of their PM2.5 concentrations. Together, the quantified organosulfates accounted for < 0.3 % of organic carbon mass in PM2.5. To gain insights into other organosulfates in PM2.5 collected from Centreville, semi-quantitative analysis was employed by way of monitoring characteristic product ions of organosulfates (HSO4- at m/z 97 and SO4- ṡ at m/z 96) and evaluating relative signal strength by HILIC-TQD. Molecular formulas of organosulfates were determined by high-resolution time-of-flight (TOF) mass spectrometry. The major organosulfate signal across all samples corresponded to 2-methyltetrol sulfates, which accounted for 42-62 % of the total bisulfate ion signal. Conversely, glycolic acid sulfate, the most abundant organosulfate quantified in this study, was 0

  5. 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

  6. The Measles Vaccination Narrative in Twitter: A Quantitative Analysis

    PubMed Central

    Radzikowski, Jacek; Jacobsen, Kathryn H; Croitoru, Arie; Crooks, Andrew; Delamater, Paul L

    2016-01-01

    Background The emergence of social media is providing an alternative avenue for information exchange and opinion formation on health-related issues. Collective discourse in such media leads to the formation of a complex narrative, conveying public views and perceptions. Objective This paper presents a study of Twitter narrative regarding vaccination in the aftermath of the 2015 measles outbreak, both in terms of its cyber and physical characteristics. We aimed to contribute to the analysis of the data, as well as presenting a quantitative interdisciplinary approach to analyze such open-source data in the context of health narratives. Methods We collected 669,136 tweets referring to vaccination from February 1 to March 9, 2015. These tweets were analyzed to identify key terms, connections among such terms, retweet patterns, the structure of the narrative, and connections to the geographical space. Results The data analysis captures the anatomy of the themes and relations that make up the discussion about vaccination in Twitter. The results highlight the higher impact of stories contributed by news organizations compared to direct tweets by health organizations in communicating health-related information. They also capture the structure of the antivaccination narrative and its terms of reference. Analysis also revealed the relationship between community engagement in Twitter and state policies regarding child vaccination. Residents of Vermont and Oregon, the two states with the highest rates of non-medical exemption from school-entry vaccines nationwide, are leading the social media discussion in terms of participation. Conclusions The interdisciplinary study of health-related debates in social media across the cyber-physical debate nexus leads to a greater understanding of public concerns, views, and responses to health-related issues. Further coalescing such capabilities shows promise towards advancing health communication, thus supporting the design of more

  7. Quantitative analysis of routine chemical constituents in tobacco by near-infrared spectroscopy and support vector machine.

    PubMed

    Zhang, Yong; Cong, Qian; Xie, Yunfei; JingxiuYang; Zhao, Bing

    2008-12-15

    It is important to monitor quality of tobacco during the production of cigarette. Therefore, in order to scientifically control the tobacco raw material and guarantee the cigarette quality, fast and accurate determination routine chemical of constituents of tobacco, including the total sugar, reducing sugar, Nicotine, the total nitrogen and so on, is needed. In this study, 50 samples of tobacco from different cultivation areas were surveyed by near-infrared (NIR) spectroscopy, and the spectral differences provided enough quantitative analysis information for the tobacco. Partial least squares regression (PLSR), artificial neural network (ANN), and support vector machine (SVM), were applied. The quantitative analysis models of 50 tobacco samples were studied comparatively in this experiment using PLSR, ANN, radial basis function (RBF) SVM regression, and the parameters of the models were also discussed. The spectrum variables of 50 samples had been compressed through the wavelet transformation technology before the models were established. The best experimental results were obtained using the (RBF) SVM regression with gamma=1.5, 1.3, 0.9, and 0.1, separately corresponds to total sugar, reducing sugar, Nicotine, and total nitrogen, respectively. Finally, compared with the back propagation (BP-ANN) and PLSR approach, SVM algorithm showed its excellent generalization for quantitative analysis results, while the number of samples for establishing the model is smaller. The overall results show that NIR spectroscopy combined with SVM can be efficiently utilized for rapid and accurate analysis of routine chemical compositions in tobacco. Simultaneously, the research can serve as the technical support and the foundation of quantitative analysis of other NIR applications.

  8. Quantitative analysis of routine chemical constituents in tobacco by near-infrared spectroscopy and support vector machine

    NASA Astrophysics Data System (ADS)

    Zhang, Yong; Cong, Qian; Xie, Yunfei; Yang, Jingxiu; Zhao, Bing

    2008-12-01

    It is important to monitor quality of tobacco during the production of cigarette. Therefore, in order to scientifically control the tobacco raw material and guarantee the cigarette quality, fast and accurate determination routine chemical of constituents of tobacco, including the total sugar, reducing sugar, Nicotine, the total nitrogen and so on, is needed. In this study, 50 samples of tobacco from different cultivation areas were surveyed by near-infrared (NIR) spectroscopy, and the spectral differences provided enough quantitative analysis information for the tobacco. Partial least squares regression (PLSR), artificial neural network (ANN), and support vector machine (SVM), were applied. The quantitative analysis models of 50 tobacco samples were studied comparatively in this experiment using PLSR, ANN, radial basis function (RBF) SVM regression, and the parameters of the models were also discussed. The spectrum variables of 50 samples had been compressed through the wavelet transformation technology before the models were established. The best experimental results were obtained using the (RBF) SVM regression with γ = 1.5, 1.3, 0.9, and 0.1, separately corresponds to total sugar, reducing sugar, Nicotine, and total nitrogen, respectively. Finally, compared with the back propagation (BP-ANN) and PLSR approach, SVM algorithm showed its excellent generalization for quantitative analysis results, while the number of samples for establishing the model is smaller. The overall results show that NIR spectroscopy combined with SVM can be efficiently utilized for rapid and accurate analysis of routine chemical compositions in tobacco. Simultaneously, the research can serve as the technical support and the foundation of quantitative analysis of other NIR applications.

  9. The ALHAMBRA survey: accurate merger fractions derived by PDF analysis of photometrically close pairs

    NASA Astrophysics Data System (ADS)

    López-Sanjuan, C.; Cenarro, A. J.; Varela, J.; Viironen, K.; Molino, A.; Benítez, N.; Arnalte-Mur, P.; Ascaso, B.; Díaz-García, L. A.; Fernández-Soto, A.; Jiménez-Teja, Y.; Márquez, I.; Masegosa, J.; Moles, M.; Pović, M.; Aguerri, J. A. L.; Alfaro, E.; Aparicio-Villegas, T.; Broadhurst, T.; Cabrera-Caño, J.; Castander, F. J.; Cepa, J.; Cerviño, M.; Cristóbal-Hornillos, D.; Del Olmo, A.; González Delgado, R. M.; Husillos, C.; Infante, L.; Martínez, V. J.; Perea, J.; Prada, F.; Quintana, J. M.

    2015-04-01

    Aims: Our goal is to develop and test a novel methodology to compute accurate close-pair fractions with photometric redshifts. Methods: We improved the currently used methodologies to estimate the merger fraction fm from photometric redshifts by (i) using the full probability distribution functions (PDFs) of the sources in redshift space; (ii) including the variation in the luminosity of the sources with z in both the sample selection and the luminosity ratio constrain; and (iii) splitting individual PDFs into red and blue spectral templates to reliably work with colour selections. We tested the performance of our new methodology with the PDFs provided by the ALHAMBRA photometric survey. Results: The merger fractions and rates from the ALHAMBRA survey agree excellently well with those from spectroscopic work for both the general population and red and blue galaxies. With the merger rate of bright (MB ≤ -20-1.1z) galaxies evolving as (1 + z)n, the power-law index n is higher for blue galaxies (n = 2.7 ± 0.5) than for red galaxies (n = 1.3 ± 0.4), confirming previous results. Integrating the merger rate over cosmic time, we find that the average number of mergers per galaxy since z = 1 is Nmred = 0.57 ± 0.05 for red galaxies and Nmblue = 0.26 ± 0.02 for blue galaxies. Conclusions: Our new methodology statistically exploits all the available information provided by photometric redshift codes and yields accurate measurements of the merger fraction by close pairs from using photometric redshifts alone. Current and future photometric surveys will benefit from this new methodology. Based on observations collected at the German-Spanish Astronomical Center, Calar Alto, jointly operated by the Max-Planck-Institut für Astronomie (MPIA) at Heidelberg and the Instituto de Astrofísica de Andalucía (CSIC).The catalogues, probabilities, and figures of the ALHAMBRA close pairs detected in Sect. 5.1 are available at http://https://cloud.iaa.csic.es/alhambra/catalogues/ClosePairs

  10. Membrane chromatographic immunoassay method for rapid quantitative analysis of specific serum antibodies.

    PubMed

    Ghosh, Raja

    2006-02-05

    This paper discusses a membrane chromatographic immunoassay method for rapid detection and quantitative analysis of specific serum antibodies. A type of polyvinylidine fluoride (PVDF) microfiltration membrane was used in the method for its ability to reversibly and specifically bind IgG antibodies from antiserum samples by hydrophobic interaction. Using this form of selective antibody binding and enrichment an affinity membrane with antigen binding ability was obtained in-situ. This was done by passing a pulse of diluted antiserum sample through a stack of microporous PVDF membranes. The affinity membrane thus formed was challenged with a pulse of antigen solution and the amount of antigen bound was accurately determined using chromatographic methods. The antigen binding correlated well with the antibody loading on the membrane. This method is direct, rapid and accurate, does not involve any chemical reaction, and uses very few reagents. Moreover, the same membrane could be repeatedly used for sequential immunoassays on account of the reversible nature of the antibody binding. Proof of concept of this method is provided using human hemoglobin as model antigen and rabbit antiserum against human hemoglobin as the antibody source.

  11. The Quantitative Overhead Analysis for Effective Task Migration in Biosensor Networks

    PubMed Central

    Kim, Tae-Kyung; Eom, Jung-Ho; Chung, Tai-Myoung

    2013-01-01

    We present a quantitative overhead analysis for effective task migration in biosensor networks. A biosensor network is the key technology which can automatically provide accurate and specific parameters of a human in real time. Biosensor nodes are typically very small devices, so the use of computing resources is restricted. Due to the limitation of nodes, the biosensor network is vulnerable to an external attack against a system for exhausting system availability. Since biosensor nodes generally deal with sensitive and privacy data, their malfunction can bring unexpected damage to system. Therefore, we have to use a task migration process to avoid the malfunction of particular biosensor nodes. Also, it is essential to accurately analyze overhead to apply a proper migration process. In this paper, we calculated task processing time of nodes to analyze system overhead and compared the task processing time applied to a migration process and a general method. We focused on a cluster ratio and different processing time between biosensor nodes in our simulation environment. The results of performance evaluation show that task execution time is greatly influenced by a cluster ratio and different processing time of biosensor nodes. In the results, the proposed algorithm reduces total task execution time in a migration process. PMID:24187668

  12. Quantitative safety assessment of computer based I and C systems via modular Markov analysis

    SciTech Connect

    Elks, C. R.; Yu, Y.; Johnson, B. W.

    2006-07-01

    This paper gives a brief overview of the methodology based on quantitative metrics for evaluating digital I and C system that has been under development at the Univ. of Virginia for a number years. Our quantitative assessment methodology is based on three well understood and extensively practiced disciplines in the dependability assessment field: (1) System level fault modeling and fault injection, (2) safety and coverage based dependability modeling methods, and (3) statistical estimation of model parameters used for safety predication. There are two contributions of this paper; the first contribution is related to incorporating design flaw information into homogenous Markov models when such data is available. The second is to introduce a Markov modeling method for managing the modeling complexities of large distributed I and C systems for the predication of safety and reliability. The method is called Modular Markov Chain analysis. This method allows Markov models of the system to be composed in a modular manner. In doing so, it address two important issues. (1) The models are more visually representative of the functional the system. (2) Important failure dependencies that naturally occur in complex systems are modeled accurately with our approach. (authors)

  13. A novel procedure of quantitation of virus based on microflow cytometry analysis.

    PubMed

    Vazquez, Diego; López-Vázquez, Carmen; Cutrín, Juan Manuel; Dopazo, Carlos P

    2016-03-01

    The accurate and fast titration of viruses is a critical step in research laboratories and biotechnology industries. Different approaches are commonly applied which either are time consuming (like the plaque and endpoint dilution assays) or do not ensure quantification of only infective particles (like quantitative real-time PCR). In the last decade, a methodology based on the analysis of infected cells by flow cytometry and fluorescence-activated cell sorting (FACS) has been reported as a fast and reliable test for the titration of some viruses. However, this technology needs expensive equipment and expert technicians to operate it. Recently, the "lab on a chip" integrated devices have brought about the miniaturization of this equipment, turning this technology into an affordable and easy-to-use alternative to traditional flow cytometry. In the present study, we have designed a microflow cytometry (μFC) procedure for the quantitation of viruses, using the infectious pancreatic necrosis virus (IPNV) as a model. The optimization of conditions and validation of the method are reported here.

  14. Quantitative human chorionic gonadotropin analysis. I. Comparison of an immunoradiometric assay and a radioimmunoassay

    SciTech Connect

    Shapiro, A.I.; Wu, T.F.; Ballon, S.C.; Lamb, E.J.

    1984-01-01

    An immunoradiometric assay (IRMA) for the quantitative analysis of human chorionic gonadotropin (hCG) was evaluated for specificity, sensitivity, accuracy and precision. The results were compared with those of the conventional radioimmunoassay (RIA) used in our laboratory. The IRMA is a solid-phase, double-antibody immunoassay that sandwiches the intact hCG molecule between the two antibodies. It has specificity, accuracy, and precision which are similar to those of the RIA. The RIA is based upon the assumptions that the antigenicity of the tracer is not altered by the iodination process and that the antibody reacts equally with all of the antigens, including the radiolabeled antigen. The IRMA does not use radiolabeled antigens and thus is free of the assumptions made in the conventional RIA. The IRMA may be more accurate at the lower limits of the assay because it does not require logarithmic transformations. Since the IRMA does not measure the free beta-subunit of hCG, it cannot be endorsed as the sole technique to quantitate hCG in patients with gestational trophoblastic neoplasia until the significance of the free beta-subunit in these patients is determined.

  15. Quantitative Analysis of Mutant Subclones in Chronic Myeloid Leukemia: Comparison of Different Methodological Approaches.

    PubMed

    Preuner, Sandra; Barna, Agnes; Frommlet, Florian; Czurda, Stefan; Konstantin, Byrgazov; Alikian, Mary; Machova Polakova, Katerina; Sacha, Tomasz; Richter, Johan; Lion, Thomas; Gabriel, Christian

    2016-04-29

    Identification and quantitative monitoring of mutant BCR-ABL1 subclones displaying resistance to tyrosine kinase inhibitors (TKIs) have become important tasks in patients with Ph-positive leukemias. Different technologies have been established for patient screening. Various next-generation sequencing (NGS) platforms facilitating sensitive detection and quantitative monitoring of mutations in the ABL1-kinase domain (KD) have been introduced recently, and are expected to become the preferred technology in the future. However, broad clinical implementation of NGS methods has been hampered by the limited accessibility at different centers and the current costs of analysis which may not be regarded as readily affordable for routine diagnostic monitoring. It is therefore of interest to determine whether NGS platforms can be adequately substituted by other methodological approaches. We have tested three different techniques including pyrosequencing, LD (ligation-dependent)-PCR and NGS in a series of peripheral blood specimens from chronic myeloid leukemia (CML) patients carrying single or multiple mutations in the BCR-ABL1 KD. The proliferation kinetics of mutant subclones in serial specimens obtained during the course of TKI-treatment revealed similar profiles via all technical approaches, but individual specimens showed statistically significant differences between NGS and the other methods tested. The observations indicate that different approaches to detection and quantification of mutant subclones may be applicable for the monitoring of clonal kinetics, but careful calibration of each method is required for accurate size assessment of mutant subclones at individual time points.

  16. An integrative variant analysis pipeline for accurate genotype/haplotype inference in population NGS data.

    PubMed

    Wang, Yi; Lu, James; Yu, Jin; Gibbs, Richard A; Yu, Fuli

    2013-05-01

    Next-generation sequencing is a powerful approach for discovering genetic variation. Sensitive variant calling and haplotype inference from population sequencing data remain challenging. We describe methods for high-quality discovery, genotyping, and phasing of SNPs for low-coverage (approximately 5×) sequencing of populations, implemented in a pipeline called SNPTools. Our pipeline contains several innovations that specifically address challenges caused by low-coverage population sequencing: (1) effective base depth (EBD), a nonparametric statistic that enables more accurate statistical modeling of sequencing data; (2) variance ratio scoring, a variance-based statistic that discovers polymorphic loci with high sensitivity and specificity; and (3) BAM-specific binomial mixture modeling (BBMM), a clustering algorithm that generates robust genotype likelihoods from heterogeneous sequencing data. Last, we develop an imputation engine that refines raw genotype likelihoods to produce high-quality phased genotypes/haplotypes. Designed for large population studies, SNPTools' input/output (I/O) and storage aware design leads to improved computing performance on large sequencing data sets. We apply SNPTools to the International 1000 Genomes Project (1000G) Phase 1 low-coverage data set and obtain genotyping accuracy comparable to that of SNP microarray.

  17. High-accurate optical vector analysis based on optical single-sideband modulation

    NASA Astrophysics Data System (ADS)

    Xue, Min; Pan, Shilong

    2016-11-01

    Most of the efforts devoted to the area of optical communications were on the improvement of the optical spectral efficiency. Varies innovative optical devices are thus developed to finely manipulate the optical spectrum. Knowing the spectral responses of these devices, including the magnitude, phase and polarization responses, is of great importance for their fabrication and application. To achieve high-resolution characterization, optical vector analyzers (OVAs) based on optical single-sideband (OSSB) modulation have been proposed and developed. Benefiting from the mature and highresolution microwave technologies, the OSSB-based OVA can potentially achieve a resolution of sub-Hz. However, the accuracy is restricted by the measurement errors induced by the unwanted first-order sideband and the high-order sidebands in the OSSB signal, since electrical-to-optical conversion and optical-to-electrical conversion are essentially required to achieve high-resolution frequency sweeping and extract the magnitude and phase information in the electrical domain. Recently, great efforts have been devoted to improve the accuracy of the OSSB-based OVA. In this paper, the influence of the unwanted-sideband induced measurement errors and techniques for implementing high-accurate OSSB-based OVAs are discussed.

  18. Design of an accurate wireless data logger for vibration analysis with Android interface.

    PubMed

    Blanco, J R; Menéndez, J; Ferrero, F J; Campo, J C; Valledor, M

    2016-12-01

    In this work a new accurate wireless data logger using the Android interface was developed to monitor vibrations at low-cost. The new data logger is completely autonomous and extremely reduced in size. This instrument enables data collection wirelessly and the ability to display it on any tablet or smartphone with operating system Android. The prototype allows the monitoring of any industrial system with minimal investment in material and installation costs. The data logger is capable of making 12.8 kSPS enough to sample up to 5 kHz signals. The basic specification of the data logger includes a high resolution 1-axis piezoelectric accelerometer with a working range of ±30 G. In addition to the acceleration measurements, temperature can also be recorded. The data logger was tested during a 6-month period in industrial environments. The details of the specific hardware and software design are described. The proposed technology can be easily transferred to many other areas of industrial monitoring.

  19. Design of an accurate wireless data logger for vibration analysis with Android interface

    NASA Astrophysics Data System (ADS)

    Blanco, J. R.; Menéndez, J.; Ferrero, F. J.; Campo, J. C.; Valledor, M.

    2016-12-01

    In this work a new accurate wireless data logger using the Android interface was developed to monitor vibrations at low-cost. The new data logger is completely autonomous and extremely reduced in size. This instrument enables data collection wirelessly and the ability to display it on any tablet or smartphone with operating system Android. The prototype allows the monitoring of any industrial system with minimal investment in material and installation costs. The data logger is capable of making 12.8 kSPS enough to sample up to 5 kHz signals. The basic specification of the data logger includes a high resolution 1-axis piezoelectric accelerometer with a working range of ±30 G. In addition to the acceleration measurements, temperature can also be recorded. The data logger was tested during a 6-month period in industrial environments. The details of the specific hardware and software design are described. The proposed technology can be easily transferred to many other areas of industrial monitoring.

  20. Quantitative XPS analysis of silica-supported Cu Co oxides

    NASA Astrophysics Data System (ADS)

    Cesar, Deborah V.; Peréz, Carlos A.; Schmal, Martin; Salim, Vera Maria M.

    2000-04-01

    Copper-cobalt oxides with Cu/Co=5:5, 15:15 and 35:35 bulk ratio have been prepared by deposition-precipitation method at constant pH from copper and cobalt nitrate solutions. Different oxides were obtained by decomposition of the precursors at 673 K for 7 h in air and analyzed by X-ray diffraction (XRD), transmission electron microscopy (TEM) and X-ray photoelectron spectroscopy (XPS). XRD data showed the formation of different oxide phases; for the bulk atomic ratio of 15Cu:15Co, a phase containing Cu and Co with spinel-like structure was observed, while the other bimetallic oxides presented CuO and Co 3O 4 as distinct phases. The XPS qualitative analysis has shown that all samples exhibited Cu 2+ and Co 3+ species at the surface. The Cu-Co spinel presented a displacement in Cu 2p binding energy value. A mathematical model was proposed from relative intensity ratios, which allowed the determination of the oxide particle thickness and the fraction of coverage at the support. This model described accurately the system and showed that cobalt improved the copper dispersion.

  1. 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.

  2. Quantitative Analysis of Various Metalloprotein Compositional Stoichiometries with Simultaneous PIXE and NRA

    NASA Astrophysics Data System (ADS)

    McCubbin, Andrew; Deyoung, Paul; Peaslee, Graham; Sibley, Megan; Warner, Joshua

    2013-04-01

    Stoichiometric characterization has been carried out on multiple metalloproteins using a combination of Ion Beam Analysis methods and a newly modified preparation technique. Particle Induced X-ray emission (PIXE) spectroscopy is a non-destructive ion beam analysis technique well suited to determine the concentrations of heavy elements. Nuclear Reaction Analysis (NRA) is a technique which measures the areal density of a thin target from scattering cross sections of 3.4 MeV protons. A combination of NRA and PIXE has been developed to provide a quantitative technique for the determination of stoichiometric metal ion ratios in metalloproteins. About one third of all proteins are metalloproteins, and most do not have well determined stoichiometric compositions for the metals they contain. Current work focuses on establishing a standard method in which to prepare protein samples. The method involves placing drops of protein solutions on aluminized polyethylene terephthalate (Mylar) and allowing them to dry. This technique has been tested for several proteins of known stoichiometry to determine cofactor content and has proven to be a reliable analysis method, accurately determining metal stoichiometry in cytochrome c, superoxide dismutase, concanavalin A, vitamin B12, and hemoglobin.

