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Sample records for quantitative analysis aqua

  1. Analysis of leaf area index products from combination of MODIS Terra and Aqua data

    E-print Network

    Myneni, Ranga B.

    of testing for the next version (Collection 5) of the MODerate resolution Imaging Spectroradiometer (MODIS. Index terms: MODIS; Terra; Aqua; Leaf area index 1. Introduction The MODerate resolution Imaging Spectroradiometer (MODIS) on board NASA's Terra and Aqua platforms is designed for monitoring of the Earth

  2. 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.

  3. Book Reviews Quantitative Syntax Analysis

    E-print Network

    between QL and computational linguistics. Quantitative Syntax Analysis is a recent work on QL by Reinhard linguistics in general. © 2012 Association for Computational Linguistics In the first chapter, K¨ohler points when it comes to processing real texts. And that is why in computational linguistics, "devout executors

  4. Improved centroid moment tensor analyses in the NIED AQUA (Accurate and QUick Analysis system for source parameters)

    NASA Astrophysics Data System (ADS)

    Kimura, H.; Asano, Y.; Matsumoto, T.

    2012-12-01

    The rapid determination of hypocentral parameters and their transmission to the public are valuable components of disaster mitigation. We have operated an automatic system for this purpose—termed the Accurate and QUick Analysis system for source parameters (AQUA)—since 2005 (Matsumura et al., 2006). In this system, the initial hypocenter, the moment tensor (MT), and the centroid moment tensor (CMT) solutions are automatically determined and posted on the NIED Hi-net Web site (www.hinet.bosai.go.jp). This paper describes improvements made to the AQUA to overcome limitations that became apparent after the 2011 Tohoku Earthquake (05:46:17, March 11, 2011 in UTC). The improvements included the processing of NIED F-net velocity-type strong motion records, because NIED F-net broadband seismographs are saturated for great earthquakes such as the 2011 Tohoku Earthquake. These velocity-type strong motion seismographs provide unsaturated records not only for the 2011 Tohoku Earthquake, but also for recording stations located close to the epicenters of M>7 earthquakes. We used 0.005-0.020 Hz records for M>7.5 earthquakes, in contrast to the 0.01-0.05 Hz records employed in the original system. The initial hypocenters determined based on arrival times picked by using seismograms recorded by NIED Hi-net stations can have large errors in terms of magnitude and hypocenter location, especially for great earthquakes or earthquakes located far from the onland Hi-net network. The size of the 2011 Tohoku Earthquake was initially underestimated in the AQUA to be around M5 at the initial stage of rupture. Numerous aftershocks occurred at the outer rise east of the Japan trench, where a great earthquake is anticipated to occur. Hence, we modified the system to repeat the MT analyses assuming a larger size, for all earthquakes for which the magnitude was initially underestimated. We also broadened the search range of centroid depth for earthquakes located far from the onland Hi-net network. After implementing the above improvements, the CMT solution for the 2011 Tohoku Earthquake was successfully determined with a moment magnitude (Mw) of 8.6 (9.04 × 10^21 Nm). The focal mechanisms and centroid depths of the 2011 Tohoku Earthquake and M>7 aftershocks, as obtained using the improved system, are in agreement with those from the GlobalCMT. The sizes of these earthquakes are also consistent with those of GlobalCMT, with differences of less than Mw 0.1 except for the mainshock (Mw9.1, 5.31 × 10^22 Nm, GlobalCMT). This discrepancy may indicate that the bandwidth used in the analysis is insufficient for an earthquake of this size. To address this shortcoming, we used 0.0025-0.0100 Hz records and obtained a magnitude of Mw8.9 (3.35 × 10^22 Nm). This result is consistent with the GlobalCMT and other results (e.g., Mw 9.0, 3.43 × 10^22 Nm reported by Ozawa et al., 2011; Mw9.0, 4.42 × 10^22 Nm reported by Suzuki et al., 2011). Using the improved system, the CMT analysis for the 2011 Tohoku Earthquake is estimated to be completed within 12 minutes of the origin time.

  5. Quantitative Analysis of Glaciated Landscapes

    NASA Astrophysics Data System (ADS)

    Huerta, A. D.

    2005-12-01

    The evolution of glaciated mountains is at the heart of the debate over Late Cenozoic linkages between climate and tectonics. Traditionally, the development of high summit elevations is attributed to tectonic processes. However, much of the high elevation of the Transantarctic Mountains can be attributed solely to uplift in response to glacial erosion (Stern et al., 2005). The Transantarctic Mountains (TAM) provide an unparalleled opportunity to study glacial erosion. The mountain range has experienced glacial conditions since Oligocene time. In the higher and dryer regions of the TAM there is only a thin veneer of ice and snow draping the topography. In these regions landforms that were shaped during earlier climatic conditions are preserved. In fact, both glacial and fluvial landforms dating as far back as 18 Ma are preserved locally. In addition, the TAM are ideal for studying glacial erosion since the range has experienced minimal tectonic uplift since late Oligocene time, thus isolating the erosion signal from any tectonic signal. With the advent of digital data sets and GIS methodologies, quantitative analysis can identify key aspects of glaciated landscape morphology, and thus develop powerful analytical techniques for objective study of glaciation. Inspection of USGS topographic maps of the TAM reveals that mountain tops display an extreme range of glacial modification. For example, in the Mt. Rabot region (83°-84° S), mountain peaks are strongly affected by glaciation; cirque development is advanced with cirque diameters on the range of several kilometers, and cirque confluence has resulted in the formation of ``knife-edge'' arêtes up to 10 km long. In contrast, in the Mt. Murchison area (73°-74° S) cirque development is youthful, and there is minimal development of arêtes. Preliminary work indicates that analysis of DEM's and contour lines can be used to distinguish degree of glaciation. In particular, slope, curvature, and power spectrum analysis reveal characteristics that capture the development of cirques and arêtes.

  6. Quantitative analysis of masculinity perceptions 

    E-print Network

    Cima, Brian Norman

    2002-01-01

    This study was conducted using a modified version of the Brannon's Masculinity index, designed to measure quantitatively the ideologies of American masculinity. Included is an extensive literature review and an explanation ...

  7. Aqua CERES First Light

    NASA Technical Reports Server (NTRS)

    2002-01-01

    NASA's latest Earth Observing System satellite-Aqua-is dedicated to advancing our understanding of Earth's water cycle. Launched on May 4, 2002, Aqua has successfully completed its checkout period and is fully operational. Using multiple instruments, Aqua data and images are crucial toward improving our knowledge of global climate change. The Clouds and the Earth's Radiant Energy System (CERES) instrument is one of six on board the Aqua satellite. CERES detects the amount of outgoing heat and reflected sunlight leaving the planet. A detailed understanding of how clouds affect the energy balance is essential for better climate change predictions. These Aqua images show CERES measurements over the United States from June 22, 2002. Clear ocean regions, shown in dark blue on the left image, reflect the least amount of sunlight back to space. Clear land areas, shown in lighter blue, reflect more solar energy. Clouds and snow-covered surfaces, shown in white and green, reflect the greatest amounts of sunlight back to space. Clear warm regions, shown in yellow over much of the western United States on the right image, emit the most heat. High, cold clouds, shown in blue and white, significantly reduce the amount of heat lost to space. Aqua is part of NASA's Earth Science Enterprise, a long-term research effort dedicated to understanding and protecting our home planet. Through the study of Earth, NASA will help to provide sound science to policy and economic decision makers so as to better life here, while developing the technologies needed to explore the universe and search for life beyond our home planet. Click to read details on the launch and deployment of Aqua; or read the Aqua fact sheet for more information about the mission. Image courtesy CERES Science Team, NASA Langley Research Center

  8. QUANTITATIVE PATTERN RECOGNITION USING NONLINEAR MODELBASED ANALYSIS

    E-print Network

    Abidi, Mongi A.

    A nonlinear model­based approach is taken to quantitatively analyze time series data gener- ated by analyticalQUANTITATIVE PATTERN RECOGNITION USING NONLINEAR MODEL­BASED ANALYSIS A Dissertation Presented program and data interpretation module (DIM) functional leader, for his valuable guidance in the world

  9. Radisson Blu Aqua Hotel Chicago Radisson Blu Aqua Hotel Chicago

    E-print Network

    He, Chuan

    Radisson Blu Aqua Hotel Chicago Radisson Blu Aqua Hotel Chicago 221 North Columbus Drive Chicago and are subject to availability. Ask for the University of Chicago rate. Offer is available to all faculty, staff The Radisson Blu Aqua Hotel Chicago is an architectural marvel built for the 21st century. Situated near

  10. 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 loading of an image No. of bits in a word: 32 No. of processors used: 1 Has the code been vectorized or parallelized?: No No of lines in distributed program, including test data, etc.:138 946 No. of bytes in distributed program, including test data, etc.:15 166 675 Distribution format: tar.gz Nature of physical problem: Quantification of image data (e.g., for discrimination of molecular species in gels or fluorescent molecular probes in cell cultures) requires proprietary or complex software packages, which might not include the relevant statistical parameters or make the analysis of multiple images a tedious procedure for the general user. Method of solution: Tool for conversion of RGB bitmap image into luminance-linear image and extraction of luminance histogram, probability distribution, and statistical parameters (average brightness, standard deviation, variance, minimal and maximal brightness, mode, skewness and kurtosis of histogram and median of probability distribution) with possible selection of region of interest (ROI) and lower and upper threshold levels. Restrictions on the complexity of the problem: Does not incorporate application-specific functions (e.g., morphometric analysis) Typical running time: Seconds (depending on image size and processor speed) Unusual features of the program: None

  11. Aqua Education and Public Outreach

    NASA Astrophysics Data System (ADS)

    Graham, S. M.; Parkinson, C. L.; Chambers, L. H.; Ray, S. E.

    2011-12-01

    NASA's Aqua satellite was launched on May 4, 2002, with six instruments designed to collect data about the Earth's atmosphere, biosphere, hydrosphere, and cryosphere. Since the late 1990s, the Aqua mission has involved considerable education and public outreach (EPO) activities, including printed products, formal education, an engineering competition, webcasts, and high-profile multimedia efforts. The printed products include Aqua and instrument brochures, an Aqua lithograph, Aqua trading cards, NASA Fact Sheets on Aqua, the water cycle, and weather forecasting, and an Aqua science writers' guide. On-going formal education efforts include the Students' Cloud Observations On-Line (S'COOL) Project, the MY NASA DATA Project, the Earth System Science Education Alliance, and, in partnership with university professors, undergraduate student research modules. Each of these projects incorporates Aqua data into its inquiry-based framework. Additionally, high school and undergraduate students have participated in summer internship programs. An earlier formal education activity was the Aqua Engineering Competition, which was a high school program sponsored by the NASA Goddard Space Flight Center, Morgan State University, and the Baltimore Museum of Industry. The competition began with the posting of a Round 1 Aqua-related engineering problem in December 2002 and concluded in April 2003 with a final round of competition among the five finalist teams. The Aqua EPO efforts have also included a wide range of multimedia products. Prior to launch, the Aqua team worked closely with the Special Projects Initiative (SPI) Office to produce a series of live webcasts on Aqua science and the Cool Science website aqua.nasa.gov/coolscience, which displays short video clips of Aqua scientists and engineers explaining the many aspects of the Aqua mission. These video clips, the Aqua website, and numerous presentations have benefited from dynamic visualizations showing the Aqua launch, instrument deployments, instrument sensing, and the Aqua orbit. More recently, in 2008 the Aqua team worked with the ViewSpace production team from the Space Telescope Science Institute to create an 18-minute ViewSpace feature showcasing the science and applications of the Aqua mission. Then in 2010 and 2011, Aqua and other NASA Earth-observing missions partnered with National CineMedia on the "Know Your Earth" (KYE) project. During January and July 2010 and 2011, KYE ran 2-minute segments highlighting questions that promoted global climate literacy on lobby LCD screens in movie theaters throughout the U.S. Among the ongoing Aqua EPO efforts is the incorporation of Aqua data sets onto the Dynamic Planet, a large digital video globe that projects a wide variety of spherical data sets. Aqua also has a highly successful collaboration with EarthSky communications on the production of an Aqua/EarthSky radio show and podcast series. To date, eleven productions have been completed and distributed via the EarthSky network. In addition, a series of eight video podcasts (i.e., vodcasts) are under production by NASA Goddard TV in conjunction with Aqua personnel, highlighting various aspects of the Aqua mission.

  12. 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.

  13. Analysis of Raman Lidar and Radiosonde Measurements from the AWEX-G Field Campaign and Its Relation to Aqua Validation

    NASA Technical Reports Server (NTRS)

    Whiteman, D. N.; Russo, F.; Demoz, B.; Miloshevich, L. M.; Veselovskii, I.; Hannon, S.; Wang, Z.; Vomel, H.; Schmidlin, F.; Lesht, B.; Moore, P. J.; Beebe, A. S.; Gambacorta, A.; Barnet, C.

    2006-01-01

    Early work within the Aqua validation activity revealed there to be large differences in water vapor measurement accuracy among the various technologies in use for providing validation data. The validation measurements were made at globally distributed sites making it difficult to isolate the sources of the apparent measurement differences among the various sensors, which included both Raman lidar and radiosonde. Because of this, the AIRS Water Vapor Experiment-Ground (AWEX-G) was held in October-November 2003 with the goal of bringing validation technologies to a common site for intercomparison and resolving the measurement discrepancies. Using the University of Colorado Cryogenic Frostpoint Hygrometer (CFH) as the water vapor reference, the AWEX-G field campaign permitted correction techniques to be validated for Raman lidar, Vaisala RS80-H and RS90/92 that significantly improve the absolute accuracy of water vapor measurements from these systems particularly in the upper troposphere. Mean comparisons of radiosondes and lidar are performed demonstrating agreement between corrected sensors and the CFH to generally within 5% thereby providing data of sufficient accuracy for Aqua validation purposes. Examples of the use of the correction techniques in radiance and retrieval comparisons are provided and discussed.

  14. Analysis of Raman Lidar and radiosonde measurements from the AWEX-G field campaign and its relation to Aqua validation

    NASA Technical Reports Server (NTRS)

    Whiteman, D. N.; Russo, F.; Demoz, B.; Miloshevich, L. M.; Veselovskii, I.; Hannon, S.; Wang, Z.; Vomel, H.; Schmidlin, F.; Lesht, B.

    2005-01-01

    Early work within the Aqua validation activity revealed there to be large differences in water vapor measurement accuracy among the various technologies in use for providing validation data. The validation measurements were made at globally distributed sites making it difficult to isolate the sources of the apparent measurement differences among the various sensors, which included both Raman lidar and radiosonde. Because of this, the AIRS Water Vapor Experiment-Ground (AWEX-G) was held in October - November, 2003 with the goal of bringing validation technologies to a common site for intercomparison and resolution of the measurement discrepancies. Using the University of Colorado Cryogenic Frostpoint Hygrometer (CFH) as the water vapor reference, the AWEX-G field campaign resulted in new correction techniques for both Raman lidar, Vaisala RS80-H and RS90/92 measurements that significantly improve the absolute accuracy of those measurement systems particularly in the upper troposphere. Mean comparisons of radiosondes and lidar are performed demonstrating agreement between corrected sensors and the CFH to generally within 5% thereby providing data of sufficient accuracy for Aqua validation purposes. Examples of the use of the correction techniques in radiance and retrieval comparisons are provided and discussed.

  15. Christhin: Quantitative Analysis of Thin Layer Chromatography

    E-print Network

    Barchiesi, Maximiliano; Renaudo, Carlos; Rossi, Pablo; Pramparo, María de Carmen; Nepote, Valeria; Grosso, Nelson Ruben; Gayol, María Fernanda

    2012-01-01

    Manual for Christhin 0.1.36 Christhin (Chromatography Riser Thin) is software developed for the quantitative analysis of data obtained from thin-layer chromatographic techniques (TLC). Once installed on your computer, the program is very easy to use, and provides data quickly and accurately. This manual describes the program, and reading should be enough to use it properly.

  16. Journal of Quantitative Analysis in Manuscript 1416

    E-print Network

    Redner, Sidney

    Journal of Quantitative Analysis in Sports Manuscript 1416 Random Walk Picture of Basketball of Basketball Scoring Alan Gabel and Sidney Redner Abstract We present evidence, based on play­by­play data from all 6087 games from the 2006/07-- 2009/10 seasons of the National Basketball Association (NBA

  17. 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…

  18. 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

  19. Quantitative analysis of colony morphology in yeast

    PubMed Central

    Ruusuvuori, Pekka; Lin, Jake; Scott, Adrian C.; Tan, Zhihao; Sorsa, Saija; Kallio, Aleksi; Nykter, Matti; Yli-Harja, Olli; Shmulevich, Ilya; Dudley, Aimée M.

    2014-01-01

    Microorganisms often form multicellular structures such as biofilms and structured colonies that can influence the organism’s virulence, drug resistance, and adherence to medical devices. Phenotypic classification of these structures has traditionally relied on qualitative scoring systems that limit detailed phenotypic comparisons between strains. Automated imaging and quantitative analysis have the potential to improve the speed and accuracy of experiments designed to study the genetic and molecular networks underlying different morphological traits. For this reason, we have developed a platform that uses automated image analysis and pattern recognition to quantify phenotypic signatures of yeast colonies. Our strategy enables quantitative analysis of individual colonies, measured at a single time point or over a series of time-lapse images, as well as the classification of distinct colony shapes based on image-derived features. Phenotypic changes in colony morphology can be expressed as changes in feature space trajectories over time, thereby enabling the visualization and quantitative analysis of morphological development. To facilitate data exploration, results are plotted dynamically through an interactive Yeast Image Analysis web application (YIMAA; http://yimaa.cs.tut.fi) that integrates the raw and processed images across all time points, allowing exploration of the image-based features and principal components associated with morphological development. PMID:24447135

  20. COX-2 Expression and Survival in Patients with Locally Advanced Cervical Cancer Treated with Chemoradiotherapy and Celecoxib: A Quantitative Immunohistochemical Analysis of RTOG C0128

    PubMed Central

    Doll, Corinne M; Winter, Kathryn; Gaffney, David K; Ryu, Janice K; Jhingran, Anuja; Dicker, Adam P; Weidhaas, Joanne B; Miller, Brigitte E; Magliocco, Anthony M

    2015-01-01

    Purpose To measure expression of COX-2 and CD34 in pre-treatment tumor biopsies from patients on the RTOG C0128 phase II study, and to correlate expression of these biomarkers, using quantitative immunohistochemistry (IHC), with clinical outcome parameters. Methods and Materials Pre-treatment biopsies were placed into tissue microarrays. COX-2 and CD34 expression were measured using automated quantitative IHC (AQUA®). Cox regression models and Fisher's exact test were used to explore associations between expression of the biomarkers and clinical endpoints. Results 84 patients were accrued between 2001 and 2004; 78 were eligible and analyzable. Pathology specimen submission was optional; COX-2 expression was determined for 37 (47%) of patients, and CD34 scoring was determined for 34 (44%) of patients. Median follow-up was 44.5 months. In tumors where COX-2 data was available, 6 of 37 (16%) patients had local-regional failure; 4 of these patients had tumors with COX-2 scores below the AQUA® score median [HR=0.39; 95%CI= (0.07, 2.16); p=0.28]. Of the 8 patients with DFS failures, 5 had tumors with COX-2 levels below the median [HR=0.49; 95%CI= (0.12, 2.04); p=0.32]. The 4 patients who died all had COX-2 levels below the median value. COX-2 levels below the median were associated with worse 2-year survival (Fisher's p=0.046). There was no statistically significant association between CD34 status and clinical outcome. Conclusions Low COX-2 expression measured by AQUA® was associated with worse overall survival in this subset of patients available for analysis from RTOG C0128. Application of AQUA® technology, in a larger study, will be required to definitively evaluate the association COX-2 with clinical outcome in cervical cancer. PMID:23221733

  1. 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.

  2. 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

  3. Quantitative analysis of spirality in elliptical galaxies

    NASA Astrophysics Data System (ADS)

    Dojcsak, Levente; Shamir, Lior

    2014-04-01

    We use an automated galaxy morphology analysis method to quantitatively measure the spirality of galaxies classified manually as elliptical. The data set used for the analysis consists of 60,518 galaxy images with redshift obtained by the Sloan Digital Sky Survey (SDSS) and classified manually by Galaxy Zoo, as well as the RC3 and NA10 catalogues. We measure the spirality of the galaxies by using the Ganalyzer method, which transforms the galaxy image to its radial intensity plot to detect galaxy spirality that is in many cases difficult to notice by manual observation of the raw galaxy image. Experimental results using manually classified elliptical and S0 galaxies with redshift <0.3 suggest that galaxies classified manually as elliptical and S0 exhibit a nonzero signal for the spirality. These results suggest that the human eye observing the raw galaxy image might not always be the most effective way of detecting spirality and curves in the arms of galaxies.