  3. Evaluating Multiplexed Quantitative Phosphopeptide Analysis on a Hybrid Quadrupole Mass Filter/Linear Ion Trap/Orbitrap Mass Spectrometer

    PubMed Central

    2015-01-01

    As a driver for many biological processes, phosphorylation remains an area of intense research interest. Advances in multiplexed quantitation utilizing isobaric tags (e.g., TMT and iTRAQ) have the potential to create a new paradigm in quantitative proteomics. New instrumentation and software are propelling these multiplexed workflows forward, which results in more accurate, sensitive, and reproducible quantitation across tens of thousands of phosphopeptides. This study assesses the performance of multiplexed quantitative phosphoproteomics on the Orbitrap Fusion mass spectrometer. Utilizing a two-phosphoproteome model of precursor ion interference, we assessed the accuracy of phosphopeptide quantitation across a variety of experimental approaches. These methods included the use of synchronous precursor selection (SPS) to enhance TMT reporter ion intensity and accuracy. We found that (i) ratio distortion remained a problem for phosphopeptide analysis in multiplexed quantitative workflows, (ii) ratio distortion can be overcome by the use of an SPS-MS3 scan, (iii) interfering ions generally possessed a different charge state than the target precursor, and (iv) selecting only the phosphate neutral loss peak (single notch) for the MS3 scan still provided accurate ratio measurements. Remarkably, these data suggest that the underlying cause of interference may not be due to coeluting and cofragmented peptides but instead from consistent, low level background fragmentation. Finally, as a proof-of-concept 10-plex experiment, we compared phosphopeptide levels from five murine brains to five livers. In total, the SPS-MS3 method quantified 38 247 phosphopeptides, corresponding to 11 000 phosphorylation sites. With 10 measurements recorded for each phosphopeptide, this equates to more than 628 000 binary comparisons collected in less than 48 h. PMID:25521595

  4. Note: Alignment/focus dependent core-line sensitivity for quantitative chemical analysis in hard x-ray photoelectron spectroscopy using a hemispherical electron analyzer

    SciTech Connect

    Weiland, Conan; Browning, Raymond; Karlin, Barry A.; Fischer, Daniel A.; Woicik, Joseph C.

    2013-03-15

    X-ray photoelectron spectroscopy is an established technique for quantitative chemical analysis requiring accurate peak intensity analysis. We present evidence of focus/alignment dependence of relative peak intensities for peaks over a broad kinetic energy range with a hemispherical electron analyzer operated in a position imaging mode. A decrease of over 50% in the Ag 2p{sub 3/2} to Ag 3d ratio is observed in a Ag specimen. No focus/alignment dependence is observed when using an angular imaging mode, necessitating the use of angular mode for quantitative chemical analysis.

  5. Note: Alignment/focus dependent core-line sensitivity for quantitative chemical analysis in hard x-ray photoelectron spectroscopy using a hemispherical electron analyzer.

    PubMed

    Weiland, Conan; Browning, Raymond; Karlin, Barry A; Fischer, Daniel A; Woicik, Joseph C

    2013-03-01

    X-ray photoelectron spectroscopy is an established technique for quantitative chemical analysis requiring accurate peak intensity analysis. We present evidence of focus∕alignment dependence of relative peak intensities for peaks over a broad kinetic energy range with a hemispherical electron analyzer operated in a position imaging mode. A decrease of over 50% in the Ag 2p₃/₂ to Ag 3d ratio is observed in a Ag specimen. No focus∕alignment dependence is observed when using an angular imaging mode, necessitating the use of angular mode for quantitative chemical analysis.

  6. Quantitative texture analysis of talc in mantle hydrated mylonites

    NASA Astrophysics Data System (ADS)

    Benitez-Perez, J. M.; Gomez Barreiro, J.; Wenk, H. R.; Vogel, S. C.; Soda, Y.; Voltolini, M.; Martinez-Catalan, J. R.

    2014-12-01

    A quantitative texture analysis of talc-serpentinite mylonites developed in highly deformed ultramafic rocks from different orogenic contexts have been done with neutorn diffraction at HIPPO (Los Álamos National Laboratory). Mineral assemblage, metamorphic evolution and deformative fabric of these samples could be correlated with those verified along the shallow levels (<100km; <5GPa) of a subduction zone. The hydration of mantle (ultramafic) rocks at those levels it is likely to occur dynamically, with important implications on seismogenesis. Given the high anisotropy of the major phases in the samples (i.e. talc and antigorite) it is expected to influence seismic anisotropy of the whole system, in the presence of texture. However to date there was no data on the crystallographic preferred orientation of talc and examples of antigorite textures are very limited. We explore the contribution of talc texture to the seismic anisotropy of mantle hydrated mylonites. Acknowledgements: This work has been funded by research project CGL2011-22728 of Spanish Ministry of Economy and Competitiveness. JGB and JMBP are grateful to the Ramón y Cajal and FPI funding programs. Access to HIPPO (LANSCE) to conduct diffraction experiments is kindly acknowledged.

  7. Quantitative Analysis of Cellular Metabolic Dissipative, Self-Organized Structures

    PubMed Central

    de la Fuente, Ildefonso Martínez

    2010-01-01

    One of the most important goals of the postgenomic era is understanding the metabolic dynamic processes and the functional structures generated by them. Extensive studies during the last three decades have shown that the dissipative self-organization of the functional enzymatic associations, the catalytic reactions produced during the metabolite channeling, the microcompartmentalization of these metabolic processes and the emergence of dissipative networks are the fundamental elements of the dynamical organization of cell metabolism. Here we present an overview of how mathematical models can be used to address the properties of dissipative metabolic structures at different organizational levels, both for individual enzymatic associations and for enzymatic networks. Recent analyses performed with dissipative metabolic networks have shown that unicellular organisms display a singular global enzymatic structure common to all living cellular organisms, which seems to be an intrinsic property of the functional metabolism as a whole. Mathematical models firmly based on experiments and their corresponding computational approaches are needed to fully grasp the molecular mechanisms of metabolic dynamical processes. They are necessary to enable the quantitative and qualitative analysis of the cellular catalytic reactions and also to help comprehend the conditions under which the structural dynamical phenomena and biological rhythms arise. Understanding the molecular mechanisms responsible for the metabolic dissipative structures is crucial for unraveling the dynamics of cellular life. PMID:20957111

  8. Separation and quantitative analysis of alkyl sulfate ethoxymers by HPLC.

    PubMed

    Morvan, Julien; Hubert-Roux, Marie; Agasse, Valérie; Cardinael, Pascal; Barbot, Florence; Decock, Gautier; Bouillon, Jean-Philippe

    2008-01-01

    Separation of alkyl sulfate ethoxymers is investigated on various high-performance liquid chromatography (HPLC) stationary phases: Acclaim C18 Surfactant, Surfactant C8, and Hypercarb. For a fixed alkyl chain length, ethoxymers are eluted in the order of increasing number of ethoxylated units on Acclaim C18 Surfactant, whereas a reversed elution order is observed on Surfactant C8 and Hypercarb. Moreover, on an Acclaim C18 Surfactant column, non-ethoxylated compounds are eluted in their ethoxymers distribution and the use of sodium acetate additive in mobile phase leads to a co-elution of ethoxymers. HPLC stationary phases dedicated to surfactants analysis are evaluated by means of the Tanaka test. Surfactant C8 presents a great silanol activity whereas Acclaim C18 Surfactant shows a high steric selectivity. For alkyl sulfates, linearity of the calibration curve and limits of detection and quantitation are evaluated. The amount of sodium laureth sulfate raw material found in commercial body product is in agreement with the specification of the manufacturer.

  9. Quantitative analysis of 3-OH oxylipins in fermentation yeast.

    PubMed

    Potter, Greg; Xia, Wei; Budge, Suzanne M; Speers, R Alex

    2017-02-01

    Despite the ubiquitous distribution of oxylipins in plants, animals, and microbes, and the application of numerous analytical techniques to study these molecules, 3-OH oxylipins have never been quantitatively assayed in yeasts. The formation of heptafluorobutyrate methyl ester derivatives and subsequent analysis with gas chromatography - negative chemical ionization - mass spectrometry allowed for the first determination of yeast 3-OH oxylipins. The concentration of 3-OH 10:0 (0.68-4.82 ng/mg dry cell mass) in the SMA strain of Saccharomyces pastorianus grown in laboratory-scale beverage fermentations was elevated relative to oxylipin concentrations in plant tissues and macroalgae. In fermenting yeasts, the onset of 3-OH oxylipin formation has been related to fermentation progression and flocculation initiation. When the SMA strain was grown in laboratory-scale fermentations, the maximal sugar consumption rate preceded the lowest concentration of 3-OH 10:0 by ∼4.5 h and a distinct increase in 3-OH 10:0 concentration by ∼16.5 h.

  10. Quantitative analysis of brain magnetic resonance imaging for hepatic encephalopathy

    NASA Astrophysics Data System (ADS)

    Syh, Hon-Wei; Chu, Wei-Kom; Ong, Chin-Sing

    1992-06-01

    High intensity lesions around ventricles have recently been observed in T1-weighted brain magnetic resonance images for patients suffering hepatic encephalopathy. The exact etiology that causes magnetic resonance imaging (MRI) gray scale changes has not been totally understood. The objective of our study was to investigate, through quantitative means, (1) the amount of changes to brain white matter due to the disease process, and (2) the extent and distribution of these high intensity lesions, since it is believed that the abnormality may not be entirely limited to the white matter only. Eleven patients with proven haptic encephalopathy and three normal persons without any evidence of liver abnormality constituted our current data base. Trans-axial, sagittal, and coronal brain MRI were obtained on a 1.5 Tesla scanner. All processing was carried out on a microcomputer-based image analysis system in an off-line manner. Histograms were decomposed into regular brain tissues and lesions. Gray scale ranges coded as lesion were then brought back to original images to identify distribution of abnormality. Our results indicated the disease process involved pallidus, mesencephalon, and subthalamic regions.

  11. Quantitative SERS sensors for environmental analysis of naphthalene.

    PubMed

    Péron, O; Rinnert, E; Toury, T; Lamy de la Chapelle, M; Compère, C

    2011-03-07

    In the investigation of chemical pollutants, such as PAHs (Polycyclic Aromatic Hydrocarbons) at low concentration in aqueous medium, Surface-Enhanced Raman Scattering (SERS) stands for an alternative to the inherent low cross-section of normal Raman scattering. Indeed, SERS is a very sensitive spectroscopic technique due to the excitation of the surface plasmon modes of the nanostructured metallic film. The surface of quartz substrates was coated with a hydrophobic film obtained by silanization and subsequently reacted with polystyrene (PS) beads coated with gold nanoparticles. The hydrophobic surface of the SERS substrates pre-concentrates non-polar molecules such as naphthalene. Under laser excitation, the SERS-active substrates allow the detection and the identification of the target molecules localized close to the gold nanoparticles. The morphology of the SERS substrates based on polystyrene beads surrounded by gold nanoparticles was characterized by scanning electron microscopy (SEM). Furthermore, the Raman fingerprint of the polystyrene stands for an internal spectral reference. To this extent, an innovative method to detect and to quantify organic molecules, as naphthalene in the range of 1 to 20 ppm, in aqueous media was carried out. Such SERS-active substrates tend towards an application as quantitative SERS sensors for the environmental analysis of naphthalene.

  12. Quantitative Financial Analysis of Alternative Energy Efficiency Shareholder Incentive Mechanisms

    SciTech Connect

    Cappers, Peter; Goldman, Charles; Chait, Michele; Edgar, George; Schlegel, Jeff; Shirley, Wayne

    2008-08-03

    Rising energy prices and climate change are central issues in the debate about our nation's energy policy. Many are demanding increased energy efficiency as a way to help reduce greenhouse gas emissions and lower the total cost of electricity and energy services for consumers and businesses. Yet, as the National Action Plan on Energy Efficiency (NAPEE) pointed out, many utilities continue to shy away from seriously expanding their energy efficiency program offerings because they claim there is insufficient profit-motivation, or even a financial disincentive, when compared to supply-side investments. With the recent introduction of Duke Energy's Save-a-Watt incentive mechanism and ongoing discussions about decoupling, regulators and policymakers are now faced with an expanded and diverse landscape of financial incentive mechanisms, Determining the 'right' way forward to promote deep and sustainable demand side resource programs is challenging. Due to the renaissance that energy efficiency is currently experiencing, many want to better understand the tradeoffs in stakeholder benefits between these alternative incentive structures before aggressively embarking on a path for which course corrections can be time-consuming and costly. Using a prototypical Southwest utility and a publicly available financial model, we show how various stakeholders (e.g. shareholders, ratepayers, etc.) are affected by these different types of shareholder incentive mechanisms under varying assumptions about program portfolios. This quantitative analysis compares the financial consequences associated with a wide range of alternative incentive structures. The results will help regulators and policymakers better understand the financial implications of DSR program incentive regulation.

  13. Quantitative analysis of plasma interleiukin-6 by immunoassay on microchip

    NASA Astrophysics Data System (ADS)

    Abe, K.; Hashimoto, Y.; Yatsushiro, S.; Yamamura, S.; Tanaka, M.; Ooie, T.; Baba, Y.; Kataoka, M.

    2012-03-01

    Sandwich enzyme-linked immunoassay (ELISA) is one of the most frequently employed assays for clinical diagnosis, since this enables the investigator to identify specific protein biomarkers. However, the conventional assay using a 96-well microtitration plate is time- and sample-consuming, and therefore is not suitable for rapid diagnosis. To overcome these drawbacks, we performed a sandwich ELISA on a microchip. We employed the piezoelectric inkjet printing for deposition and fixation of 1st antibody on the microchannnel surface (300 μm width and 100 μm depth). Model analyte was interleukin-6 (IL-6) which was one of the inflammatory cytokine. After blocking the microchannel, antigen, biotin-labeled 2nd antibody, and avidin-labeled peroxidase were infused into the microchannel and incubated for 20 min, 10 min, and 5 min, respectively. This assay could detect 2 pg/ml and quantitatively measure the range of 0-32 pg/ml. Liner regression analysis of plasma IL-6 concentration obtained by microchip and conventional methods exhibited a significant relationship (R2 = 0.9964). This assay reduced the time for the antigen-antibody reaction to 1/6, and the consumption of samples and reagents to 1/50 compared with the conventional method. This assay enables us to determine plasma IL-6 with accuracy, high sensitivity, time saving ability, and low consumption of sample and reagents, and thus will be applicable to clinic diagnosis.

  14. Quantitative produced water analysis using mobile 1H NMR

    NASA Astrophysics Data System (ADS)

    Wagner, Lisabeth; Kalli, Chris; Fridjonsson, Einar O.; May, Eric F.; Stanwix, Paul L.; Graham, Brendan F.; Carroll, Matthew R. J.; Johns, Michael L.

    2016-10-01

    Measurement of oil contamination of produced water is required in the oil and gas industry to the (ppm) level prior to discharge in order to meet typical environmental legislative requirements. Here we present the use of compact, mobile 1H nuclear magnetic resonance (NMR) spectroscopy, in combination with solid phase extraction (SPE), to meet this metrology need. The NMR hardware employed featured a sufficiently homogeneous magnetic field, such that chemical shift differences could be used to unambiguously differentiate, and hence quantitatively detect, the required oil and solvent NMR signals. A solvent system consisting of 1% v/v chloroform in tetrachloroethylene was deployed, this provided a comparable 1H NMR signal intensity for the oil and the solvent (chloroform) and hence an internal reference 1H signal from the chloroform resulting in the measurement being effectively self-calibrating. The measurement process was applied to water contaminated with hexane or crude oil over the range 1-30 ppm. The results were validated against known solubility limits as well as infrared analysis and gas chromatography.

  15. Quantitative analysis of dynamic association in live biological fluorescent samples.

    PubMed

    Ruusuvuori, Pekka; Paavolainen, Lassi; Rutanen, Kalle; Mäki, Anita; Huttunen, Heikki; Marjomäki, Varpu

    2014-01-01

    Determining vesicle localization and association in live microscopy may be challenging due to non-simultaneous imaging of rapidly moving objects with two excitation channels. Besides errors due to movement of objects, imaging may also introduce shifting between the image channels, and traditional colocalization methods cannot handle such situations. Our approach to quantifying the association between tagged proteins is to use an object-based method where the exact match of object locations is not assumed. Point-pattern matching provides a measure of correspondence between two point-sets under various changes between the sets. Thus, it can be used for robust quantitative analysis of vesicle association between image channels. Results for a large set of synthetic images shows that the novel association method based on point-pattern matching demonstrates robust capability to detect association of closely located vesicles in live cell-microscopy where traditional colocalization methods fail to produce results. In addition, the method outperforms compared Iterated Closest Points registration method. Results for fixed and live experimental data shows the association method to perform comparably to traditional methods in colocalization studies for fixed cells and to perform favorably in association studies for live cells.

  16. High throughput, quantitative analysis of human osteoclast differentiation and activity.

    PubMed

    Diepenhorst, Natalie A; Nowell, Cameron J; Rueda, Patricia; Henriksen, Kim; Pierce, Tracie; Cook, Anna E; Pastoureau, Philippe; Sabatini, Massimo; Charman, William N; Christopoulos, Arthur; Summers, Roger J; Sexton, Patrick M; Langmead, Christopher J

    2017-02-15

    Osteoclasts are multinuclear cells that degrade bone under both physiological and pathophysiological conditions. Osteoclasts are therefore a major target of osteoporosis therapeutics aimed at preserving bone. Consequently, analytical methods for osteoclast activity are useful for the development of novel biomarkers and/or pharmacological agents for the treatment of osteoporosis. The nucleation state of an osteoclast is indicative of its maturation and activity. To date, activity is routinely measured at the population level with only approximate consideration of the nucleation state (an 'osteoclast population' is typically defined as cells with ≥3 nuclei). Using a fluorescent substrate for tartrate-resistant acid phosphatase (TRAP), a routinely used marker of osteoclast activity, we developed a multi-labelled imaging method for quantitative measurement of osteoclast TRAP activity at the single cell level. Automated image analysis enables interrogation of large osteoclast populations in a high throughput manner using open source software. Using this methodology, we investigated the effects of receptor activator of nuclear factor kappa-B ligand (RANK-L) on osteoclast maturation and activity and demonstrated that TRAP activity directly correlates with osteoclast maturity (i.e. nuclei number). This method can be applied to high throughput screening of osteoclast-targeting compounds to determine changes in maturation and activity.

  17. Electrochemical valveless flow microsystems for ultra fast and accurate analysis of total isoflavones with integrated calibration.

    PubMed

    Blasco, Antonio Javier; Crevillén, Agustín González; de la Fuente, Pedro; González, María Cristina; Escarpa, Alberto

    2007-04-01

    A novel strategy integrating methodological calibration and analysis on board on a planar first-generation microfluidics system for the determination of total isoflavones in soy samples is proposed. The analytical strategy is conceptually proposed and successfully demonstrated on the basis of (i) the microchip design (with the possibility to use both reservoirs), (ii) the analytical characteristics of the developed method (statically zero intercept and excellent robustness between calibration slopes, RSDs < 5%), (iii) the irreversible electrochemical behaviour of isoflavone oxidation (no significant electrode fouling effect was observed between calibration and analysis runs) and (iv) the inherent versatility of the electrochemical end-channel configurations (possibility of use different pumping and detection media). Repeatability obtained in both standard (calibration) and real soy samples (analysis) with values of RSD less than 1% for the migration times indicated the stability of electroosmotic flow (EOF) during both integrated operations. The accuracy (an error of less than 6%) is demonstrated for the first time in these microsystems using a documented secondary standard from the Drug Master File (SW/1211/03) as reference material. Ultra fast calibration and analysis of total isoflavones in soy samples was integrated successfully employing 60 s each; enhancing notably the analytical performance of these microdevices with an important decrease in overall analysis times (less than 120 s) and with an increase in accuracy by a factor of 3.

  18. Quantitative Analysis of Intracellular Fluorescent Foci in Live Bacteria

    PubMed Central

    Moolman, M. Charl; Kerssemakers, Jacob W.J.; Dekker, Nynke H.

    2015-01-01

    Fluorescence microscopy has revolutionized in vivo cellular biology. Through the specific labeling of a protein of interest with a fluorescent protein, one is able to study movement and colocalization, and even count individual proteins in a live cell. Different algorithms exist to quantify the total intensity and position of a fluorescent focus. Although these algorithms have been rigorously studied for in vitro conditions, which are greatly different than the in-homogenous and variable cellular environments, their exact limits and applicability in the context of a live cell have not been thoroughly and systematically evaluated. In this study, we quantitatively characterize the influence of different background subtraction algorithms on several focus analysis algorithms. We use, to our knowledge, a novel approach to assess the sensitivity of the focus analysis algorithms to background removal, in which simulated and experimental data are combined to maintain full control over the sensitivity of a focus within a realistic background of cellular fluorescence. We demonstrate that the choice of algorithm and the corresponding error are dependent on both the brightness of the focus, and the cellular context. Expectedly, focus intensity estimation and localization accuracy suffer in all algorithms at low focus to background ratios, with the bacteroidal background subtraction in combination with the median excess algorithm, and the region of interest background subtraction in combination with a two-dimensional Gaussian fit algorithm, performing the best. We furthermore show that the choice of background subtraction algorithm is dependent on the expression level of the protein under investigation, and that the localization error is dependent on the distance of a focus from the bacterial edge and pole. Our results establish a set of guidelines for what signals can be analyzed to give a targeted spatial and intensity accuracy within a bacterial cell. PMID:26331246

  19. Communication about vaccinations in Italian websites: a quantitative analysis.

    PubMed

    Tafuri, Silvio; Gallone, Maria S; Gallone, Maria F; Zorico, Ivan; Aiello, Valeria; Germinario, Cinzia

    2014-01-01

    Babies' parents and people who look for information about vaccination often visit anti-vaccine movement's websites, blogs by naturopathic physicians or natural and alternative medicine practitioners. The aim of this work is to provide a quantitative analysis on the type of information available to Italian people regarding vaccination and a quality analysis of websites retrieved through our searches. A quality score was created to evaluate the technical level of websites. A research was performed through Yahoo, Google, and MSN using the keywords "vaccine" and "vaccination," with the function "OR" in order to identify the most frequently used websites. The 2 keywords were input in Italian, and the first 15 pages retrieved by each search engine were analyzed. 149 websites were selected through this methodology. Fifty-three per cent of the websites belonged to associations, groups, or scientific companies, 32.2% (n = 48) consisted of a personal blog and 14.8% (n = 22) belonged to some of the National Health System offices. Among all analyzed websites, 15.4% (n = 23) came from anti-vaccine movement groups. 37.6% reported webmaster name, 67.8% webmaster e-mail, 28.6% indicated the date of the last update and 46.6% the author's name. The quality score for government sites was higher on average than anti-vaccine websites; although, government sites don't use Web 2.0 functions, as the forums.: National Health System institutions who have to promote vaccination cannot avoid investing in web communication because it cannot be managed by private efforts but must be the result of Public Health, private and scientific association, and social movement synergy.

  20. Accurate and noninvasive embryos screening during in vitro fertilization (IVF) assisted by Raman analysis of embryos culture medium Accurate and noninvasive embryos screening during IVF

    NASA Astrophysics Data System (ADS)

    Shen, A. G.; Peng, J.; Zhao, Q. H.; Su, L.; Wang, X. H.; Hu, J. M.; Yang, J.

    2012-04-01

    In combination with morphological evaluation tests, we employ Raman spectroscopy to select higher potential reproductive embryos during in vitro fertilization (IVF) based on chemical composition of embryos culture medium. In this study, 57 Raman spectra are acquired from both higher and lower quality embryos culture medium (ECM) from 10 patients which have been preliminarily confirmed by clinical assay. Data are fit by using a linear combination model of least squares method in which 12 basis spectra represent the chemical features of ECM. The final fitting coefficients provide insight into the chemical compositions of culture medium samples and are subsequently used as criterion to evaluate the quality of embryos. The relative fitting coefficients ratios of sodium pyruvate/albumin and phenylalanine/albumin seem act as key roles in the embryo screening, attaining 85.7% accuracy in comparison with clinical pregnancy. The good results demonstrate that Raman spectroscopy therefore is an important candidate for an accurate and noninvasive screening of higher quality embryos, which potentially decrease the time-consuming clinical trials during IVF.