  4. 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 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. Electronic supplementary information (ESI) available: Derivation and implementation of unbiased feature measurement, calculation of empirical distribution of single particle areas, calculation of self-similarity dimensions by regression on cluster data, and validation of image analysis algorithms. See DOI: 10.1039/c5nr00809c

  5. Quantitative proteomic analysis of single pancreatic islets

    PubMed Central

    Waanders, Leonie F.; Chwalek, Karolina; Monetti, Mara; Kumar, Chanchal; Lammert, Eckhard; Mann, Matthias

    2009-01-01

    Technological developments make mass spectrometry (MS)-based proteomics a central pillar of biochemical research. MS has been very successful in cell culture systems, where sample amounts are not limiting. To extend its capabilities to extremely small, physiologically distinct cell types isolated from tissue, we developed a high sensitivity chromatographic system that measures nanogram protein mixtures for 8 h with very high resolution. This technology is based on splitting gradient effluents into a capture capillary and provides an inherent technical replicate. In a single analysis, this allowed us to characterize kidney glomeruli isolated by laser capture microdissection to a depth of more than 2,400 proteins. From pooled pancreatic islets of Langerhans, another type of “miniorgan,” we obtained an in-depth proteome of 6,873 proteins, many of them involved in diabetes. We quantitatively compared the proteome of single islets, containing 2,000–4,000 cells, treated with high or low glucose levels, and covered most of the characteristic functions of beta cells. Our ultrasensitive analysis recapitulated known hyperglycemic changes but we also find components up-regulated such as the mitochondrial stress regulator Park7. Direct proteomic analysis of functionally distinct cellular structures opens up perspectives in physiology and pathology. PMID:19846766

  6. Quantitative local analysis of nonlinear systems

    NASA Astrophysics Data System (ADS)

    Topcu, Ufuk

    This thesis investigates quantitative methods for local robustness and performance analysis of nonlinear dynamical systems with polynomial vector fields. We propose measures to quantify systems' robustness against uncertainties in initial conditions (regions-of-attraction) and external disturbances (local reachability/gain analysis). S-procedure and sum-of-squares relaxations are used to translate Lyapunov-type characterizations to sum-of-squares optimization problems. These problems are typically bilinear/nonconvex (due to local analysis rather than global) and their size grows rapidly with state/uncertainty space dimension. Our approach is based on exploiting system theoretic interpretations of these optimization problems to reduce their complexity. We propose a methodology incorporating simulation data in formal proof construction enabling more reliable and efficient search for robustness and performance certificates compared to the direct use of general purpose solvers. This technique is adapted both to region-of-attraction and reachability analysis. We extend the analysis to uncertain systems by taking an intentionally simplistic and potentially conservative route, namely employing parameter-independent rather than parameter-dependent certificates. The conservatism is simply reduced by a branch-and-hound type refinement procedure. The main thrust of these methods is their suitability for parallel computing achieved by decomposing otherwise challenging problems into relatively tractable smaller ones. We demonstrate proposed methods on several small/medium size examples in each chapter and apply each method to a benchmark example with an uncertain short period pitch axis model of an aircraft. Additional practical issues leading to a more rigorous basis for the proposed methodology as well as promising further research topics are also addressed. We show that stability of linearized dynamics is not only necessary but also sufficient for the feasibility of the formulations in region-of-attraction analysis. Furthermore, we generalize an upper bound refinement procedure in local reachability/gain analysis which effectively generates non-polynomial certificates from polynomial ones. Finally, broader applicability of optimization-based tools stringently depends on the availability of scalable/hierarchial algorithms. As an initial step toward this direction, we propose a local small-gain theorem and apply to stability region analysis in the presence of unmodeled dynamics.

  7. 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…

  8. QUANTITATIVE TRAIT LOCUS ANALYSIS AND METABOLIC PATHWAYS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The development of molecular markers for crop plants has enabled research on the genetic basis of quantitative traits. However, despite more than a decade of these studies, called quantitative trait locus (QTL) analyses, the molecular basis for variation in most agronomic traits is still largely unk...

  9. Aqua 10 Years After Launch

    NASA Technical Reports Server (NTRS)

    Parkinson, Claire L.

    2013-01-01

    A little over ten years ago, in the early morning hours of May 4, 2002, crowds of spectators stood anxiously watching as the Delta II rocket carrying NASA's Aqua spacecraft lifted off from its launch pad at Vandenberg Air Force Base in California at 2:55 a.m. The rocket quickly went through a low-lying cloud cover, after which the main portion of the rocket fell to the waters below and the rockets second stage proceeded to carry Aqua south across the Pacific, onward over Antarctica, and north to Africa, where the spacecraft separated from the rocket 59.5 minutes after launch. Then, 12.5 minutes later, the solar array unfurled over Europe, and Aqua was on its way in the first of what by now have become over 50,000 successful orbits of the Earth.

  10. Errors in Quantitative Image Analysis due to

    E-print Network

    Rubin, Daniel L.

    multiple series using four scanners such that the histogram of pixel intensities varied enough to provoke is derived from relative contrast across tissues [6], change in signal with acquisition conditions [2 change over time [5]. The concept of "quantitative imaging" implies a direct or modeled relationship

  11. Large-Scale Quantitative Analysis of Painting Arts

    E-print Network

    Jeong, Hawoong

    Large-Scale Quantitative Analysis of Painting Arts Daniel Kim1 , Seung-Woo Son2 & Hawoong Jeong3 has made rapid progress, researchers have come to a point where it is possible to perform statistical digital image processing techniques, we investigate three quantitative measures of images ­ the usage

  12. A Quantitative Proteomics Analysis of Subcellular Proteome Localization and

    E-print Network

    Lamond, Angus I.

    A Quantitative Proteomics Analysis of Subcellular Proteome Localization and Changes Induced by DNA-based proteomics to provide an unbiased, quantitative, and high throughput approach for measuring the subcellular distribution of the proteome, termed "spa- tial proteomics." The spatial proteomics method analyzes a whole

  13. Use quantitative analysis to manage fire risk

    SciTech Connect

    Mowrer, D.S.

    1995-04-01

    By incorporating quantitative engineering tools into fire-risk evaluations, safety engineers and managers can mitigate hazards caused by pressurized oil. Fire remains the number one factor for unscheduled downtime, lost production and equipment damage. Pressurized oil is a common and sometimes underestimated fire hazard. This hazard exists in many industrial facilities and can fuel a pool fire or an intense torch fire. Standard sprinkler protection does not affect torch fires, and either roil fire type can rapidly weaken structural steel members to the point of failure. Two case histories show how safety engineers using quantitative tools analyze fire hazards presented by pressurized oil and reduce its risks. The techniques are simple-to-use and are readily available.

  14. Francesca Vitale, Ann-Christin Rudolphi, Barbara Bland Aqua reports 2013:16

    E-print Network

    , which includes collection of otoliths for age analysis, was done on the most important commercial species. In total 4 447 otoliths were collected from 12 different species. #12;Aqua reports 2013:16 4

  15. A QUANTITATIVE ANALYSIS OF DISTANT OPEN CLUSTERS

    SciTech Connect

    Janes, Kenneth A.; Hoq, Sadia

    2011-03-15

    The oldest open star clusters are important for tracing the history of the Galactic disk, but many of the more distant clusters are heavily reddened and projected against the rich stellar background of the Galaxy. We have undertaken an investigation of several distant clusters (Berkeley 19, Berkeley 44, King 25, NGC 6802, NGC 6827, Berkeley 52, Berkeley 56, NGC 7142, NGC 7245, and King 9) to develop procedures for separating probable cluster members from the background field. We next created a simple quantitative approach for finding approximate cluster distances, reddenings, and ages. We first conclude that with the possible exception of King 25 they are probably all physical clusters. We also find that for these distant clusters our typical errors are about {+-}0.07 in E(B - V), {+-}0.15 in log(age), and {+-}0.25 in (m - M){sub o}. The clusters range in age from 470 Myr to 7 Gyr and range from 7.1 to 16.4 kpc from the Galactic center.

  16. Quantitative analysis of HIV-1 preintegration complexes.

    PubMed

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

    2009-04-01

    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

  17. Multiple quantitative trait analysis using bayesian networks.

    PubMed

    Scutari, Marco; Howell, Phil; Balding, David J; Mackay, Ian

    2014-09-01

    Models for genome-wide prediction and association studies usually target a single phenotypic trait. However, in animal and plant genetics it is common to record information on multiple phenotypes for each individual that will be genotyped. Modeling traits individually disregards the fact that they are most likely associated due to pleiotropy and shared biological basis, thus providing only a partial, confounded view of genetic effects and phenotypic interactions. In this article we use data from a Multiparent Advanced Generation Inter-Cross (MAGIC) winter wheat population to explore Bayesian networks as a convenient and interpretable framework for the simultaneous modeling of multiple quantitative traits. We show that they are equivalent to multivariate genetic best linear unbiased prediction (GBLUP) and that they are competitive with single-trait elastic net and single-trait GBLUP in predictive performance. Finally, we discuss their relationship with other additive-effects models and their advantages in inference and interpretation. MAGIC populations provide an ideal setting for this kind of investigation because the very low population structure and large sample size result in predictive models with good power and limited confounding due to relatedness. PMID:25236454

  18. Using fire tests for quantitative risk analysis

    SciTech Connect

    Ling, W.C.T.; Williamson, R.B.

    1980-03-01

    Fires can be considered a causal chain-of-events in which the growth and spread of fire may cause damage and injury if it is rapid enough to overcome the barriers placed in its way. Fire tests for fire resistance of the barriers can be used in a quantitative risk assessment. The fire growth and spread is modelled in a State Transition Model (STM). The fire barriers are presented as part of the Fire Protection Model (FPM) which is based on a portion of the NFPA Decision Tree. An Emergency Equivalent Network is introduced to couple the Fire Growth Model (FGM) and the FPM so that the spread of fire beyond the room-of-origin can be computed. An example is presented in which a specific building floor plan is analyzed to obtain the shortest expected time for fire to spread between two points. To obtain the probability and time for each link in the network, data from the results of fire tests were used. These results were found to be lacking and new standards giving better data are advocated.

  19. 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.

  20. Multiple Quantitative Trait Analysis Using Bayesian Networks

    PubMed Central

    Scutari, Marco; Howell, Phil; Balding, David J.; Mackay, Ian

    2014-01-01

    Models for genome-wide prediction and association studies usually target a single phenotypic trait. However, in animal and plant genetics it is common to record information on multiple phenotypes for each individual that will be genotyped. Modeling traits individually disregards the fact that they are most likely associated due to pleiotropy and shared biological basis, thus providing only a partial, confounded view of genetic effects and phenotypic interactions. In this article we use data from a Multiparent Advanced Generation Inter-Cross (MAGIC) winter wheat population to explore Bayesian networks as a convenient and interpretable framework for the simultaneous modeling of multiple quantitative traits. We show that they are equivalent to multivariate genetic best linear unbiased prediction (GBLUP) and that they are competitive with single-trait elastic net and single-trait GBLUP in predictive performance. Finally, we discuss their relationship with other additive-effects models and their advantages in inference and interpretation. MAGIC populations provide an ideal setting for this kind of investigation because the very low population structure and large sample size result in predictive models with good power and limited confounding due to relatedness. PMID:25236454

  1. 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.

  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. In aqua vivo EPID dosimetry

    SciTech Connect

    Wendling, Markus; McDermott, Leah N.; Mans, Anton; Olaciregui-Ruiz, Igor; Pecharroman-Gallego, Raul; Sonke, Jan-Jakob; Stroom, Joep; Herk, Marcel J.; Mijnheer, Ben van

    2012-01-15

    Purpose: At the Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital in vivo dosimetry using an electronic portal imaging device (EPID) has been implemented for almost all high-energy photon treatments of cancer with curative intent. Lung cancer treatments were initially excluded, because the original back-projection dose-reconstruction algorithm uses water-based scatter-correction kernels and therefore does not account for tissue inhomogeneities accurately. The aim of this study was to test a new method, in aqua vivo EPID dosimetry, for fast dose verification of lung cancer irradiations during actual patient treatment. Methods: The key feature of our method is the dose reconstruction in the patient from EPID images, obtained during the actual treatment, whereby the images have been converted to a situation as if the patient consisted entirely of water; hence, the method is termed in aqua vivo. This is done by multiplying the measured in vivo EPID image with the ratio of two digitally reconstructed transmission images for the unit-density and inhomogeneous tissue situation. For dose verification, a comparison is made with the calculated dose distribution with the inhomogeneity correction switched off. IMRT treatment verification is performed for each beam in 2D using a 2D {gamma} evaluation, while for the verification of volumetric-modulated arc therapy (VMAT) treatments in 3D a 3D {gamma} evaluation is applied using the same parameters (3%, 3 mm). The method was tested using two inhomogeneous phantoms simulating a tumor in lung and measuring its sensitivity for patient positioning errors. Subsequently five IMRT and five VMAT clinical lung cancer treatments were investigated, using both the conventional back-projection algorithm and the in aqua vivo method. The verification results of the in aqua vivo method were statistically analyzed for 751 lung cancer patients treated with IMRT and 50 lung cancer patients treated with VMAT. Results: The improvements by applying the in aqua vivo approach are considerable. The percentage of {gamma} values {<=}1 increased on average from 66.2% to 93.1% and from 43.6% to 97.5% for the IMRT and VMAT cases, respectively. The corresponding mean {gamma} value decreased from 0.99 to 0.43 for the IMRT cases and from 1.71 to 0.40 for the VMAT cases, which is similar to the accepted clinical values for the verification of IMRT treatments of prostate, rectum, and head-and-neck cancers. The deviation between the reconstructed and planned dose at the isocenter diminished on average from 5.3% to 0.5% for the VMAT patients and was almost the same, within 1%, for the IMRT cases. The in aqua vivo verification results for IMRT and VMAT treatments of a large group of patients had a mean {gamma} of approximately 0.5, a percentage of {gamma} values {<=}1 larger than 89%, and a difference of the isocenter dose value less than 1%. Conclusions: With the in aqua vivo approach for the verification of lung cancer treatments (IMRT and VMAT), we can achieve results with the same accuracy as obtained during in vivo EPID dosimetry of sites without large inhomogeneities.

  4. 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.

  5. 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. PMID:26456251

  6. 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.

  7. A Full Snow Season in Yellowstone: A Database of Restored Aqua Band 6

    NASA Technical Reports Server (NTRS)

    Gladkova, Irina; Grossberg, Michael; Bonev, George; Romanov, Peter; Riggs, George; Hall, Dorothy

    2013-01-01

    The algorithms for estimating snow extent for the Moderate Resolution Imaging Spectroradiometer (MODIS) optimally use the 1.6- m channel which is unavailable for MODIS on Aqua due to detector damage. As a test bed to demonstrate that Aqua band 6 can be restored, we chose the area surrounding Yellowstone and Grand Teton national parks. In such rugged and difficult-to-access terrain, satellite images are particularly important for providing an estimation of snow-cover extent. For the full 2010-2011 snow season covering the Yellowstone region, we have used quantitative image restoration to create a database of restored Aqua band 6. The database includes restored radiances, normalized vegetation index, normalized snow index, thermal data, and band-6-based snow-map products. The restored Aqua-band-6 data have also been regridded and combined with Terra data to produce a snow-cover map that utilizes both Terra and Aqua snow maps. Using this database, we show that the restored Aqua-band-6-based snow-cover extent has a comparable performance with respect to ground stations to the one based on Terra. The result of a restored band 6 from Aqua is that we have an additional band-6 image of the Yellowstone region each day. This image can be used to mitigate cloud occlusion, using the same algorithms used for band 6 on Terra. We show an application of this database of restored band-6 images to illustrate the value of creating a cloud gap filling using the National Aeronautics and Space Administration s operational cloud masks and data from both Aqua and Terra.

  8. 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.

  9. Aqua's First 10 Years: An Overview

    NASA Technical Reports Server (NTRS)

    Parkinson, Claire L.

    2012-01-01

    NASA's Aqua spacecraft was launched at 2:55 a.m. on May 4, 2002, from Vandenberg Air Force Base in California, into a near-polar, sun-synchronous orbit at an altitude of 705 km. Aqua carries six Earth-observing instruments to collect data on water in all its forms (liquid, vapor, and solid) and on a wide variety of additional Earth system variables (Parkinson 2003). The design lifetime for Aqua's prime mission was 6 years, and Aqua is now well into its extended mission, approaching 10 years of successful operations. The Aqua data have been used for hundreds of scientific studies and continue to be used for scientific discovery and numerous practical applications.

  10. 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

  11. Trace Environmental Quantitative Analysis: Principles, Techniques and Applications, 2nd

    E-print Network

    Natelson, Douglas

    Trace Environmental Quantitative Analysis: Principles, Techniques and Applications, 2nd Edition teaching relevant laboratory courses. In this 2nd edition, Loconto has expanded the instrumental section provide the high temporal and spatial resolution data needed to study environmental system dynamics. I

  12. Perceptual Analysis of Talking Avatar Head Movements: A Quantitative Perspective

    E-print Network

    Deng, Zhigang

    Perceptual Analysis of Talking Avatar Head Movements: A Quantitative Perspective Xiaohan Ma Dept@cs.uh.edu ABSTRACT Lifelike interface agents (e.g. talking avatars) have been in- creasingly used in human-head motion characteristics of talk- ing avatars. Specifically, we quantify the correlation be- tween

  13. Early Child Grammars: Qualitative and Quantitative Analysis of Morphosyntactic Production

    ERIC Educational Resources Information Center

    Legendre, Geraldine

    2006-01-01

    This article reports on a series of 5 analyses of spontaneous production of verbal inflection (tense and person-number agreement) by 2-year-olds acquiring French as a native language. A formal analysis of the qualitative and quantitative results is developed using the unique resources of Optimality Theory (OT; Prince & Smolensky, 2004). It is…

  14. Quantitative Analysis of Simulated Erosion for Different Soils

    E-print Network

    Franklin, W. Randolph

    Quantitative Analysis of Simulated Erosion for Different Soils Zhongxian Chen chenz5@cs Hurricane Katrina. We present a computer simulation of erosion to study the de- velopment of the rills and gullies that form along an earthen embankment during overtopping. We have coupled 3D Smoothed Particle

  15. RETINAL DISORDERS Quantitative analysis of central visual field defects

    E-print Network

    Arizona, University of

    RETINAL DISORDERS Quantitative analysis of central visual field defects in macular edema using levels of contrast in one eye of 37 patients with diabetic macular edema (DME, n=16) and exudative age . Amslergrid . Contrast sensitivity. Diabetic macular edema . Macular edema . Scotomas Introduction Amsler grid

  16. 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...

  17. Quantitative Methods Inquires ANALYSIS AND COMPARISON OF UNDER FIVE CHILD

    E-print Network

    de Leon, Alex R.

    Quantitative Methods Inquires 1 ANALYSIS AND COMPARISON OF UNDER FIVE CHILD MORTALITY BETWEEN RURAL Research, Bangladesh (ICDDR,B) Abstract: Knowledge of factors that affect the under-five year child from rich family and the 2nd or 3rd child have lower risk of death compared to poor and 1st child

  18. Quantitative Analysis of Incorrectly-Configured Bogon-Filter Detection

    E-print Network

    Roughan, Matthew

    1 Quantitative Analysis of Incorrectly-Configured Bogon-Filter Detection Jon Arnold, Olaf Maennel. It is common for network operators to filter out address space which is known to be unallocated ("bogon announced prefixes. Unfortunately, some ISPs still do not configure their bogon filters via lists published

  19. Quantitative analysis of volume images -electron microscopic tomography of HIV

    E-print Network

    Nyström, Ingela

    Quantitative analysis of volume images - electron microscopic tomography of HIV Ingela Nystr syndrome (AIDS), namely human immunode#12;ciency virus (HIV), produced by electron microscopic tomography by the HIV Structure Group at the Dept. of Biochemistry, Uppsala University. The algorithms are used

  20. Quantitative Analysis of the Effective Functional Structure in Yeast Glycolysis

    E-print Network

    Cortes, Jesus

    Quantitative Analysis of the Effective Functional Structure in Yeast Glycolysis Ildefonso M. De la the technique of Transfer Entropy. The data were obtained by means of a yeast glycolytic model formed by three-core of the metabolic system, behaving for all conditions as the main source of the effective causal flows in yeast

  1. Quantitative Analysis of the Full Bitcoin Transaction Graph

    E-print Network

    International Association for Cryptologic Research (IACR)

    Quantitative Analysis of the Full Bitcoin Transaction Graph Dorit Ron and Adi Shamir Department.ron,adi.shamir}@weizmann.ac.il Abstract. The Bitcoin scheme is a rare example of a large scale global payment system in which all and how they spend their bitcoins, the balance of bitcoins they keep in their accounts, and how they move

  2. Quantitative Analysis for Authentication of Low-cost RFID Tags

    E-print Network

    Paparrizos, Ioannis; Petridou, Sophia

    2011-01-01

    Formal analysis techniques are widely used today in order to verify and analyze communication protocols. In this work, we launch a quantitative verification analysis for the low- cost Radio Frequency Identification (RFID) protocol proposed by Song and Mitchell. The analysis exploits a Discrete-Time Markov Chain (DTMC) using the well-known PRISM model checker. We have managed to represent up to 100 RFID tags communicating with a reader and quantify each RFID session according to the protocol's computation and transmission cost requirements. As a consequence, not only does the proposed analysis provide quantitative verification results, but also it constitutes a methodology for RFID designers who want to validate their products under specific cost requirements.

  3. 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.

  4. 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

  5. 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. PMID:24889823

  6. Aqua-vanadyl ion interaction with Nafion® membranes

    DOE PAGESBeta

    Vijayakumar, Murugesan; Govind, Niranjan; Li, Bin; Wei, Xiaoliang; Nie, Zimin; Thevuthasan, Suntharampillai; Sprenkle, Vince L.; Wang, Wei

    2015-03-23

    Lack of comprehensive understanding about the interactions between Nafion membrane and battery electrolytes prevents the straightforward tailoring of optimal materials for redox flow battery applications. In this work, we analyzed the interaction between aqua-vanadyl cation and sulfonic sites within the pores of Nafion membranes using combined theoretical and experimental X-ray spectroscopic methods. Molecular level interactions, namely, solvent share and contact pair mechanisms are discussed based on Vanadium and Sulfur K-edge spectroscopic analysis.

  7. An Improved Quantitative Analysis Method for Plant Cortical Microtubules

    PubMed Central

    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. PMID:24744684

  8. Analysis of the influence of river discharge and wind on the Ebro turbid plume using MODIS-Aqua and MODIS-Terra data

    NASA Astrophysics Data System (ADS)

    Fernández-Nóvoa, D.; Mendes, R.; deCastro, M.; Dias, J. M.; Sánchez-Arcilla, A.; Gómez-Gesteira, M.

    2015-02-01

    The turbid plume formed at many river mouths influences the adjacent coastal area because it transports sediments, nutrients, and pollutants. The effects of the main forcings affecting the Ebro turbid plume were analyzed using data obtained from the Moderate Resolution Imaging Spectroradiometer (MODIS) sensor onboard the Aqua and Terra satellites over the period 2003-2011. Composite images were obtained for days under certain river discharge conditions (different flow regimes) and different types of wind (alongshore and cross-shore winds) in order to obtain a representative plume pattern for each situation. River discharge was the main driver of the Ebro River plume, followed by wind as the secondary force and regional oceanic circulation as the third one. Turbid plume extension increased monotonically with increased river discharge. Under high river discharge conditions (> 355 m3 s- 1), wind distributed the plume in the dominant wind direction. Seaward winds (mistral) produced the largest extension of the plume (1893 km2), whereas southern alongshore winds produced the smallest one (1325 km2). Northern alongshore winds induced the highest mean turbid value of the plume, and southern alongshore winds induced the lowest one. Regardless of the wind condition, more than 70% of the plume extension was located south of the river mouth influenced by the regional oceanic circulation.

  9. A quantitative analysis of coupled oscillations using mobile accelerometer sensors

    NASA Astrophysics Data System (ADS)

    Castro-Palacio, Juan Carlos; Velázquez-Abad, Luisberis; Giménez, Fernando; Monsoriu, Juan A.

    2013-05-01

    In this paper, smartphone acceleration sensors were used to perform a quantitative analysis of mechanical coupled oscillations. Symmetric and asymmetric normal modes were studied separately in the first two experiments. In the third, a coupled oscillation was studied as a combination of the normal modes. Results indicate that acceleration sensors of smartphones, which are very familiar to students, represent valuable measurement instruments for introductory and first-year physics courses.

  10. 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.

  11. 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)

  12. Quantitative Motion Analysis in Two and Three Dimensions.

    PubMed

    Wessels, Deborah J; Lusche, Daniel F; Kuhl, Spencer; Scherer, Amanda; Voss, Edward; Soll, David R

    2016-01-01

    This chapter describes 2D quantitative methods for motion analysis as well as 3D motion analysis and reconstruction methods. Emphasis is placed on the analysis of dynamic cell shape changes that occur through extension and retraction of force generating structures such as pseudopodia and lamellipodia. Quantitative analysis of these structures is an underutilized tool in the field of cell migration. Our intent, therefore, is to present methods that we developed in an effort to elucidate mechanisms of basic cell motility, directed cell motion during chemotaxis, and metastasis. We hope to demonstrate how application of these methods can more clearly define alterations in motility that arise due to specific mutations or disease and hence, suggest mechanisms or pathways involved in normal cell crawling and treatment strategies in the case of disease. In addition, we present a 4D tumorigenesis model for high-resolution analysis of cancer cells from cell lines and human cancer tissue in a 3D matrix. Use of this model led to the discovery of the coalescence of cancer cell aggregates and unique cell behaviors not seen in normal cells or normal tissue. Graphic illustrations to visually display and quantify cell shape are presented along with algorithms and formulae for calculating select 2D and 3D motion analysis parameters. PMID:26498790

  13. Quantitative Epistasis Analysis and Pathway Inference from Genetic Interaction Data

    PubMed Central

    Phenix, Hilary; Morin, Katy; Batenchuk, Cory; Parker, Jacob; Abedi, Vida; Yang, Liu; Tepliakova, Lioudmila; Perkins, Theodore J.; Kærn, Mads

    2011-01-01

    Inferring regulatory and metabolic network models from quantitative genetic interaction data remains a major challenge in systems biology. Here, we present a novel quantitative model for interpreting epistasis within pathways responding to an external signal. The model provides the basis of an experimental method to determine the architecture of such pathways, and establishes a new set of rules to infer the order of genes within them. The method also allows the extraction of quantitative parameters enabling a new level of information to be added to genetic network models. It is applicable to any system where the impact of combinatorial loss-of-function mutations can be quantified with sufficient accuracy. We test the method by conducting a systematic analysis of a thoroughly characterized eukaryotic gene network, the galactose utilization pathway in Saccharomyces cerevisiae. For this purpose, we quantify the effects of single and double gene deletions on two phenotypic traits, fitness and reporter gene expression. We show that applying our method to fitness traits reveals the order of metabolic enzymes and the effects of accumulating metabolic intermediates. Conversely, the analysis of expression traits reveals the order of transcriptional regulatory genes, secondary regulatory signals and their relative strength. Strikingly, when the analyses of the two traits are combined, the method correctly infers ?80% of the known relationships without any false positives. PMID:21589890

  14. 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. PMID:26095427

  15. Quantitative epistasis analysis and pathway inference from genetic interaction data.

    PubMed

    Phenix, Hilary; Morin, Katy; Batenchuk, Cory; Parker, Jacob; Abedi, Vida; Yang, Liu; Tepliakova, Lioudmila; Perkins, Theodore J; Kærn, Mads

    2011-05-01

    Inferring regulatory and metabolic network models from quantitative genetic interaction data remains a major challenge in systems biology. Here, we present a novel quantitative model for interpreting epistasis within pathways responding to an external signal. The model provides the basis of an experimental method to determine the architecture of such pathways, and establishes a new set of rules to infer the order of genes within them. The method also allows the extraction of quantitative parameters enabling a new level of information to be added to genetic network models. It is applicable to any system where the impact of combinatorial loss-of-function mutations can be quantified with sufficient accuracy. We test the method by conducting a systematic analysis of a thoroughly characterized eukaryotic gene network, the galactose utilization pathway in Saccharomyces cerevisiae. For this purpose, we quantify the effects of single and double gene deletions on two phenotypic traits, fitness and reporter gene expression. We show that applying our method to fitness traits reveals the order of metabolic enzymes and the effects of accumulating metabolic intermediates. Conversely, the analysis of expression traits reveals the order of transcriptional regulatory genes, secondary regulatory signals and their relative strength. Strikingly, when the analyses of the two traits are combined, the method correctly infers ~80% of the known relationships without any false positives. PMID:21589890

  16. Universal Quantitative NMR Analysis of Complex Natural Samples

    PubMed Central

    Simmler, Charlotte; Napolitano, José G.; McAlpine, James B.; Chen, Shao-Nong; Pauli, Guido F.

    2013-01-01

    Nuclear Magnetic Resonance (NMR) is a universal and quantitative analytical technique. Being a unique structural tool, NMR also competes with metrological techniques for purity determination and reference material analysis. In pharmaceutical research, applications of quantitative NMR (qNMR) cover mostly the identification and quantification of drug and biological metabolites. Offering an unbiased view of the sample composition, and the possibility to simultaneously quantify multiple compounds, qNMR has become the method of choice for metabolomic studies and quality control of complex natural samples such as foods, plants or herbal remedies, and biofluids. In this regard, NMR-based metabolomic studies, dedicated to both the characterization of herbal remedies and clinical diagnosis, have increased considerably. PMID:24484881

  17. Quantitative analysis of microtubule orientation in interdigitated leaf pavement cells.

    PubMed

    Akita, Kae; Higaki, Takumi; Kutsuna, Natsumaro; Hasezawa, Seiichiro

    2015-01-01

    Leaf pavement cells are shaped like a jigsaw puzzle in most dicotyledon species. Molecular genetic studies have identified several genes required for pavement cells morphogenesis and proposed that microtubules play crucial roles in the interdigitation of pavement cells. In this study, we performed quantitative analysis of cortical microtubule orientation in leaf pavement cells in Arabidopsis thaliana. We captured confocal images of cortical microtubules in cotyledon leaf epidermis expressing GFP-tubulin? and quantitatively evaluated the microtubule orientations relative to the pavement cell growth axis using original image processing techniques. Our results showed that microtubules kept parallel orientations to the growth axis during pavement cell growth. In addition, we showed that immersion treatment of seed cotyledons in solutions containing tubulin polymerization and depolymerization inhibitors decreased pavement cell complexity. Treatment with oryzalin and colchicine inhibited the symmetric division of guard mother cells. PMID:26039484

  18. 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.

  19. Fluorescent foci quantitation for high-throughput analysis

    PubMed Central

    Ledesma-Fernández, Elena; Thorpe, Peter H.

    2015-01-01

    A number of cellular proteins localize to discrete foci within cells, for example DNA repair proteins, microtubule organizing centers, P bodies or kinetochores. It is often possible to measure the fluorescence emission from tagged proteins within these foci as a surrogate for the concentration of that specific protein. We wished to develop tools that would allow quantitation of fluorescence foci intensities in high-throughput studies. As proof of principle we have examined the kinetochore, a large multi-subunit complex that is critical for the accurate segregation of chromosomes during cell division. Kinetochore perturbations lead to aneuploidy, which is a hallmark of cancer cells. Hence, understanding kinetochore homeostasis and regulation are important for a global understanding of cell division and genome integrity. The 16 budding yeast kinetochores colocalize within the nucleus to form a single focus. Here we have created a set of freely-available tools to allow high-throughput quantitation of kinetochore foci fluorescence. We use this ‘FociQuant’ tool to compare methods of kinetochore quantitation and we show proof of principle that FociQuant can be used to identify changes in kinetochore protein levels in a mutant that affects kinetochore function. This analysis can be applied to any protein that forms discrete foci in cells. PMID:26290880

  20. 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.

  1. Chromatin immunoprecipitation: optimization, quantitative analysis and data normalization

    PubMed Central

    Haring, Max; Offermann, Sascha; Danker, Tanja; Horst, Ina; Peterhansel, Christoph; Stam, Maike

    2007-01-01

    Background Chromatin remodeling, histone modifications and other chromatin-related processes play a crucial role in gene regulation. A very useful technique to study these processes is chromatin immunoprecipitation (ChIP). ChIP is widely used for a few model systems, including Arabidopsis, but establishment of the technique for other organisms is still remarkably challenging. Furthermore, quantitative analysis of the precipitated material and normalization of the data is often underestimated, negatively affecting data quality. Results We developed a robust ChIP protocol, using maize (Zea mays) as a model system, and present a general strategy to systematically optimize this protocol for any type of tissue. We propose endogenous controls for active and for repressed chromatin, and discuss various other controls that are essential for successful ChIP experiments. We experienced that the use of quantitative PCR (QPCR) is crucial for obtaining high quality ChIP data and we explain why. The method of data normalization has a major impact on the quality of ChIP analyses. Therefore, we analyzed different normalization strategies, resulting in a thorough discussion of the advantages and drawbacks of the various approaches. Conclusion Here we provide a robust ChIP protocol and strategy to optimize the protocol for any type of tissue; we argue that quantitative real-time PCR (QPCR) is the best method to analyze the precipitates, and present comprehensive insights into data normalization. PMID:17892552

  2. Quantitative analysis of neutral glycosphingolipids from human lymphocyte subpopulations.

    PubMed Central

    Schwarting, G A

    1980-01-01

    The glycosphingolipids of normal human lymphocytes from individual donors were analysed by high-pressure liquid chromatography. In addition, purified T- and B-lymphocytes were examined separately. Lactosylceramide was shown to be the major neutral glycosphingolipid in human lymphocytes, and monohexosylceramide, trihexosylceramide, globoside and paragloboside were all detected in smaller amounts. Analysis of purified B- and T-cell fractions revealed that each of these populations contained a similar qualitative profile for neutral glycosphingolipids, but that quantitatively, B-cells contained several times more of each glycosphingolipid per cell than did T-cells. PMID:6971095

  3. Neutron diffractometer INES for quantitative phase analysis of archaeological objects

    NASA Astrophysics Data System (ADS)

    Imberti, S.; Kockelmann, W.; Celli, M.; Grazzi, F.; Zoppi, M.; Botti, A.; Sodo, A.; Imperiale, M. Leo; de Vries-Melein, M.; Visser, D.; Postma, H.

    2008-03-01

    With the Italian Neutron Experimental Station (INES) a new general purpose neutron powder diffractometer is available at ISIS, characterized by a high resolution at low d-spacings, and particularly suited for the quantitative phase analysis of a wide range of archaeological materials. Time-of-flight neutron diffraction is notable for being a non-destructive technique, allowing a reliable determination of the phase compositions of multiphase artefacts, with or without superficial corrosion layers. A selection of archaeometric studies carried out during the first year of the INES user programme is presented here to demonstrate the capabilities of the instrument.

  4. 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.

  5. 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.

  6. 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

  7. Quantitative proteomic and phosphoproteomic analysis of Trypanosoma cruzi amastigogenesis.

    PubMed

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

    2014-12-01

    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

  8. 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 ?-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 C??C? 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

  9. 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.

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

    NASA Astrophysics Data System (ADS)

    Haaland, David M.

    1992-03-01

    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 mid- or near-infrared spectra of the blood. Progress toward the noninvasive determination of glucose levels in diabetics is an ultimate goal of this research.

  11. Quantitative analysis of intermolecular interactions in orthorhombic rubrene.

    PubMed

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

    2015-09-01

    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 ?-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 C??C? 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

  12. Quantitative analysis of volume images: electron microscopic tomography of HIV

    NASA Astrophysics Data System (ADS)

    Nystroem, Ingela; Bengtsson, Ewert W.; Nordin, Bo G.; Borgefors, Gunilla

    1994-05-01

    Three-dimensional objects should be represented by 3D images. So far, most of the evaluation of images of 3D objects have been done visually, either by looking at slices through the volumes or by looking at 3D graphic representations of the data. In many applications a more quantitative evaluation would be valuable. Our application is the analysis of volume images of the causative agent of the acquired immune deficiency syndrome (AIDS), namely human immunodeficiency virus (HIV), produced by electron microscopic tomography (EMT). A structural analysis of the virus is of importance. The representation of some of the interesting structural features will depend on the orientation and the position of the object relative to the digitization grid. We describe a method of defining orientation and position of objects based on the moment of inertia of the objects in the volume image. In addition to a direct quantification of the 3D object a quantitative description of the convex deficiency may provide valuable information about the geometrical properties. The convex deficiency is the volume object subtracted from its convex hull. We describe an algorithm for creating an enclosing polyhedron approximating the convex hull of an arbitrarily shaped object.

  13. 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

  14. Quantitatively understanding cellular uptake of gold nanoparticles via radioactivity analysis

    PubMed Central

    Shao, Xia; Schnau, Paul; Qian, Wei; Wang, Xueding

    2015-01-01

    The development of multifunctional gold nanoparticles (AuNPs) underwent an explosion in the last two decades. However, many questions regarding detailed surface chemistry and how they are affecting the behaviors of AuNPs in vivo and in vitro still need to be addressed before AuNPs can be widely adapted into clinical settings. In this work, radioactivity analysis was employed for quantitative evaluation of I-125 radiolabeled AuNPs uptakes by cancer cells. Facilitated with this new method, we have conducted initial bioevaluation of surfactant-free AuNPs produced by femtosecond laser ablation. Cellular uptake of AuNPs as a function of the RGD density on the AuNP surface, as well as a function of time, has been quantified. The radioactivity analysis may shed light on the dynamic interactions of AuNPs with cancer cells, and help achieve optimized designs of AuNPs for future clinical applications. PMID:26405436

  15. 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. PMID:25782471

  16. 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.

  17. BiDirectional optical communication with AquaOptical II

    E-print Network

    Doniec, Marek Wojciech

    This paper describes AquaOptical II, a bidirectional, high data-rate, long-range, underwater optical communication system. The system uses the software radio principle. Each AquaOptical II modem can be programmed to transmit ...

  18. 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.

  19. 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 can now be used to enhance the conformational determination of globular proteins on the basis of their CD spectra. PMID:1304345

  20. 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/). PMID:25913743

  1. 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

  2. Fractal Spectrum Technique for Quantitative Analysis of Volcanic Particle Shapes

    NASA Astrophysics Data System (ADS)

    Maria, A. H.; Carey, S. N.

    2001-12-01

    The shapes of volcanic particles reflect numerous eruptive parameters (e.g. magma viscosity, volatile content, degree of interaction with water) and are useful for understanding fragmentation and transport processes associated with volcanic eruptions. However, quantitative analysis of volcanic particle shapes has proven difficult due to their morphological complexity and variability. Shape analysis based on fractal geometry has been successfully applied to a wide variety of particles and appears to be well suited for describing complex features. The technique developed and applied to volcanic particles in this study uses fractal data produced by dilation of the 2-D particle boundary to produce a full spectrum of fractal dimensions over a range of scales for each particle. Multiple fractal dimensions, which can be described as a fractal spectrum curve, are calculated by taking the first derivative of data points on a standard Richardson plot. Quantitative comparisons are carried out using multivariate statistical techniques such as cluster and principal components analysis. Compared with previous fractal methods that express shape in terms of only one or two fractal dimensions, use of multiple fractal dimensions results in more effective discrimination between samples. In addition, the technique eliminates the subjectivity associated with selecting linear segments on Richardson plots for fractal dimension calculation, and allows direct comparison of particles as long as instantaneous dimensions used as input to multivariate analyses are selected at the same scales for each particle. Applications to samples from well documented eruptions (e.g. Mt. St. Helens, Tambora, Surtsey) indicate that the fractal spectrum technique provides a useful means of characterizing volcanic particles and can be helpful for identifying the products of specific fragmentation processes (volatile exsolution, phreatomagmatic, quench granulation) and modes of volcanic deposition (tephra fall, pyroclastic flow, blast/surge).

  3. Quantitative analysis of multiple sclerosis: a feasibility study

    NASA Astrophysics Data System (ADS)

    Li, Lihong; Li, Xiang; Wei, Xinzhou; Sturm, Deborah; Lu, Hongbing; Liang, Zhengrong

    2006-03-01

    Multiple Sclerosis (MS) is an inflammatory and demyelinating disorder of the central nervous system with a presumed immune-mediated etiology. For treatment of MS, the measurements of white matter (WM), gray matter (GM), and cerebral spinal fluid (CSF) are often used in conjunction with clinical evaluation to provide a more objective measure of MS burden. In this paper, we apply a new unifying automatic mixture-based algorithm for segmentation of brain tissues to quantitatively analyze MS. The method takes into account the following effects that commonly appear in MR imaging: 1) The MR data is modeled as a stochastic process with an inherent inhomogeneity effect of smoothly varying intensity; 2) A new partial volume (PV) model is built in establishing the maximum a posterior (MAP) segmentation scheme; 3) Noise artifacts are minimized by a priori Markov random field (MRF) penalty indicating neighborhood correlation from tissue mixture. The volumes of brain tissues (WM, GM) and CSF are extracted from the mixture-based segmentation. Experimental results of feasibility studies on quantitative analysis of MS are presented.

  4. 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. PMID:21375327

  5. Improvements to Direct Quantitative Analysis of Multiple MicroRNAs Facilitating Faster Analysis

    E-print Network

    Krylov, Sergey

    Information ABSTRACT: Studies suggest that patterns of deregulation in sets of microRNA (miRNA) can be used as cancer diagnostic and prognostic biomarkers. Establishing a "miRNA finger- print"-based diagnosticImprovements to Direct Quantitative Analysis of Multiple MicroRNAs Facilitating Faster Analysis

  6. Quantitative analysis of creatinine in urine by metalized nanostructured parylene

    NASA Astrophysics Data System (ADS)

    Wang, Hui; Malvadkar, Niranjan; Koytek, S.; Bylander, J.; Reeves, W. Brian; Demirel, Melik C.

    2010-03-01

    A highly accurate, real-time multisensor agent monitor for biomarker detection is required for early detection of kidney diseases. Urine creatinine level can provide useful information on the status of the kidney. We prepare nanostructured surface-enhanced Raman spectroscopy (SERS) substrates without template or lithography, which provides controllable, well-organized nanostructures on the surface, for the quantitative analysis of creatinine concentration in urine. We present our work on sensitivity of the SERS substrate to urine samples collected from diabetic patients and healthy persons. We report the preparation of a new type of SERS substrate, which provides fast (<10 s), highly sensitive (creatinine concentration <0.5 ?g/mL) and reproducible (<5% variation) detection of urine. Our method to analyze the creatinine level in urine is in good agreement with the enzymatic method.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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

  14. Quantitative Medical Image Analysis for Clinical Development of Therapeutics

    NASA Astrophysics Data System (ADS)

    Analoui, Mostafa

    There has been significant progress in development of therapeutics for prevention and management of several disease areas in recent years, leading to increased average life expectancy, as well as of quality of life, globally. However, due to complexity of addressing a number of medical needs and financial burden of development of new class of therapeutics, there is a need for better tools for decision making and validation of efficacy and safety of new compounds. Numerous biological markers (biomarkers) have been proposed either as adjunct to current clinical endpoints or as surrogates. Imaging biomarkers are among rapidly increasing biomarkers, being examined to expedite effective and rational drug development. Clinical imaging often involves a complex set of multi-modality data sets that require rapid and objective analysis, independent of reviewer's bias and training. In this chapter, an overview of imaging biomarkers for drug development is offered, along with challenges that necessitate quantitative and objective image analysis. Examples of automated and semi-automated analysis approaches are provided, along with technical review of such methods. These examples include the use of 3D MRI for osteoarthritis, ultrasound vascular imaging, and dynamic contrast enhanced MRI for oncology. Additionally, a brief overview of regulatory requirements is discussed. In conclusion, this chapter highlights key challenges and future directions in this area.