  1. How to Construct More Accurate Student Models: Comparing and Optimizing Knowledge Tracing and Performance Factor Analysis

    ERIC Educational Resources Information Center

    Gong, Yue; Beck, Joseph E.; Heffernan, Neil T.

    2011-01-01

    Student modeling is a fundamental concept applicable to a variety of intelligent tutoring systems (ITS). However, there is not a lot of practical guidance on how to construct and train such models. This paper compares two approaches for student modeling, Knowledge Tracing (KT) and Performance Factors Analysis (PFA), by evaluating their predictive…

  2. Solid rocket booster internal flow analysis by highly accurate adaptive computational methods

    NASA Technical Reports Server (NTRS)

    Huang, C. Y.; Tworzydlo, W.; Oden, J. T.; Bass, J. M.; Cullen, C.; Vadaketh, S.

    1991-01-01

    The primary objective of this project was to develop an adaptive finite element flow solver for simulating internal flows in the solid rocket booster. Described here is a unique flow simulator code for analyzing highly complex flow phenomena in the solid rocket booster. New methodologies and features incorporated into this analysis tool are described.

  3. Quantitative analysis of continuous intracranial pressure recordings in symptomatic patients with extracranial shunts

    PubMed Central

    Eide, P

    2003-01-01

    Objectives: To explore the outcome of management of possible shunt related symptoms using intracranial pressure (ICP) monitoring, and to identify potential methodological limitations with the current strategies of ICP assessment. Methods: The distribution of persistent symptoms related to extracranial shunt treatment was compared before and after management of shunt failure in 69 consecutive hydrocephalic cases. Management was heavily based on ICP monitoring (calculation of mean ICP and visual determination of plateau waves). After the end of patient management, all ICP curves were re-evaluated using a quantitative method and software (SensometricsTM pressure analyser). The ICP curves were presented as a matrix of numbers of ICP elevations (20 to 35 mm Hg) or depressions (-10 to -5 mm Hg) of different durations (0.5, 1, or 5 minutes). The numbers of ICP elevations/depressions standardised to 10 hours recording time were calculated to allow comparisons of ICP between individuals. Results: After ICP monitoring and management of the putative shunt related symptoms, the symptoms remained unchanged in as many as 58% of the cases, with the highest percentages in those patients with ICP considered normal or too low at the time of ICP monitoring. The quantitative analysis revealed a high frequency of ICP elevations (20 to 35 mm Hg lasting 0.5 to 1 minute) and ICP depressions (-10 to -5 mm Hg lasting 0.5, 1, or 5 minutes), particularly in patients with ICP considered normal. Conclusions: The value of continuous ICP monitoring with ICP analysis using current criteria appears doubtful in the management of possible shunt related symptoms. This may reflect limitations in the strategies of ICP analysis. Calculation of the exact numbers of ICP elevations and depressions may provide a more accurate description of the ICP profile. PMID:12531957

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

    PubMed

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

    2015-01-10

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

  5. Practical implementation of an accurate method for multilevel design sensitivity analysis

    NASA Technical Reports Server (NTRS)

    Nguyen, Duc T.

    1987-01-01

    Solution techniques for handling large scale engineering optimization problems are reviewed. Potentials for practical applications as well as their limited capabilities are discussed. A new solution algorithm for design sensitivity is proposed. The algorithm is based upon the multilevel substructuring concept to be coupled with the adjoint method of sensitivity analysis. There are no approximations involved in the present algorithm except the usual approximations introduced due to the discretization of the finite element model. Results from the six- and thirty-bar planar truss problems show that the proposed multilevel scheme for sensitivity analysis is more effective (in terms of computer incore memory and the total CPU time) than a conventional (one level) scheme even on small problems. The new algorithm is expected to perform better for larger problems and its applications on the new generation of computer hardwares with 'parallel processing' capability is very promising.

  6. Software for quantitative analysis of radiotherapy: overview, requirement analysis and design solutions.

    PubMed

    Zhang, Lanlan; Hub, Martina; Mang, Sarah; Thieke, Christian; Nix, Oliver; Karger, Christian P; Floca, Ralf O

    2013-06-01

    Radiotherapy is a fast-developing discipline which plays a major role in cancer care. Quantitative analysis of radiotherapy data can improve the success of the treatment and support the prediction of outcome. In this paper, we first identify functional, conceptional and general requirements on a software system for quantitative analysis of radiotherapy. Further we present an overview of existing radiotherapy analysis software tools and check them against the stated requirements. As none of them could meet all of the demands presented herein, we analyzed possible conceptional problems and present software design solutions and recommendations to meet the stated requirements (e.g. algorithmic decoupling via dose iterator pattern; analysis database design). As a proof of concept we developed a software library "RTToolbox" following the presented design principles. The RTToolbox is available as open source library and has already been tested in a larger-scale software system for different use cases. These examples demonstrate the benefit of the presented design principles.

  7. 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

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

    SciTech Connect

    Larimer, Curtis J.; Winder, Eric M.; Jeters, Robert T.; Prowant, Matthew S.; Nettleship, Ian; Addleman, Raymond S.; Bonheyo, George 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 were 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.

  9. Column precipitation chromatography: an approach to quantitative analysis of eigencolloids.

    PubMed

    Breynaert, E; Maes, A

    2005-08-01

    A new column precipitation chromatography (CPC) technique, capable of quantitatively measuring technetium eigencolloids in aqueous solutions, is presented. The CPC technique is based on the destabilization and precipitation of eigencolloids by polycations in a confined matrix. Tc(IV) colloids can be quantitatively determined from their precipitation onto the CPC column (separation step) and their subsequent elution upon oxidation to pertechnetate by peroxide (elution step). A clean-bed particle removal model was used to explain the experimental results.

  10. Apparatus for use in rapid and accurate controlled-potential coulometric analysis

    DOEpatents

    Frazzini, Thomas L.; Holland, Michael K.; Pietri, Charles E.; Weiss, Jon R.

    1981-01-01

    An apparatus for controlled-potential coulometric analysis of a solution includes a cell to contain the solution to be analyzed and a plurality of electrodes to contact the solution in the cell. Means are provided to stir the solution and to control the atmosphere above it. A potentiostat connected to the electrodes controls potential differences among the electrodes. An electronic circuit connected to the potentiostat provides analog-to-digital conversion and displays a precise count of charge transfer during a desired chemical process. This count provides a measure of the amount of an unknown substance in the solution.

  11. Advances in Proteomics Data Analysis and Display Using an Accurate Mass and Time Tag Approach

    PubMed Central

    Zimmer, Jennifer S.D.; Monroe, Matthew E.; Qian, Wei-Jun; Smith, Richard D.

    2007-01-01

    Proteomics has recently demonstrated utility in understanding cellular processes on the molecular level as a component of systems biology approaches and for identifying potential biomarkers of various disease states. The large amount of data generated by utilizing high efficiency (e.g., chromatographic) separations coupled to high mass accuracy mass spectrometry for high-throughput proteomics analyses presents challenges related to data processing, analysis, and display. This review focuses on recent advances in nanoLC-FTICR-MS-based proteomics approaches and the accompanying data processing tools that have been developed to display and interpret the large volumes of data being produced. PMID:16429408

  12. Quantitative analysis of harmonic convergence in mosquito auditory interactions.

    PubMed

    Aldersley, Andrew; Champneys, Alan; Homer, Martin; Robert, Daniel

    2016-04-01

    This article analyses the hearing and behaviour of mosquitoes in the context of inter-individual acoustic interactions. The acoustic interactions of tethered live pairs of Aedes aegypti mosquitoes, from same and opposite sex mosquitoes of the species, are recorded on independent and unique audio channels, together with the response of tethered individual mosquitoes to playbacks of pre-recorded flight tones of lone or paired individuals. A time-dependent representation of each mosquito's non-stationary wing beat frequency signature is constructed, based on Hilbert spectral analysis. A range of algorithmic tools is developed to automatically analyse these data, and used to perform a robust quantitative identification of the 'harmonic convergence' phenomenon. The results suggest that harmonic convergence is an active phenomenon, which does not occur by chance. It occurs for live pairs, as well as for lone individuals responding to playback recordings, whether from the same or opposite sex. Male-female behaviour is dominated by frequency convergence at a wider range of harmonic combinations than previously reported, and requires participation from both partners in the duet. New evidence is found to show that male-male interactions are more varied than strict frequency avoidance. Rather, they can be divided into two groups: convergent pairs, typified by tightly bound wing beat frequencies, and divergent pairs, that remain widely spaced in the frequency domain. Overall, the results reveal that mosquito acoustic interaction is a delicate and intricate time-dependent active process that involves both individuals, takes place at many different frequencies, and which merits further enquiry.

  13. Quantitative analysis of harmonic convergence in mosquito auditory interactions

    PubMed Central

    Aldersley, Andrew; Champneys, Alan; Robert, Daniel

    2016-01-01

    This article analyses the hearing and behaviour of mosquitoes in the context of inter-individual acoustic interactions. The acoustic interactions of tethered live pairs of Aedes aegypti mosquitoes, from same and opposite sex mosquitoes of the species, are recorded on independent and unique audio channels, together with the response of tethered individual mosquitoes to playbacks of pre-recorded flight tones of lone or paired individuals. A time-dependent representation of each mosquito's non-stationary wing beat frequency signature is constructed, based on Hilbert spectral analysis. A range of algorithmic tools is developed to automatically analyse these data, and used to perform a robust quantitative identification of the ‘harmonic convergence’ phenomenon. The results suggest that harmonic convergence is an active phenomenon, which does not occur by chance. It occurs for live pairs, as well as for lone individuals responding to playback recordings, whether from the same or opposite sex. Male–female behaviour is dominated by frequency convergence at a wider range of harmonic combinations than previously reported, and requires participation from both partners in the duet. New evidence is found to show that male–male interactions are more varied than strict frequency avoidance. Rather, they can be divided into two groups: convergent pairs, typified by tightly bound wing beat frequencies, and divergent pairs, that remain widely spaced in the frequency domain. Overall, the results reveal that mosquito acoustic interaction is a delicate and intricate time-dependent active process that involves both individuals, takes place at many different frequencies, and which merits further enquiry. PMID:27053654

  14. Quantitative analysis of flavanones and chalcones from willow bark.

    PubMed

    Freischmidt, A; Untergehrer, M; Ziegler, J; Knuth, S; Okpanyi, S; Müller, J; Kelber, O; Weiser, D; Jürgenliemk, G

    2015-09-01

    Willow bark extracts are used for the treatment of fever, pain and inflammation. Recent clinical and pharmacological research revealed that not only the salicylic alcohol derivatives, but also the polyphenols significantly contribute to these effects. Quantitative analysis of the European Pharmacopoeia still focuses on the determination of the salicylic alcohol derivatives. The objective of the present study was the development of an effective quantification method for the determination of as many flavanone and chalcone glycosides as possible in Salix purpurea and other Salix species as well as commercial preparations thereof. As Salix species contain a diverse spectrum of the glycosidated flavanones naringenin, eriodictyol, and the chalcone chalconaringenin, a subsequent acidic and enzymatic hydrolysis was developed to yield naringenin and eriodictyol as aglycones, which were quantified by HPLC. The 5-O-glucosides were cleaved with 11.5% TFA before subsequent hydrolysis of the 7-O-glucosides with an almond β-glucosidase at pH 6-7. The method was validated with regard to LOD, LOQ, intraday and interday precision, accuracy, stability, recovery, time of hydrolysis, robustness and applicability to extracts. All 5-O- and 7-O-glucosides of naringenin, eriodictyol and chalconaringenin were completely hydrolysed and converted to naringenin and eriodictyol. The LOD of the HPLC method was 0.77 μM of naringenin and 0.45 μM of eriodictyol. The LOQ was 2.34 μM of naringenin and 1.35 μM for eriodictyol. The method is robust with regard to sample weight, but susceptible concerning enzyme deterioration. The developed method is applicable to the determination of flavanone and chalcone glycosides in willow bark and corresponding preparations.

  15. Hydrocarbons on Phoebe, Iapetus, and Hyperion: Quantitative Analysis

    NASA Technical Reports Server (NTRS)

    Cruikshank, Dale P.; MoreauDalleOre, Cristina; Pendleton, Yvonne J.; Clark, Roger Nelson

    2012-01-01

    We present a quantitative analysis of the hydrocarbon spectral bands measured on three of Saturn's satellites, Phoebe, Iaperus, and Hyperion. These bands, measured with the Cassini Visible-Infrared Mapping Spectrometer on close fly-by's of these satellites, are the C-H stretching modes of aromatic hydrocarbons at approximately 3.28 micrometers (approximately 3050 per centimeter), and the are four blended bands of aliphatic -CH2- and -CH3 in the range approximately 3.36-3.52 micrometers (approximately 2980- 2840 per centimeter) bably indicating the presence of polycyclic aromatic hydrocarbons (PAH), is unusually strong in comparison to the aliphatic bands, resulting in a unique signarure among Solar System bodies measured so far, and as such offers a means of comparison among the three satellites. The ratio of the C-H bands in aromatic molecules to those in aliphatic molecules in the surface materials of Phoebe, NAro:NAliph approximately 24; for Hyperion the value is approximately 12, while laperus shows an intermediate value. In view of the trend of the evolution (dehydrogenation by heat and radiation) of aliphatic complexes toward more compact molecules and eventually to aromatics, the relative abundances of aliphatic -CH2- and -CH3- is an indication of the lengths of the molecular chain structures, hence the degree of modification of the original material. We derive CH2:CH3 approximately 2.2 in the spectrum of low-albedo material on laperus; this value is the same within measurement errors to the ratio in the diffuse interstellar medium. The similarity in the spectral signatures of the three satellites, plus the apparent weak trend of aromatic/aliphatic abundance from Phoebe to Hyperion, is consistent with, and effectively confirms that the source of the hydrocarbon-bearing material is Phoebe, and that the appearance of that material on the other two satellites arises from the deposition of the inward-spiraling dust that populates the Phoebe ring.

  16. Quantitative Analysis of the Effective Functional Structure in Yeast Glycolysis

    PubMed Central

    De la Fuente, Ildefonso M.; Cortes, Jesus M.

    2012-01-01

    The understanding of the effective functionality that governs the enzymatic self-organized processes in cellular conditions is a crucial topic in the post-genomic era. In recent studies, Transfer Entropy has been proposed as a rigorous, robust and self-consistent method for the causal quantification of the functional information flow among nonlinear processes. Here, in order to quantify the functional connectivity for the glycolytic enzymes in dissipative conditions we have analyzed different catalytic patterns using the technique of Transfer Entropy. The data were obtained by means of a yeast glycolytic model formed by three delay differential equations where the enzymatic rate equations of the irreversible stages have been explicitly considered. These enzymatic activity functions were previously modeled and tested experimentally by other different groups. The results show the emergence of a new kind of dynamical functional structure, characterized by changing connectivity flows and a metabolic invariant that constrains the activity of the irreversible enzymes. In addition to the classical topological structure characterized by the specific location of enzymes, substrates, products and feedback-regulatory metabolites, an effective functional structure emerges in the modeled glycolytic system, which is dynamical and characterized by notable variations of the functional interactions. The dynamical structure also exhibits a metabolic invariant which constrains the functional attributes of the enzymes. Finally, in accordance with the classical biochemical studies, our numerical analysis reveals in a quantitative manner that the enzyme phosphofructokinase is the key-core of the metabolic system, behaving for all conditions as the main source of the effective causal flows in yeast glycolysis. PMID:22393350

  17. High performance thin layer chromatography (HPTLC) and high performance liquid chromatography (HPLC) for the qualitative and quantitative analysis of Calendula officinalis-advantages and limitations.

    PubMed

    Loescher, Christine M; Morton, David W; Razic, Slavica; Agatonovic-Kustrin, Snezana

    2014-09-01

    Chromatography techniques such as HPTLC and HPLC are commonly used to produce a chemical fingerprint of a plant to allow identification and quantify the main constituents within the plant. The aims of this study were to compare HPTLC and HPLC, for qualitative and quantitative analysis of the major constituents of Calendula officinalis and to investigate the effect of different extraction techniques on the C. officinalis extract composition from different parts of the plant. The results found HPTLC to be effective for qualitative analysis, however, HPLC was found to be more accurate for quantitative analysis. A combination of the two methods may be useful in a quality control setting as it would allow rapid qualitative analysis of herbal material while maintaining accurate quantification of extract composition.

  18. Toward a highly accurate ambulatory system for clinical gait analysis via UWB radios.

    PubMed

    Shaban, Heba A; Abou el-Nasr, Mohamad; Buehrer, R Michael

    2010-03-01

    In this paper, we propose and investigate a low-cost and low-complexity wireless ambulatory human locomotion tracking system that provides a high ranging accuracy (intersensor distance) suitable for the assessment of clinical gait analysis using wearable ultra wideband (UWB) transceivers. The system design and transceiver performance are presented in additive-white-gaussian noise and realistic channels, using industry accepted channel models for body area networks. The proposed system is theoretically capable of providing a ranging accuracy of 0.11 cm error at distances equivalent to interarker distances, at an 18 dB SNR in realistic on-body UWB channels. Based on real measurements, it provides the target ranging accuracy at an SNR = 20 dB. The achievable accuracy is ten times better than the accuracy reported in the literature for the intermarker-distance measurement. This makes it suitable for use in clinical gait analysis, and for the characterization and assessment of unstable mobility diseases, such as Parkinson's disease.

  19. Automated system for fast and accurate analysis of SF6 injected in the surface ocean.

    PubMed

    Koo, Chul-Min; Lee, Kitack; Kim, Miok; Kim, Dae-Ok

    2005-11-01

    This paper describes an automated sampling and analysis system for the shipboard measurement of dissolved sulfur hexafluoride (SF6) in surface marine environments into which SF6 has been deliberately released. This underway system includes a gas chromatograph associated with an electron capture detector, a fast and highly efficient SF6-extraction device, a global positioning system, and a data acquisition system based on Visual Basic 6.0/C 6.0. This work is distinct from previous studies in that it quantifies the efficiency of the SF6-extraction device and its carryover effect and examines the effect of surfactant on the SF6-extraction efficiency. Measurements can be continuously performed on seawater samples taken from a seawater line installed onboard a research vessel. The system runs on an hourly cycle during which one set of four SF6 standards is measured and SF6 derived from the seawater stream is subsequently analyzed for the rest of each 1 h period. This state-of-art system was successfully used to trace a water mass carrying Cochlodinium polykrikoides, which causes harmful algal blooms (HAB) in the coastal waters of southern Korea. The successful application of this analysis system in tracing the HAB-infected water mass suggests that the SF6 detection method described in this paper will improve the quality of the future study of biogeochemical processes in the marine environment.

  20. Combining multiple regression and principal component analysis for accurate predictions for column ozone in Peninsular Malaysia

    NASA Astrophysics Data System (ADS)

    Rajab, Jasim M.; MatJafri, M. Z.; Lim, H. S.

    2013-06-01

    This study encompasses columnar ozone modelling in the peninsular Malaysia. Data of eight atmospheric parameters [air surface temperature (AST), carbon monoxide (CO), methane (CH4), water vapour (H2Ovapour), skin surface temperature (SSKT), atmosphere temperature (AT), relative humidity (RH), and mean surface pressure (MSP)] data set, retrieved from NASA's Atmospheric Infrared Sounder (AIRS), for the entire period (2003-2008) was employed to develop models to predict the value of columnar ozone (O3) in study area. The combined method, which is based on using both multiple regressions combined with principal component analysis (PCA) modelling, was used to predict columnar ozone. This combined approach was utilized to improve the prediction accuracy of columnar ozone. Separate analysis was carried out for north east monsoon (NEM) and south west monsoon (SWM) seasons. The O3 was negatively correlated with CH4, H2Ovapour, RH, and MSP, whereas it was positively correlated with CO, AST, SSKT, and AT during both the NEM and SWM season periods. Multiple regression analysis was used to fit the columnar ozone data using the atmospheric parameter's variables as predictors. A variable selection method based on high loading of varimax rotated principal components was used to acquire subsets of the predictor variables to be comprised in the linear regression model of the atmospheric parameter's variables. It was found that the increase in columnar O3 value is associated with an increase in the values of AST, SSKT, AT, and CO and with a drop in the levels of CH4, H2Ovapour, RH, and MSP. The result of fitting the best models for the columnar O3 value using eight of the independent variables gave about the same values of the R (≈0.93) and R2 (≈0.86) for both the NEM and SWM seasons. The common variables that appeared in both regression equations were SSKT, CH4 and RH, and the principal precursor of the columnar O3 value in both the NEM and SWM seasons was SSKT.

  1. Duplicate portion sampling combined with spectrophotometric analysis affords the most accurate results when assessing daily dietary phosphorus intake.

    PubMed

    Navarro-Alarcon, Miguel; Zambrano, Esmeralda; Moreno-Montoro, Miriam; Agil, Ahmad; Olalla, Manuel

    2012-08-01

    The assessment of daily dietary phosphorus (P) intake is a major concern in human nutrition because of its relationship with Ca and Mg metabolism and osteoporosis. Within this context, we hypothesized that several of the methods available for the assessment of daily dietary intake of P are equally accurate and reliable, although few studies have been conducted to confirm this. The aim of this study then was to evaluate daily dietary P intake, which we did by 3 methods: duplicate portion sampling of 108 hospital meals, combined either with spectrophotometric analysis or the use of food composition tables, and 24-hour dietary recall for 3 consecutive days plus the use of food composition tables. The mean P daily dietary intakes found were 1106 ± 221, 1480 ± 221, and 1515 ± 223 mg/d, respectively. Daily dietary intake of P determined by spectrophotometric analysis was significantly lower (P < .001) and closer to dietary reference intakes for adolescents aged from 14 to 18 years (88.5%) and adult subjects (158.1%) compared with the other 2 methods. Duplicate portion sampling with P analysis takes into account the influence of technological and cooking processes on the P content of foods and meals and therefore afforded the most accurate and reliable P daily dietary intakes. The use of referred food composition tables overestimated daily dietary P intake. No adverse effects in relation to P nutrition (deficiencies or toxic effects) were encountered.

  2. Simulating Expert Clinical Comprehension: Adapting Latent Semantic Analysis to Accurately Extract Clinical Concepts from Psychiatric Narrative

    PubMed Central

    Cohen, Trevor; Blatter, Brett; Patel, Vimla

    2008-01-01

    Cognitive studies reveal that less-than-expert clinicians are less able to recognize meaningful patterns of data in clinical narratives. Accordingly, psychiatric residents early in training fail to attend to information that is relevant to diagnosis and the assessment of dangerousness. This manuscript presents cognitively motivated methodology for the simulation of expert ability to organize relevant findings supporting intermediate diagnostic hypotheses. Latent Semantic Analysis is used to generate a semantic space from which meaningful associations between psychiatric terms are derived. Diagnostically meaningful clusters are modeled as geometric structures within this space and compared to elements of psychiatric narrative text using semantic distance measures. A learning algorithm is defined that alters components of these geometric structures in response to labeled training data. Extraction and classification of relevant text segments is evaluated against expert annotation, with system-rater agreement approximating rater-rater agreement. A range of biomedical informatics applications for these methods are suggested. PMID:18455483

  3. Computer-implemented system and method for automated and highly accurate plaque analysis, reporting, and visualization

    NASA Technical Reports Server (NTRS)

    Kemp, James Herbert (Inventor); Talukder, Ashit (Inventor); Lambert, James (Inventor); Lam, Raymond (Inventor)

    2008-01-01

    A computer-implemented system and method of intra-oral analysis for measuring plaque removal is disclosed. The system includes hardware for real-time image acquisition and software to store the acquired images on a patient-by-patient basis. The system implements algorithms to segment teeth of interest from surrounding gum, and uses a real-time image-based morphing procedure to automatically overlay a grid onto each segmented tooth. Pattern recognition methods are used to classify plaque from surrounding gum and enamel, while ignoring glare effects due to the reflection of camera light and ambient light from enamel regions. The system integrates these components into a single software suite with an easy-to-use graphical user interface (GUI) that allows users to do an end-to-end run of a patient record, including tooth segmentation of all teeth, grid morphing of each segmented tooth, and plaque classification of each tooth image.

  4. An Accurate Method for Free Vibration Analysis of Structures with Application to Plates

    NASA Astrophysics Data System (ADS)

    KEVORKIAN, S.; PASCAL, M.

    2001-10-01

    In this work, the continuous element method which has been used as an alternative to the finite element method of vibration analysis of frames is applied to more general structures like 3-D continuum and rectangular plates. The method is based on the concept of the so-called impedance matrix giving in the frequency domain, the linear relation between the generalized displacements of the boundaries and the generalized forces exerted on these boundaries. For a 3-D continuum, the concept of impedance matrix is introduced assuming a particular kind of boundary conditions. For rectangular plates, this new development leads to the solution of vibration problems for boundary conditions other than the simply supported ones.

  5. Accurate wavelength calibration in the near-infrared for multielement analysis without the need for reference spectra

    SciTech Connect

    Asimellis, George; Giannoudakos, Aggelos; Kompitsas, Michael

    2006-12-10

    A new technique has been developed for an instant, precise, and accurate wavelength calibration over a wide pixel array for simultaneous, multielement spectral analysis based on an inverse numerical solution to the grating dispersion function.This technique is applicable to multielement analytical applications such as laser-induced breakdown spectroscopy (LIBS), particularly when using high-density gratings in the upper visible and in the near-infrared, where nonmetallic elements are detected.This application overcomes the need to use reference spectra for each window of observation and is tested on a commercially available LIBS instrument.

  6. Quantitative PCR analysis of salivary pathogen burden in periodontitis

    PubMed Central

    Salminen, Aino; Kopra, K. A. Elisa; Hyvärinen, Kati; Paju, Susanna; Mäntylä, Päivi; Buhlin, Kåre; Nieminen, Markku S.; Sinisalo, Juha; Pussinen, Pirkko J.

    2015-01-01

    Our aim was to investigate the value of salivary concentrations of four major periodontal pathogens and their combination in diagnostics of periodontitis. The Parogene study included 462 dentate subjects (mean age 62.9 ± 9.2 years) with coronary artery disease (CAD) diagnosis who underwent an extensive clinical and radiographic oral examination. Salivary levels of four major periodontal bacteria were measured by quantitative real-time PCR (qPCR). Median salivary concentrations of Porphyromonas gingivalis, Tannerella forsythia, and Prevotella intermedia, as well as the sum of the concentrations of the four bacteria, were higher in subjects with moderate to severe periodontitis compared to subjects with no to mild periodontitis. Median salivary Aggregatibacter actinomycetemcomitans concentrations did not differ significantly between the subjects with no to mild periodontitis and subjects with moderate to severe periodontitis. In logistic regression analysis adjusted for age, gender, diabetes, and the number of teeth and implants, high salivary concentrations of P. gingivalis, T. forsythia, and P. intermedia were significantly associated with moderate to severe periodontitis. When looking at different clinical and radiographic parameters of periodontitis, high concentrations of P. gingivalis and T. forsythia were significantly associated with the number of 4–5 mm periodontal pockets, ≥6 mm pockets, and alveolar bone loss (ABL). High level of T. forsythia was associated also with bleeding on probing (BOP). The combination of the four bacteria, i.e., the bacterial burden index, was associated with moderate to severe periodontitis with an odds ratio (OR) of 2.40 (95% CI 1.39–4.13). When A. actinomycetemcomitans was excluded from the combination of the bacteria, the OR was improved to 2.61 (95% CI 1.51–4.52). The highest OR 3.59 (95% CI 1.94–6.63) was achieved when P. intermedia was further excluded from the combination and only the levels of P. gingivalis and

  7. Quantitative PCR analysis of salivary pathogen burden in periodontitis.

    PubMed

    Salminen, Aino; Kopra, K A Elisa; Hyvärinen, Kati; Paju, Susanna; Mäntylä, Päivi; Buhlin, Kåre; Nieminen, Markku S; Sinisalo, Juha; Pussinen, Pirkko J

    2015-01-01

    Our aim was to investigate the value of salivary concentrations of four major periodontal pathogens and their combination in diagnostics of periodontitis. The Parogene study included 462 dentate subjects (mean age 62.9 ± 9.2 years) with coronary artery disease (CAD) diagnosis who underwent an extensive clinical and radiographic oral examination. Salivary levels of four major periodontal bacteria were measured by quantitative real-time PCR (qPCR). Median salivary concentrations of Porphyromonas gingivalis, Tannerella forsythia, and Prevotella intermedia, as well as the sum of the concentrations of the four bacteria, were higher in subjects with moderate to severe periodontitis compared to subjects with no to mild periodontitis. Median salivary Aggregatibacter actinomycetemcomitans concentrations did not differ significantly between the subjects with no to mild periodontitis and subjects with moderate to severe periodontitis. In logistic regression analysis adjusted for age, gender, diabetes, and the number of teeth and implants, high salivary concentrations of P. gingivalis, T. forsythia, and P. intermedia were significantly associated with moderate to severe periodontitis. When looking at different clinical and radiographic parameters of periodontitis, high concentrations of P. gingivalis and T. forsythia were significantly associated with the number of 4-5 mm periodontal pockets, ≥6 mm pockets, and alveolar bone loss (ABL). High level of T. forsythia was associated also with bleeding on probing (BOP). The combination of the four bacteria, i.e., the bacterial burden index, was associated with moderate to severe periodontitis with an odds ratio (OR) of 2.40 (95% CI 1.39-4.13). When A. actinomycetemcomitans was excluded from the combination of the bacteria, the OR was improved to 2.61 (95% CI 1.51-4.52). The highest OR 3.59 (95% CI 1.94-6.63) was achieved when P. intermedia was further excluded from the combination and only the levels of P. gingivalis and T

  8. A Quantitative Analysis of the Behavioral Checklist of the Movement ABC Motor Test

    ERIC Educational Resources Information Center

    Ruiz, Luis Miguel; Gomez, Marta; Graupera, Jose Luis; Gutierrez, Melchor; Linaza, Jose Luis

    2007-01-01

    The fifth section of the Henderson and Sugden's Movement ABC Checklist is part of the general Checklist that accompanies The Movement ABC Battery. The authors maintain that the analysis of this section must be mainly qualitative instead of quantitative. The main objective of this study was to employ a quantitative analysis of this behavioural…

  9. Quantitative proton nuclear magnetic resonance for the structural and quantitative analysis of atropine sulfate.

    PubMed

    Shen, Shi; Yao, Jing; Shi, Yaqin

    2014-02-01

    This study assessed a general method of quantitative nuclear magnetic resonance (qNMR) for the calibration of atropine sulfate (Active Pharmaceutical Ingredient, API) as reference standard. The spectra were acquired in D2O using maleic acid as the internal standard. Conformational behaviors of tropane ring were observed and studied by means of NMR and ROESY experiments at different temperature, which showed that the azine methyl group was at equilibrium for axial and equatorial conformations at room temperature. Signal delay and monitor signals of qNMR experimentation were optimized for quantification. The study reported here validated the method's linearity, range, limit of quantification, stability and precision. The results were consistent with the results obtained from mass balance approach.

  10. Derivation of a quantitative minimal model from a detailed elementary-step mechanism supported by mathematical coupling analysis

    NASA Astrophysics Data System (ADS)

    Shaik, O. S.; Kammerer, J.; Gorecki, J.; Lebiedz, D.

    2005-12-01

    Accurate experimental data increasingly allow the development of detailed elementary-step mechanisms for complex chemical and biochemical reaction systems. Model reduction techniques are widely applied to obtain representations in lower-dimensional phase space which are more suitable for mathematical analysis, efficient numerical simulation, and model-based control tasks. Here, we exploit a recently implemented numerical algorithm for error-controlled computation of the minimum dimension required for a still accurate reduced mechanism based on automatic time scale decomposition and relaxation of fast modes. We determine species contributions to the active (slow) dynamical modes of the reaction system and exploit this information in combination with quasi-steady-state and partial-equilibrium approximations for explicit model reduction of a novel detailed chemical mechanism for the Ru-catalyzed light-sensitive Belousov-Zhabotinsky reaction. The existence of a minimum dimension of seven is demonstrated to be mandatory for the reduced model to show good quantitative consistency with the full model in numerical simulations. We derive such a maximally reduced seven-variable model from the detailed elementary-step mechanism and demonstrate that it reproduces quantitatively accurately the dynamical features of the full model within a given accuracy tolerance.

  11. Quantitative hopanoid analysis enables robust pattern detection and comparison between laboratories.

    PubMed

    Wu, C-H; Kong, L; Bialecka-Fornal, M; Park, S; Thompson, A L; Kulkarni, G; Conway, S J; Newman, D K

    2015-07-01

    Hopanoids are steroid-like lipids from the isoprenoid family that are produced primarily by bacteria. Hopanes, molecular fossils of hopanoids, offer the potential to provide insight into environmental transitions on the early Earth, if their sources and biological functions can be constrained. Semiquantitative methods for mass spectrometric analysis of hopanoids from cultures and environmental samples have been developed in the last two decades. However, the structural diversity of hopanoids, and possible variability in their ionization efficiencies on different instruments, have thus far precluded robust quantification and hindered comparison of results between laboratories. These ionization inconsistencies give rise to the need to calibrate individual instruments with purified hopanoids to reliably quantify hopanoids. Here, we present new approaches to obtain both purified and synthetic quantification standards. We optimized 2-methylhopanoid production in Rhodopseudomonas palustris TIE-1 and purified 2Me-diplopterol, 2Me-bacteriohopanetetrol (2Me-BHT), and their unmethylated species (diplopterol and BHT). We found that 2-methylation decreases the signal intensity of diplopterol between 2 and 34% depending on the instrument used to detect it, but decreases the BHT signal less than 5%. In addition, 2Me-diplopterol produces 10× higher ion counts than equivalent quantities of 2Me-BHT. Similar deviations were also observed using a flame ionization detector for signal quantification in GC. In LC-MS, however, 2Me-BHT produces 11× higher ion counts than 2Me-diplopterol but only 1.2× higher ion counts than the sterol standard pregnane acetate. To further improve quantification, we synthesized tetradeuterated (D4) diplopterol, a precursor for a variety of hopanoids. LC-MS analysis on a mixture of (D4)-diplopterol and phospholipids showed that under the influence of co-eluted phospholipids, the D4-diplopterol internal standard quantifies diplopterol more accurately than

  12. Quantitative hopanoid analysis enables robust pattern detection and comparison between laboratories

    PubMed Central

    Wu, C-H; Kong, L; Bialecka-Fornal, M; Park, S; Thompson, A L; Kulkarni, G; Conway, S J; Newman, D K

    2015-01-01

    Hopanoids are steroid-like lipids from the isoprenoid family that are produced primarily by bacteria. Hopanes, molecular fossils of hopanoids, offer the potential to provide insight into environmental transitions on the early Earth, if their sources and biological functions can be constrained. Semiquantitative methods for mass spectrometric analysis of hopanoids from cultures and environmental samples have been developed in the last two decades. However, the structural diversity of hopanoids, and possible variability in their ionization efficiencies on different instruments, have thus far precluded robust quantification and hindered comparison of results between laboratories. These ionization inconsistencies give rise to the need to calibrate individual instruments with purified hopanoids to reliably quantify hopanoids. Here, we present new approaches to obtain both purified and synthetic quantification standards. We optimized 2-methylhopanoid production in Rhodopseudomonas palustris TIE-1 and purified 2Me-diplopterol, 2Me-bacteriohopanetetrol (2Me-BHT), and their unmethylated species (diplopterol and BHT). We found that 2-methylation decreases the signal intensity of diplopterol between 2 and 34% depending on the instrument used to detect it, but decreases the BHT signal less than 5%. In addition, 2Me-diplopterol produces 10× higher ion counts than equivalent quantities of 2Me-BHT. Similar deviations were also observed using a flame ionization detector for signal quantification in GC. In LC-MS, however, 2Me-BHT produces 11× higher ion counts than 2Me-diplopterol but only 1.2× higher ion counts than the sterol standard pregnane acetate. To further improve quantification, we synthesized tetradeuterated (D4) diplopterol, a precursor for a variety of hopanoids. LC-MS analysis on a mixture of (D4)-diplopterol and phospholipids showed that under the influence of co-eluted phospholipids, the D4-diplopterol internal standard quantifies diplopterol more accurately than

  13. A Cost-Benefit and Accurate Method for Assessing Microalbuminuria: Single versus Frequent Urine Analysis.

    PubMed

    Hemmati, Roholla; Gharipour, Mojgan; Khosravi, Alireza; Jozan, Mahnaz

    2013-01-01

    Background. The purpose of this study was to answer the question whether a single testing for microalbuminuria results in a reliable conclusion leading costs saving. Methods. This current cross-sectional study included a total of 126 consecutive persons. Microalbuminuria was assessed by collection of two fasting random urine specimens on arrival to the clinic as well as one week later in the morning. Results. In overall, 17 out of 126 participants suffered from microalbuminuria that, among them, 12 subjects were also diagnosed as microalbuminuria once assessing this factor with a sensitivity of 70.6%, a specificity of 100%, a PPV of 100%, a NPV of 95.6%, and an accuracy of 96.0%. The measured sensitivity, specificity, PVV, NPV, and accuracy in hypertensive patients were 73.3%, 100%, 100%, 94.8%, and 95.5%, respectively. Also, these rates in nonhypertensive groups were 50.0%, 100%, 100%, 97.3%, and 97.4%, respectively. According to the ROC curve analysis, a single measurement of UACR had a high value for discriminating defected from normal renal function state (c = 0.989). Urinary albumin concentration in a single measurement had also high discriminative value for diagnosis of damaged kidney (c = 0.995). Conclusion. The single testing of both UACR and urine albumin level rather frequent testing leads to high diagnostic sensitivity, specificity, and accuracy as well as high predictive values in total population and also in hypertensive subgroups.

  14. Integrative subcellular proteomic analysis allows accurate prediction of human disease-causing genes

    PubMed Central

    Zhao, Li; Chen, Yiyun; Bajaj, Amol Onkar; Eblimit, Aiden; Xu, Mingchu; Soens, Zachry T.; Wang, Feng; Ge, Zhongqi; Jung, Sung Yun; He, Feng; Li, Yumei; Wensel, Theodore G.; Qin, Jun; Chen, Rui

    2016-01-01

    Proteomic profiling on subcellular fractions provides invaluable information regarding both protein abundance and subcellular localization. When integrated with other data sets, it can greatly enhance our ability to predict gene function genome-wide. In this study, we performed a comprehensive proteomic analysis on the light-sensing compartment of photoreceptors called the outer segment (OS). By comparing with the protein profile obtained from the retina tissue depleted of OS, an enrichment score for each protein is calculated to quantify protein subcellular localization, and 84% accuracy is achieved compared with experimental data. By integrating the protein OS enrichment score, the protein abundance, and the retina transcriptome, the probability of a gene playing an essential function in photoreceptor cells is derived with high specificity and sensitivity. As a result, a list of genes that will likely result in human retinal disease when mutated was identified and validated by previous literature and/or animal model studies. Therefore, this new methodology demonstrates the synergy of combining subcellular fractionation proteomics with other omics data sets and is generally applicable to other tissues and diseases. PMID:26912414

  15. Laser-Ablation Sampling for Accurate Analysis of Sulfur in Edible Salts.

    PubMed

    Lee, Yonghoon; Chirinos, Jose; Gonzalez, Jhanis; Oropeza, Dayana; Zorba, Vassilia; Mao, Xianglei; Yoo, Jonghyun; Russo, Richard E

    2017-04-01

    We evaluated the performance of laser ablation analysis techniques such as laser-induced breakdown spectroscopy (LIBS), laser ablation inductively coupled optical emission spectrometry (LA-ICP-OES), and laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS), in comparison with that of ICP-OES using aqueous solutions for the quantification of sulfur (S) in edible salts from different geographical origins. We found that the laser ablation based sampling techniques were not influenced by loss of S, which was observed in ICP-OES with aqueous solutions for a certain salt upon their dissolution in aqueous solutions, originating from the formation of volatile species and precipitates upon their dilution in water. Although detection of S using direct laser sampling with LA-ICP-MS has well-known isobaric and polyatomic interferences, LIBS and LA-ICP-OES showed good accuracy in the detection of S for all salts. LIBS also provided the ability to identify the dominant chemical form in which S is present in salts. Correlation between S and oxygen, observed in LIBS spectra, provided chemical information about the presence of S(2-) or [Formula: see text], which are associated with the origin and quality of edible salts.

  16. Accurate analysis of taurine, anserine, carnosine and free amino acids in a cattle muscle biopsy sample.

    PubMed

    Imanari, Mai; Higuchi, Mikito; Shiba, Nobuya; Watanabe, Akira

    2010-06-01

    We have established an analysis method for some free amino acids (FAAs), as well as taurine (Tau), anserine (Ans) and carnosine (Car), in a fresh biopsy sample from cattle muscle. A series of model biopsy samples, corresponding to the mixtures of lean meat, fat and connective tissue, was prepared and showed high correlation coefficients between the compound concentration and the 3-methylhistidine (3-MeHis) content derived from hydrolysis of the biopsy sample (r = 0.74-0.95, P < 0.01). Interference from blood contamination could not be neglected, because the concentration of some FAAs in blood was comparable to that in muscle. However, it was possible to control the contamination of Tau, Ans, Car, glutamic acid, glutamine, asparatic acid and alanine to less than 5.0% when the blood contamination was controlled to less than 23%.These results suggest the necessity of measuring 3-MeHis as an index of lean meat and hemoglobin as an index of blood contamination when compounds in muscle biopsy samples are evaluated. We have carried out a series of these analyses using one biopsy sample and reveal differences in Tau, Ans, Car and some FAAs in beef muscle after different feeding regimes.

  17. Accurate determination of the diffusion coefficient of proteins by Fourier analysis with whole column imaging detection.

    PubMed

    Zarabadi, Atefeh S; Pawliszyn, Janusz

    2015-02-17

    Analysis in the frequency domain is considered a powerful tool to elicit precise information from spectroscopic signals. In this study, the Fourier transformation technique is employed to determine the diffusion coefficient (D) of a number of proteins in the frequency domain. Analytical approaches are investigated for determination of D from both experimental and data treatment viewpoints. The diffusion process is modeled to calculate diffusion coefficients based on the Fourier transformation solution to Fick's law equation, and its results are compared to time domain results. The simulations characterize optimum spatial and temporal conditions and demonstrate the noise tolerance of the method. The proposed model is validated by its application for the electropherograms from the diffusion path of a set of proteins. Real-time dynamic scanning is conducted to monitor dispersion by employing whole column imaging detection technology in combination with capillary isoelectric focusing (CIEF) and the imaging plug flow (iPF) experiment. These experimental techniques provide different peak shapes, which are utilized to demonstrate the Fourier transformation ability in extracting diffusion coefficients out of irregular shape signals. Experimental results confirmed that the Fourier transformation procedure substantially enhanced the accuracy of the determined values compared to those obtained in the time domain.

  18. Accurate modeling of antennas for radiating short pulses, FDTD analysis and experimental measurements

    NASA Astrophysics Data System (ADS)

    Maloney, James G.; Smith, Glenn S.

    1993-01-01

    Antennas used to radiate short pulses often require different design rules that those that are used to radiate essentially time-harmonic signals. The finite-difference time-domain (FDTD) method is a very flexible numerical approach that can be used to treat a variety of electromagnetic problems in the time domain. It is well suited to the analysis and design of antennas for radiating short pulses; however, several advances had to be made before the method could be applied to this problem. In this paper, we will illustrate the use of the FDTD method with two antennas designed for the radiation of short pulses. The first is a simple, two-dimensional geometry, and open-ended parallel-plate waveguide, while the second is a three-dimensional, rotationally symmetric geometry, a conical monopole fed through an image by a coaxial transmission line. Both antennas are 'optimized' according to given criteria by adjusting geometrical parameters and including resistive loading that varies continuously with position along the antenna. The predicted performance for the conical monopole antenna is compared with experimental measurements; this verifies the optimization and demonstrates the practicality of the design.

  19. Borehole flowmeter logging for the accurate design and analysis of tracer tests.

    PubMed

    Basiricò, Stefano; Crosta, Giovanni B; Frattini, Paolo; Villa, Alberto; Godio, Alberto

    2015-04-01

    Tracer tests often give ambiguous interpretations that may be due to the erroneous location of sampling points and/or the lack of flow rate measurements through the sampler. To obtain more reliable tracer test results, we propose a methodology that optimizes the design and analysis of tracer tests in a cross borehole mode by using vertical borehole flow rate measurements. Experiments using this approach, herein defined as the Bh-flow tracer test, have been performed by implementing three sequential steps: (1) single-hole flowmeter test, (2) cross-hole flowmeter test, and (3) tracer test. At the experimental site, core logging, pumping tests, and static water-level measurements were previously carried out to determine stratigraphy, fracture characteristics, and bulk hydraulic conductivity. Single-hole flowmeter testing makes it possible to detect the presence of vertical flows as well as inflow and outflow zones, whereas cross-hole flowmeter testing detects the presence of connections along sets of flow conduits or discontinuities intercepted by boreholes. Finally, the specific pathways and rates of groundwater flow through selected flowpaths are determined by tracer testing. We conclude that the combined use of single and cross-borehole flowmeter tests is fundamental to the formulation of the tracer test strategy and interpretation of the tracer test results.

  20. Cortical Up State Activity Is Enhanced After Seizures: A Quantitative Analysis

    PubMed Central

    Gerkin, Richard C.; Clem, Roger L.; Shruti, Sonal; Kass, Robert E.; Barth, Alison L.