  15. Aqua Reticulata: topology of liquid water networks

    E-print Network

    Hyde, Stephen

    at oxygen vertices (the net nodes), with four edges at each vertex. second, liquid water is a mixture of two145 VI Aqua Reticulata: topology of liquid water networks Stephen T. Hyde department of Applied explored the notion of structure at the atomic scale in liquid water.1 While not the earliest attempt

  16. AquaTRAIN MCRTN Geogenic Chemicals in

    E-print Network

    Politècnica de Catalunya, Universitat

    irrigating rice paddies ­ Biggest contamination in the world! #12;Arsenic volatilization: BackgroundAquaTRAIN MCRTN Geogenic Chemicals in Groundwaters and Soils. Measuring arsenic volatileMeasuring arsenic volatile species in the environment usingspecies in the environment using a new chemoa new chemo

  17. 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) the use of a narrow frequency band for acquisition, (3) the inability to identify P and S waves given the small sample size, and (4) acquisition using a narrow amplitude range given a low signal to noise ratio. Moving forward to the final stage of this thesis, with the ability to characterize the sources of AE, we applied our method to study an engineering problem. We chose hydraulic fracturing because of its obvious importance in the future of Canadian energy production. During a hydraulic fracture treatment, whether in a lab or in the field, energy is added to the system via hydraulic pressure. The injection energy, which is on the order of 10 J in the lab and and 100 GJ in the field, is used in the creation of new fracture surface area, the radiation of elastic waves, and aseismic deformation. In the field, it has been consistently shown that the amount of induced seismic energy radiated is between 1e-7 % and 1e-3 % of the injection energy. We tested these findings by calculating the AE energy as a percentage of the injection energy and found that for eight laboratory hydraulic fracture experiments, the seismic energy ranged from 7.02e-08 % to 1.24e-04 % of the injection energy. These results support those made in the field, which concludes that seismic energy projection is a very small component of the hydraulic fracture energy budget and that the dominant energy budget term is aseismic deformation.

  18. 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

  19. Quantitative DNA methylation analysis of candidate genes in cervical cancer.

    PubMed

    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

  20. 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.

  1. Quantitative analysis of PPT1 interactome in human neuroblastoma cells

    PubMed Central

    Scifo, Enzo; Szwajda, Agnieszka; Soliymani, Rabah; Pezzini, Francesco; Bianchi, Marzia; Dapkunas, Arvydas; D?bski, Janusz; Uusi-Rauva, Kristiina; Dadlez, Micha?; Gingras, Anne-Claude; Tyynelä, Jaana; Simonati, Alessandro; Jalanko, Anu; Baumann, Marc H.; Lalowski, Maciej

    2015-01-01

    Mutations in the CLN1 gene that encodes Palmitoyl protein thioesterase 1 (PPT1) or CLN1, cause Infantile NCL (INCL, MIM#256730). PPT1 removes long fatty acid chains such as palmitate from modified cysteine residues of proteins. The data shown here result from isolated protein complexes from PPT1-expressing SH-SY5Y stable cells that were subjected to single step affinity purification coupled to mass spectrometry (AP-MS). Prior to the MS analysis, we utilised a modified filter-aided sample preparation (FASP) protocol. Based on label free quantitative analysis of the data by SAINT, 23 PPT1 interacting partners (IP) were identified. A dense connectivity in PPT1 network was further revealed by functional coupling and extended network analyses, linking it to mitochondrial ATP synthesis coupled protein transport and thioester biosynthetic process. Moreover, the terms: inhibition of organismal death, movement disorders and concentration of lipid were predicted to be altered in the PPT1 network. Data presented here are related to Scifo et al. (J. Proteomics, 123 (2015) 42–53). PMID:26217791

  2. A new LEED instrument for quantitative spot profile analysis

    NASA Astrophysics Data System (ADS)

    Scheithauer, U.; Meyer, G.; Henzler, M.

    1986-12-01

    A new instrument for spot profile analysis of electron diffraction (SPA-LEED) has been set up. The instrument works either with a transparent phosphor screen for visual inspection of the pattern or in its main mode with a channeltron for the measurement of the intensity. The diffraction pattern is recorded with a fixed channeltron position by scanning the beam over the channeltron aperture using two sets of electrostatic deflection plates. The scanning range covers about 30°. The intensity may vary over five orders of magnitude. The SPA-LEED system was checked with the Si(111) 7 × 7 surface. A full width at half maximum of 0.3% of the normal reflex distance corresponding to a transfer width of 110 nm is reproducibly obtained. Under optimum conditions the transfer width rose up to about 200 nm. Initial high resolution measurements have been performed on the system Pb on Cu(111). The results demonstrate the possibilities of the new instrument for qualitative and quantitative analysis.

  3. Inside single cells: quantitative analysis with advanced optics and nanomaterials.

    PubMed

    Cui, Yi; Irudayaraj, Joseph

    2015-01-01

    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. 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

  4. Optimal display conditions for quantitative analysis of stereoscopic cerebral angiograms

    SciTech Connect

    Charland, P.; Peters, T.

    1996-10-01

    For several years the authors have been using a stereoscopic display as a tool in the planning of stereotactic neurosurgical techniques. This PC-based workstation allows the surgeon to interact with and view vascular images in three dimensions, as well as to perform quantitative analysis of the three-dimensional (3-D) space. Some of the perceptual issues relevant to the presentation of medical images on this stereoscopic display were addressed in five experiments. The authors show that a number of parameters--namely the shape, color, and depth cue, associated with a cursor--as well as the image filtering and observer position, have a role in improving the observer`s perception of a 3-D image and his ability to localize points within the stereoscopically presented 3-D image. However, an analysis of the results indicates that while varying these parameters can lead to an effect on the performance of individual observers, the effects are not consistent across observers, and the mean accuracy remains relatively constant under the different experimental conditions.

  5. Quantitative diet analysis of four mesopredators from a coral reef.

    PubMed

    Ashworth, E C; Depczynski, M; Holmes, T H; Wilson, S K

    2014-04-01

    The diets of four common mesopredator fishes were examined in the back-reef habitat of a subtropical fringing reef system during the summer months. Quantitative gut content analyses revealed that crustaceans, represented >60% of ingested prey (% mass) by the latticed sand-perch Parapercis clathrata, brown dottyback Pseudochromis fuscus and half-moon grouper Epinephelus rivulatus. Dietary analyses also provided insights into ontogenetic shifts. Juvenile P. fuscus ingested large numbers of crustaceans (amphipods and isopods); these small prey were rarely found in larger individuals (<1% of ingested mass). Fishes also made an important contribution to the diets of all three species representing 10-30% of ingested mass. Conversely, the sand lizardfish Synodus dermatogenys fed exclusively on fishes including clupeids, gobies and labrids. Differences in the gut contents of the four species recorded were not apparent using stable isotope analysis of muscle tissues. The similarity of ?(13) C values in muscle tissues suggested that carbon within prey was derived from primary producers, with comparable carbon isotope signatures to corals and macroalgae, whilst similarities in ?(15) N values indicated that all four species belonged to the same trophic level. Thus, interspecific differences between mesopredator diets were undetectable when using stable isotope analysis which suggests that detailed elucidation of trophic pathways requires gut content analyses. PMID:24641257

  6. 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; Rodriguez, Henry; Rodland, Karin D.; Liu, Tao; Smith, Richard D.

    2015-01-01

    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, and 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.

  7. Nanotechnology patents in the automotive industry (a quantitative & qualitative analysis).

    PubMed

    Prasad, Raghavendra; Bandyopadhyay, Tapas K

    2014-01-01

    The aim of the article is to present a trend in patent filings for application of nanotechnology to the automobile sector across the world, using the keyword-based patent search. Overviews of the patents related to nano technology in the automobile industry have been provided. The current work has started from the worldwide patent search to find the patents on nanotechnology in the automobile industry and classify the patents according to the various parts of an automobile to which they are related and the solutions which they are providing. In the next step various graphs have been produced to get an insight into various trends. In next step, analysis of patents in various classifications, have been performed. The trends shown in graphs provide the quantitative analysis whereas; the qualitative analysis has been done in another section. The classifications of patents based on the solution they provide have been performed by reading the claims, titles, abstract and full texts separately. Patentability of nano technology inventions have been discussed in a view to give an idea of requirements and statutory bars to the patentability of nanotechnology inventions. Another objective of the current work is to suggest appropriate framework for the companies regarding use of nano technology in the automobile industry and a suggestive strategy for patenting of the inventions related to the same. For example, US Patent, with patent number US2008-019426A1 discusses the invention related to Lubricant composition. This patent has been studied and classified to fall under classification of automobile parts. After studying this patent, it is deduced that, the problem of friction in engine is being solved by this patent. One classification is the "automobile part" based while other is the basis of "problem being solved". Hence, two classifications, namely reduction in friction and engine were created. Similarly, after studying all the patents, a similar matrix has been created. PMID:25336172

  8. 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.

  9. Quantitative analysis of enzymatic fractionation of multiple substrate mixtures.

    PubMed

    Kaki, Shiva Shanker; Adlercreutz, Patrick

    2013-01-01

    The enzymatic conversion of mixtures of multiple substrates was studied quantitatively, based on established methodology used for the enzymatic kinetic resolution of racemic mixtures, involving the use of competitive factors: ratios of specificity constants (k(cat)/K(M)) of substrate pairs. The competitive factors of the substrates were defined in relation to a reference substrate. These competitive factors were used to predict the composition of the reaction mixture as a function of the degree of conversion of the reaction. The methodology was evaluated using three different lipases to hydrolyze a model mixture of four fatty acid methyl esters and for the esterification of a mixture of the same fatty acids in free form with ethanol. In most cases, the competitive factors determined from the initial phase of the reactions predicted the product composition during the rest of the reaction very well. The slowest reacting fatty acid was erucic acid (both in free form and as methyl ester), which was thus enriched in the remaining substrate fraction, while the other fatty acids: lauric acid, palmitic acid and oleic acid were converted faster. Simulations of the compositions of reaction mixtures with different values of the competitive factors were carried out to provide an overview of what could be achieved using enzymatic enrichment. Possible applications include reactions involving homologous substrates and mixtures of multiple isomers. The analysis presented provides guidelines that can be useful in the screening and development of enzymes for enzymatic enrichment applications. PMID:22811287

  10. Quantitative phase imaging applied to laser damage detection and analysis.

    PubMed

    Douti, Dam-Bé L; Chrayteh, Mhamad; Aknoun, Sherazade; Doualle, Thomas; Hecquet, Christophe; Monneret, Serge; Gallais, Laurent

    2015-10-01

    We investigate phase imaging as a measurement method for laser damage detection and analysis of laser-induced modification of optical materials. Experiments have been conducted with a wavefront sensor based on lateral shearing interferometry associated with a high-magnification optical microscope. The system has been used for the in-line observation of optical thin films and bulk samples, laser irradiated in two different conditions: 500 fs pulses at 343 and 1030 nm, and millisecond to second irradiation with a CO2 laser at 10.6 ?m. We investigate the measurement of the laser-induced damage threshold of optical material by detection and phase changes and show that the technique realizes high sensitivity with different optical path measurements lower than 1 nm. Additionally, the quantitative information on the refractive index or surface modification of the samples under test that is provided by the system has been compared to classical metrology instruments used for laser damage or laser ablation characterization (an atomic force microscope, a differential interference contrast microscope, and an optical surface profiler). An accurate in-line measurement of the morphology of laser-ablated sites, from few nanometers to hundred microns in depth, is shown. PMID:26479612

  11. Limits of normality of quantitative thoracic CT analysis

    PubMed Central

    2013-01-01

    Introduction Although computed tomography (CT) is widely used to investigate different pathologies, quantitative data from normal populations are scarce. Reference values may be useful to estimate the anatomical or physiological changes induced by various diseases. Methods We analyzed 100 helical CT scans taken for clinical purposes and referred as nonpathological by the radiologist. Profiles were manually outlined on each CT scan slice and each voxel was classified according to its gas/tissue ratio. For regional analysis, the lungs were divided into 10 sterno-vertebral levels. Results We studied 53 males and 47 females (age 64 ± 13 years); males had a greater total lung volume, lung gas volume and lung tissue. Noninflated tissue averaged 7 ± 4% of the total lung weight, poorly inflated tissue averaged 18 ± 3%, normally inflated tissue averaged 65 ± 8% and overinflated tissue averaged 11 ± 7%. We found a significant correlation between lung weight and subject's height (P <0.0001, r2 = 0.49); the total lung capacity in a supine position was 4,066 ± 1,190 ml, ~1,800 ml less than the predicted total lung capacity in a sitting position. Superimposed pressure averaged 2.6 ± 0.5 cmH2O. Conclusion Subjects without lung disease present significant amounts of poorly inflated and overinflated tissue. Normal lung weight can be predicted from patient's height with reasonable confidence. PMID:23706034

  12. Quantitative analysis by digital processing of streakline flow visualization images

    NASA Astrophysics Data System (ADS)

    Borleteau, J.-P.; Cognet, G.

    1986-01-01

    An experimental technique is described for the quantitative analysis of smoke filament (streakline) flow visualization images. The streakline, smoke droplets emitted by a point source, is illuminated by a sheet of laser light. The 1-2 micron diameter droplets trace the diffusive motions in the flow. Fast photography is performed to record the streaklines using ASA 400 film (an 800 ASA film system is under development). The film frames are scanned by a video camera linked to a mainframe (PDP 11-34) computer to digitize the images within a 256 x 256 pixel grid with 256 gray levels. Sample results are provided from a study of the entrained mixing layer of two plane parallel flows at speeds of 2 and 1 m/sec, respectively. The photography was performed at 600 frames/sec with 1/3000 sec exposures, yielding a spatial resolution of 1.5 mm. The method furnishes data for calculating the probability distribution for the presence of an oil droplet at any point of the flow, as well as recording the turbulent structures which form. Correlations between the vertical displacements of the droplets and the longitudinal speed of the flow permit calculating the frequency of passage of the vortices.

  13. 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.

  14. Quantitative Proteomics Analysis of Vitreous Humor from Diabetic Retinopathy Patients.

    PubMed

    Loukovaara, Sirpa; Nurkkala, Helka; Tamene, Fitsum; Gucciardo, Erika; Liu, Xiaonan; Repo, Pauliina; Lehti, Kaisa; Varjosalo, Markku

    2015-12-01

    Initial triggers for diabetic retinopathy (DR) are hyperglycemia-induced oxidative stress and advanced glycation end-products. The most pathological structural changes occur in retinal microvasculature, but the overall development of DR is multifactorial, with a complex interplay of microvascular, neurodegenerative, genetic/epigenetic, immunological, and secondary inflammation-related factors. Although several individual factors and pathways have been associated with retinopathy, a systems level understanding of the disease is lacking. To address this, we performed mass spectrometry based label-free quantitative proteomics analysis of 138 vitreous humor samples from patients with nonproliferative DR or the more severe proliferative form of the disease. Additionally, we analyzed samples from anti-VEGF (vascular endothelial growth factor) (bevacizumab)-treated patients from both groups. In our study, we identified 2482 and quantified the abundancy of 1351 vitreous proteins. Of these, the abundancy of 230 proteins was significantly higher in proliferative retinopathy compared with nonproliferative retinopathy. This specific subset of proteins was linked to inflammation, complement, and coagulation cascade proteins, protease inhibitors, apolipoproteins, immunoglobulins, and cellular adhesion molecules, reflecting the multifactorial nature of the disease. The identification of the key molecules of the disease is critical for the development of new therapeutic molecules and for the new use of existing drugs. PMID:26490944

  15. Quantitative analysis of biomedical samples using synchrotron radiation microbeams

    NASA Astrophysics Data System (ADS)

    Ektessabi, Ali; Shikine, Shunsuke; Yoshida, Sohei

    2001-07-01

    X-ray fluorescence (XRF) using a synchrotron radiation (SR) microbeam was applied to investigate distributions and concentrations of elements in single neurons of patients with neurodegenerative diseases. In this paper we introduce a computer code that has been developed to quantify the trace elements and matrix elements at the single cell level. This computer code has been used in studies of several important neurodegenerative diseases such as Alzheimer's disease (AD), Parkinson's disease (PD) and parkinsonism-dementia complex (PDC), as well as in basic biological experiments to determine the elemental changes in cells due to incorporation of foreign metal elements. The substantial nigra (SN) tissue obtained from the autopsy specimens of patients with Guamanian parkinsonism-dementia complex (PDC) and control cases were examined. Quantitative XRF analysis showed that neuromelanin granules of Parkinsonian SN contained higher levels of Fe than those of the control. The concentrations were in the ranges of 2300-3100 ppm and 2000-2400 ppm respectively. On the contrary, Zn and Ni in neuromelanin granules of SN tissue from the PDC case were lower than those of the control. Especially Zn was less than 40 ppm in SN tissue from the PDC case while it was 560-810 ppm in the control. These changes are considered to be closely related to the neuro-degeneration and cell death.

  16. 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. PMID:24607988

  17. 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…

  18. 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)

  19. 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.

  20. Quantitative analysis of the effective functional structure in yeast glycolysis.

    PubMed

    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

  1. 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 ?-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 ?M of naringenin and 0.45 ?M of eriodictyol. The LOQ was 2.34 ?M of naringenin and 1.35 ?M 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. PMID:26492639

  2. Descriptive Quantitative Analysis of Rearfoot Alignment Radiographic Parameters.

    PubMed

    Meyr, Andrew J; Wagoner, Matthew R

    2015-01-01

    Although the radiographic parameters of the transverse talocalcaneal angle (tTCA), calcaneocuboid angle (CCA), talar head uncovering (THU), calcaneal inclination angle (CIA), talar declination angle (TDA), lateral talar-first metatarsal angle (lTFA), and lateral talocalcaneal angle (lTCA) form the basis of the preoperative evaluation and procedure selection for pes planovalgus deformity, the so-called normal values of these measurements are not well-established. The objectives of the present study were to retrospectively evaluate the descriptive statistics of these radiographic parameters (tTCA, CCA, THU, CIA, TDA, lTFA, and lTCA) in a large population, and, second, to determine an objective basis for defining "normal" versus "abnormal" measurements. As a secondary outcome, the relationship of these variables to the body mass index was assessed. Anteroposterior and lateral foot radiographs from 250 consecutive patients without a history of previous foot and ankle surgery and/or trauma were evaluated. The results revealed a mean measurement of 24.12°, 13.20°, 74.32%, 16.41°, 26.64°, 8.37°, and 43.41° for the tTCA, CCA, THU, CIA, TDA, lTFA, and lTCA, respectively. These were generally in line with the reported historical normal values. Descriptive statistical analysis demonstrated that the tTCA, THU, and TDA met the standards to be considered normally distributed but that the CCA, CIA, lTFA, and lTCA demonstrated data characteristics of both parametric and nonparametric distributions. Furthermore, only the CIA (R = -0.2428) and lTCA (R = -0.2449) demonstrated substantial correlation with the body mass index. No differentiations in deformity progression were observed when the radiographic parameters were plotted against each other to lead to a quantitative basis for defining "normal" versus "abnormal" measurements. PMID:26002682

  3. Quantitative analysis of analgoantipyretics in dosage form using planar chromatography.

    PubMed

    Franeta, J T; Agbaba, D D; Eric, S M; Pavkov, S P; Vladimirov, S D; Aleksic, M B

    2001-03-01

    In the therapy of pain of weaker genesis, frequently used drugs usually represent a mix of analgoantipyretics of different chemical structures, mostly derivatives of salicylic acid, pyrazolone and p-aminophenol as well as derivatives of propionic and acetylsalicylic acid. For the determination of these drugs, different chromatographic methods have been applied, mostly HPLC, due to the the lower polarity (pyrazolones derivatives) and thermolability, as well as nonvolatility of compounds investigated. TLC method, considering advantages which include simplicity, reasonable sensitivity, rapidity, excellent resolving power and low cost has been successfully explored for the determination of analgoantipyretic compounds. The aim of this work was to develop a simple and rapid HPTLC method for the determination of acetylsalicylic acid, paracetamol, caffeine and phenobarbitone in dosage form. The determination of analgoantipyretics were performed on pre-coated HPTLC silica gel plates (10 x 20 cm(2)) by development in the mobile phase dichlormethane-ethyl acetate-cyclohexane-isopropanol-0.1 M HCL-formic acid (9:8:3:1.5:0.2:0.2 v/v/v/v/v/v). Migration distances (68.6+0.2 mm, 54.1+0.1 mm, 36.4+0.14 mm and 85.9+0.11 mm for acetylsalicylic acid, paracetamol, caffeine and phenobarbitone, respectively) with low RSD values (0.13--0.39%) showed a satisfactory reproductivity of the chromatographic system. TLC scanner was used for direct evaluation of the chromatograms in the reflectance/absorbance mode. Established calibration curves (r>0.999), precision (0.3--1.02%) and detection limits, as well as recovery values (96.51--98.1%) were validated and found to be satisfactory. The method was found to be reproducible and convenient for the quantitative analysis of compounds investigated in their dosage forms. PMID:11248516

  4. 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

  5. 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 T. forsythia were used. Salivary diagnostics of periodontitis has potential especially in large-scale population studies and health promotion. The cumulative strategy appears to be useful in the analysis of salivary bacteria as markers of periodontitis. PMID:26484315

  6. 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 (?-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. PMID:23775063

  7. 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…

  8. Speeding Up SMT-Based Quantitative Program Analysis

    E-print Network

    Seshia, Sanjit A.

    the amount of information leaked about secret data through a program's output channels. Such information can, which seeks to compute the amount of information leaked by a program. Much of the work in this area has time, number of bits leaked, memory used, etc.) for basic blocks. Then, to obtain the quantitative

  9. 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...

  10. On the quantitative analysis of Deep Belief Networks 

    E-print Network

    Salakhutdinov, Ruslan; Murray, Iain

    2008-01-01

    with approximate inference, can be used to estimate a lower bound on the log-probability that a DBN model with multiple hidden layers assigns to the test data. This is, to our knowledge, the first step towards obtaining quantitative results that would allow us...

  11. Genome-Wide Analysis of Expression Quantitative Trait Loci in Breast Cancer - Nicholas Knoblauch, TCGA Scientitifc Symposium 2012

    Cancer.gov

    Home News and Events Multimedia Library Videos Genome-Wide Analysis of Expression Quantitative Trait Loci in Breast Cancer - Nicholas Knoblauch Genome-Wide Analysis of Expression Quantitative Trait Loci in Breast Cancer - Nicholas Knoblauch, TCGA

  12. Quantitative analysis of directional spontaneous emission spectra from light sources in photonic crystals

    E-print Network

    Vos, Willem L.