    2011-01-01

    In the neocortex, neurons participate in epochs of elevated activity, or Up states, during periods of quiescent wakefulness, slow-wave sleep, and general anesthesia. The regulation of firing during and between Up states is of great interest because it can reflect the underlying connectivity and excitability of neurons within the network. Automated analysis of the onset and characteristics of Up state firing across different experiments and conditions requires a robust and accurate method for Up state detection. Using measurements of membrane potential mean and variance calculated from whole-cell recordings of neurons from control and postseizure tissue, the authors have developed such a method. This quantitative and automated method is independent of cell- or condition-dependent variability in underlying noise or tonic firing activity. Using this approach, the authors show that Up state frequency and firing rates are significantly increased in layer 2/3 neocortical neurons 24 hours after chemo-convulsant-induced seizure. Down states in postseizure tissue show greater membrane-potential variance characterized by increased synaptic activity. Previously, the authors have found that postseizure increase in excitability is linked to a gain-of-function in BK channels, and blocking BK channels in vitro and in vivo can decrease excitability and eliminate seizures. Thus, the authors also assessed the effect of BK-channel antagonists on Up state properties in control and postseizure neurons. These data establish a robust and broadly applicable algorithm for Up state detection and analysis, provide a quantitative description of how prior seizures increase spontaneous firing activity in cortical networks, and show how BK-channel antagonists reduce this abnormal activity. PMID:21127407

  1. Flow injection combined with ICP-MS for accurate high throughput analysis of elemental impurities in pharmaceutical products according to USP <232>/<233>.

    PubMed

    Fischer, Lisa; Zipfel, Barbara; Koellensperger, Gunda; Kovac, Jessica; Bilz, Susanne; Kunkel, Andrea; Venzago, Cornel; Hann, Stephan

    2014-07-01

    New guidelines of the United States Pharmacopeia (USP), European Pharmacopeia (EP) and international organization (ICH, International Conference on Harmonization) regulating elemental impurity limits in pharmaceuticals seal the end of unspecific analysis of metal(oid)s as outlined in USP <231> and EP 2.4.8. Chapter USP <232> and EP 5.20 as well as drafts from ICH Q3D specify both daily doses and concentration limits of metallic impurities in pharmaceutical final products and in active pharmaceutical ingredients (API) and excipients. In chapters USP <233> and EP 2.4.20 method implementation, validation and quality control during the analytical process are described. By contrast with the--by now--applied methods, substance specific quantitative analysis features new basic requirements, further, significantly lower detection limits ask for the necessity of a general changeover of the methodology toward sensitive multi element analysis by ICP-AES and ICP-MS, respectively. A novel methodological approach based on flow injection analysis and ICP-SFMS/ICP-QMS for the quick and accurate analysis of Cd, Pb, As, Hg, Ir, Os, Pd, Pt, Rh, Ru, Cr, Mo, Ni, V, Cu, Mn, Fe and Zn in drug products by prior dilution, dissolution or microwave assisted closed vessel digestion according to the regulations is presented. In comparison to the acquisition of continuous signals, this method is advantageous with respect to the unprecedented high sample throughput due to a total analysis time of approximately 30s and the low sample consumption of below 50 μL, while meeting the strict USP demands on detection/quantification limits, precision and accuracy.

  2. Quantitative Analysis by Isotopic Dilution Using Mass Spectroscopy: The Determination of Caffeine by GC-MS.

    ERIC Educational Resources Information Center

    Hill, Devon W.; And Others

    1988-01-01

    Describes a laboratory technique for quantitative analysis of caffeine by an isotopic dilution method for coupled gas chromatography-mass spectroscopy. Discusses caffeine analysis and experimental methodology. Lists sample caffeine concentrations found in common products. (MVL)

  3. Preoperative misdiagnosis analysis and accurate distinguish intrathymic cyst from small thymoma on computed tomography

    PubMed Central

    Li, Xin; Han, Xingpeng; Sun, Wei; Wang, Meng; Jing, Guohui

    2016-01-01

    Background To evaluate the role of computed tomography (CT) in preoperative diagnosis of intrathymic cyst and small thymoma, and determine the best CT threshold for distinguish intrathymic cyst from small thymoma. Methods We retrospectively reviewed the medical records of 30 patients (17 intrathymic cyst and 13 small thymoma) who had undergone mediastinal masses resection (with diameter less than 3 cm) under thoracoscope between January 2014 and July 2015 at our hospital. Clinical and CT features were compared and receiver-operating characteristics curve (ROC) analysis was performed. Results The CT value of small thymoma [39.5 HU (IQR, 33.7–42.2 HU)] was significantly higher than intrathymic cyst [25.8 HU (IQR, 22.3–29.3 HU), P=0.004]. When CT value was 31.2 HU, it could act as a threshold for identification of small thymoma and intrathymic cyst (the sensitivity and specificity was 92.3% and 82.4%, respectively). The ΔCT value of enhanced CT value with the non-enhanced CT value was significantly different between small thymoma [18.7 HU (IQR, 10.9–19.0 HU)] and intrathymic cyst [4.3 HU (IQR, 3.0–11.7 HU), P=0.04]. The density was more homogenous in intrathymic cyst than small thymoma, and the contour of the intrathymic cyst was more smoothly than small thymoma. Conclusions Preoperative CT scans could help clinicians to identify intrathymic cyst and small thymoma, and we recommend 31.2 HU as the best thresholds. Contrast-enhanced CT scans is useful for further identification of the two diseases. PMID:27621863

  4. Whole-Genome Sequencing Analysis Accurately Predicts Antimicrobial Resistance Phenotypes in Campylobacter spp.

    PubMed

    Zhao, S; Tyson, G H; Chen, Y; Li, C; Mukherjee, S; Young, S; Lam, C; Folster, J P; Whichard, J M; McDermott, P F

    2015-10-30

    The objectives of this study were to identify antimicrobial resistance genotypes for Campylobacter and to evaluate the correlation between resistance phenotypes and genotypes using in vitro antimicrobial susceptibility testing and whole-genome sequencing (WGS). A total of 114 Campylobacter species isolates (82 C. coli and 32 C. jejuni) obtained from 2000 to 2013 from humans, retail meats, and cecal samples from food production animals in the United States as part of the National Antimicrobial Resistance Monitoring System were selected for study. Resistance phenotypes were determined using broth microdilution of nine antimicrobials. Genomic DNA was sequenced using the Illumina MiSeq platform, and resistance genotypes were identified using assembled WGS sequences through blastx analysis. Eighteen resistance genes, including tet(O), blaOXA-61, catA, lnu(C), aph(2″)-Ib, aph(2″)-Ic, aph(2')-If, aph(2″)-Ig, aph(2″)-Ih, aac(6')-Ie-aph(2″)-Ia, aac(6')-Ie-aph(2″)-If, aac(6')-Im, aadE, sat4, ant(6'), aad9, aph(3')-Ic, and aph(3')-IIIa, and mutations in two housekeeping genes (gyrA and 23S rRNA) were identified. There was a high degree of correlation between phenotypic resistance to a given drug and the presence of one or more corresponding resistance genes. Phenotypic and genotypic correlation was 100% for tetracycline, ciprofloxacin/nalidixic acid, and erythromycin, and correlations ranged from 95.4% to 98.7% for gentamicin, azithromycin, clindamycin, and telithromycin. All isolates were susceptible to florfenicol, and no genes associated with florfenicol resistance were detected. There was a strong correlation (99.2%) between resistance genotypes and phenotypes, suggesting that WGS is a reliable indicator of resistance to the nine antimicrobial agents assayed in this study. WGS has the potential to be a powerful tool for antimicrobial resistance surveillance programs.

  5. Microchromatography of hemoglobins. VIII. A general qualitative and quantitative method in plastic drinking straws and the quantitative analysis of Hb-F.

    PubMed

    Schroeder, W A; Pace, L A

    1978-03-01

    The microchromatographic procedure for the quantitative analysis of the hemoglobin components in a hemolysate uses columns of DEAE-cellulose in a plastic drinking straw with a glycine-KCN-NaCl developer. Not only may the method be used for the quantitative analysis of Hb-F but also for the analysis of the varied components in mixtures of hemoglobins.

  6. Geographical classification of Epimedium based on HPLC fingerprint analysis combined with multi-ingredients quantitative analysis.

    PubMed

    Xu, Ning; Zhou, Guofu; Li, Xiaojuan; Lu, Heng; Meng, Fanyun; Zhai, Huaqiang

    2017-05-01

    A reliable and comprehensive method for identifying the origin and assessing the quality of Epimedium has been developed. The method is based on analysis of HPLC fingerprints, combined with similarity analysis, hierarchical cluster analysis (HCA), principal component analysis (PCA) and multi-ingredient quantitative analysis. Nineteen batches of Epimedium, collected from different areas in the western regions of China, were used to establish the fingerprints and 18 peaks were selected for the analysis. Similarity analysis, HCA and PCA all classified the 19 areas into three groups. Simultaneous quantification of the five major bioactive ingredients in the Epimedium samples was also carried out to confirm the consistency of the quality tests. These methods were successfully used to identify the geographical origin of the Epimedium samples and to evaluate their quality.

  7. Whole-Genome Sequencing Analysis Accurately Predicts Antimicrobial Resistance Phenotypes in Campylobacter spp.

    PubMed Central

    Tyson, G. H.; Chen, Y.; Li, C.; Mukherjee, S.; Young, S.; Lam, C.; Folster, J. P.; Whichard, J. M.; McDermott, P. F.

    2015-01-01

    The objectives of this study were to identify antimicrobial resistance genotypes for Campylobacter and to evaluate the correlation between resistance phenotypes and genotypes using in vitro antimicrobial susceptibility testing and whole-genome sequencing (WGS). A total of 114 Campylobacter species isolates (82 C. coli and 32 C. jejuni) obtained from 2000 to 2013 from humans, retail meats, and cecal samples from food production animals in the United States as part of the National Antimicrobial Resistance Monitoring System were selected for study. Resistance phenotypes were determined using broth microdilution of nine antimicrobials. Genomic DNA was sequenced using the Illumina MiSeq platform, and resistance genotypes were identified using assembled WGS sequences through blastx analysis. Eighteen resistance genes, including tet(O), blaOXA-61, catA, lnu(C), aph(2″)-Ib, aph(2″)-Ic, aph(2′)-If, aph(2″)-Ig, aph(2″)-Ih, aac(6′)-Ie-aph(2″)-Ia, aac(6′)-Ie-aph(2″)-If, aac(6′)-Im, aadE, sat4, ant(6′), aad9, aph(3′)-Ic, and aph(3′)-IIIa, and mutations in two housekeeping genes (gyrA and 23S rRNA) were identified. There was a high degree of correlation between phenotypic resistance to a given drug and the presence of one or more corresponding resistance genes. Phenotypic and genotypic correlation was 100% for tetracycline, ciprofloxacin/nalidixic acid, and erythromycin, and correlations ranged from 95.4% to 98.7% for gentamicin, azithromycin, clindamycin, and telithromycin. All isolates were susceptible to florfenicol, and no genes associated with florfenicol resistance were detected. There was a strong correlation (99.2%) between resistance genotypes and phenotypes, suggesting that WGS is a reliable indicator of resistance to the nine antimicrobial agents assayed in this study. WGS has the potential to be a powerful tool for antimicrobial resistance surveillance programs. PMID:26519386

  8. Quantitatively estimating defects in graphene devices using discharge current analysis method

    PubMed Central

    Jung, Ukjin; Lee, Young Gon; Kang, Chang Goo; Lee, Sangchul; Kim, Jin Ju; Hwang, Hyeon June; Lim, Sung Kwan; Ham, Moon-Ho; Lee, Byoung Hun

    2014-01-01

    Defects of graphene are the most important concern for the successful applications of graphene since they affect device performance significantly. However, once the graphene is integrated in the device structures, the quality of graphene and surrounding environment could only be assessed using indirect information such as hysteresis, mobility and drive current. Here we develop a discharge current analysis method to measure the quality of graphene integrated in a field effect transistor structure by analyzing the discharge current and examine its validity using various device structures. The density of charging sites affecting the performance of graphene field effect transistor obtained using the discharge current analysis method was on the order of 1014/cm2, which closely correlates with the intensity ratio of the D to G bands in Raman spectroscopy. The graphene FETs fabricated on poly(ethylene naphthalate) (PEN) are found to have a lower density of charging sites than those on SiO2/Si substrate, mainly due to reduced interfacial interaction between the graphene and the PEN. This method can be an indispensable means to improve the stability of devices using a graphene as it provides an accurate and quantitative way to define the quality of graphene after the device fabrication. PMID:24811431

  9. Electroencephalographic Data Analysis With Visibility Graph Technique for Quantitative Assessment of Brain Dysfunction.

    PubMed

    Bhaduri, Susmita; Ghosh, Dipak

    2015-07-01

    Usual techniques for electroencephalographic (EEG) data analysis lack some of the important properties essential for quantitative assessment of the progress of the dysfunction of the human brain. EEG data are essentially nonlinear and this nonlinear time series has been identified as multi-fractal in nature. We need rigorous techniques for such analysis. In this article, we present the visibility graph as the latest, rigorous technique that can assess the degree of multifractality accurately and reliably. Moreover, it has also been found that this technique can give reliable results with test data of comparatively short length. In this work, the visibility graph algorithm has been used for mapping a time series-EEG signals-to a graph to study complexity and fractality of the time series through investigation of its complexity. The power of scale-freeness of visibility graph has been used as an effective method for measuring fractality in the EEG signal. The scale-freeness of the visibility graph has also been observed after averaging the statistically independent samples of the signal. Scale-freeness of the visibility graph has been calculated for 5 sets of EEG data patterns varying from normal eye closed to epileptic. The change in the values is analyzed further, and it has been observed that it reduces uniformly from normal eye closed to epileptic.

  10. Quantitatively estimating defects in graphene devices using discharge current analysis method.

    PubMed

    Jung, Ukjin; Lee, Young Gon; Kang, Chang Goo; Lee, Sangchul; Kim, Jin Ju; Hwang, Hyeon June; Lim, Sung Kwan; Ham, Moon-Ho; Lee, Byoung Hun

    2014-05-08

    Defects of graphene are the most important concern for the successful applications of graphene since they affect device performance significantly. However, once the graphene is integrated in the device structures, the quality of graphene and surrounding environment could only be assessed using indirect information such as hysteresis, mobility and drive current. Here we develop a discharge current analysis method to measure the quality of graphene integrated in a field effect transistor structure by analyzing the discharge current and examine its validity using various device structures. The density of charging sites affecting the performance of graphene field effect transistor obtained using the discharge current analysis method was on the order of 10(14)/cm(2), which closely correlates with the intensity ratio of the D to G bands in Raman spectroscopy. The graphene FETs fabricated on poly(ethylene naphthalate) (PEN) are found to have a lower density of charging sites than those on SiO2/Si substrate, mainly due to reduced interfacial interaction between the graphene and the PEN. This method can be an indispensable means to improve the stability of devices using a graphene as it provides an accurate and quantitative way to define the quality of graphene after the device fabrication.

  11. Quantitatively estimating defects in graphene devices using discharge current analysis method

    NASA Astrophysics Data System (ADS)

    Jung, Ukjin; Lee, Young Gon; Kang, Chang Goo; Lee, Sangchul; Kim, Jin Ju; Hwang, Hyeon June; Lim, Sung Kwan; Ham, Moon-Ho; Lee, Byoung Hun

    2014-05-01

    Defects of graphene are the most important concern for the successful applications of graphene since they affect device performance significantly. However, once the graphene is integrated in the device structures, the quality of graphene and surrounding environment could only be assessed using indirect information such as hysteresis, mobility and drive current. Here we develop a discharge current analysis method to measure the quality of graphene integrated in a field effect transistor structure by analyzing the discharge current and examine its validity using various device structures. The density of charging sites affecting the performance of graphene field effect transistor obtained using the discharge current analysis method was on the order of 1014/cm2, which closely correlates with the intensity ratio of the D to G bands in Raman spectroscopy. The graphene FETs fabricated on poly(ethylene naphthalate) (PEN) are found to have a lower density of charging sites than those on SiO2/Si substrate, mainly due to reduced interfacial interaction between the graphene and the PEN. This method can be an indispensable means to improve the stability of devices using a graphene as it provides an accurate and quantitative way to define the quality of graphene after the device fabrication.

  12. Quantitative analysis of eugenol in clove extract by a validated HPLC method.

    PubMed

    Yun, So-Mi; Lee, Myoung-Heon; Lee, Kwang-Jick; Ku, Hyun-Ok; Son, Seong-Wan; Joo, Yi-Seok

    2010-01-01

    Clove (Eugenia caryophyllata) is a well-known medicinal plant used for diarrhea, digestive disorders, or in antiseptics in Korea. Eugenol is the main active ingredient of clove and has been chosen as a marker compound for the chemical evaluation or QC of clove. This paper reports the development and validation of an HPLC-diode array detection (DAD) method for the determination of eugenol in clove. HPLC separation was accomplished on an XTerra RP18 column (250 x 4.6 mm id, 5 microm) with an isocratic mobile phase of 60% methanol and DAD at 280 nm. Calibration graphs were linear with very good correlation coefficients (r2 > 0.9999) from 12.5 to 1000 ng/mL. The LOD was 0.81 and the LOQ was 2.47 ng/mL. The method showed good intraday precision (%RSD 0.08-0.27%) and interday precision (%RSD 0.32-1.19%). The method was applied to the analysis of eugenol from clove cultivated in various countries (Indonesia, Singapore, and China). Quantitative analysis of the 15 clove samples showed that the content of eugenol varied significantly, ranging from 163 to 1049 ppb. The method of determination of eugenol by HPLC is accurate to evaluate the quality and safety assurance of clove, based on the results of this study.

  13. Quantitative analysis of the central-chest lymph nodes based on 3D MDCT image data

    NASA Astrophysics Data System (ADS)

    Lu, Kongkuo; Bascom, Rebecca; Mahraj, Rickhesvar P. M.; Higgins, William E.

    2009-02-01

    Lung cancer is the leading cause of cancer death in the United States. In lung-cancer staging, central-chest lymph nodes and associated nodal stations, as observed in three-dimensional (3D) multidetector CT (MDCT) scans, play a vital role. However, little work has been done in relation to lymph nodes, based on MDCT data, due to the complicated phenomena that give rise to them. Using our custom computer-based system for 3D MDCT-based pulmonary lymph-node analysis, we conduct a detailed study of lymph nodes as depicted in 3D MDCT scans. In this work, the Mountain lymph-node stations are automatically defined by the system. These defined stations, in conjunction with our system's image processing and visualization tools, facilitate lymph-node detection, classification, and segmentation. An expert pulmonologist, chest radiologist, and trained technician verified the accuracy of the automatically defined stations and indicated observable lymph nodes. Next, using semi-automatic tools in our system, we defined all indicated nodes. Finally, we performed a global quantitative analysis of the characteristics of the observed nodes and stations. This study drew upon a database of 32 human MDCT chest scans. 320 Mountain-based stations (10 per scan) and 852 pulmonary lymph nodes were defined overall from this database. Based on the numerical results, over 90% of the automatically defined stations were deemed accurate. This paper also presents a detailed summary of central-chest lymph-node characteristics for the first time.

  14. ArrayExplorer, a program in Visual Basic for robust and accurate filter cDNA array analysis.

    PubMed

    Patriotis, P C; Querec, T D; Gruver, B N; Brown, T R; Patriotis, C

    2001-10-01

    Determining the dynamics in the global regulation of gene expression holds the promise of bringing a better understanding of the processes that govern physiological cell growth regulation and its disruption during the development of disease. The advent for cDNA arrays has created the possibility for the parallel analysis of expression of thousands of genes in a given cell population, simultaneously. The level of expression of a given set of genes within the studied tissue corresponds to the intensity of a labeled cDNA probe synthesized from the studied tissue RNA and bound specifically to the cDNAs of the genes spotted on the array. The accurate extraction of gene expression intensity values is essential for further data analysis and the interpretation of the obtained results. Here, we describe a new array image-processing software developed in Microsoft Visual Basic, the ArrayExplorer, which provides a user-friendly, multiple-window interface and a number of automatic and manual features that facilitate a reliable, robust, and accurate extraction of gene intensity values from filter-array images.

  15. Accurate quantitation of Ki67-positive proliferating hepatocytes in rabbit liver by a multicolor immunohistochemical (IHC) approach analyzed with automated tissue and cell segmentation software.

    PubMed

    van der Loos, Chris M; de Boer, Onno J; Mackaaij, Claire; Hoekstra, Lisette T; van Gulik, Thomas M; Verheij, Joanne

    2013-01-01

    Determination of hepatocyte proliferation activity is hampered by the presence of Ki67-positive non-parenchymal cells. We validated a multicolor immunohistochemical (IHC) approach using multispectral tissue and cell segmentation software. Portal vein branches to the cranial liver lobes of 10 rabbits were embolized, leading to atrophy of the cranial lobes and hyperplasia of the caudal lobes. Slides from cranial and caudal lobes (n=20) were double-stained (CK8+18 and Ki67) and triple-stained (CK8+18, Ki67, and CD31). The Ki67 proliferation index was calculated using automated tissue and cell segmentation software and compared with manual counting by two independent observers. A substantial variation was seen in the number of Ki67-positive hepatocytes in the different specimens in both double and triple staining (range, 0-50). Correlation coefficients between manual counting and the digital analysis were 0.76 for observer 1 (p<0.001) and 0.78 for observer 2 (p<0.001) with double staining and R(2) = 0.91 for observer 1 and R(2) = 0.89 for observer 2, p<0.001 with triple staining. In conclusion, in rabbit, the hepatocellular proliferation index can be reliably determined using automated tissue and cell segmentation software in combination with IHC multiple staining. Our findings may be useful in clinical practice when Ki67 proliferation index yields prognostic significance.

  16. Barcoding T Cell Calcium Response Diversity with Methods for Automated and Accurate Analysis of Cell Signals (MAAACS)

    PubMed Central

    Sergé, Arnauld; Bernard, Anne-Marie; Phélipot, Marie-Claire; Bertaux, Nicolas; Fallet, Mathieu; Grenot, Pierre; Marguet, Didier; He, Hai-Tao; Hamon, Yannick

    2013-01-01

    We introduce a series of experimental procedures enabling sensitive calcium monitoring in T cell populations by confocal video-microscopy. Tracking and post-acquisition analysis was performed using Methods for Automated and Accurate Analysis of Cell Signals (MAAACS), a fully customized program that associates a high throughput tracking algorithm, an intuitive reconnection routine and a statistical platform to provide, at a glance, the calcium barcode of a population of individual T-cells. Combined with a sensitive calcium probe, this method allowed us to unravel the heterogeneity in shape and intensity of the calcium response in T cell populations and especially in naive T cells, which display intracellular calcium oscillations upon stimulation by antigen presenting cells. PMID:24086124

  17. Teaching Quantitative Reasoning for Nonscience Majors through Carbon Footprint Analysis

    ERIC Educational Resources Information Center

    Boose, David L.

    2014-01-01

    Quantitative reasoning is a key intellectual skill, applicable across disciplines and best taught in the context of authentic, relevant problems. Here, I describe and assess a laboratory exercise that has students calculate their "carbon footprint" and evaluate the impacts of various behavior choices on that footprint. Students gather…

  18. MOLD SPECIFIC QUANTITATIVE PCR: THE EMERGING STANDARD IN MOLD ANALYSIS

    EPA Science Inventory

    Today I will talk about the use of quantitative or Real time PCR for the standardized identification and quantification of molds. There are probably at least 100,000 species of molds or fungi. But there are actually about 100 typically found indoors. Some pose a threat to human...

  19. Quantitative and Qualitative Analysis of Biomarkers in Fusarium verticillioides

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In this study, a combination HPLC-DART-TOF-MS system was utilized to identify and quantitatively analyze carbohydrates in wild type and mutant strains of Fusarium verticillioides. Carbohydrate fractions were isolated from F. verticillioides cellular extracts by HPLC using a cation-exchange size-excl...

  20. A new quantitative method for gunshot residue analysis by ion beam analysis.

    PubMed

    Christopher, Matthew E; Warmenhoeven, John-William; Romolo, Francesco S; Donghi, Matteo; Webb, Roger P; Jeynes, Christopher; Ward, Neil I; Kirkby, Karen J; Bailey, Melanie J

    2013-08-21

    Imaging and analyzing gunshot residue (GSR) particles using the scanning electron microscope equipped with an energy dispersive X-ray spectrometer (SEM-EDS) is a standard technique that can provide important forensic evidence, but the discrimination power of this technique is limited due to low sensitivity to trace elements and difficulties in obtaining quantitative results from small particles. A new, faster method using a scanning proton microbeam and Particle Induced X-ray Emission (μ-PIXE), together with Elastic Backscattering Spectrometry (EBS) is presented for the non-destructive, quantitative analysis of the elemental composition of single GSR particles. In this study, the GSR particles were all Pb, Ba, Sb. The precision of the method is assessed. The grouping behaviour of different makes of ammunition is determined using multivariate analysis. The protocol correctly groups the cartridges studied here, with a confidence >99%, irrespective of the firearm or population of particles selected.

  1. Structural and Quantitative Analysis of Three C-Glycosylflavones by Variable Temperature Proton Quantitative Nuclear Magnetic Resonance

    PubMed Central

    Liu, Yang; Dai, Zhong

    2017-01-01

    Quantitative nuclear magnetic resonance is a powerful tool in drug analysis because of its speed, precision, and efficiency. In present study, the application of variable temperature proton quantitative nuclear magnetic resonance (VT-1H-qNMR) for the calibration of three C-glycosylflavones including orientin, isoorientin, and schaftoside as reference substances was reported. Since there was conformational equilibrium due to the restricted rotation around the C(sp3)-C(sp2) bond in C-glycosylflavones, the conformational behaviors were investigated by VT-NMR and verified by molecular mechanics (MM) calculation. The VT-1H-qNMR method was validated including the linearity, limit of quantification, precision, and stability. The results were consistent with those obtained from mass balance approach. VT-1H-qNMR can be deployed as an effective tool in analyzing C-glycosylflavones. PMID:28243484

  2. iTRAQ-Based Quantitative Proteomic Analysis Identified HSC71 as a Novel Serum Biomarker for Renal Cell Carcinoma

    PubMed Central

    Zhang, Yushi; Cai, Yi; Yu, Hongyan; Li, Hanzhong

    2015-01-01

    Renal cell carcinoma (RCC) is one of the most lethal urologic cancers and about 80% of RCC are of the clear-cell type (ccRCC). However, there are no serum biomarkers for the accurate diagnosis of RCC. In this study, we performed a quantitative proteomic analysis on serum samples from ccRCC patients and control group by using isobaric tag for relative and absolute quantitation (iTRAQ) labeling and LC-MS/MS analysis to access differentially expressed proteins. Overall, 16 proteins were significantly upregulated (ratio > 1.5) and 14 proteins were significantly downregulated (ratio < 0.67) in early-stage ccRCC compared to control group. HSC71 was selected and subsequently validated by Western blot in six independent sets of patients. ELISA subsequently confirmed HSC71 as a potential serum biomarker for distinguishing RCC from benign urologic disease with an operating characteristic curve (ROC) area under the curve (AUC) of 0.86 (95% confidence interval (CI), 0.76~0.96), achieving sensitivity of 87% (95% CI 69%~96%) at a specificity of 80% (95% CI 61~92%) with a threshold of 15 ng/mL. iTRAQ-based quantitative proteomic analysis led to identification of serum HSC71 as a novel serum biomarker of RCC, particularly useful in early diagnosis of ccRCC. PMID:26425554

  3. Exploring Valid Reference Genes for Quantitative Real-Time PCR Analysis in Sesamia inferens (Lepidoptera: Noctuidae)

    PubMed Central

    Sun, Meng; Lu, Ming-Xing; Tang, Xiao-Tian; Du, Yu-Zhou

    2015-01-01

    The pink stem borer, Sesamia inferens, which is endemic in China and other parts of Asia, is a major pest of rice and causes significant yield loss in this host plant. Very few studies have addressed gene expression in S. inferens. Quantitative real-time PCR (qRT-PCR) is currently the most accurate and sensitive method for gene expression analysis. In qRT-PCR, data are normalized using reference genes, which help control for internal differences and reduce error between samples. In this study, seven candidate reference genes, 18S ribosomal RNA (18S rRNA), elongation factor 1 (EF1), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), ribosomal protein S13 (RPS13), ribosomal protein S20 (RPS20), tubulin (TUB), and β-actin (ACTB) were evaluated for their suitability in normalizing gene expression under different experimental conditions. The results indicated that three genes (RPS13, RPS20, and EF1) were optimal for normalizing gene expression in different insect tissues (head, epidermis, fat body, foregut, midgut, hindgut, Malpighian tubules, haemocytes, and salivary glands). 18S rRNA, EF1, and GAPDH were best for normalizing expression with respect to developmental stages and sex (egg masses; first, second, third, fourth, fifth, and sixth instar larvae; male and female pupae; and one-day-old male and female adults). 18S rRNA, RPS20, and TUB were optimal for fifth instars exposed to different temperatures (−8, −6, −4, −2, 0, and 27°C). To validate this recommendation, the expression profile of a target gene heat shock protein 83 gene (hsp83) was investigated, and results showed the selection was necessary and effective. In conclusion, this study describes reference gene sets that can be used to accurately measure gene expression in S. inferens. PMID:25585250

  4. Exploring valid reference genes for quantitative real-time PCR analysis in Sesamia inferens (Lepidoptera: Noctuidae).

    PubMed

    Sun, Meng; Lu, Ming-Xing; Tang, Xiao-Tian; Du, Yu-Zhou

    2015-01-01

    The pink stem borer, Sesamia inferens, which is endemic in China and other parts of Asia, is a major pest of rice and causes significant yield loss in this host plant. Very few studies have addressed gene expression in S. inferens. Quantitative real-time PCR (qRT-PCR) is currently the most accurate and sensitive method for gene expression analysis. In qRT-PCR, data are normalized using reference genes, which help control for internal differences and reduce error between samples. In this study, seven candidate reference genes, 18S ribosomal RNA (18S rRNA), elongation factor 1 (EF1), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), ribosomal protein S13 (RPS13), ribosomal protein S20 (RPS20), tubulin (TUB), and β-actin (ACTB) were evaluated for their suitability in normalizing gene expression under different experimental conditions. The results indicated that three genes (RPS13, RPS20, and EF1) were optimal for normalizing gene expression in different insect tissues (head, epidermis, fat body, foregut, midgut, hindgut, Malpighian tubules, haemocytes, and salivary glands). 18S rRNA, EF1, and GAPDH were best for normalizing expression with respect to developmental stages and sex (egg masses; first, second, third, fourth, fifth, and sixth instar larvae; male and female pupae; and one-day-old male and female adults). 18S rRNA, RPS20, and TUB were optimal for fifth instars exposed to different temperatures (-8, -6, -4, -2, 0, and 27°C). To validate this recommendation, the expression profile of a target gene heat shock protein 83 gene (hsp83) was investigated, and results showed the selection was necessary and effective. In conclusion, this study describes reference gene sets that can be used to accurately measure gene expression in S. inferens.

  5. Quantitative Analysis of Volatile Impurities in Diallyldimethylammonium Chloride Monomer Solution by Gas Chromatography Coupled with Liquid-Liquid Extraction

    PubMed Central

    Wang, Haiying; Wang, Weixin

    2017-01-01

    The quantitative analysis method for volatile impurities in diallyldimethylammonium chloride (DADMAC) monomer solution was established in this paper. The volatile impurities were quantitatively analyzed with trichloromethane as extraction solvent and n-hexane as internal standard by using gas chromatography (GC) coupled with solvent extraction, and the chromatographic conditions, quantitative methods, and extraction conditions were systematically investigated in detail. The results showed that excellent linear relationships of 5 volatile impurities (dimethylamine, allyldimethylamine, allyl chloride, allyl alcohol, and allyl aldehyde) were obtained in the range of 1–100 mg·L−1. The method also showed good specificity, recovery (95.0%–107.5%), and relative standard deviation (RSD, 1.40%–7.67%). This method could accurately detect the whole volatile impurities in DADMAC monomer solution quantitatively in one time with a low detection limit. Furthermore, this method is conducive to the preparation of highly pure DADMAC monomer and the development of national and international standards of the DADMAC monomer product quality, and the results could provide a strong foundation for the regulation and mechanism research of impurities on monomer reactivity in polymerization. PMID:28243255

  6. Development of a Tool for the Rapid Quantitative Analysis of Multiple Gamma Spectra

    SciTech Connect

    HODGE, CHRISTOPHERA.

    2004-06-28

    Often multiple gamma spectra are acquired for the quantitative measurement of process holdup, filter banks, waste containers, D and D objects, or other such items. These spectra can represent data for single items, background data, and multiple assays of the same item or multiple areas representative of a single process area. The spectra are often collected under differing circumstances with regard to attenuating materials, distances, assay times, relative backgrounds, and many other such parameters. Quantitative results, and associated errors, are often dependent on multiple calibration constants, assays of varying isotopes, source geometries (point, line, or area), background averaging, Compton effects, and the accurate analysis, i.e. region of interest, of the raw gamma spectra. A tool has been developed to assist in this endeavor. The calculations have been quality checked so that the tool can readily be used with assurance that the calculations are consistent and correct. This tool allows for multiple spectra (up to 150) to be compared and manipulated. The tool has features for: dynamic average background subtraction; accounting for varying Compton effects; different calibration constants; up to three attenuating materials; any gamma energy; and variance in collection parameters such as distance, angle, assay times, and isotope. Selections of point, line, or area calculations are easily specified. The tool has a report writer that allows for averaging over multiple assays, graphing of activity (e.g., graphing activity in a sump allows the hot spots to be identified), and presentation of results with associated error components or MLDs. The resulting database allows for easy self-documentation and archiving.

  7. Quantitative and integrative analysis of paracrine hepatocyte activation by nonparenchymal cells upon lipopolysaccharide induction.

    PubMed

    Beuke, Katharina; Schildberg, Frank A; Pinna, Federico; Albrecht, Ute; Liebe, Roman; Bissinger, Michaela; Schirmacher, Peter; Dooley, Steven; Bode, Johannes G; Knolle, Percy A; Kummer, Ursula; Breuhahn, Kai; Sahle, Sven

    2017-03-01

    Gut-derived bacterial lipopolysaccharides (LPS) stimulate the secretion of tumour necrosis factor (TNF) from liver macrophages (MCs), liver sinusoidal endothelial cells (LSECs) and hepatic stellate cells (HSCs), which control the acute phase response in hepatocytes through activation of the NF-κB pathway. The individual and cooperative impact of nonparenchymal cells on this clinically relevant response has not been analysed in detail due to technical limitations. To gain an integrative view on this complex inter- and intracellular communication, we combined a multiscale mathematical model with quantitative, time-resolved experimental data of different primary murine liver cell types. We established a computational model for TNF-induced NF-κB signalling in hepatocytes, accurately describing dose-responsiveness for physiologically relevant cytokine concentrations. TNF secretion profiles were quantitatively measured for all nonparenchymal cell types upon LPS stimulation. This novel approach allowed the analysis of individual and collective paracrine TNF-mediated NF-κB induction in hepatocytes, revealing strongest effects of MCs and LSECs on hepatocellular NF-κB signalling. Simulations suggest that both cell types act together to maximize the NF-κB pathway response induced by low LPS concentrations (0.1 and 1 ng/mL). Higher LPS concentrations (≥ 5 ng/mL) induced sufficient TNF levels from MCs or LSECs to induce a strong and nonadjustable pathway response. Importantly, these simulations also revealed that the initial cytokine secretion (1-2 h after stimulation) rather than final TNF level (10 h after stimulation) defines the hepatocellular NF-κB response. This raises the question whether the current experimental standard of single high-dose cytokine administration is suitable to mimic in vivo cytokine exposure.

  8. Quantitative compositional analysis of sedimentary materials using thermal emission spectroscopy: 1. Application to sedimentary rocks

    NASA Astrophysics Data System (ADS)

    Thorpe, Michael T.; Rogers, A. Deanne; Bristow, Thomas F.; Pan, Cong

    2015-11-01

    Thermal emission spectroscopy is used to determine the mineralogy of sandstone and mudstone rocks as part of an investigation of linear spectral mixing between sedimentary constituent phases. With widespread occurrences of sedimentary rocks on the surface of Mars, critical examination of the accuracy associated with quantitative models of mineral abundances derived from thermal emission spectra of sedimentary materials is necessary. Although thermal emission spectroscopy has been previously proven to be a viable technique to obtain quantitative mineralogy from igneous and metamorphic materials, sedimentary rocks, with natural variation of composition, compaction, and grain size, have yet to be examined. In this work, we present an analysis of the thermal emission spectral (~270-1650 cm-1) characteristics of a suite of 13 sandstones and 14 mudstones. X-ray diffraction and traditional point counting procedures were all evaluated in comparison with thermal emission spectroscopy. Results from this work are consistent with previous thermal emission spectroscopy studies and indicate that bulk rock mineral abundances can be estimated within 11.2% for detrital grains (i.e., quartz and feldspars) and 14.8% for all other mineral phases present in both sandstones and mudstones, in comparison to common in situ techniques used for determining bulk rock composition. Clay-sized to fine silt-sized grained phase identification is less accurate, with differences from the known ranging from ~5 to 24% on average. Nevertheless, linear least squares modeling of thermal emission spectra is an advantageous technique for determining abundances of detrital grains and sedimentary matrix and for providing a rapid classification of clastic rocks.

  9. Fourier Transform Mass Spectrometry and Nuclear Magnetic Resonance Analysis for the Rapid and Accurate Characterization of Hexacosanoylceramide.

    PubMed

    Ross, Charles W; Simonsick, William J; Bogusky, Michael J; Celikay, Recep W; Guare, James P; Newton, Randall C

    2016-06-28

    Ceramides are a central unit of all sphingolipids which have been identified as sites of biological recognition on cellular membranes mediating cell growth and differentiation. Several glycosphingolipids have been isolated, displaying immunomodulatory and anti-tumor activities. These molecules have generated considerable interest as potential vaccine adjuvants in humans. Accurate analyses of these and related sphingosine analogues are important for the characterization of structure, biological function, and metabolism. We report the complementary use of direct laser desorption ionization (DLDI), sheath flow electrospray ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) and high-field nuclear magnetic resonance (NMR) analysis for the rapid, accurate identification of hexacosanoylceramide and starting materials. DLDI does not require stringent sample preparation and yields representative ions. Sheath-flow ESI yields ions of the product and byproducts and was significantly better than monospray ESI due to improved compound solubility. Negative ion sheath flow ESI provided data of starting materials and products all in one acquisition as hexacosanoic acid does not ionize efficiently when ceramides are present. NMR provided characterization of these lipid molecules complementing the results obtained from MS analyses. NMR data was able to differentiate straight chain versus branched chain alkyl groups not easily obtained from mass spectrometry.

  10. An accurate retrieval of leaf water content from mid to thermal infrared spectra using continuous wavelet analysis.

    PubMed

    Ullah, Saleem; Skidmore, Andrew K; Naeem, Mohammad; Schlerf, Martin

    2012-10-15

    Leaf water content determines plant health, vitality, photosynthetic efficiency and is an important indicator of drought assessment. The retrieval of leaf water content from the visible to shortwave infrared spectra is well known. Here for the first time, we estimated leaf water content from the mid to thermal infrared (2.5-14.0 μm) spectra, based on continuous wavelet analysis. The dataset comprised 394 spectra from nine plant species, with different water contents achieved through progressive drying. To identify the spectral feature most sensitive to the variations in leaf water content, first the Directional Hemispherical Reflectance (DHR) spectra were transformed into a wavelet power scalogram, and then linear relations were established between the wavelet power scalogram and leaf water content. The six individual wavelet features identified in the mid infrared yielded high correlations with leaf water content (R(2)=0.86 maximum, 0.83 minimum), as well as low RMSE (minimum 8.56%, maximum 9.27%). The combination of four wavelet features produced the most accurate model (R(2)=0.88, RMSE=8.00%). The models were consistent in terms of accuracy estimation for both calibration and validation datasets, indicating that leaf water content can be accurately retrieved from the mid to thermal infrared domain of the electromagnetic radiation.

  11. Fourier Transform Mass Spectrometry and Nuclear Magnetic Resonance Analysis for the Rapid and Accurate Characterization of Hexacosanoylceramide

    PubMed Central

    Ross, Charles W.; Simonsick, William J.; Bogusky, Michael J.; Celikay, Recep W.; Guare, James P.; Newton, Randall C.

    2016-01-01

    Ceramides are a central unit of all sphingolipids which have been identified as sites of biological recognition on cellular membranes mediating cell growth and differentiation. Several glycosphingolipids have been isolated, displaying immunomodulatory and anti-tumor activities. These molecules have generated considerable interest as potential vaccine adjuvants in humans. Accurate analyses of these and related sphingosine analogues are important for the characterization of structure, biological function, and metabolism. We report the complementary use of direct laser desorption ionization (DLDI), sheath flow electrospray ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) and high-field nuclear magnetic resonance (NMR) analysis for the rapid, accurate identification of hexacosanoylceramide and starting materials. DLDI does not require stringent sample preparation and yields representative ions. Sheath-flow ESI yields ions of the product and byproducts and was significantly better than monospray ESI due to improved compound solubility. Negative ion sheath flow ESI provided data of starting materials and products all in one acquisition as hexacosanoic acid does not ionize efficiently when ceramides are present. NMR provided characterization of these lipid molecules complementing the results obtained from MS analyses. NMR data was able to differentiate straight chain versus branched chain alkyl groups not easily obtained from mass spectrometry. PMID:27367671

  12. Quantitative sectioning and noise analysis for structured illumination microscopy

    PubMed Central

    Hagen, Nathan; Gao, Liang; Tkaczyk, Tomasz S.

    2011-01-01

    Structured illumination (SI) has long been regarded as a nonquantitative technique for obtaining sectioned microscopic images. Its lack of quantitative results has restricted the use of SI sectioning to qualitative imaging experiments, and has also limited researchers’ ability to compare SI against competing sectioning methods such as confocal microscopy. We show how to modify the standard SI sectioning algorithm to make the technique quantitative, and provide formulas for calculating the noise in the sectioned images. The results indicate that, for an illumination source providing the same spatially-integrated photon flux at the object plane, and for the same effective slice thicknesses, SI sectioning can provide higher SNR images than confocal microscopy for an equivalent setup when the modulation contrast exceeds about 0.09. PMID:22274364

  13. Quantitative analysis of immobilized metalloenzymes by atomic absorption spectroscopy.

    PubMed

    Opwis, Klaus; Knittel, Dierk; Schollmeyer, Eckhard

    2004-12-01

    A new, sensitive assay for the quantitative determination of immobilized metal containing enzymes has been developed using atomic absorption spectroscopy (AAS). In contrast with conventionally used indirect methods the described quantitative AAS assay for metalloenzymes allows more exact analyses, because the carrier material with the enzyme is investigated directly. As an example, the validity and reliability of the method was examined by fixing the iron-containing enzyme catalase on cotton fabrics using different immobilization techniques. Sample preparation was carried out by dissolving the loaded fabrics in sulfuric acid before oxidising the residues with hydrogen peroxide. The iron concentrations were determined by flame atomic absorption spectrometry after calibration of the spectrometer with solutions of the free enzyme at different concentrations.

  14. Semi-quantitative spectrographic analysis and rank correlation in geochemistry

    USGS Publications Warehouse

    Flanagan, F.J.

    1957-01-01

    The rank correlation coefficient, rs, which involves less computation than the product-moment correlation coefficient, r, can be used to indicate the degree of relationship between two elements. The method is applicable in situations where the assumptions underlying normal distribution correlation theory may not be satisfied. Semi-quantitative spectrographic analyses which are reported as grouped or partly ranked data can be used to calculate rank correlations between elements. ?? 1957.

  15. Quantitative analysis of cortical pyramidal neurons after corpus callosotomy.

    PubMed

    Jacobs, Bob; Creswell, Johanna; Britt, Jonathan P; Ford, Kevin L; Bogen, Joseph E; Zaidel, Eran

    2003-07-01

    This study quantitatively explored the dendritic/spine extent of supragranular pyramidal neurons across several cortical areas in two adult male subjects who had undergone a callosotomy several decades before death. In all cortical areas, there were numerous atypical, supragranular pyramidal neurons with elongated "tap root" basilar dendrites. These atypical cells could be associated with an underlying epileptic condition and/or could represent a compensatory mechanism in response to deafferentation after callosotomy.

  16. Fluorescent microscopy approaches of quantitative soil microbial analysis

    NASA Astrophysics Data System (ADS)

    Ivanov, Konstantin; Polyanskaya, Lubov

    2015-04-01

    Classical fluorescent microscopy method was used during the last decades in various microbiological studies of terrestrial ecosystems. The method provides representative results and simple application which is allow to use it both as routine part of amplitudinous research and in small-scaled laboratories. Furthermore, depending on research targets a lot of modifications of fluorescent microscopy method were established. Combination and comparison of several approaches is an opportunity of quantitative estimation of microbial community in soil. The first analytical part of the study was dedicated to soil bacterial density estimation by fluorescent microscopy in dynamic of several 30-days experiments. The purpose of research was estimation of changes in soil bacterial community on the different soil horizons under aerobic and anaerobic conditions with adding nutrients in two experimental sets: cellulose and chitin. Was modified the nalidixic acid method for inhibition of DNA division of gram-negative bacteria, and the method provides the quantification of this bacterial group by fluorescent microscopy. Established approach allowed to estimate 3-4 times more cells of gram-negative bacteria in soil. The functions of actinomyces in soil polymer destruction are traditionally considered as dominant in comparison to gram-negative bacterial group. However, quantification of gram-negative bacteria in chernozem and peatland provides underestimation of classical notion for this bacterial group. Chitin introduction had no positive effect to gram-negative bacterial population density changes in chernozem but concurrently this nutrient provided the fast growing dynamics at the first 3 days of experiment both under aerobic and anaerobic conditions. This is confirming chitinolytic activity of gram-negative bacteria in soil organic matter decomposition. At the next part of research modified method for soil gram-negative bacteria quantification was compared to fluorescent in situ

  17. A new method of accurate broken rotor bar diagnosis based on modulation signal bispectrum analysis of motor current signals

    NASA Astrophysics Data System (ADS)

    Gu, F.; Wang, T.; Alwodai, A.; Tian, X.; Shao, Y.; Ball, A. D.

    2015-01-01

    Motor current signature analysis (MCSA) has been an effective way of monitoring electrical machines for many years. However, inadequate accuracy in diagnosing incipient broken rotor bars (BRB) has motivated many studies into improving this method. In this paper a modulation signal bispectrum (MSB) analysis is applied to motor currents from different broken bar cases and a new MSB based sideband estimator (MSB-SE) and sideband amplitude estimator are introduced for obtaining the amplitude at (1 ± 2 s)fs (s is the rotor slip and fs is the fundamental supply frequency) with high accuracy. As the MSB-SE has a good performance of noise suppression, the new estimator produces more accurate results in predicting the number of BRB, compared with conventional power spectrum analysis. Moreover, the paper has also developed an improved model for motor current signals under rotor fault conditions and an effective method to decouple the BRB current which interferes with that of speed oscillations associated with BRB. These provide theoretical supports for the new estimators and clarify the issues in using conventional bispectrum analysis.