    Quantitative analysis of directional spontaneous emission spectra from light sources in photonic disorder. Using a model comprising diffuse light transport and photonic band structure, we quantitatively of spontaneously emitted light in real photonic crystals, which is essential in the interpretation of quantum

  13. 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…

  14. Particle concentration measurement of virus samples using electrospray differential mobility analysis and quantitative amino acid analysis.

    PubMed

    Cole, Kenneth D; Pease, Leonard F; Tsai, De-Hao; Singh, Tania; Lute, Scott; Brorson, Kurt A; Wang, Lili

    2009-07-24

    Virus reference materials are needed to develop and calibrate detection devices and instruments. We used electrospray differential mobility analysis (ES-DMA) and quantitative amino acid analysis (AAA) to determine the particle concentration of three small model viruses (bacteriophages MS2, PP7, and phiX174). The biological activity, purity, and aggregation of the virus samples were measured using plaque assays, denaturing gel electrophoresis, and size-exclusion chromatography. ES-DMA was developed to count the virus particles using gold nanoparticles as internal standards. ES-DMA additionally provides quantitative measurement of the size and extent of aggregation in the virus samples. Quantitative AAA was also used to determine the mass of the viral proteins in the pure virus samples. The samples were hydrolyzed and the masses of the well-recovered amino acids were used to calculate the equivalent concentration of viral particles in the samples. The concentration of the virus samples determined by ES-DMA was in good agreement with the concentration predicted by AAA for these purified samples. The advantages and limitations of ES-DMA and AAA to characterize virus reference materials are discussed. PMID:19545873

  15. Understanding Maneuver Uncertainties during Inclination Maneuvers of the Aqua Spacecraft

    NASA Technical Reports Server (NTRS)

    McKinley, David P.

    2007-01-01

    During the Fall 2006 inclination campaign for the Aqua spacecraft it was discovered that there was significant uncertainty in the prediction of the semimajor axis change during a maneuver. The low atmospheric drag environment at the time of the maneuvers amplified the effects of this uncertainty leading to a potential violation of the spacecraft ground-track requirements. In order to understand the uncertainty, a Monte Carlo simulation was developed to characterize the expected semi-major axis change uncertainty given the observed behavior of the spacecraft propulsion and attitude control systems during a maneuver. This expected uncertainty was then used to develop new analysis tools to ensure that future inclination maneuver plans will .meet ground-track control requirements in the presence of the error.

  16. Blocking systems over an aqua planet Yongyun Hu,1

    E-print Network

    Hu, Yongyun

    Blocking systems over an aqua planet Yongyun Hu,1 Da Yang,1 and Jun Yang1 Received 15 July 2008 that forced planetary waves are critically important for blocking formation. To test whether blocking can NCAR CAM2. Results show that blockings occur frequently under the aqua-planet conditions which have

  17. 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 hybridization method (FISH). This approach was used for evaluation of contribution of each gram-negative bactera group. No significant difference between the main soil gram-negative bacterial groups (phylum Proteobacteria and Bacteroidetes) was found both under anaerobic and anaerobic conditions in chernozem in the topsoil. Thus soil gram-negative bacteria play an important ecological role in natural polymer degradation as common group of microorganisms. Another approach with using cascade filtration technique for bacterial population density estimation in chernozem was compared to classical method of fluorescent microscopy. Quantification of soil bacteria with cascade filtration provided by filters with different diameters and filtering of soil suspension in fixed amount. In comparison to the classical fluorescent microscopy method the modification with filtration of soil suspension provided to quantify more bacterial cells. Thus biomass calculation results of soil bacteria by using classical fluorescent microscopy could be underestimated and combination with cascade filtration technique allow to avoid potential experimental error. Thereby, combination and comparison of several fluorescent microscopy methods modifications established during the research provided miscellaneous approaches in soil bacteria quantification and analysis of ecological roles of soil microorganisms.

  18. 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

  19. Quantitative PCR Analysis of DNA Aptamer Pharmacokinetics in Mice

    PubMed Central

    Perschbacher, Katherine; Smestad, John A.; Peters, Justin P.; Standiford, Miranda M.; Denic, Aleksandar; Wootla, Bharath; Warrington, Arthur E.; Rodriguez, Moses

    2015-01-01

    DNA aptamer oligonucleotides and their protein conjugates show promise as therapeutics in animal models of diseases such as multiple sclerosis. These molecules are large and highly charged, raising questions about their biodistribution and pharmacokinetics in mammals. Here we exploit the power of quantitative polymerase chain reaction to accurately quantitate the tissue distribution of 40-nucleotide DNA aptamers and their streptavidin conjugates after intraperitoneal injection in mice. We show remarkably rapid distribution to peripheral tissues including the central nervous system. Modeling of tissue distribution data reveals the importance of DNA aptamer sequence, 3? modification, and protein conjugation in enhancing tissue exposure. These data help to interpret the previously observed effectiveness of aptamer conjugates, as opposed to free aptamers, in stimulating central nervous system remyelination in a mouse model of multiple sclerosis. PMID:25536292

  20. Quantitative analysis of HSV gene expression during lytic infection

    PubMed Central

    Turner, Anne-Marie W.; Arbuckle, Jesse H.; Kristie, Thomas M.

    2014-01-01

    Herpes Simplex Virus (HSV) is a human pathogen that establishes latency and undergoes periodic reactivation, resulting in chronic recurrent lytic infection. HSV lytic infection is characterized by an organized cascade of three gene classes, however successful transcription and expression of the first, the immediate early class, is critical to the overall success of viral infection. This initial event of lytic infection is also highly dependent on host cell factors. This unit uses RNA interference and small molecule inhibitors to examine the role of host and viral proteins in HSV lytic infection. Methods detailing isolation of viral and host RNA and genomic DNA, followed by quantitative real-time PCR, allow characterization of impacts on viral transcription and replication respectively. Western blot can be used to confirm quantitative PCR results. This combination of protocols represents a starting point for researchers interested in virus-host interactions during HSV lytic infection. PMID:25367270

  1. Quantitative analysis of the human T cell palmitome

    PubMed Central

    Morrison, Eliot; Kuropka, Benno; Kliche, Stefanie; Brügger, Britta; Krause, Eberhard; Freund, Christian

    2015-01-01

    Palmitoylation is a reversible post-translational modification used to inducibly compartmentalize proteins in cellular membranes, affecting the function of receptors and intracellular signaling proteins. The identification of protein “palmitomes” in several cell lines raises the question to what extent this modification is conserved in primary cells. Here we use primary T cells with acyl-biotin exchange and quantitative mass spectrometry to identify a pool of proteins previously unreported as palmitoylated in vivo. PMID:26111759

  2. 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. PMID:12838530

  3. Quantitative histochemical analysis of human artery using Raman spectroscopy.

    PubMed

    Manoharan, R; Baraga, J J; Feld, M S; Rava, R P

    1992-10-30

    We have developed a method for using near infrared Raman spectroscopy to quantitatively analyze the histochemical composition of human artery. The main contributors to bands observed in the Raman spectra of normal and atherosclerotic aorta are the proteins collagen and elastin, cholesterol lipids, and calcium hydroxyapatite. The Raman scattering cross-sections of different bands for these components have been determined in order to understand their relative contributions to the Raman spectra of biological tissue. The Raman signal is observed to behave linearly with the concentration of the components, even in a highly scattering medium such as a powder. Using these data, we have developed a linear model that can be used to extract the quantitative contribution of an individual component to the spectrum of a mixture. The model has been applied to several mixtures of known composition of tissue constituents in order to evaluate its precision and accuracy. The calculated fit coefficients from the spectra are in agreement with the measured values within experimental uncertainties. The spectra of different types of atherosclerotic aorta have also been modeled, and we have extracted quantitative information regarding the relative concentration of biological constituents in atherosclerotic aorta. PMID:1474427

  4. Visual Modeling for Aqua Ventus I off Monhegan Island, ME

    SciTech Connect

    Hanna, Luke A.; Whiting, Jonathan M.; Copping, Andrea E.

    2013-11-27

    To assist the University of Maine in demonstrating a clear pathway to project completion, PNNL has developed visualization models of the Aqua Ventus I project that accurately depict the Aqua Ventus I turbines from various points on Monhegain Island, ME and the surrounding area. With a hub height of 100 meters, the Aqua Ventus I turbines are large and may be seen from many areas on Monhegan Island, potentially disrupting important viewsheds. By developing these visualization models, which consist of actual photographs taken from Monhegan Island and the surrounding area with the Aqua Ventus I turbines superimposed within each photograph, PNNL intends to support the project’s siting and permitting process by providing the Monhegan Island community and various other stakeholders with a probable glimpse of how the Aqua Ventus I project will appear.

  5. A QUANTITATIVE ANALYSIS OF ALKALINE PHOSPHATASE ACTIVITY IN HE`EIA FISHPOND

    E-print Network

    Qiu, Bo

    Phosphatase Activity: Enzyme Kinetics & Reaction MechanismA QUANTITATIVE ANALYSIS OF ALKALINE PHOSPHATASE ACTIVITY IN HE`EIA FISHPOND A THESIS SUBMITTED of the alkaline phosphatase (APase) enzyme indicates inorganic P deficiency and the potential for utilization

  6. Lung Extraction, Lobe Segmentation and Hierarchical Region Assessment for Quantitative Analysis on High

    E-print Network

    Lung Extraction, Lobe Segmentation and Hierarchical Region Assessment for Quantitative Analysis Care Division, Brigham and Women's Hospital, Boston, MA Abstract. Regional assessment of lung disease specific to different lung regions on high resolution computed tomography (HRCT) datasets. We present

  7. Quantitative Computed Tomography Analysis of Local Chemotherapy in Liver Tissue After

    E-print Network

    Gao, Jinming

    Quantitative Computed Tomography Analysis of Local Chemotherapy in Liver Tissue After livers before and following radiofrequency ablation. Materials and Methods. Polymer matrixes containing carboplatin (a platinum-containing chemotherapeutic agent) were implanted into rat livers either immediately

  8. Automated Quantitative Analysis of Capnogram Shape for COPD–Normal and COPD–CHF Classification

    E-print Network

    Mieloszyk, Rebecca J.

    We develop an approach to quantitative analysis of carbon dioxide concentration in exhaled breath, recorded as a function of time by capnography. The generated waveform – or capnogram – is currently used in clinical practice ...

  9. Formal Specification and Quantitative Analysis of a Constellation of Navigation Satellites

    E-print Network

    Miller, Alice

    Formal Specification and Quantitative Analysis of a Constellation of Navigation Satellites a single satellite and a navigation satellite constellation and logical specification of their reliability in satellite constellations Correspondence to: Yu Lu, School of Computing Science, University of Glasgow

  10. Planetary and Space Science 56 (2008) 15961606 Geysers of Enceladus: Quantitative analysis of qualitative models

    E-print Network

    2008-01-01

    Planetary and Space Science 56 (2008) 1596­1606 Geysers of Enceladus: Quantitative analysis--lead to speculations about geophysical activities in form of cryo-volcanism or geysers at Enceladus (Haff et al., 1983

  11. Quantitative Analysis of the Human Airway Microbial Ecology Reveals a Pervasive Signature for Cystic Fibrosis

    E-print Network

    Quake, Stephen R.

    Quantitative Analysis of the Human Airway Microbial Ecology Reveals a Pervasive Signature individuals, we identified diverse microbial communities in the healthy samples, contravening conventional the CF patients revealed significant differences in microbial ecology, including differential

  12. QUANTITATIVE ANALYSIS OF 68 POLAR COMPOUNDS FROM TEN CHEMICAL CLASSES BY DIRECT AQUEOUS INJECTION GAS CHROMATOGRAPHY

    EPA Science Inventory

    Porous polymer packings have been used successfully in many applications of direct aqueous injection gas chromatography. The authors have expanded the use of aqueous injection to the quantitative analysis of 68 alcohols, acetates, ketones, ethers, sulfides, aldehydes, diols, dion...

  13. Changes in protein expression in maturing equine testis: a quantitative DIGE analysis 

    E-print Network

    Roper-Foo, Pilar

    2011-01-11

    -Foo_Final_Thesis_withappendix-FINAL-VERSION.pdf.txt Content-Type text/plain; charset=ISO-8859-1 CHANGES IN PROTEIN EXPRESSION IN MATURING EQUINE TESTIS: A QUANTITATIVE DIGE ANALYSIS Major: Genetics April 2009 Submitted to the Office of Undergraduate Research Texas A...&M University in partial fulfillment of the requirements for the designation as UNDERGRADUATE RESEARCH SCHOLAR A Senior Scholars Thesis by PILAR ROPER-FOO CHANGES IN PROTEIN EXPRESSION IN MATURING EQUINE TESTIS: A QUANTITATIVE DIGE ANALYSIS...

  14. Quantitative mineralogical analysis of hydraulic limes by X-ray diffraction

    SciTech Connect

    Mertens, G. Madau, P.; Durinck, D.; Blanpain, B.; Elsen, J.

    2007-11-15

    A combined selective dissolution/quantitative X-ray diffraction (QXRD) approach is proposed for the quantitative mineralogical phase analysis of hydraulic limes. The proposed methodology is validated by the analysis of two model mixtures. Afterwards two commercial hydraulic binders and one self-burned hydraulic quicklime were analysed. Chemical, thermal and microprobe analyses were performed to check the results. It is shown that the proposed selective dissolution/QXRD approach yields reliable quantitative mineralogical information for hydraulic limes in spite of their complex phase composition and the presence of amorphous material.

  15. A new method for quantitative analysis of multiple scelerosis using MR images

    E-print Network

    analysis of multiple sclerosis (MS) was presented. An automatic self-adaptive image segmentation algorithm Analysis, Multipl Sclerosis, Brain Atrophy 1. INTRODUCTION Multiple sclerosis (MS) is the most commonA new method for quantitative analysis of multiple scelerosis using MR images Dongqing Chen*a , Wei

  16. Quantitative analysis of a wind energy conversion model

    NASA Astrophysics Data System (ADS)

    Zucker, Florian; Gräbner, Anna; Strunz, Andreas; Meyn, Jan-Peter

    2015-03-01

    A rotor of 12 cm diameter is attached to a precision electric motor, used as a generator, to make a model wind turbine. Output power of the generator is measured in a wind tunnel with up to 15 m s-1 air velocity. The maximum power is 3.4 W, the power conversion factor from kinetic to electric energy is cp = 0.15. The v3 power law is confirmed. The model illustrates several technically important features of industrial wind turbines quantitatively.

  17. Electrospray Mass Spectrometry for Quantitative Plasma Proteome Analysis

    PubMed Central

    Wang, Hong; Hanash, Sam

    2015-01-01

    Summary Electrospray ionization mass spectrometry (ESI-MS) is an efficient soft ionization procedure for macro biomolecules. However, it is a rather delicate process to produce charged molecules for mass-to-charge ratio (m/z) based measurement. In this chapter, the mechanism of ESI is briefly presented, and the experimental pipeline for quantitative profiling of plasma proteins (prefractionation immunodepletion, protein isotope tagging, 2D-HPLC separation of intact proteins, and LC-MS) is presented as applied by our group in studies of cancer biomarker discovery. PMID:19544026

  18. Quantitative control of idealized analysis models of thin , Junzhe Zhenga

    E-print Network

    Martin, Ralph R.

    , thin plate. 1. Introduction Engineering analysis is typically performed using the finite element (FE difficulty both for the meshing process, and the finite element analysis performed using that mesh [3, 7 a theoretical analysis and practical algorithms. Our approach can compute bounds for the errors induced

  19. Quantitative phenotypic analysis of multistress response in Zygosaccharomyces rouxii complex.

    PubMed

    Solieri, Lisa; Dakal, Tikam C; Bicciato, Silvio

    2014-06-01

    Zygosaccharomyces rouxii complex comprises three yeasts clusters sourced from sugar- and salt-rich environments: haploid Zygosaccharomyces rouxii, diploid Zygosaccharomyces sapae and allodiploid/aneuploid strains of uncertain taxonomic affiliations. These yeasts have been characterized with respect to gene copy number variation, karyotype variability and change in ploidy, but functional diversity in stress responses has not been explored yet. Here, we quantitatively analysed the stress response variation in seven strains of the Z. rouxii complex by modelling growth variables via model and model-free fitting methods. Based on the spline fit as most reliable modelling method, we resolved different interstrain responses to 15 environmental perturbations. Compared with Z. rouxii CBS 732(T) and Z. sapae strains ABT301(T) and ABT601, allodiploid strain ATCC 42981 and aneuploid strains CBS 4837 and CBS 4838 displayed higher multistress resistance and better performance in glycerol respiration even in the presence of copper. ?-based logarithmic phenotypic index highlighted that ABT601 is a slow-growing strain insensitive to stress, whereas ABT301(T) grows fast on rich medium and is sensitive to suboptimal conditions. Overall, the differences in stress response could imply different adaptation mechanisms to sugar- and salt-rich niches. The obtained phenotypic profiling contributes to provide quantitative insights for elucidating the adaptive mechanisms to stress in halo- and osmo-tolerant Zygosaccharomyces yeasts. PMID:24533625

  20. QUANTITATIVE ANALYSIS OF PERIODONTAL PATHOGENS IN PERIODONTITIS AND GINGIVITIS.

    PubMed

    Scapoli, L; Girardi, A; Palmieri, A; Martinelli, M; Cura, F; Lauritano, D; Carinci, F

    2015-01-01

    Periodontal tissues surround the teeth and provide their attachment. Periodontal diseases include a mild and reversible form named gingivitis and periodontitis that is the main cause of tooth loss in adults. Gingivitis, that affects gums and coronal junctional epithelium, as well as periodontitis, that is characterized by loss of connective tissue attachment, are caused by a persistent inflammatory response promoted by alteration of periodontal biofilm. The aim of the study was to test whether the prevalence or relative amount of each species was associated with a particular clinical condition. Periodontal evaluation of 539 unrelated patients was performed by the Periodontal Screening and Recording (PSR) system. Subgingival samples were obtained from the site with the worst PSR score. A selection of eleven bacterial species was evaluated by quantitative real time PCR. Some bacterial species were found to be associated with all phases of periodontal disease, such as Tannerella forsythia, Treponema denticola, and Treponema lecithinolyticum, while other species were more specifically associated with periodontitis, such as Porphyromonas endodontalis and Porphyromonas gingivalis, or with gingivitis, such as Capnocytophaga ochracea and Campylobacter rectus. Quantitative and qualitative analyses helps to better understand the microbial changes associated with different stages of periodontal disease. PMID:26511188

  1. Qualitative and quantitative analysis of volatile constituents from latrines.

    PubMed

    Lin, Jianming; Aoll, Jackline; Niclass, Yvan; Velazco, Maria Inés; Wünsche, Laurent; Pika, Jana; Starkenmann, Christian

    2013-07-16

    More than 2.5 billion people defecate in the open. The increased commitment of private and public organizations to improving this situation is driving the research and development of new technologies for toilets and latrines. Although key technical aspects are considered by researchers when designing new technologies for developing countries, the basic aspect of offending malodors from human waste is often neglected. With the objective of contributing to technical solutions that are acceptable to global consumers, we investigated the chemical composition of latrine malodors sampled in Africa and India. Field latrines in four countries were evaluated olfactively and the odors qualitatively and quantitatively characterized with three analytical techniques. Sulfur compounds including H2S, methyl mercaptan, and dimethyl-mono-(di;tri) sulfide are important in sewage-like odors of pit latrines under anaerobic conditions. Under aerobic conditions, in Nairobi for example, paracresol and indole reached concentrations of 89 and 65 ?g/g, respectively, which, along with short chain fatty acids such as butyric acid (13 mg/g) explained the strong rancid, manure and farm yard odor. This work represents the first qualitative and quantitative study of volatile compounds sampled from seven pit latrines in a variety of geographic, technical, and economic contexts in addition to three single stools from India and a pit latrine model system. PMID:23829328

  2. Is the new AquaTrainer® snorkel valid for VO2 assessment in swimming?

    PubMed

    Baldari, C; Fernandes, R J; Meucci, M; Ribeiro, J; Vilas-Boas, J P; Guidetti, L

    2013-04-01

    The Cosmed AquaTrainer® snorkel, in connection with the K4b2 analyzer, is the most recent instrument used for real time gas analysis during swimming. This study aimed to test if a new AquaTrainer® snorkel with 2 (SV2) or 4 (SV4) valves is comparable to a standard face mask (Mask) being valid for real time gas analysis under controlled laboratory and swimming pool conditions. 9 swimmers performed 2 swimming and 3 cycling tests at 3 different workloads on separate days. Tests were performed in random order, at constant exercise load with direct turbine temperature measurements, breathing with Mask, SV4 and SV2 while cycling, and with SV2 and SV4 while swimming. A high agreement was obtained using Passing - Bablok regression analysis in oxygen consumption, carbon dioxide production, tidal volumes, pulmonary ventilation, expiratory fraction of oxygen and carbon dioxide, and heart rate comparing different conditions in swimming and cycling. Proportional and fixed differences were always rejected (95% CI always contained the value 1 for the slope and the 0 for the intercept). In conclusion, the new SV2 AquaTrainer® snorkel, can be considered a valid device for gas analysis, being comparable to the Mask and the SV4 in cycling, and to the SV4 in swimming. PMID:23041962

  3. Influence of energy straggling on quantitative PIXE analysis

    NASA Astrophysics Data System (ADS)

    Ruvalcaba, J. L.; Miranda, J.