  18. The Effects of Selection on Linkage Analysis for Quantitative Traits

    PubMed Central

    Mackinnon, M. J.; Georges, MAJ.

    1992-01-01

    The effects of within-sample selection on the outcome of analyses detecting linkage between genetic markers and quantitative traits were studied. It was found that selection by truncation for the trait of interest significantly reduces the differences between marker genotype means thus reducing the power to detect linked quantitative trait loci (QTL). The size of this reduction is a function of proportion selected, the magnitude of the QTL effect, recombination rate between the marker locus and the QTL, and the allele frequency of the QTL. Proportion selected was the most influential of these factors on bias, e.g., for an allele substitution effect of one standard deviation unit, selecting the top 80%, 50% or 20% of the population required 2,6 or 24 times the number of progeny, respectively, to offset the loss of power caused by this selection. The effect on power was approximately linear with respect to the size of gene effect, almost invariant to recombination rate, and a complex function of QTL allele frequency. It was concluded that experimental samples from animal populations which have been subjected to even minor amounts of selection will be inefficient in yielding information on linkage between markers and loci influencing the quantitative trait under selection. PMID:1459434

  19. A method to accurately quantitate intensities of (32)P-DNA bands when multiple bands appear in a single lane of a gel is used to study dNTP insertion opposite a benzo[a]pyrene-dG adduct by Sulfolobus DNA polymerases Dpo4 and Dbh.

    PubMed

    Sholder, Gabriel; Loechler, Edward L

    2015-01-01

    Quantitating relative (32)P-band intensity in gels is desired, e.g., to study primer-extension kinetics of DNA polymerases (DNAPs). Following imaging, multiple (32)P-bands are often present in lanes. Though individual bands appear by eye to be simple and well-resolved, scanning reveals they are actually skewed-Gaussian in shape and neighboring bands are overlapping, which complicates quantitation, because slower migrating bands often have considerable contributions from the trailing edges of faster migrating bands. A method is described to accurately quantitate adjacent (32)P-bands, which relies on having a standard: a simple skewed-Gaussian curve from an analogous pure, single-component band (e.g., primer alone). This single-component scan/curve is superimposed on its corresponding band in an experimentally determined scan/curve containing multiple bands (e.g., generated in a primer-extension reaction); intensity exceeding the single-component scan/curve is attributed to other components (e.g., insertion products). Relative areas/intensities are determined via pixel analysis, from which relative molarity of components is computed. Common software is used. Commonly used alternative methods (e.g., drawing boxes around bands) are shown to be less accurate. Our method was used to study kinetics of dNTP primer-extension opposite a benzo[a]pyrene-N(2)-dG-adduct with four DNAPs, including Sulfolobus solfataricus Dpo4 and Sulfolobus acidocaldarius Dbh. Vmax/Km is similar for correct dCTP insertion with Dpo4 and Dbh. Compared to Dpo4, Dbh misinsertion is slower for dATP (∼20-fold), dGTP (∼110-fold) and dTTP (∼6-fold), due to decreases in Vmax. These findings provide support that Dbh is in the same Y-Family DNAP class as eukaryotic DNAP κ and bacterial DNAP IV, which accurately bypass N(2)-dG adducts, as well as establish the scan-method described herein as an accurate method to quantitate relative intensity of overlapping bands in a single lane, whether generated

  20. Accurate Enumeration of Aspergillus brasiliensis in Hair Color and Mascara by Time-Lapse Shadow Image Analysis.

    PubMed

    Ogawa, Hiroyuki; Matsuoka, Hideaki; Saito, Mikako

    2015-01-01

    The growth of black mold (Aspergillus brasiliensis) in black-colored samples such as hair color and mascara was measured with an automatic count system based on time-lapse shadow image analysis (TSIA). A. brasiliensis suspended in a lecithin and polysorbate (LP) solution of each sample (hair color or mascara) was spread on a potato dextrose agar medium plate containing LP. The background image darkness of the agar plate could be adjusted to attain accurate colony counts. 95 colonies in hair color and 22 colonies in mascara could be automatically determined at 48 h. The accuracy of the colony counts could be confirmed from the timelapse image data. In contrast, conventional visual counting at a specified time could not determine the number of colonies or led to false colony counts.

  1. An Inexpensive Electrodeposition Device and Its Use in a Quantitative Analysis Laboratory Exercise

    ERIC Educational Resources Information Center

    Parker, Richard H.

    2011-01-01

    An experimental procedure, using an apparatus that is easy to construct, was developed to incorporate a quantitative electrogravimetric determination of the solution nickel content into an undergraduate or advanced high school quantitative analysis laboratory. This procedure produces results comparable to the procedure used for the gravimetric…

  2. Quantitative Analysis of Single Amino Acid Variant Peptides Associated with Pancreatic Cancer in Serum by an Isobaric Labeling Quantitative Method

    PubMed Central

    2015-01-01

    Single amino acid variations are highly associated with many human diseases. The direct detection of peptides containing single amino acid variants (SAAVs) derived from nonsynonymous single nucleotide polymorphisms (SNPs) in serum can provide unique opportunities for SAAV associated biomarker discovery. In the present study, an isobaric labeling quantitative strategy was applied to identify and quantify variant peptides in serum samples of pancreatic cancer patients and other benign controls. The largest number of SAAV peptides to date in serum including 96 unique variant peptides were quantified in this quantitative analysis, of which five variant peptides showed a statistically significant difference between pancreatic cancer and other controls (p-value < 0.05). Significant differences in the variant peptide SDNCEDTPEAGYFAVAVVK from serotransferrin were detected between pancreatic cancer and controls, which was further validated by selected reaction monitoring (SRM) analysis. The novel biomarker panel obtained by combining α-1-antichymotrypsin (AACT), Thrombospondin-1 (THBS1) and this variant peptide showed an excellent diagnostic performance in discriminating pancreatic cancer from healthy controls (AUC = 0.98) and chronic pancreatitis (AUC = 0.90). These results suggest that large-scale analysis of SAAV peptides in serum may provide a new direction for biomarker discovery research. PMID:25393578

  3. [Quantitative analysis method of natural gas combustion process combining wavelength selection and outlier spectra detection].

    PubMed

    Cao, Hui; Hu, Luo-Na; Zhou, Yan

    2012-10-01

    The present paper uses a combination method of wavelength selection and outlier spectra detection for quantitative analysis of nature gas combustion process based on its near infrared spectra. According to the statistical distribution of partial least squares (PLS) model coefficients and prediction errors, the method realized wavelength selection and outlier spectra detection, respectively. In contrast with PLS, PLS after leave-one-out for outlier detection (LOO-PLS), uninformative variable elimination by PLS (UVE-PLS) and UVE-PLS after leave-one-out for outlier detection (LOO-UVE-PLS), the root-mean-squared error of prediction (RMSEP) based on the method for CH4 prediction model is reduced by 14.33%, 14.33%, 10.96% and 12.21%; the RMSEP value for CO prediction model is reduced by 67.26%, 72.58%, 11.32% and 4.52%; the RMSEP value for CO2 prediction model is reduced by 5.95%, 19.7%, 36.71% and 4.04% respectively. Experimental results demonstrate that the method can significantly decrease the number of selected wavelengths, reduce model complexity and effectively detect outlier spectra. The established prediction model of analytes is more accurate as well as robust.

  4. Rapid quantitative analysis of lipids using a colorimetric method in a microplate format.

    PubMed

    Cheng, Yu-Shen; Zheng, Yi; VanderGheynst, Jean S

    2011-01-01

    A colorimetric sulfo-phospho-vanillin (SPV) method was developed for high throughput analysis of total lipids. The developed method uses a reaction mixture that is maintained in a 96-well microplate throughout the entire assay. The new assay provides the following advantages over other methods of lipid measurement: (1) background absorbance can be easily corrected for each well, (2) there is less risk of handling and transferring sulfuric acid contained in reaction mixtures, (3) color develops more consistently providing more accurate measurement of absorbance, and (4) the assay can be used for quantitative measurement of lipids extracted from a wide variety of sources. Unlike other spectrophotometric approaches that use fluorescent dyes, the optimal spectra and reaction conditions for the developed assay do not vary with the sample source. The developed method was used to measure lipids in extracts from four strains of microalgae. No significant difference was found in lipid determination when lipid content was measured using the new method and compared to results obtained using a macro-gravimetric method.

  5. A quantitative analysis of hydraulic interaction processes in stream-aquifer systems

    PubMed Central

    Wang, Wenke; Dai, Zhenxue; Zhao, Yaqian; Li, Junting; Duan, Lei; Wang, Zhoufeng; Zhu, Lin

    2016-01-01

    The hydraulic relationship between the stream and aquifer can be altered from hydraulic connection to disconnection when the pumping rate exceeds the maximum seepage flux of the streambed. This study proposes to quantitatively analyze the physical processes of stream-aquifer systems from connection to disconnection. A free water table equation is adopted to clarify under what conditions a stream starts to separate hydraulically from an aquifer. Both the theoretical analysis and laboratory tests have demonstrated that the hydraulic connectedness of the stream-aquifer system can reach a critical disconnection state when the horizontal hydraulic gradient at the free water surface is equal to zero and the vertical is equal to 1. A boundary-value problem for movement of the critical point of disconnection is established for an analytical solution of the inverted water table movement beneath the stream. The result indicates that the maximum distance or thickness of the inverted water table is equal to the water depth in the stream, and at a steady state of disconnection, the maximum hydraulic gradient at the streambed center is 2. This study helps us to understand the hydraulic phenomena of water flow near streams and accurately assess surface water and groundwater resources. PMID:26818442

  6. A quantitative analysis of hydraulic interaction processes in stream-aquifer systems.

    PubMed

    Wang, Wenke; Dai, Zhenxue; Zhao, Yaqian; Li, Junting; Duan, Lei; Wang, Zhoufeng; Zhu, Lin

    2016-01-28

    The hydraulic relationship between the stream and aquifer can be altered from hydraulic connection to disconnection when the pumping rate exceeds the maximum seepage flux of the streambed. This study proposes to quantitatively analyze the physical processes of stream-aquifer systems from connection to disconnection. A free water table equation is adopted to clarify under what conditions a stream starts to separate hydraulically from an aquifer. Both the theoretical analysis and laboratory tests have demonstrated that the hydraulic connectedness of the stream-aquifer system can reach a critical disconnection state when the horizontal hydraulic gradient at the free water surface is equal to zero and the vertical is equal to 1. A boundary-value problem for movement of the critical point of disconnection is established for an analytical solution of the inverted water table movement beneath the stream. The result indicates that the maximum distance or thickness of the inverted water table is equal to the water depth in the stream, and at a steady state of disconnection, the maximum hydraulic gradient at the streambed center is 2. This study helps us to understand the hydraulic phenomena of water flow near streams and accurately assess surface water and groundwater resources.

  7. 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.

  8. A quantitative analysis of hydraulic interaction processes in stream-aquifer systems

    SciTech Connect

    Wang, Wenke; Dai, Zhenxue; Zhao, Yaqian; Li, Junting; Duan, Lei; Wang, Zhoufeng; Zhu, Lin

    2016-01-28

    The hydraulic relationship between the stream and aquifer can be altered from hydraulic connection to disconnection when the pumping rate exceeds the maximum seepage flux of the streambed. This study proposes to quantitatively analyze the physical processes of stream-aquifer systems from connection to disconnection. A free water table equation is adopted to clarify under what conditions a stream starts to separate hydraulically from an aquifer. Both the theoretical analysis and laboratory tests have demonstrated that the hydraulic connectedness of the stream-aquifer system can reach a critical disconnection state when the horizontal hydraulic gradient at the free water surface is equal to zero and the vertical is equal to 1. A boundary-value problem for movement of the critical point of disconnection is established for an analytical solution of the inverted water table movement beneath the stream. The result indicates that the maximum distance or thickness of the inverted water table is equal to the water depth in the stream, and at a steady state of disconnection, the maximum hydraulic gradient at the streambed center is 2. In conclusion, this study helps us to understand the hydraulic phenomena of water flow near streams and accurately assess surface water and groundwater resources.

  9. A quantitative analysis of hydraulic interaction processes in stream-aquifer systems

    DOE PAGES

    Wang, Wenke; Dai, Zhenxue; Zhao, Yaqian; ...

    2016-01-28

    The hydraulic relationship between the stream and aquifer can be altered from hydraulic connection to disconnection when the pumping rate exceeds the maximum seepage flux of the streambed. This study proposes to quantitatively analyze the physical processes of stream-aquifer systems from connection to disconnection. A free water table equation is adopted to clarify under what conditions a stream starts to separate hydraulically from an aquifer. Both the theoretical analysis and laboratory tests have demonstrated that the hydraulic connectedness of the stream-aquifer system can reach a critical disconnection state when the horizontal hydraulic gradient at the free water surface is equalmore » to zero and the vertical is equal to 1. A boundary-value problem for movement of the critical point of disconnection is established for an analytical solution of the inverted water table movement beneath the stream. The result indicates that the maximum distance or thickness of the inverted water table is equal to the water depth in the stream, and at a steady state of disconnection, the maximum hydraulic gradient at the streambed center is 2. In conclusion, this study helps us to understand the hydraulic phenomena of water flow near streams and accurately assess surface water and groundwater resources.« less

  10. Self-awareness in Mild Cognitive Impairment: Quantitative evidence from systematic review and meta-analysis.

    PubMed

    Piras, Federica; Piras, Fabrizio; Orfei, Maria Donata; Caltagirone, Carlo; Spalletta, Gianfranco

    2016-02-01

    Here we quantitatively summarized evidence of impaired awareness in Mild Cognitive Impairment (MCI) and meta-analytically explored the relationship between Subjective Cognitive Complaints (SCC) and actual cognitive impairment. Twenty-three studies were included, 14 comparing awareness measures in MCI and healthy elderly subjects, and 16 also exploring the neuropsychological underpinnings of impaired awareness. Moderator analyses were conducted to determine whether self-awareness varied according to patient group, the particular state in relation to which insight was assessed, or the approach to measuring awareness. The meta-analysis shows that MCI patients have knowledge of their neuropsychological deficits and that level of awareness varies according to cognitive status, language and memory abilities. The assessment technique employed impacted on the insight phenomena. Specifically, MCI patients seem particularly accurate in evaluating the current state of their performance during an ongoing task and this could be essential in regulating their behavior so that compensative strategies are practiced and greater cognitive independence is achieved. Thus, assessment technique and cognitive status are crucial factors that influence level of awareness and should be taken into consideration in awareness evaluation and rehabilitation.

  11. MCM - 2 and Ki - 67 as proliferation markers in renal cell carcinoma: A quantitative and semi - quantitative analysis

    PubMed Central

    Mehdi, Muhammad Zain; Nagi, Abdul Hanan; Naseem, Nadia

    2016-01-01

    ABSTRACT Introduction/Background: Fuhrman nuclear grade is the most important histological parameter to predict prognosis in a patient of renal cell carcinoma (RCC). However, it suffers from inter-observer and intra-observer variation giving rise to need of a parameter that not only correlates with nuclear grade but is also objective and reproducible. Proliferation is the measure of aggressiveness of a tumour and it is strongly correlated with Fuhrman nuclear grade, clinical survival and recurrence in RCC. Ki-67 is conventionally used to assess proliferation. Mini-chromosome maintenance 2 (MCM-2) is a lesser known marker of proliferation and identifies a greater proliferation faction. This study was designed to assess the prognostic significance of MCM-2 by comparing it with Fuhrman nuclear grade and Ki-67. Material and Methods: n=50 cases of various ages, stages, histological subtypes and grades of RCC were selected for this study. Immunohistochemical staining using Ki-67(MIB-1, Mouse monoclonal antibody, Dako) and MCM-2 (Mouse monoclonal antibody, Thermo) was performed on the paraffin embedded blocks in the department of Morbid anatomy and Histopathology, University of Health Sciences, Lahore. Labeling indices (LI) were determined by two pathologists independently using quantitative and semi-quantitative analysis. Statistical analysis was carried out using SPSS 20.0. Kruskall-Wallis test was used to determine a correlation of proliferation markers with grade, and Pearson's correlate was used to determine correlation between the two proliferation markers. Results: Labeling index of MCM-2 (median=24.29%) was found to be much higher than Ki-67(median=13.05%). Both markers were significantly related with grade (p=0.00; Kruskall-Wallis test). LI of MCM-2 was found to correlate significantly with LI of Ki-67(r=0.0934;p=0.01 with Pearson's correlate). Results of semi-quantitative analysis correlated well with quantitative analysis. Conclusion: Both Ki-67 and MCM-2 are

  12. Identification of fidgety movements and prediction of CP by the use of computer-based video analysis is more accurate when based on two video recordings.

    PubMed

    Adde, Lars; Helbostad, Jorunn; Jensenius, Alexander R; Langaas, Mette; Støen, Ragnhild

    2013-08-01

    This study evaluates the role of postterm age at assessment and the use of one or two video recordings for the detection of fidgety movements (FMs) and prediction of cerebral palsy (CP) using computer vision software. Recordings between 9 and 17 weeks postterm age from 52 preterm and term infants (24 boys, 28 girls; 26 born preterm) were used. Recordings were analyzed using computer vision software. Movement variables, derived from differences between subsequent video frames, were used for quantitative analysis. Sensitivities, specificities, and area under curve were estimated for the first and second recording, or a mean of both. FMs were classified based on the Prechtl approach of general movement assessment. CP status was reported at 2 years. Nine children developed CP of whom all recordings had absent FMs. The mean variability of the centroid of motion (CSD) from two recordings was more accurate than using only one recording, and identified all children who were diagnosed with CP at 2 years. Age at assessment did not influence the detection of FMs or prediction of CP. The accuracy of computer vision techniques in identifying FMs and predicting CP based on two recordings should be confirmed in future studies.

  13. Quantitative analysis of cadmium selenide nanocrystal concentration by comparative techniques.

    PubMed

    Kuçur, Erol; Boldt, Frank M; Cavaliere-Jaricot, Sara; Ziegler, Jan; Nann, Thomas

    2007-12-01

    In this paper, we compared atomic absorption spectroscopy (AAS), anodic stripping voltammetry (ASV), and UV-vis spectroscopy for the determination of the concentration of CdSe nanocrystal (NC) solutions. The experimental results were combined with crystallographic calculations of the NC size, which led to a very accurate determination of the nanocrystal concentration--a crucial parameter for bioanalytical applications. Furthermore, such a combined approach can be extended to the determination of shell thickness of core/shell materials (e.g., CdSe/ZnS).

  14. Quantitative analysis of multi-component complex oil spills based on the least-squares support vector regression

    NASA Astrophysics Data System (ADS)

    Tan, Ailing; Zhao, Yong; Wang, Siyuan

    2016-10-01

    Quantitative analysis of the simulated complex oil spills was researched based on PSO-LS-SVR method. Forty simulated mixture oil spills samples were made with different concentration proportions of gasoline, diesel and kerosene oil, and their near infrared spectra were collected. The parameters of least squares support vector machine were optimized by particle swarm optimization algorithm. The optimal concentration quantitative models of three-component oil spills were established. The best regularization parameter C and kernel parameter σ of gasoline, diesel and kerosene model were 48.1418 and 0.1067, 53.2820 and 0.1095, 59.1689 and 0.1000 respectively. The decision coefficient R2 of the prediction model were 0.9983, 0.9907 and 0.9942 respectively. RMSEP values were 0.0753, 0.1539 and 0.0789 respectively. For gasoline, diesel fuel and kerosene oil models, the mean value and variance value of predict absolute error were -0.0176±0.0636 μL/mL, -0.0084+/-0.1941 μL/mL, and 0.00338+/-0.0726 μL/mL respectively. The results showed that each component's concentration of the oil spills samples could be detected by the NIR technology combined with PSO-LS-SVR regression method, the predict results were accurate and reliable, thus this method can provide effective means for the quantitative detection and analysis of complex marine oil spills.

  15. Study of proper conditions for quantitative atom-probe analysis

    NASA Astrophysics Data System (ADS)

    Rolander, Ulf; Andrén, Hans-Olof

    1994-03-01

    Atom-probe microanalysis is a truly quantitative method only if certain requirements are fulfilled. Field evaporation must only happen when the detector system is active; ions must travel from specimen to detector without being obstructed; and ions must be detected with the same probability regardless of mass and energy. Designs and methods to achieve these requirements are presented in the paper, such as a controlled high-voltage pulser, a detector with good and variable multi-hit resolution, ion optical alignment procedures, and a method to statistically correct for pile-up in the detector.

  16. Qualitative and quantitative analysis of monomers in polyesters for food contact materials.

    PubMed

    Brenz, Fabrian; Linke, Susanne; Simat, Thomas

    2017-02-01

    Polyesters (PESs) are gaining more importance on the food contact material (FCM) market and the variety of properties and applications is expected to be wide. In order to acquire the desired properties manufacturers can combine several FCM-approved polyvalent carboxylic acids (PCAs) and polyols as monomers. However, information about the qualitative and quantitative composition of FCM articles is often limited. The method presented here describes the analysis of PESs with the identification and quantification of 25 PES monomers (10 PCA, 15 polyols) by HPLC with diode array detection (HPLC-DAD) and GC-MS after alkaline hydrolysis. Accurate identification and quantification were demonstrated by the analysis of seven different FCM articles made of PESs. The results explained between 97.2% and 103.4% w/w of the polymer composition whilst showing equal molar amounts of PCA and polyols. Quantification proved to be precise and sensitive with coefficients of variation (CVs) below 6.0% for PES samples with monomer concentrations typically ranging from 0.02% to 75% w/w. The analysis of 15 PES samples for the FCM market revealed the presence of five different PCAs and 11 different polyols (main monomers, co-monomers, non-intentionally added substances (NIAS)) showing the wide variety of monomers in modern PESs. The presented method provides a useful tool for commercial, state and research laboratories as well as for producers and distributors facing the task of FCM risk assessment. It can be applied for the identification and quantification of migrating monomers and the prediction of oligomer compositions from the identified monomers, respectively.

  17. Chemical Fingerprint Analysis and Quantitative Analysis of Rosa rugosa by UPLC-DAD.

    PubMed

    Mansur, Sanawar; Abdulla, Rahima; Ayupbec, Amatjan; Aisa, Haji Akbar

    2016-12-21

    A method based on ultra performance liquid chromatography with a diode array detector (UPLC-DAD) was developed for quantitative analysis of five active compounds and chemical fingerprint analysis of Rosa rugosa. Ten batches of R. rugosa collected from different plantations in the Xinjiang region of China were used to establish the fingerprint. The feasibility and advantages of the used UPLC fingerprint were verified for its similarity evaluation by systematically comparing chromatograms with professional analytical software recommended by State Food and Drug Administration (SFDA) of China. In quantitative analysis, the five compounds showed good regression (R² = 0.9995) within the test ranges, and the recovery of the method was in the range of 94.2%-103.8%. The similarities of liquid chromatography fingerprints of 10 batches of R. rugosa were more than 0.981. The developed UPLC fingerprint method is simple, reliable, and validated for the quality control and identification of R. rugosa. Additionally, simultaneous quantification of five major bioactive ingredients in the R. rugosa samples was conducted to interpret the consistency of the quality test. The results indicated that the UPLC fingerprint, as a characteristic distinguishing method combining similarity evaluation and quantification analysis, can be successfully used to assess the quality and to identify the authenticity of R. rugosa.