    1996-04-01

    Examples of numerical calculations aimed to estimate the effect of proton energy straggling on quantitative PIXE are presented. Special attention has been taken to low energy PIXE and external beam PIXE. X-ray yield calculations including beam energy straggling for beam energies ranging from 0.3 to 3 MeV were carried out and the X-ray yield variations due to the energy straggling were determined. Proton energy straggling was calculated using the uncorrected Bohr's formula. K-and L-shell ionization cross sections variations were considered for the X-ray yields calculations. Results indicate that in some cases the error induced on the produced X-ray yield may be up to a few percent on low energy PIXE. For external beam PIXE and high energy PIXE the X-ray yield variations are very small (less than 0.5%).

  4. Quantitative error analysis for computer assisted navigation: a feasibility study

    PubMed Central

    Güler, Ö.; Perwög, M.; Kral, F.; Schwarm, F.; Bárdosi, Z. R.; Göbel, G.; Freysinger, W.

    2013-01-01

    Purpose The benefit of computer-assisted navigation depends on the registration process, at which patient features are correlated to some preoperative imagery. The operator-induced uncertainty in localizing patient features – the User Localization Error (ULE) - is unknown and most likely dominating the application accuracy. This initial feasibility study aims at providing first data for ULE with a research navigation system. Methods Active optical navigation was done in CT-images of a plastic skull, an anatomic specimen (both with implanted fiducials) and a volunteer with anatomical landmarks exclusively. Each object was registered ten times with 3, 5, 7, and 9 registration points. Measurements were taken at 10 (anatomic specimen and volunteer) and 11 targets (plastic skull). The active NDI Polaris system was used under ideal working conditions (tracking accuracy 0.23 mm root mean square, RMS; probe tip calibration was 0.18 mm RMS. Variances of tracking along the principal directions were measured as 0.18 mm2, 0.32 mm2, and 0.42 mm2. ULE was calculated from predicted application accuracy with isotropic and anisotropic models and from experimental variances, respectively. Results The ULE was determined from the variances as 0.45 mm (plastic skull), 0.60 mm (anatomic specimen), and 4.96 mm (volunteer). The predicted application accuracy did not yield consistent values for the ULE. Conclusions Quantitative data of application accuracy could be tested against prediction models with iso- and anisotropic noise models and revealed some discrepancies. This could potentially be due to the facts that navigation and one prediction model wrongly assume isotropic noise (tracking is anisotropic), while the anisotropic noise prediction model assumes an anisotropic registration strategy (registration is isotropic in typical navigation systems). The ULE data are presumably the first quantitative values for the precision of localizing anatomical landmarks and implanted fiducials. Submillimetric localization is possible for implanted screws; anatomic landmarks are not suitable for high-precision clinical navigation. PMID:23387758

  5. Aqua at TRW, August 2001, being positioned for lowering into the thermal vacuum chamber. (Photo by Sally Aristei.) Front cover: The computer rendering of the Aqua spacecraft was done by Reto Stckli, based on earlier versions by TRW.

    E-print Network

    mission aimed at improving our understanding of the Earth/atmosphere system, along with changes occurring within it, through the monitoring and analysis of dozens of Earth variables from a space-based plat- form orbiting the Earth. Aqua is part of the Earth Observing System (EOS), an international Earth

  6. Quantitative assessment of human motion using video motion analysis

    NASA Technical Reports Server (NTRS)

    Probe, John D.

    1990-01-01

    In the study of the dynamics and kinematics of the human body, a wide variety of technologies was developed. Photogrammetric techniques are well documented and are known to provide reliable positional data from recorded images. Often these techniques are used in conjunction with cinematography and videography for analysis of planar motion, and to a lesser degree three-dimensional motion. Cinematography has been the most widely used medium for movement analysis. Excessive operating costs and the lag time required for film development coupled with recent advances in video technology have allowed video based motion analysis systems to emerge as a cost effective method of collecting and analyzing human movement. The Anthropometric and Biomechanics Lab at Johnson Space Center utilizes the video based Ariel Performance Analysis System to develop data on shirt-sleeved and space-suited human performance in order to plan efficient on orbit intravehicular and extravehicular activities. The system is described.

  7. Probabilistic reliability analysis, quantitative safety goals, and nuclear licensing in the United Kingdom.

    PubMed

    Cannell, W

    1987-09-01

    Although unpublicized, the use of quantitative safety goals and probabilistic reliability analysis for licensing nuclear reactors has become a reality in the United Kingdom. This conclusion results from an examination of the process leading to the licensing of the Sizewell B PWR in England. The licensing process for this reactor has substantial implications for nuclear safety standards in Britain, and is examined in the context of the growing trend towards quantitative safety goals in the United States. PMID:3685540

  8. Quantitative Brightness Analysis of Fluorescence Intensity Fluctuations in E. Coli

    PubMed Central

    Hur, Kwang-Ho; Mueller, Joachim D.

    2015-01-01

    The brightness measured by fluorescence fluctuation spectroscopy specifies the average stoichiometry of a labeled protein in a sample. Here we extended brightness analysis, which has been mainly applied in eukaryotic cells, to prokaryotic cells with E. coli serving as a model system. The small size of the E. coli cell introduces unique challenges for applying brightness analysis that are addressed in this work. Photobleaching leads to a depletion of fluorophores and a reduction of the brightness of protein complexes. In addition, the E. coli cell and the point spread function of the instrument only partially overlap, which influences intensity fluctuations. To address these challenges we developed MSQ analysis, which is based on the mean Q-value of segmented photon count data, and combined it with the analysis of axial scans through the E. coli cell. The MSQ method recovers brightness, concentration, and diffusion time of soluble proteins in E. coli. We applied MSQ to measure the brightness of EGFP in E. coli and compared it to solution measurements. We further used MSQ analysis to determine the oligomeric state of nuclear transport factor 2 labeled with EGFP expressed in E. coli cells. The results obtained demonstrate the feasibility of quantifying the stoichiometry of proteins by brightness analysis in a prokaryotic cell. PMID:26099032

  9. Depression in Parkinson's disease: a quantitative and qualitative analysis.

    PubMed Central

    Gotham, A M; Brown, R G; Marsden, C D

    1986-01-01

    Depression is a common feature of Parkinson's disease, a fact of both clinical and theoretical significance. Assessment of depression in Parkinson's disease is complicated by overlapping symptomatology in the two conditions, making global assessments based on observer or self-ratings of doubtful validity. The present study aimed to provide both a quantitative and qualitative description of the nature of the depressive changes found in Parkinson's disease as compared with normal elderly subjects and arthritis patients. As with previous studies, the patients with Parkinson's disease scored significantly higher than normal controls on various self-ratings of depression and anxiety but, in this study, did not differ from those with arthritis. Qualitatively, both the Parkinson's disease and the arthritis groups had depression characterised by pessimism and hopelessness, decreased motivation and drive, and increased concern with health. In contrast, the negative affective feelings of guilt, self-blame and worthlessness were absent in both patient groups. This pattern of depression was significantly associated with severity of illness and functional disability. However, these factors account for only a modest proportion of the variability in test scores. Probable unexplored factors are individual differences in coping style and availability of support. PMID:3701347

  10. Quantitative analysis of task selection for brain-computer interfaces

    NASA Astrophysics Data System (ADS)

    Llera, Alberto; Gómez, Vicenç; Kappen, Hilbert J.

    2014-10-01

    Objective. To assess quantitatively the impact of task selection in the performance of brain-computer interfaces (BCI). Approach. We consider the task-pairs derived from multi-class BCI imagery movement tasks in three different datasets. We analyze for the first time the benefits of task selection on a large-scale basis (109 users) and evaluate the possibility of transferring task-pair information across days for a given subject. Main results. Selecting the subject-dependent optimal task-pair among three different imagery movement tasks results in approximately 20% potential increase in the number of users that can be expected to control a binary BCI. The improvement is observed with respect to the best task-pair fixed across subjects. The best task-pair selected for each subject individually during a first day of recordings is generally a good task-pair in subsequent days. In general, task learning from the user side has a positive influence in the generalization of the optimal task-pair, but special attention should be given to inexperienced subjects. Significance. These results add significant evidence to existing literature that advocates task selection as a necessary step towards usable BCIs. This contribution motivates further research focused on deriving adaptive methods for task selection on larger sets of mental tasks in practical online scenarios.

  11. Temporal Kinetics and Quantitative Analysis of Cryptococcus neoformans Nonlytic Exocytosis

    PubMed Central

    Stukes, Sabriya A.; Cohen, Hillel W.

    2014-01-01

    Cryptococcus neoformans is a facultative intracellular pathogen and the causative agent of cryptococcosis, a disease that is often fatal to those with compromised immune systems. C. neoformans has the capacity to escape phagocytic cells through a process known as nonlytic exocytosis whereby the cryptococcal cell is released from the macrophage into the extracellular environment, leaving both the host and pathogen alive. Little is known about the mechanism behind nonlytic exocytosis, but there is evidence that both the fungal and host cells contribute to the process. In this study, we used time-lapse movies of C. neoformans-infected macrophages to delineate the kinetics and quantitative aspects of nonlytic exocytosis. We analyzed approximately 800 macrophages containing intracellular C. neoformans and identified 163 nonlytic exocytosis events that were further characterized into three subcategories: type I (complete emptying of macrophage), type II (partial emptying of macrophage), and type III (cell-to-cell transfer). The majority of type I and II events occurred after several hours of intracellular residence, whereas type III events occurred significantly (P < 0.001) earlier in the course of macrophage infection. Our results show that nonlytic exocytosis is a morphologically and temporally diverse process that occurs relatively rapidly in the course of macrophage infection. PMID:24595144

  12. Analysis of quantitative trait loci for behavioral laterality in mice.

    PubMed Central

    Roubertoux, Pierre L; Le Roy, Isabelle; Tordjman, Sylvie; Cherfou, Améziane; Migliore-Samour, Danièle

    2003-01-01

    Laterality is believed to have genetic components, as has been deduced from family studies in humans and responses to artificial selection in mice, but these genetic components are unknown and the underlying physiological mechanisms are still a subject of dispute. We measured direction of laterality (preferential use of left or right paws) and degree of laterality (absolute difference between the use of left and right paws) in C57BL/6ByJ (B) and NZB/BlNJ (N) mice and in their F(1) and F(2) intercrosses. Measurements were taken of both forepaws and hind paws. Quantitative trait loci (QTL) did not emerge for direction but did for degree of laterality. One QTL for forepaw (LOD score = 5.6) and the second QTL for hind paw (LOD score = 7.2) were both located on chromosome 4 and their peaks were within the same confidence interval. A QTL for plasma luteinizing hormone concentration was also found in the confidence interval of these two QTL. These results suggest that the physiological mechanisms underlying degree of laterality react to gonadal steroids. PMID:12663540

  13. Quantitative analysis on electric dipole energy in Rashba band splitting

    PubMed Central

    Hong, Jisook; Rhim, Jun-Won; Kim, Changyoung; Ryong Park, Seung; Hoon Shim, Ji

    2015-01-01

    We report on quantitative comparison between the electric dipole energy and the Rashba band splitting in model systems of Bi and Sb triangular monolayers under a perpendicular electric field. We used both first-principles and tight binding calculations on p-orbitals with spin-orbit coupling. First-principles calculation shows Rashba band splitting in both systems. It also shows asymmetric charge distributions in the Rashba split bands which are induced by the orbital angular momentum. We calculated the electric dipole energies from coupling of the asymmetric charge distribution and external electric field, and compared it to the Rashba splitting. Remarkably, the total split energy is found to come mostly from the difference in the electric dipole energy for both Bi and Sb systems. A perturbative approach for long wave length limit starting from tight binding calculation also supports that the Rashba band splitting originates mostly from the electric dipole energy difference in the strong atomic spin-orbit coupling regime. PMID:26323493

  14. Space-to-Ground Communication for Columbus: A Quantitative Analysis.

    PubMed

    Uhlig, Thomas; Mannel, Thurid; Fortunato, Antonio; Illmer, Norbert

    2015-01-01

    The astronauts on board the International Space Station (ISS) are only the most visible part of a much larger team engaged around the clock in the performance of science and technical activities in space. The bulk of such team is scattered around the globe in five major Mission Control Centers (MCCs), as well as in a number of smaller payload operations centres. Communication between the crew in space and the flight controllers at those locations is an essential element and one of the key drivers to efficient space operations. Such communication can be carried out in different forms, depending on available technical assets and the selected operational approach for the activity at hand. This paper focuses on operational voice communication and provides a quantitative overview of the balance achieved in the Columbus program between collaborative space/ground operations and autonomous on-board activity execution. An interpretation of the current situation is provided, together with a description of potential future approaches for deep space exploration missions. PMID:26290898

  15. Quantitative Analysis of Synaptic Release at the Photoreceptor Synapse

    PubMed Central

    Duncan, Gabriel; Rabl, Katalin; Gemp, Ian; Heidelberger, Ruth; Thoreson, Wallace B.

    2010-01-01

    Abstract Exocytosis from the rod photoreceptor is stimulated by submicromolar Ca2+ and exhibits an unusually shallow dependence on presynaptic Ca2+. To provide a quantitative description of the photoreceptor Ca2+ sensor for exocytosis, we tested a family of conventional and allosteric computational models describing the final Ca2+-binding steps leading to exocytosis. Simulations were fit to two measures of release, evoked by flash-photolysis of caged Ca2+: exocytotic capacitance changes from individual rods and postsynaptic currents of second-order neurons. The best simulations supported the occupancy of only two Ca2+ binding sites on the rod Ca2+ sensor rather than the typical four or five. For most models, the on-rates for Ca2+ binding and maximal fusion rate were comparable to those of other neurons. However, the off-rates for Ca2+ unbinding were unexpectedly slow. In addition to contributing to the high-affinity of the photoreceptor Ca2+ sensor, slow Ca2+ unbinding may support the fusion of vesicles located at a distance from Ca2+ channels. In addition, partial sensor occupancy due to slow unbinding may contribute to the linearization of the first synapse in vision. PMID:20483317

  16. Neuropeptidomics: Mass spectrometry-based qualitative and quantitative analysis

    PubMed Central

    Yin, Ping; Hou, Xiaowen; Romanova, Elena V.; Sweedler, Jonathan V.

    2013-01-01

    Neuropeptidomics refers to a global characterization approach for the investigation of neuropeptides, often under specific physiological conditions. Neuropeptides comprise a complex set of signaling molecules that are involved in regulatory functions and behavioral control in the nervous system. Neuropeptidomics is inherently challenging because neuropeptides are spatially, temporally and chemically heterogeneous, making them difficult to predict in silico from genomic information. Mature neuropeptides are produced from intricate enzymatic processing of precursor proteins/prohormones via a range of post-translational modifications, resulting in multiple final peptide products from each prohormone gene. Although there are several methods for targeted peptide studies, mass spectrometry (MS), with its qualitative and quantitative capabilities, is ideally suited to the task. MS provides fast, sensitive, accurate, and high-throughput peptidomic analyses of neuropeptides without requiring prior knowledge of the peptide sequences. Aided by liquid chromatography (LC) separations and bioinformatics, MS is quickly becoming a leading technique in neuropeptidomics. This chapter describes several LC-MS analytical methods to identify, characterize and quantify neuropeptides, while emphasizing the sample preparation steps so integral to experimental success. PMID:21922411

  17. Space-to-Ground Communication for Columbus: A Quantitative Analysis

    PubMed Central

    Uhlig, Thomas; Mannel, Thurid; Fortunato, Antonio; Illmer, Norbert

    2015-01-01

    The astronauts on board the International Space Station (ISS) are only the most visible part of a much larger team engaged around the clock in the performance of science and technical activities in space. The bulk of such team is scattered around the globe in five major Mission Control Centers (MCCs), as well as in a number of smaller payload operations centres. Communication between the crew in space and the flight controllers at those locations is an essential element and one of the key drivers to efficient space operations. Such communication can be carried out in different forms, depending on available technical assets and the selected operational approach for the activity at hand. This paper focuses on operational voice communication and provides a quantitative overview of the balance achieved in the Columbus program between collaborative space/ground operations and autonomous on-board activity execution. An interpretation of the current situation is provided, together with a description of potential future approaches for deep space exploration missions. PMID:26290898

  18. Quantitative MRI analysis of salivary glands in sickle cell disease

    PubMed Central

    Liao, J; Saito, N; Ozonoff, A; Jara, H; Steinberg, M; Sakai, O

    2012-01-01

    Objectives The purpose of this prospective study was to characterize the MR relaxometric features of the major salivary glands in patients with sickle cell disease (SCD). Methods 15 patients with SCD (aged 19.8–43.6 years) and 12 controls were imaged with the mixed turbo-spin echo pulse sequence. The major salivary glands were manually segmented and T1, T2 and secular T2 relaxometry histograms were modelled with Gaussian functions. Results Shortened T1 relaxation times were seen solely in the submandibular glands of patients with SCD (747.5 ± 54.8 ms vs 807.1 ± 38.3 ms, p < 0.001). Slight T2 and secular T2 shortening were seen in the parotid gland; however, this difference was not significant (p = 0.07). The sublingual gland showed no changes under MR relaxometry. There was no difference in glandular volumes, and no correlation was demonstrated between history of blood transfusion and salivary gland relaxometry. Conclusions Patients with SCD exhibited changes in quantitative MRI T1 relaxometry histograms of the submandibular glands. PMID:23166360

  19. Quantitative textural analysis of ilmenite in Apollo 17 high-titanium mare basalts

    E-print Network

    Quantitative textural analysis of ilmenite in Apollo 17 high-titanium mare basalts Patrick H in the investigation of basalt crystallization. We present the first compre- hensive crystal size distribution analysis of Apollo 17 high-titanium lunar basalts, with a focus on ilmenite. Crystal size distributions of ilmenite

  20. Quantitative analysis of gene expression in living adult neural stem cells by gene trapping

    E-print Network

    Cai, Long

    , processes such as differentiation are controlled by tightly regulated genes that are only expressed analysis of gene expression, making the system less affected by background fluorescence and cell density14Quantitative analysis of gene expression in living adult neural stem cells by gene trapping John R

  1. Kinetic Analysis of Amylase Using Quantitative Benedict's and Iodine Starch Reagents

    ERIC Educational Resources Information Center

    Cochran, Beverly; Lunday, Deborah; Miskevich, Frank

    2008-01-01

    Quantitative analysis of carbohydrates is a fundamental analytical tool used in many aspects of biology and chemistry. We have adapted a technique developed by Mathews et al. using an inexpensive scanner and open-source image analysis software to quantify amylase activity using both the breakdown of starch and the appearance of glucose. Breakdown…

  2. A Quantitative Content Analysis of Mercer University MEd, EdS, and Doctoral Theses

    ERIC Educational Resources Information Center

    Randolph, Justus J.; Gaiek, Lura S.; White, Torian A.; Slappey, Lisa A.; Chastain, Andrea; Harris, Rose Prejean

    2010-01-01

    Quantitative content analysis of a body of research not only helps budding researchers understand the culture, language, and expectations of scholarship, it helps identify deficiencies and inform policy and practice. Because of these benefits, an analysis of a census of 980 Mercer University MEd, EdS, and doctoral theses was conducted. Each thesis…

  3. A QUANTITATIVE ANALYSIS OF MIXED-TO-PURE PIXEL CONVERSION (MPCV)

    E-print Network

    Chang, Chein-I

    9 A QUANTITATIVE ANALYSIS OF MIXED-TO-PURE PIXEL CONVERSION (MPCV) Over the past years many a standardized HYDICE data set with custom-designed detection and classification criteria. The algorithms analysis (LDA). In order to compare mixed pixel classification (MPC) algorithms against pure pixel

  4. A Quantitative Analysis of the Extrinsic and Intrinsic Turnover Factors of Relational Database Support Professionals

    ERIC Educational Resources Information Center

    Takusi, Gabriel Samuto

    2010-01-01

    This quantitative analysis explored the intrinsic and extrinsic turnover factors of relational database support specialists. Two hundred and nine relational database support specialists were surveyed for this research. The research was conducted based on Hackman and Oldham's (1980) Job Diagnostic Survey. Regression analysis and a univariate ANOVA…

  5. Quantitative proteomics analysis of adsorbed plasma proteins classifies nanoparticles with different surface properties and size

    SciTech Connect

    Zhang, Haizhen; Burnum, Kristin E.; Luna, Maria L.; Petritis, Brianne O.; Kim, Jong Seo; Qian, Weijun; Moore, Ronald J.; Heredia-Langner, Alejandro; Webb-Robertson, Bobbie-Jo M.; Thrall, Brian D.; Camp, David G.; Smith, Richard D.; Pounds, Joel G.; Liu, Tao

    2011-12-01

    In biofluids (e.g., blood plasma) nanoparticles are readily embedded in layers of proteins that can affect their biological activity and biocompatibility. Herein, we report a study on the interactions between human plasma proteins and nanoparticles with a controlled systematic variation of properties using stable isotope labeling and liquid chromatography-mass spectrometry (LC-MS) based quantitative proteomics. Novel protocol has been developed to simplify the isolation of nanoparticle bound proteins and improve the reproducibility. Plasma proteins associated with polystyrene nanoparticles with three different surface chemistries and two sizes as well as for four different exposure times (for a total of 24 different samples) were identified and quantified by LC-MS analysis. Quantitative comparison of relative protein abundances were achieved by spiking an 18 O-labeled 'universal reference' into each individually processed unlabeled sample as an internal standard, enabling simultaneous application of both label-free and isotopic labeling quantitation across the sample set. Clustering analysis of the quantitative proteomics data resulted in distinctive pattern that classifies the nanoparticles based on their surface properties and size. In addition, data on the temporal study indicated that the stable protein 'corona' that was isolated for the quantitative analysis appeared to be formed in less than 5 minutes. The comprehensive results obtained herein using quantitative proteomics have potential implications towards predicting nanoparticle biocompatibility.

  6. [Study on the multivariate quantitative analysis method for steel alloy elements using LIBS].

    PubMed

    Gu, Yan-hong; Li, Ying; Tian, Ye; Lu, Yuan

    2014-08-01

    Quantitative analysis of steel alloys was carried out using laser induced breakdown spectroscopy (LIBS) taking into account the complex matrix effects in steel alloy samples. The laser induced plasma was generated by a Q-switched Nd:YAG laser operating at 1064 nm with pulse width of 10 ns and repeated frequency of 10 Hz. The LIBS signal was coupled to the echelle spectrometer and recorded by a high sensitive ICCD detector. To get the best experimental conditions, some parameters, such as the detection delay, the CCDs integral gate width and the detecting position from the sample surface, were optimized. The experimental results showed that the optimum detection delay time was 1.5 micros, the optimal CCDs integral gate width was 2 micros and the best detecting position was 1.5 mm below the alloy sample's surface. The samples used in the experiments are ten standard steel alloy samples and two unknown steel alloy samples. The quantitative analysis was investigated with the optimum experimental parameters. Elements Cr and Ni in steel alloy samples were taken as the detection targets. The analysis was carried out with the methods based on conditional univariate quantitative analysis, multiple linear regression and partial least squares (PLS) respectively. It turned out that the correlation coefficients of calibration curves are not very high in the conditional univariate calibration method. The analysis results were obtained with the unsatisfied relative errors for the two predicted samples. So the con- ditional univariate quantitative analysis method can't effectively serve the quantitative analysis purpose for multi-components and complex matrix steel alloy samples. And with multiple linear regression method, the analysis accuracy was improved effectively. The method based on partial least squares (PLS) turned out to be the best method among all the three quantitative analysis methods applied. Based on PLS, the correlation coefficient of calibration curve for Cr is 0.981 and that for Ni is 0.995. The concentrations of Cr and Ni in two target samples were determined using PLS calibration method, and the relative errors for the two unknown steel alloy samples are lower than 6.62% and 1.49% respectively. The obtained results showed that in the quantitative analysis of steel alloys, the matrix effect would be reduced effectively and the quantitative analysis accuracy would be improved by the PLS calibration method. PMID:25508749

  7. [Study on the multivariate quantitative analysis method for steel alloy elements using LIBS].

    PubMed

    Gu, Yan-hong; Li, Ying; Tian, Ye; Lu, Yuan

    2014-08-01

    Quantitative analysis of steel alloys was carried out using laser induced breakdown spectroscopy (LIBS) taking into account the complex matrix effects in steel alloy samples. The laser induced plasma was generated by a Q-switched Nd:YAG laser operating at 1064 nm with pulse width of 10 ns and repeated frequency of 10 Hz. The LIBS signal was coupled to the echelle spectrometer and recorded by a high sensitive ICCD detector. To get the best experimental conditions, some parameters, such as the detection delay, the CCDs integral gate width and the detecting position from the sample surface, were optimized. The experimental results showed that the optimum detection delay time was 1.5 micros, the optimal CCDs integral gate width was 2 micros and the best detecting position was 1.5 mm below the alloy sample's surface. The samples used in the experiments are ten standard steel alloy samples and two unknown steel alloy samples. The quantitative analysis was investigated with the optimum experimental parameters. Elements Cr and Ni in steel alloy samples were taken as the detection targets. The analysis was carried out with the methods based on conditional univariate quantitative analysis, multiple linear regression and partial least squares (PLS) respectively. It turned out that the correlation coefficients of calibration curves are not very high in the conditional univariate calibration method. The analysis results were obtained with the unsatisfied relative errors for the two predicted samples. So the con- ditional univariate quantitative analysis method can't effectively serve the quantitative analysis purpose for multi-components and complex matrix steel alloy samples. And with multiple linear regression method, the analysis accuracy was improved effectively. The method based on partial least squares (PLS) turned out to be the best method among all the three quantitative analysis methods applied. Based on PLS, the correlation coefficient of calibration curve for Cr is 0.981 and that for Ni is 0.995. The concentrations of Cr and Ni in two target samples were determined using PLS calibration method, and the relative errors for the two unknown steel alloy samples are lower than 6.62% and 1.49% respectively. The obtained results showed that in the quantitative analysis of steel alloys, the matrix effect would be reduced effectively and the quantitative analysis accuracy would be improved by the PLS calibration method. PMID:25474970

  8. Quantitative assessment of human motion using video motion analysis

    NASA Technical Reports Server (NTRS)

    Probe, John D.

    1993-01-01

    In the study of the dynamics and kinematics of the human body a wide variety of technologies has been developed. Photogrammetric techniques are well documented and are known to provide reliable positional data from recorded images. Often these techniques are used in conjunction with cinematography and videography for analysis of planar motion, and to a lesser degree three-dimensional motion. Cinematography has been the most widely used medium for movement analysis. Excessive operating costs and the lag time required for film development, coupled with recent advances in video technology, have allowed video based motion analysis systems to emerge as a cost effective method of collecting and analyzing human movement. The Anthropometric and Biomechanics Lab at Johnson Space Center utilizes the video based Ariel Performance Analysis System (APAS) to develop data on shirtsleeved and space-suited human performance in order to plan efficient on-orbit intravehicular and extravehicular activities. APAS is a fully integrated system of hardware and software for biomechanics and the analysis of human performance and generalized motion measurement. Major components of the complete system include the video system, the AT compatible computer, and the proprietary software.

  9. Quantitative histology analysis of the ovarian tumour microenvironment

    PubMed Central

    Lan, Chunyan; Heindl, Andreas; Huang, Xin; Xi, Shaoyan; Banerjee, Susana; Liu, Jihong; Yuan, Yinyin

    2015-01-01

    Concerted efforts in genomic studies examining RNA transcription and DNA methylation patterns have revealed profound insights in prognostic ovarian cancer subtypes. On the other hand, abundant histology slides have been generated to date, yet their uses remain very limited and largely qualitative. Our goal is to develop automated histology analysis as an alternative subtyping technology for ovarian cancer that is cost-efficient and does not rely on DNA quality. We developed an automated system for scoring primary tumour sections of 91 late-stage ovarian cancer to identify single cells. We demonstrated high accuracy of our system based on expert pathologists’ scores (cancer?=?97.1%, stromal?=?89.1%) as well as compared to immunohistochemistry scoring (correlation?=?0.87). The percentage of stromal cells in all cells is significantly associated with poor overall survival after controlling for clinical parameters including debulking status and age (multivariate analysis p?=?0.0021, HR?=?2.54, CI?=?1.40–4.60) and progression-free survival (multivariate analysis p?=?0.022, HR?=?1.75, CI?=?1.09–2.82). We demonstrate how automated image analysis enables objective quantification of microenvironmental composition of ovarian tumours. Our analysis reveals a strong effect of the tumour microenvironment on ovarian cancer progression and highlights the potential of therapeutic interventions that target the stromal compartment or cancer-stroma signalling in the stroma-high, late-stage ovarian cancer subset. PMID:26573438

  10. Quantitative histology analysis of the ovarian tumour microenvironment.

    PubMed

    Lan, Chunyan; Heindl, Andreas; Huang, Xin; Xi, Shaoyan; Banerjee, Susana; Liu, Jihong; Yuan, Yinyin

    2015-01-01

    Concerted efforts in genomic studies examining RNA transcription and DNA methylation patterns have revealed profound insights in prognostic ovarian cancer subtypes. On the other hand, abundant histology slides have been generated to date, yet their uses remain very limited and largely qualitative. Our goal is to develop automated histology analysis as an alternative subtyping technology for ovarian cancer that is cost-efficient and does not rely on DNA quality. We developed an automated system for scoring primary tumour sections of 91 late-stage ovarian cancer to identify single cells. We demonstrated high accuracy of our system based on expert pathologists' scores (cancer?=?97.1%, stromal?=?89.1%) as well as compared to immunohistochemistry scoring (correlation?=?0.87). The percentage of stromal cells in all cells is significantly associated with poor overall survival after controlling for clinical parameters including debulking status and age (multivariate analysis p?=?0.0021, HR?=?2.54, CI?=?1.40-4.60) and progression-free survival (multivariate analysis p?=?0.022, HR?=?1.75, CI?=?1.09-2.82). We demonstrate how automated image analysis enables objective quantification of microenvironmental composition of ovarian tumours. Our analysis reveals a strong effect of the tumour microenvironment on ovarian cancer progression and highlights the potential of therapeutic interventions that target the stromal compartment or cancer-stroma signalling in the stroma-high, late-stage ovarian cancer subset. PMID:26573438

  11. Automated quantitative analysis of ventilation-perfusion lung scintigrams

    SciTech Connect

    Burton, G.H.; Vernon, P.; Seed, W.A.

    1984-05-01

    An automated computer analysis of ventilation (Kr-81m) and perfusion (Tc-99m) lung images has been devised that produces a graphical image of the distribution of ventilation and perfusion, and of ventilation-perfusion ratios. The analysis has overcome the following problems: the identification of the midline between two lungs and the lung boundaries, the exclusion of extrapulmonary radioactivity, the superimposition of lung images of different sizes, and the format for presentation of the data. Therefore, lung images of different sizes and shapes may be compared with each other. The analysis has been used to develop normal ranges from 55 volunteers. Comparison of younger and older age groups of men and women show small but significant differences in the distribution of ventilation and perfusion, but no differences in ventilation-perfusion ratios.

  12. 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.

  13. Epilepsy surgery failure in children: a quantitative and qualitative analysis

    PubMed Central

    Englot, Dario J.; Han, Seunggu J.; Rolston, John D.; Ivan, Michael E.; Kuperman, Rachel A.; Chang, Edward F.; Gupta, Nalin; Sullivan, Joseph E.; Auguste, Kurtis I.

    2015-01-01

    Object Resection is a safe and effective treatment option for children with pharmacoresistant focal epilepsy, but some patients continue experience seizures after surgery. While most studies of pediatric epilepsy surgery focus on predictors of postoperative seizure outcome, these factors are often not modifiable, and the reasons for surgical failure may remain unclear. Methods The authors performed a retrospective cohort study of children and adolescents who received focal resective surgery for pharmacoresistant epilepsy. Both quantitative and qualitative analyses of factors associated with persistent postoperative seizures were conducted. Results Records were reviewed from 110 patients, ranging in age from 6 months to 19 years at the time of surgery, who underwent a total of 115 resections. At a mean 3.1-year follow-up, 76% of patients were free of disabling seizures (Engel Class I outcome). Seizure freedom was predicted by temporal lobe surgery compared with extra-temporal resection, tumor or mesial temporal sclerosis compared with cortical dysplasia or other pathologies, and by a lower preoperative seizure frequency. Factors associated with persistent seizures (Engel Class II–IV outcome) included residual epileptogenic tissue adjacent to the resection cavity (40%), an additional epileptogenic zone distant from the resection cavity (32%), and the presence of a hemispheric epilepsy syndrome (28%). Conclusions While seizure outcomes in pediatric epilepsy surgery may be improved by the use of high-resolution neuroimaging and invasive electrographic studies, a more aggressive resection should be considered in certain patients, including hemispherectomy if a hemispheric epilepsy syndrome is suspected. Family counseling regarding treatment expectations is critical, and reoperation may be warranted in select cases. PMID:25127098

  14. Quantitative analysis of wrist electrodermal activity during sleep.

    PubMed

    Sano, Akane; Picard, Rosalind W; Stickgold, Robert

    2014-12-01

    We present the first quantitative characterization of electrodermal activity (EDA) patterns on the wrists of healthy adults during sleep using dry electrodes. We compare the new results on the wrist to the prior findings on palmar or finger EDA by characterizing data measured from 80 nights of sleep consisting of 9 nights of wrist and palm EDA from 9 healthy adults sleeping at home, 56 nights of wrist and palm EDA from one healthy adult sleeping at home, and 15 nights of wrist EDA from 15 healthy adults in a sleep laboratory, with the latter compared to concurrent polysomnography. While high frequency patterns of EDA called "storms" were identified by eye in the 1960s, we systematically compare thresholds for automatically detecting EDA peaks and establish criteria for EDA storms. We found that more than 80% of the EDA peaks occurred in non-REM sleep, specifically during slow-wave sleep (SWS) and non-REM stage 2 sleep (NREM2). Also, EDA amplitude is higher in SWS than in other sleep stages. Longer EDA storms were more likely to occur in the first two quarters of sleep and during SWS and NREM2. We also found from the home studies (65 nights) that EDA levels were higher and the skin conductance peaks were larger and more frequent when measured on the wrist than when measured on the palm. These EDA high frequency peaks and high amplitude were sometimes associated with higher skin temperature, but more work is needed looking at neurological and other EDA elicitors in order to elucidate their complete behavior. PMID:25286449

  15. Regression Commonality Analysis: A Technique for Quantitative Theory Building

    ERIC Educational Resources Information Center

    Nimon, Kim; Reio, Thomas G., Jr.

    2011-01-01

    When it comes to multiple linear regression analysis (MLR), it is common for social and behavioral science researchers to rely predominately on beta weights when evaluating how predictors contribute to a regression model. Presenting an underutilized statistical technique, this article describes how organizational researchers can use commonality…

  16. Reflectance spectroscopy: quantitative analysis techniques for remote sensing applications.

    USGS Publications Warehouse

    Clark, R.N.; Roush, T.L.

    1984-01-01

    Several methods for the analysis of remotely sensed reflectance data are compared, including empirical methods and scattering theories, both of which are important for solving remote sensing problems. The concept of the photon mean path length and the implications for use in modeling reflectance spectra are presented.-from Authors

  17. Label-Free Quantitative Proteomics and N-terminal Analysis of Human Metastatic Lung Cancer Cells

    PubMed Central

    Min, Hophil; Han, Dohyun; Kim, Yikwon; Cho, Jee Yeon; Jin, Jonghwa; Kim, Youngsoo

    2014-01-01

    Proteomic analysis is helpful in identifying cancer-associated proteins that are differentially expressed and fragmented that can be annotated as dysregulated networks and pathways during metastasis. To examine meta-static process in lung cancer, we performed a proteomics study by label-free quantitative analysis and N-terminal analysis in 2 human non-small-cell lung cancer cell lines with disparate metastatic potentials—NCI-H1703 (primary cell, stage I) and NCI-H1755 (metastatic cell, stage IV). We identified 2130 proteins, 1355 of which were common to both cell lines. In the label-free quantitative analysis, we used the NSAF normalization method, resulting in 242 differential expressed proteins. For the N-terminal proteome analysis, 325 N-terminal peptides, including 45 novel fragments, were identified in the 2 cell lines. Based on two proteomic analysis, 11 quantitatively expressed proteins and 8 N-terminal peptides were enriched for the focal adhesion pathway. Most proteins from the quantitative analysis were upregulated in metastatic cancer cells, whereas novel fragment of CRKL was detected only in primary cancer cells. This study increases our understanding of the NSCLC metastasis proteome. PMID:24805778

  18. Building No. 905, showing typical aqua medias or rain hoods ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Building No. 905, showing typical aqua medias or rain hoods - Presidio of San Francisco, Enlisted Men's Barracks Type, West end of Crissy Field, between Pearce & Maudlin Streets, San Francisco, San Francisco County, CA

  19. Jmfrvrden frn provfisken Aqua reports 2013:18

    E-print Network

    Vattenmyndigheten Framsida: Magnus Kokkin lägger nät i Pahajärvi. Foto: Anders Kinnerbäck. Baksida: Röding från Njalakjaure. Foto: Magnus Kokkin. #12;Aqua reports 2013:18 Sammanfattning Rapporten består av jämförelsevärden

  20. Rdingen i Rostujvri Aqua reports 2013:14

    E-print Network

    Författarna Framsida: Rostujávri. Foto: Johan Hammar. Baksida: Ron B. Greer (t.v.) och Olof Idivuoma (t.h.) ogillar de ekologiska förändringarna i Rostujávri. Foto: Johan Hammar. #12;Aqua reports 2013:14 Förord Det

  1. Calibration Adjustments to the MODIS Aqua Ocean Color Bands

    NASA Technical Reports Server (NTRS)

    Meister, Gerhard

    2012-01-01

    After the end of the SeaWiFS mission in 2010 and the MERIS mission in 2012, the ocean color products of the MODIS on Aqua are the only remaining source to continue the ocean color climate data record until the VIIRS ocean color products become operational (expected for summer 2013). The MODIS on Aqua is well beyond its expected lifetime, and the calibration accuracy of the short wavelengths (412nm and 443nm) has deteriorated in recent years_ Initially, SeaWiFS data were used to improve the MODIS Aqua calibration, but this solution was not applicable after the end of the SeaWiFS mission_ In 2012, a new calibration methodology was applied by the MODIS calibration and support team using desert sites to improve the degradation trending_ This presentation presents further improvements to this new approach. The 2012 reprocessing of the MODIS Aqua ocean color products is based on the new methodology.

  2. Aqua satellite orbiting the Earth - Duration: 116 seconds.

    NASA Video Gallery

    This animation shows the Aqua satellite orbiting the Earth on August 27, 2005 by revealing MODIS true-color imagery for that day. This animation is on a cartesian map projection, so the satellite w...

  3. Enabling Quantitative Analysis in Ambient Ionization Mass Spectrometry: Internal Standard Coated Capillary Samplers

    PubMed Central

    Liu, Jiangjiang; Cooks, R. Graham; Ouyang, Zheng

    2013-01-01

    We describe a sampling method using glass capillaries for quantitative analysis of trace analytes in small volumes of complex mixtures (~1 ?L) using ambient ionization mass spectrometry. The internal surface of a sampling glass capillary was coated with internal standard then used to draw liquid sample and so transfer both the analyte and internal standard in a single fixed volume onto a substrate for analysis. The internal standard was automatically mixed into the sample during this process and the volumes of the internal standard solution and sample are both fixed by the capillary volume. Precision in quantitation is insensitive to variations in length of the capillary, making the preparation of the sampling capillary simple and providing a robust sampling protocol. Significant improvements in quantitation accuracy were obtained for analysis of 1 ?L samples using various ambient ionization methods. PMID:23731380

  4. Quantitative land cover change analysis using fuzzy segmentation

    NASA Astrophysics Data System (ADS)

    Lizarazo, Ivan

    2012-04-01

    Fuzzy image segmentation was proposed recently as an alternative GEOBIA method for conducting discrete land cover classification. In this paper, a variant of fuzzy segmentation is applied for continuous land cover change analysis. The method comprises two main stages: (i) estimation of compositional land cover for each data by fuzzy segmentation; and (ii) change analysis using a fuzzy change matrix. The fuzzy segmentation stage outputs fuzzy-crisp and crisp-fuzzy image regions whose spectral and geometric properties are measured to populate the set of predictors used to estimate land cover at single dates. The variant of fuzzy image segmentation is implemented using advanced machine learning techniques and tested in a rapidly urbanizing area using Landsat multi-spectral imagery. Experimental results suggest that the method produces accurate characterization of continuous land cover classes. Thus, the proposed method is potentially useful for enhancing the current GEOBIA perspective which focuses mainly on discrete land cover classifications.

  5. Integrated quantitative fractal polarimetric analysis of monolayer lung cancer cells

    NASA Astrophysics Data System (ADS)

    Shrestha, Suman; Zhang, Lin; Quang, Tri; Farrahi, Tannaz; Narayan, Chaya; Deshpande, Aditi; Na, Ying; Blinzler, Adam; Ma, Junyu; Liu, Bo; Giakos, George C.

    2014-05-01

    Digital diagnostic pathology has become one of the most valuable and convenient advancements in technology over the past years. It allows us to acquire, store and analyze pathological information from the images of histological and immunohistochemical glass slides which are scanned to create digital slides. In this study, efficient fractal, wavelet-based polarimetric techniques for histological analysis of monolayer lung cancer cells will be introduced and different monolayer cancer lines will be studied. The outcome of this study indicates that application of fractal, wavelet polarimetric principles towards the analysis of squamous carcinoma and adenocarcinoma cancer cell lines may be proved extremely useful in discriminating among healthy and lung cancer cells as well as differentiating among different lung cancer cells.