  18. A Quantitative Proteomic Analysis of In Vitro Assembled Chromatin*

    PubMed Central

    Völker-Albert, Moritz Carl; Pusch, Miriam Caroline; Fedisch, Andreas; Schilcher, Pierre; Schmidt, Andreas; Imhof, Axel

    2016-01-01

    The structure of chromatin is critical for many aspects of cellular physiology and is considered to be the primary medium to store epigenetic information. It is defined by the histone molecules that constitute the nucleosome, the positioning of the nucleosomes along the DNA and the non-histone proteins that associate with it. These factors help to establish and maintain a largely DNA sequence-independent but surprisingly stable structure. Chromatin is extensively disassembled and reassembled during DNA replication, repair, recombination or transcription in order to allow the necessary factors to gain access to their substrate. Despite such constant interference with chromatin structure, the epigenetic information is generally well maintained. Surprisingly, the mechanisms that coordinate chromatin assembly and ensure proper assembly are not particularly well understood. Here, we use label free quantitative mass spectrometry to describe the kinetics of in vitro assembled chromatin supported by an embryo extract prepared from preblastoderm Drosophila melanogaster embryos. The use of a data independent acquisition method for proteome wide quantitation allows a time resolved comparison of in vitro chromatin assembly. A comparison of our in vitro data with proteomic studies of replicative chromatin assembly in vivo reveals an extensive overlap showing that the in vitro system can be used for investigating the kinetics of chromatin assembly in a proteome-wide manner. PMID:26811354

  19. Quantitative analysis of biopolymers by matrix-assisted laser desorption

    SciTech Connect

    Tang, K.; Allman, S.L.; Jones, R.B.; Chen, C.H. )

    1993-08-01

    During the past few years, major efforts have been made to use mass spectrometry to measure biopolymers because of the great potential benefit to biological and medical research. Although the theoretical details of laser desorption and ionization mechanisms of MALDI are not yet fully understood, several models have been presented to explain the production of large biopolymer ions. In brief, it is very difficult to obtain reliable measurements of the absolute quantity of analytes by MALDI. If MALDI is going to become a routine analytical tool, it is obvious that quantitative measurement capability must be pursued. Oligonucleotides and protein samples used in this work were purchased from commercial sources. Nicotinic acid was used as matrix for both types of biopolymers. From this experiment, it is seen that it is difficult to obtain absolute quantitative measurements of biopolymers using MALDI. However, internal calibration with molecules having similar chemical properties can be used to resolve these difficulties. Chemical reactions between biopolymers must be avoided to prevent the destruction of the analyte materials. 10 refs., 8 figs.

  20. Quantitative Spectral Analysis of Evolved Low-Mass Stars

    NASA Astrophysics Data System (ADS)

    Werner, Klaus; Rauch, Thomas; Kruk, Jeffrey W.

    2009-09-01

    The hydrogen-deficiency in extremely hot post-AGB stars of spectral class PG1159 is probably caused by a (very) late helium-shell flash or a AGB final thermal pulse that consumes the hydrogen envelope, exposing the usually-hidden intershell region. Thus, the photospheric element abundances of these stars allow us to draw conclusions about details of nuclear burning and mixing processes in the precursor AGB stars. We compare predicted element abundances to those determined by quantitative spectral analyses performed with advanced non-LTE model atmospheres. A good qualitative and quantitative agreement is found for many species (He, C, N, O, Ne, F, Si, Ar) but discrepancies for others (P, S, Fe) point at shortcomings in stellar evolution models for AGB stars. Almost all of the chemical trace elements in these hot stars can only be identified in the UV spectral range. The Far Ultraviolet Spectroscopic Explorer and the Hubble Space Telescope played a crucial role for this research.

  1. Quantitative analysis of radiation-induced changes in sperm morphology

    SciTech Connect

    Young, I.T.; Gledhill, B.L.; Lake, S.; Wyrobek, A.J.

    1982-09-01

    When developing spermatogenic cells are exposed to radiation, chemical carcinogens or mutagens, the transformation in the morphology of the mature sperm can be used to determine the severity of the exposure. In this study five groups of mice with three mice per group received testicular doses of X irradiation at dosage levels ranging from 0 rad to 120 rad. A random sample of 100 mature sperm per mouse was analyzed five weeks later for the quantitative morphologic transformation as a function of dosage level. The cells were stained with gallocyanin chrome alum (GCA) so that only the DNA in the sperm head was visible. The ACUity quantitative microscopy system at Lawrence Livermore National Laboratory was used to scan the sperm at a sampling density of 16 points per linear micrometer and with 256 brightness levels per point. The contour of each cell was extracted using conventional thresholding techniques on the high-contrast images. For each contour a variety of shape features was then computed to characterize the morphology of that cell. Using the control group and the distribution of their shape features to establish the variability of a normal sperm population, the 95% limits on normal morphology were established. Using only four shape features, a doubling dose of approximately 39 rad was determined. That is, at 39 rad exposure the percentage of abnormal cells was twice that occurring in the control population. This compared to a doubling dose of approximately 70 rad obtained from a concurrent visual procedure.

  2. Quantitative Raman spectroscopy for the analysis of carrot bioactives.

    PubMed

    Killeen, Daniel P; Sansom, Catherine E; Lill, Ross E; Eason, Jocelyn R; Gordon, Keith C; Perry, Nigel B

    2013-03-20

    Rapid quantitative near-infrared Fourier transform Raman analyses of the key phytonutrients in carrots, polyacetylenes and carotenoids, are reported here for the first time. Solvent extracts of 31 carrot lines were analyzed for these phytonutrients by conventional methods, polyacetylenes by GC-FID and carotenoids by visible spectrophotometry. Carotenoid concentrations were 0-5586 μg g(-1) dry weight (DW). Polyacetylene concentrations were 74-4846 μg g(-1) DW, highest in wild carrots. The polyacetylenes were falcarinol, 6-1237 μg g(-1) DW; falcarindiol, 42-3475 μg g(-1) DW; and falcarindiol 3-acetate, 27-649 μg g(-1) DW. Strong Raman bands for carotenoids gave good correlation to results by visible spectrophotometry. A chemometric model capable of quantitating carotenoids from Raman data was developed. A classification model for rapidly distinguishing carrots with high and low polyacetylene (limit of detection = 1400 μg g(-1)) concentrations based on Raman spectral intensity in the region of 2250 cm(-1) was produced.

  3. Quantitative Sulfur Analysis using Stand-off Laser-Induced Breakdown Spectroscopy

    NASA Astrophysics Data System (ADS)

    Dyar, M. D.; Tucker, J. M.; Clegg, S. M.; Barefield, J. E.; Wiens, R. C.

    2008-12-01

    The laser-induced breakdown spectrometer (LIBS) in the ChemCam instrument on Mars Science Laboratory has the capability to produce robust, quantitative analyses not only for major elements, but also for a large range of light elements and trace elements that are of great interest to geochemists. However, sulfur presents a particular challenge because it reacts easily with oxygen in the plasma and because the brightest S emission lines lie outside ChemCam's spectral range. This work was undertaken within the context of our larger effort to identify and compensate for matrix effects, which are chemical properties of the material that influence the ratio of a given emission line to the abundance of the element producing that line. Samples for this study include two suites of rocks: a suite of 12 samples that are mixtures of sulfate minerals and host rocks, generally with high S contents (0.1-26.0 wt% S), and a large suite of 118 igneous rocks from varying parageneses with S contents in the 0-2 wt% range. These compositions provide several different types of matrices to challenge our calibration procedures. Samples were analyzed under ChemCam-like conditions: a Nd:YAG laser producing 17 mJ per 10ns pulse was directed onto samples positioned 5-9 m away from the laser and tele­scope. The samples were placed in a vacuum chamber filled with 7 Torr CO2 to replicate the Martian surface pressure as the atmospheric pressure influences the LIBS plasma. Some of the LIBS plasma emission is collected with a telescope and transmitted through a 1 m, 300 um, 0.22NA optical fiber connected to a commercial Ocean Optics spectrometer. We are testing and comparing three different strategies to evaluate sulfur contents. 1) We have calculated regression lines comparing the intensity at each channel to the S content. This analysis shows that there are dozens of S emission lines in the ChemCam wavelength range that are suitable for use in quantitative analysis, even in the presence of Fe. 2

  4. QUANTITATIVE CT ANALYSIS, AIRFLOW OBSTRUCTION AND LUNG CANCER IN THE PITTSBURGH LUNG SCREENING STUDY

    PubMed Central

    Wilson, David O; Leader, Joseph K; Fuhrman, Carl R; Reilly, John J; Sciurba, Frank C.; Weissfeld, Joel L

    2011-01-01

    Background To study the relationship between emphysema, airflow obstruction and lung cancer in a high risk population we performed quantitative analysis of screening computed tomography (CT) scans. Methods Subjects completed questionnaires, spirometry and low-dose helical chest CT. Analyses compared cases and controls according to automated quantitative analysis of lung parenchyma and airways measures. Results Our case-control study of 117 matched pairs of lung cancer cases and controls did not reveal any airway or lung parenchymal findings on quantitative analysis of screening CT scans that were associated with increased lung cancer risk. Airway measures including wall area %, lumen perimeter, lumen area and average wall HU, and parenchymal measures including lung fraction < −910 Hounsfield Units (HU), were not statistically different between cases and controls. Conclusions The relationship between visual assessment of emphysema and increased lung cancer risk could not be verified by quantitative analysis of low-dose screening CT scans in a high risk tobacco exposed population. PMID:21610523

  5. Grid-Enabled Quantitative Analysis of Breast Cancer

    DTIC Science & Technology

    2010-10-01

    large-scale, multi-modality computerized image analysis . The central hypothesis of this research is that large-scale image analysis for breast cancer...research, we designed a pilot study utilizing large scale parallel Grid computing harnessing nationwide infrastructure for medical image analysis . Also

  6. Anniversary Paper: History and status of CAD and quantitative image analysis: The role of Medical Physics and AAPM

    SciTech Connect

    Giger, Maryellen L.; Chan, Heang-Ping; Boone, John

    2008-12-15

    algorithms using appropriate cases to measure performance and robustness; conducting observer studies with which to evaluate radiologists in the diagnostic task without and with the use of the computer aid; and ultimately assessing performance with a clinical trial. Medical physicists also have an important role in quantitative imaging, by validating the quantitative integrity of scanners and developing imaging techniques, and image analysis tools that extract quantitative data in a more accurate and automated fashion. As imaging systems become more complex and the need for better quantitative information from images grows, the future includes the combined research efforts from physicists working in CAD with those working on quantitative imaging systems to readily yield information on morphology, function, molecular structure, and more--from animal imaging research to clinical patient care. A historical review of CAD and a discussion of challenges for the future are presented here, along with the extension to quantitative image analysis.

  7. Anniversary Paper: History and status of CAD and quantitative image analysis: The role of Medical Physics and AAPM

    PubMed Central

    Giger, Maryellen L.; Chan, Heang-Ping; Boone, John

    2008-01-01

    algorithms using appropriate cases to measure performance and robustness; conducting observer studies with which to evaluate radiologists in the diagnostic task without and with the use of the computer aid; and ultimately assessing performance with a clinical trial. Medical physicists also have an important role in quantitative imaging, by validating the quantitative integrity of scanners and developing imaging techniques, and image analysis tools that extract quantitative data in a more accurate and automated fashion. As imaging systems become more complex and the need for better quantitative information from images grows, the future includes the combined research efforts from physicists working in CAD with those working on quantitative imaging systems to readily yield information on morphology, function, molecular structure, and more—from animal imaging research to clinical patient care. A historical review of CAD and a discussion of challenges for the future are presented here, along with the extension to quantitative image analysis. PMID:19175137

  8. [Qualitative and quantitative analysis of dodecatetraenamides A, B in Asari Radix et Rhizoma].

    PubMed

    Xie, De-mei; Liu, Guang-xue; Xu, Feng; Shang, Ming-ying; Zhang, Zi-wei; Wang, Xuan; Cai, Shao-qing

    2015-02-01

    and production area, the average contents of the two constituents in latter were up to (1.59 ± 0.75) mg · g(-1) and (2.90 ± 1.17) mg · g(-1), respectively, significantly higher than that in A. sieboldii var. seoulense (dodecatetraenamide A were (0.78 ± 0.52) mg · g(-1), dodecatetraenamide B were (1.69 ± 0.83) mg · g(-1)) (P < 0.05). The content of the dodecatetraenamide A in overground part was in the range of 0.11-0.33 mg · g(-1), dodecatetraenamide B was 0. 24-0.60 mg · g(-1), which were much lower than that of the underground part of ARR (dodecatetraenamide A was in the range of 0.73-3.89 mg · g(-1), dodecatetraenamide B was 2.11-6.24 mg · g(-1)). The method was certified to be simple, accurate and reliable and could be used for qualitative and quantitative analysis of dodecatetraenamide A and B in different species of ARR, also can be used for the comprehensive quality control of traditional Chinese medicine, Asari Radix et Rhizoma.

  9. Accurate Analysis of the Change in Volume, Location, and Shape of Metastatic Cervical Lymph Nodes During Radiotherapy

    SciTech Connect

    Takao, Seishin; Tadano, Shigeru; Taguchi, Hiroshi; Yasuda, Koichi; Onimaru, Rikiya; Ishikawa, Masayori; Bengua, Gerard; Suzuki, Ryusuke; Shirato, Hiroki

    2011-11-01

    Purpose: To establish a method for the accurate acquisition and analysis of the variations in tumor volume, location, and three-dimensional (3D) shape of tumors during radiotherapy in the era of image-guided radiotherapy. Methods and Materials: Finite element models of lymph nodes were developed based on computed tomography (CT) images taken before the start of treatment and every week during the treatment period. A surface geometry map with a volumetric scale was adopted and used for the analysis. Six metastatic cervical lymph nodes, 3.5 to 55.1 cm{sup 3} before treatment, in 6 patients with head and neck carcinomas were analyzed in this study. Three fiducial markers implanted in mouthpieces were used for the fusion of CT images. Changes in the location of the lymph nodes were measured on the basis of these fiducial markers. Results: The surface geometry maps showed convex regions in red and concave regions in blue to ensure that the characteristics of the 3D tumor geometries are simply understood visually. After the irradiation of 66 to 70 Gy in 2 Gy daily doses, the patterns of the colors had not changed significantly, and the maps before and during treatment were strongly correlated (average correlation coefficient was 0.808), suggesting that the tumors shrank uniformly, maintaining the original characteristics of the shapes in all 6 patients. The movement of the gravitational center of the lymph nodes during the treatment period was everywhere less than {+-}5 mm except in 1 patient, in whom the change reached nearly 10 mm. Conclusions: The surface geometry map was useful for an accurate evaluation of the changes in volume and 3D shapes of metastatic lymph nodes. The fusion of the initial and follow-up CT images based on fiducial markers enabled an analysis of changes in the location of the targets. Metastatic cervical lymph nodes in patients were suggested to decrease in size without significant changes in the 3D shape during radiotherapy. The movements of the

  10. Quantitative Anatomic Analysis of the Native Ligamentum Teres

    PubMed Central

    Mikula, Jacob D.; Slette, Erik L.; Chahla, Jorge; Brady, Alex W.; Locks, Renato; Trindade, Christiano A. C.; Rasmussen, Matthew T.; LaPrade, Robert F.; Philippon, Marc J.

    2017-01-01

    Background: While recent studies have addressed the biomechanical function of the ligamentum teres and provided descriptions of ligamentum teres reconstruction techniques, its detailed quantitative anatomy remains relatively undocumented. Moreover, there is a lack of consensus in the literature regarding the number and morphology of the acetabular attachments of the ligamentum teres. Purpose: To provide a clinically relevant quantitative anatomic description of the native human ligamentum teres. Study Design: Descriptive laboratory study. Methods: Ten human cadaveric hemipelvises, complete with femurs (mean age, 59.6 years; range, 47-65 years), were dissected free of all extra-articular soft tissues to isolate the ligamentum teres and its attachments. A coordinate measuring device was used to quantify the attachment areas and their relationships to pertinent open and arthroscopic landmarks on both the acetabulum and the femur. The clock face reference system was utilized to describe acetabular anatomy, and all anatomic relationships were described using the mean and 95% confidence intervals. Results: There were 6 distinct attachments to the acetabulum and 1 to the femur. The areas of the acetabular and femoral attachment footprints of the ligamentum teres were 434 mm2 (95% CI, 320-549 mm2) and 84 mm2 (95% CI, 65-104 mm2), respectively. The 6 acetabular clock face locations were as follows: anterior attachment, 4:53 o’clock (95% CI, 4:45-5:02); posterior attachment, 6:33 o’clock (95% CI, 6:23-6:43); ischial attachment, 8:07 o’clock (95% CI, 7:47-8:26); iliac attachment, 1:49 o’clock (95% CI, 1:04-2:34); and a smaller pubic attachment that was located at 3:50 o’clock (95% CI, 3:41-4:00). The ischial attachment possessed the largest cross-sectional attachment area (127.3 mm2; 95% CI, 103.0-151.7 mm2) of all the acetabular attachments of the ligamentum teres. Conclusion: The most important finding of this study was that the human ligamentum teres had 6

  11. Bridging the gaps for global sustainable development: a quantitative analysis.

    PubMed

    Udo, Victor E; Jansson, Peter Mark

    2009-09-01

    Global human progress occurs in a complex web of interactions between society, technology and the environment as driven by governance and infrastructure management capacity among nations. In our globalizing world, this complex web of interactions over the last 200 years has resulted in the chronic widening of economic and political gaps between the haves and the have-nots with consequential global cultural and ecosystem challenges. At the bottom of these challenges is the issue of resource limitations on our finite planet with increasing population. The problem is further compounded by pleasure-driven and poverty-driven ecological depletion and pollution by the haves and the have-nots respectively. These challenges are explored in this paper as global sustainable development (SD) quantitatively; in order to assess the gaps that need to be bridged. Although there has been significant rhetoric on SD with very many qualitative definitions offered, very few quantitative definitions of SD exist. The few that do exist tend to measure SD in terms of social, energy, economic and environmental dimensions. In our research, we used several human survival, development, and progress variables to create an aggregate SD parameter that describes the capacity of nations in three dimensions: social sustainability, environmental sustainability and technological sustainability. Using our proposed quantitative definition of SD and data from relatively reputable secondary sources, 132 nations were ranked and compared. Our comparisons indicate a global hierarchy of needs among nations similar to Maslow's at the individual level. As in Maslow's hierarchy of needs, nations that are struggling to survive are less concerned with environmental sustainability than advanced and stable nations. Nations such as the United States, Canada, Finland, Norway and others have higher SD capacity, and thus, are higher on their hierarchy of needs than nations such as Nigeria, Vietnam, Mexico and other

  12. Quantitation of phosphorus excretion in sheep by compartmental analysis

    SciTech Connect

    Schneider, K.M.; Boston, R.C.; Leaver, D.D.

    1987-04-01

    The control of phosphorus excretion in sheep has been examined by constructing a kinetic model that contains a mechanistic set of connections between blood and gastrointestinal tract. The model was developed using experimental data from chaff-fed sheep and gives an accurate description of the absorption and excretion of /sup 32/P phosphorus in feces and urine of the ruminating sheep. These results indicated the main control site for phosphorus excretion in the ruminating sheep was the gastrointestinal tract, whereas for the non-ruminating sheep fed the liquid diet, control was exerted by the kidney. A critical factor in the induction of adaptation of phosphorus reabsorption by the kidney was the reduction in salivation, and since this response occurred independently of marked changes in the delivery of phosphorus to the kidney, a humoral factor may be involved in this communication between salivary gland and kidney.

  13. Quantitative interpretation of mineral hyperspectral images based on principal component analysis and independent component analysis methods.

    PubMed

    Jiang, Xiping; Jiang, Yu; Wu, Fang; Wu, Fenghuang

    2014-01-01

    Interpretation of mineral hyperspectral images provides large amounts of high-dimensional data, which is often complicated by mixed pixels. The quantitative interpretation of hyperspectral images is known to be extremely difficult when three types of information are unknown, namely, the number of pure pixels, the spectrum of pure pixels, and the mixing matrix. The problem is made even more complex by the disturbance of noise. The key to interpreting abstract mineral component information, i.e., pixel unmixing and abundance inversion, is how to effectively reduce noise, dimension, and redundancy. A three-step procedure is developed in this study for quantitative interpretation of hyperspectral images. First, the principal component analysis (PCA) method can be used to process the pixel spectrum matrix and keep characteristic vectors with larger eigenvalues. This can effectively reduce the noise and redundancy, which facilitates the abstraction of major component information. Second, the independent component analysis (ICA) method can be used to identify and unmix the pixels based on the linear mixed model. Third, the pure-pixel spectrums can be normalized for abundance inversion, which gives the abundance of each pure pixel. In numerical experiments, both simulation data and actual data were used to demonstrate the performance of our three-step procedure. Under simulation data, the results of our procedure were compared with theoretical values. Under the actual data measured from core hyperspectral images, the results obtained through our algorithm are compared with those of similar software (Mineral Spectral Analysis 1.0, Nanjing Institute of Geology and Mineral Resources). The comparisons show that our method is effective and can provide reference for quantitative interpretation of hyperspectral images.

  14. 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

  15. Torpedo electromotor system development: a quantitative analysis of synaptogenesis.

    PubMed

    Fox, G Q; Kötting, D

    1984-04-10

    Synaptogenesis in the electric organ of Torpedo marmorato has been studied quantitatively at the ultrastructural level of observation. In addition to establishing the normal developmental time course for this event we were interested in determining whether a gradient of synaptogenesis might be present because the electric organ produces several morphologically recognizable spatiotemporal gradients during its early ontogeny. These gradients genesis of electrocyte columns, both gradients of which are operative for periods of weeks. No gradient of synaptogenesis was found, indicating this to be a synchronous process. The idea is advanced that synaptogenesis in the electric organ is modulated by extrinsic influences, many of which may originate from the target electrocytes which, by this time, have become synchronized in their development.

  16. Microfluidic platform for the quantitative analysis of leukocyte migration signatures.

    PubMed

    Boneschansker, Leo; Yan, Jun; Wong, Elisabeth; Briscoe, David M; Irimia, Daniel

    2014-09-03

    Leukocyte migration into tissues is characteristic of inflammation. It is usually measured in vitro as the average displacement of populations of cells towards a chemokine gradient, not acknowledging other patterns of cell migration. Here, we designed and validated a microfluidic migration platform to simultaneously analyse four qualitative migration patterns: chemoattraction, -repulsion, -kinesis and -inhibition, using single-cell quantitative metrics of direction, speed, persistence and fraction of cells responding. We find that established chemokines, complement component 5a and IL-8 induce chemoattraction and repulsion in equal proportions, resulting in the dispersal of cells. These migration signatures are characterized by high persistence and speed and are independent of the chemokine dose or receptor expression. Furthermore, we find that twice as many T lymphocytes migrate away than towards stromal cell-derived factor 1 and their directional migration patterns are not persistent. Overall, our platform helps discover migratory signature responses and uncovers an avenue for precise characterization of leukocyte migration and therapeutic modulators.

  17. MICROFLUIDIC PLATFORM FOR THE QUANTITATIVE ANALYSIS OF LEUKOCYTE MIGRATION SIGNATURES

    PubMed Central

    Wong, Elisabeth; Briscoe, David M.;