  6. Quantitative liquid chromatographic analysis of anthracyclines in biological fluids.

    PubMed

    Maudens, Kristof E; Stove, Christophe P; Lambert, Willy E

    2011-09-01

    Anthracyclines are amongst the most widely used drugs in oncology, being part of the treatment regimen in most patients receiving systemic chemotherapy. This review provides a comprehensive summary of the sample preparation techniques and chromatographic methods that have been developed during the last two decades for the analysis of the 4 most administered anthracyclines, doxorubicin, epirubicin, daunorubicin and idarubicin in plasma, serum, saliva or urine, within the context of clinical and pharmacokinetic studies or for assessing occupational exposure. Following deproteinization, liquid-liquid extraction, solid phase extraction or a combination of these techniques, the vast majority of methods utilizes reversed-phase C18 stationary phases for liquid chromatographic separation, followed by fluorescence detection, or, more recently, tandem mass spectrometric detection. Some pros and cons of the different techniques are addressed, in addition to potential pitfalls that may be encountered in the analysis of this class of compounds. PMID:21840776

  7. Quantitative analysis of structural neuroimaging of mesial temporal lobe epilepsy

    PubMed Central

    Memarian, Negar; Thompson, Paul M; Engel, Jerome; Staba, Richard J

    2013-01-01

    Mesial temporal lobe epilepsy (MTLE) is the most common of the surgically remediable drug-resistant epilepsies. MRI is the primary diagnostic tool to detect anatomical abnormalities and, when combined with EEG, can more accurately identify an epileptogenic lesion, which is often hippocampal sclerosis in cases of MTLE. As structural imaging technology has advanced the surgical treatment of MTLE and other lesional epilepsies, so too have the analysis techniques that are used to measure different structural attributes of the brain. These techniques, which are reviewed here and have been used chiefly in basic research of epilepsy and in studies of MTLE, have identified different types and the extent of anatomical abnormalities that can extend beyond the affected hippocampus. These results suggest that structural imaging and sophisticated imaging analysis could provide important information to identify networks capable of generating spontaneous seizures and ultimately help guide surgical therapy that improves postsurgical seizure-freedom outcomes. PMID:24319498

  8. Quantitative Analysis of PMLA Nanoconjugate Components after Backbone Cleavage

    PubMed Central

    Ding, Hui; Patil, Rameshwar; Portilla-Arias, Jose; Black, Keith L.; Ljubimova, Julia Y.; Holler, Eggehard

    2015-01-01

    Multifunctional polymer nanoconjugates containing multiple components show great promise in cancer therapy, but in most cases complete analysis of each component is difficult. Polymalic acid (PMLA) based nanoconjugates have demonstrated successful brain and breast cancer treatment. They consist of multiple components including targeting antibodies, Morpholino antisense oligonucleotides (AONs), and endosome escape moieties. The component analysis of PMLA nanoconjugates is extremely difficult using conventional spectrometry and HPLC method. Taking advantage of the nature of polyester of PMLA, which can be cleaved by ammonium hydroxide, we describe a method to analyze the content of antibody and AON within nanoconjugates simultaneously using SEC-HPLC by selectively cleaving the PMLA backbone. The selected cleavage conditions only degrade PMLA without affecting the integrity and biological activity of the antibody. Although the amount of antibody could also be determined using the bicinchoninic acid (BCA) method, our selective cleavage method gives more reliable results and is more powerful. Our approach provides a new direction for the component analysis of polymer nanoconjugates and nanoparticles. PMID:25894227

  9. Quantitative analysis of calcium spikes in noisy fluorescent background.

    PubMed

    Janicek, Radoslav; Hotka, Matej; Zahradníková, Alexandra; Zahradníková, Alexandra; Zahradník, Ivan

    2013-01-01

    Intracellular calcium signals are studied by laser-scanning confocal fluorescence microscopy. The required spatio-temporal resolution makes description of calcium signals difficult because of the low signal-to-noise ratio. We designed a new procedure of calcium spike analysis based on their fitting with a model. The accuracy and precision of calcium spike description were tested on synthetic datasets generated either with randomly varied spike parameters and Gaussian noise of constant amplitude, or with constant spike parameters and Gaussian noise of various amplitudes. Statistical analysis was used to evaluate the performance of spike fitting algorithms. The procedure was optimized for reliable estimation of calcium spike parameters and for dismissal of false events. A new algorithm was introduced that corrects the acquisition time of pixels in line-scan images that is in error due to sequential acquisition of individual pixels along the space coordinate. New software was developed in Matlab and provided for general use. It allows interactive dissection of temporal profiles of calcium spikes from x-t images, their fitting with predefined function(s) and acceptance of results on statistical grounds, thus allowing efficient analysis and reliable description of calcium signaling in cardiac myocytes down to the in situ function of ryanodine receptors. PMID:23741324

  10. 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

  11. Segmentation of vascular structures and hematopoietic cells in 3D microscopy images and quantitative analysis

    NASA Astrophysics Data System (ADS)

    Mu, Jian; Yang, Lin; Kamocka, Malgorzata M.; Zollman, Amy L.; Carlesso, Nadia; Chen, Danny Z.

    2015-03-01

    In this paper, we present image processing methods for quantitative study of how the bone marrow microenvironment changes (characterized by altered vascular structure and hematopoietic cell distribution) caused by diseases or various factors. We develop algorithms that automatically segment vascular structures and hematopoietic cells in 3-D microscopy images, perform quantitative analysis of the properties of the segmented vascular structures and cells, and examine how such properties change. In processing images, we apply local thresholding to segment vessels, and add post-processing steps to deal with imaging artifacts. We propose an improved watershed algorithm that relies on both intensity and shape information and can separate multiple overlapping cells better than common watershed methods. We then quantitatively compute various features of the vascular structures and hematopoietic cells, such as the branches and sizes of vessels and the distribution of cells. In analyzing vascular properties, we provide algorithms for pruning fake vessel segments and branches based on vessel skeletons. Our algorithms can segment vascular structures and hematopoietic cells with good quality. We use our methods to quantitatively examine the changes in the bone marrow microenvironment caused by the deletion of Notch pathway. Our quantitative analysis reveals property changes in samples with deleted Notch pathway. Our tool is useful for biologists to quantitatively measure changes in the bone marrow microenvironment, for developing possible therapeutic strategies to help the bone marrow microenvironment recovery.

  12. Quantitative analysis of mouse corpus callosum from electron microscopy images

    PubMed Central

    West, Kathryn L.; Kelm, Nathaniel D.; Carson, Robert P.; Does, Mark D.

    2015-01-01

    This article provides morphometric analysis of 72 electron microscopy images from control (n=4) and hypomyelinated (n=2) mouse corpus callosum. Measures of axon diameter and g-ratio were tabulated across all brains from two regions of the corpus callosum and a non-linear relationship between axon diameter and g-ratio was observed. These data are related to the accompanying research article comparing multiple methods of measuring g-ratio entitled ‘A revised model for estimating g-ratio from MRI’ (West et al., NeuroImage, 2015). PMID:26504893

  13. Quantitative analysis of mouse corpus callosum from electron microscopy images.

    PubMed

    West, Kathryn L; Kelm, Nathaniel D; Carson, Robert P; Does, Mark D

    2015-12-01

    This article provides morphometric analysis of 72 electron microscopy images from control (n=4) and hypomyelinated (n=2) mouse corpus callosum. Measures of axon diameter and g-ratio were tabulated across all brains from two regions of the corpus callosum and a non-linear relationship between axon diameter and g-ratio was observed. These data are related to the accompanying research article comparing multiple methods of measuring g-ratio entitled 'A revised model for estimating g-ratio from MRI' (West et al., NeuroImage, 2015). PMID:26504893

  14. Some remarks on the quantitative analysis of behavior

    PubMed Central

    Marr, M. Jackson

    1989-01-01

    This paper discusses similarities between the mathematization of operant behavior and the early history of the most mathematical of sciences—physics. Galileo explored the properties of motion without dealing with the causes of motion, focusing on changes in motion. Newton's dynamics were concerned with the action of forces as causes of change. Skinner's rationale for using rate to describe behavior derived from an interest in changes in rate. Reinforcement has played the role of force in the dynamics of behavior. Behavioral momentum and maximization have received mathematical formulations in behavior analysis. Yet to be worked out are the relations between molar and molecular formulations of behavioral theory. PMID:22478028

  15. Identifying severity of electroporation through quantitative image analysis

    NASA Astrophysics Data System (ADS)

    Morshed, Bashir I.; Shams, Maitham; Mussivand, Tofy

    2011-04-01

    Electroporation is the formation of reversible hydrophilic pores in the cell membrane under electric fields. Severity of electroporation is challenging to measure and quantify. An image analysis method is developed, and the initial results with a fabricated microfluidic device are reported. The microfluidic device contains integrated microchannels and coplanar interdigitated electrodes allowing low-voltage operation and low-power consumption. Noninvasive human buccal cell samples were specifically stained, and electroporation was induced. Captured image sequences were analyzed for pixel color ranges to quantify the severity of electroporation. The method can detect even a minor occurrence of electroporation and can perform comparative studies.

  16. Quantitative Analysis of Guanine Nucleotide Exchange Factors (GEFs) as Enzymes

    PubMed Central

    Randazzo, Paul A; Jian, Xiaoying; Chen, Pei-Wen; Zhai, Peng; Soubias, Olivier; Northup, John K

    2014-01-01

    The proteins that possess guanine nucleotide exchange factor (GEF) activity, which include about ~800 G protein coupled receptors (GPCRs),1 15 Arf GEFs,2 81 Rho GEFs,3 8 Ras GEFs,4 and others for other families of GTPases,5 catalyze the exchange of GTP for GDP on all regulatory guanine nucleotide binding proteins. Despite their importance as catalysts, relatively few exchange factors (we are aware of only eight for ras superfamily members) have been rigorously characterized kinetically.5–13 In some cases, kinetic analysis has been simplistic leading to erroneous conclusions about mechanism (as discussed in a recent review14). In this paper, we compare two approaches for determining the kinetic properties of exchange factors: (i) examining individual equilibria, and; (ii) analyzing the exchange factors as enzymes. Each approach, when thoughtfully used,14,15 provides important mechanistic information about the exchange factors. The analysis as enzymes is described in further detail. With the focus on the production of the biologically relevant guanine nucleotide binding protein complexed with GTP (G•GTP), we believe it is conceptually simpler to connect the kinetic properties to cellular effects. Further, the experiments are often more tractable than those used to analyze the equilibrium system and, therefore, more widely accessible to scientists interested in the function of exchange factors. PMID:25332840

  17. 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).

  18. 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.

  19. Quantitative real-time single particle analysis of virions

    PubMed Central

    Heider, Susanne; Metzner, Christoph

    2014-01-01

    Providing information about single virus particles has for a long time been mainly the domain of electron microscopy. More recently, technologies have been developed—or adapted from other fields, such as nanotechnology—to allow for the real-time quantification of physical virion particles, while supplying additional information such as particle diameter concomitantly. These technologies have progressed to the stage of commercialization increasing the speed of viral titer measurements from hours to minutes, thus providing a significant advantage for many aspects of virology research and biotechnology applications. Additional advantages lie in the broad spectrum of virus species that may be measured and the possibility to determine the ratio of infectious to total particles. A series of disadvantages remain associated with these technologies, such as a low specificity for viral particles. In this review we will discuss these technologies by comparing four systems for real-time single virus particle analysis and quantification. PMID:24999044

  20. Quantitative analysis of the debonding structure of soft adhesives

    E-print Network

    François Tanguy; Matteo Nicoli; Anke Lindner; Costantino Creton

    2013-05-03

    We experimentally investigate the growth dynamics of cavities nucleating during the first stages of debonding of three different model adhesives. The material properties of these adhesives range from a more liquid-like material to a soft viscoelastic solid and are carefully characterized by small strain oscillatory shear rheology as well as large strain uniaxial extension. The debonding experiments are performed on a probe tack set-up. Using high contrast images of the debonding process and precise image analysis tools we quantify the total projected area of the cavities, the average cavity shape and growth rate and link these observations to the material properties. These measurements are then used to access corrected effective stress and strain curves that can be directly compared to the results from the uniaxial extension.

  1. Quantitative radiographic analysis of fiber reinforced polymer composites.

    PubMed

    Baidya, K P; Ramakrishna, S; Rahman, M; Ritchie, A

    2001-01-01

    X-ray radiographic examination of the bone fracture healing process is a widely used method in the treatment and management of patients. Medical devices made of metallic alloys reportedly produce considerable artifacts that make the interpretation of radiographs difficult. Fiber reinforced polymer composite materials have been proposed to replace metallic alloys in certain medical devices because of their radiolucency, light weight, and tailorable mechanical properties. The primary objective of this paper is to provide a comparable radiographic analysis of different fiber reinforced polymer composites that are considered suitable for biomedical applications. Composite materials investigated consist of glass, aramid (Kevlar-29), and carbon reinforcement fibers, and epoxy and polyether-ether-ketone (PEEK) matrices. The total mass attenuation coefficient of each material was measured using clinical X-rays (50 kev). The carbon fiber reinforced composites were found to be more radiolucent than the glass and kevlar fiber reinforced composites. PMID:11261603

  2. Automated monitoring and quantitative analysis of feeding behaviour in Drosophila

    PubMed Central

    Itskov, Pavel M.; Moreira, José-Maria; Vinnik, Ekaterina; Lopes, Gonçalo; Safarik, Steve; Dickinson, Michael H.; Ribeiro, Carlos

    2014-01-01

    Food ingestion is one of the defining behaviours of all animals, but its quantification and analysis remain challenging. This is especially the case for feeding behaviour in small, genetically tractable animals such as Drosophila melanogaster. Here, we present a method based on capacitive measurements, which allows the detailed, automated and high-throughput quantification of feeding behaviour. Using this method, we were able to measure the volume ingested in single sips of an individual, and monitor the absorption of food with high temporal resolution. We demonstrate that flies ingest food by rhythmically extending their proboscis with a frequency that is not modulated by the internal state of the animal. Instead, hunger and satiety homeostatically modulate the microstructure of feeding. These results highlight similarities of food intake regulation between insects, rodents, and humans, pointing to a common strategy in how the nervous systems of different animals control food intake. PMID:25087594

  3. Quantitative Analysis of Spectral Impacts on Silicon Photodiode Radiometers: Preprint

    SciTech Connect

    Myers, D. R.

    2011-04-01

    Inexpensive broadband pyranometers with silicon photodiode detectors have a non-uniform spectral response over the spectral range of 300-1100 nm. The response region includes only about 70% to 75% of the total energy in the terrestrial solar spectral distribution from 300 nm to 4000 nm. The solar spectrum constantly changes with solar position and atmospheric conditions. Relative spectral distributions of diffuse hemispherical irradiance sky radiation and total global hemispherical irradiance are drastically different. This analysis convolves a typical photodiode response with SMARTS 2.9.5 spectral model spectra for different sites and atmospheric conditions. Differences in solar component spectra lead to differences on the order of 2% in global hemispherical and 5% or more in diffuse hemispherical irradiances from silicon radiometers. The result is that errors of more than 7% can occur in the computation of direct normal irradiance from global hemispherical irradiance and diffuse hemispherical irradiance using these radiometers.

  4. Quantitative space-bandwidth product analysis in digital holography.

    PubMed

    Claus, Daniel; Iliescu, Daciana; Bryanston-Cross, Peter

    2011-12-01

    The space-bandwidth product (SBP) is a measure for the information capacity an optical system possesses. The two information processing steps in digital holography, recording, and reconstruction are analyzed with respect to the SBP. The recording setups for a Fresnel hologram, Fourier hologram, and image-plane hologram, which represent the most commonly used setup configurations in digital holography, are investigated. For the recording process, the required SBP to ensure the recording of the entire object information is calculated. This is accomplished by analyzing the recorded interference pattern in the hologram-plane. The paraxial diffraction model is used in order to simulate the light propagation from the object to hologram-plane. The SBP in the reconstruction process is represented by the product of the reconstructed field-of-view and spatial frequency bandwidth. The outcome of this analysis results in the best SBP adapted digital holographic setup. PMID:22192996

  5. Quantitative Analysis of Genealogy Using Digitised Family Trees

    E-print Network

    Fire, Micheal; Elovici, Yuval

    2014-01-01

    Driven by the popularity of television shows such as Who Do You Think You Are? many millions of users have uploaded their family tree to web projects such as WikiTree. Analysis of this corpus enables us to investigate genealogy computationally. The study of heritage in the social sciences has led to an increased understanding of ancestry and descent but such efforts are hampered by difficult to access data. Genealogical research is typically a tedious process involving trawling through sources such as birth and death certificates, wills, letters and land deeds. Decades of research have developed and examined hypotheses on population sex ratios, marriage trends, fertility, lifespan, and the frequency of twins and triplets. These can now be tested on vast datasets containing many billions of entries using machine learning tools. Here we survey the use of genealogy data mining using family trees dating back centuries and featuring profiles on nearly 7 million individuals based in over 160 countries. These data a...

  6. Analysis of mixed cell cultures with quantitative digital holographic phase microscopy

    NASA Astrophysics Data System (ADS)

    Kemper, Björn; Wibbeling, Jana; Ketelhut, Steffi

    2014-05-01

    In order to study, for example, the influence of pharmaceuticals or pathogens on different cell types under identical measurement conditions and to analyze interactions between different cellular specimens a minimally-invasive quantitative observation of mixed cell cultures is of particular interest. Quantitative phase microscopy (QPM) provides high resolution detection of optical path length changes that is suitable for stain-free minimally-invasive live cell analysis. Due to low light intensities for object illumination, QPM minimizes the interaction with the sample and is in particular suitable for long term time-lapse investigations, e.g., for the detection of cell morphology alterations due to drugs and toxins. Furthermore, QPM has been demonstrated to be a versatile tool for the quantification of cellular growth, the extraction morphological parameters and cell motility. We studied the feasibility of QPM for the analysis of mixed cell cultures. It was explored if quantitative phase images provide sufficient information to distinguish between different cell types and to extract cell specific parameters. For the experiments quantitative phase imaging with digital holographic microscopy (DHM) was utilized. Mixed cell cultures with different types of human pancreatic tumor cells were observed with quantitative DHM phase contrast up to 35 h. The obtained series of quantitative phase images were evaluated by adapted algorithms for image segmentation. From the segmented images the cellular dry mass and the mean cell thickness were calculated and used in the further analysis as parameters to quantify the reliability the measurement principle. The obtained results demonstrate that it is possible to characterize the growth of cell types with different morphologies in a mixed cell culture separately by consideration of specimen size and cell thickness in the evaluation of quantitative DHM phase images.

  7. Scalp Surgery: Quantitative Analysis of Follicular Unit Growth

    PubMed Central

    Caruana, Giorgia

    2015-01-01

    Background: Over the years, different kinds of hair transplantation have been compared in an attempt to overcome male pattern alopecia and, at the same time, maximize both the survival and growth rate of grafted hair. In this study, we have assessed the survival and growth rate of follicular units (FU) in an in vitro model, as compared with that of conventional hair micrografts, to experimentally evaluate and elaborate on the differences between these 2 approaches in hair transplantation procedures. Methods: Group A (control; n = 100 follicles) was composed of hair micrografts, whereas FUs were assigned to Group B (experimental; n = 100 follicles, n = 35 FUs). Each group was cultured for a period of 10 days; the total stretch of follicles was measured soon after the harvest and 10 days later. The Kruskal-Wallis one-way analysis of variance on ranks test was used to perform statistical analysis. Results: The growth rate of follicles from Group A (mean 10-day shaft growth rate = 0.30 mm) proved to be statistically different compared with that of Group B (mean 10-day shaft growth rate = 0.23 mm). Conversely, our data did not show any significant difference between the survival rate of hair grafts from these 2 groups. Conclusions: Our data highlighted a reduced FU shaft growth compared with that of hair micrografts, corroborating, to a certain extent, the hypothesis that a significant amount of adipose tissue surrounding the follicle included in the graft may result in an inadequate nourishment supply to follicular cells. PMID:26579345

  8. Quantitative proteomic analysis of the brainstem following lethal sarin exposure.

    PubMed

    Meade, Mitchell L; Hoffmann, Andrea; Makley, Meghan K; Snider, Thomas H; Schlager, John J; Gearhart, Jeffery M

    2015-06-22

    The brainstem represents a major tissue area affected by sarin organophosphate poisoning due to its function in respiratory and cardiovascular control. While the acute toxic effects of sarin on brainstem-related responses are relatively unknown, other brain areas e.g., cortex or cerebellum, have been studied more extensively. The study objective was to analyze the guinea pig brainstem toxicology response following sarin (2×LD50) exposure by proteome pathway analysis to gain insight into the complex regulatory mechanisms that lead to impairment of respiratory and cardiovascular control. Guinea pig exposure to sarin resulted in the typical acute behavior/physiology outcomes with death between 15 and 25min. In addition, brain and blood acetylcholinesterase activity was significantly reduced in the presence of sarin to 95%, and 89%, respectively, of control values. Isobaric-tagged (iTRAQ) liquid chromatography tandem mass spectrometry (LC-MS/MS) identified 198 total proteins of which 23% were upregulated, and 18% were downregulated following sarin exposure. Direct gene ontology (GO) analysis revealed a sarin-specific broad-spectrum proteomic profile including glutamate-mediated excitotoxicity, calcium overload, energy depletion responses, and compensatory carbohydrate metabolism, increases in ROS defense, DNA damage and chromatin remodeling, HSP response, targeted protein degradation (ubiquitination) and cell death response. With regards to the sarin-dependent effect on respiration, our study supports the potential interference of sarin with CO2/H(+) sensitive chemoreceptor neurons of the brainstem retrotrapezoid nucleus (RTN) that send excitatory glutamergic projections to the respiratory centers. In conclusion, this study gives insight into the brainstem broad-spectrum proteome following acute sarin exposure and the gained information will assist in the development of novel countermeasures. PMID:25842371

  9. Analysis of 129I in Groundwater Samples: Direct and Quantitative Results below the Drinking Water Standard

    SciTech Connect

    Brown, Christopher F.; Geiszler, Keith N.; Lindberg, Michael J.

    2007-03-03

    Due to its long half-life (15.7 million years) and relatively unencumbered migration in subsurface environments, 129I has been recognized as a contaminant of concern at numerous federal, private, and international facilities. In order to understand the long-term risk associated with 129I at these locations, quantitative analysis of groundwater samples must be performed. However, the ability to quantitatively assess the 129I content in groundwater samples requires specialized extraction and sophisticated analytical techniques, which are complicated and not always available to the general scientific community. This paper highlights an analytical method capable of directly quantifying 129I in groundwater samples at concentrations below the MCL without the need for sample pre-concentration. Samples were analyzed on a Perkin Elmer ELAN DRC II ICP-MS after minimal dilution using O2 as the reaction gas. Analysis of continuing calibration verification standards indicated that the DRC mode could be used for quantitative analysis of 129I in samples below the drinking water standard (0.0057 ng/ml or 1 pCi/L). The low analytical detection limit of 129I analysis in the DRC mode coupled with minimal sample dilution (1.02x) resulted in a final sample limit of quantification of 0.0051 ng/ml. Subsequent analysis of three groundwater samples containing 129I resulted in fully quantitative results in the DRC mode, and spike recovery analyses performed on all three samples confirmed that the groundwater matrix did not adversely impact the analysis of 129I in the DRC mode. This analytical approach has been proven to be a cost-effective, high-throughput technique for the direct, quantitative analysis of 129I in groundwater samples at concentrations below the current MCL.

  10. Quantitative interferometric microscopic flow cytometer with expanded principal component analysis method

    NASA Astrophysics Data System (ADS)

    Wang, Shouyu; Jin, Ying; Yan, Keding; Xue, Liang; Liu, Fei; Li, Zhenhua

    2014-11-01

    Quantitative interferometric microscopy is used in biological and medical fields and a wealth of applications are proposed in order to detect different kinds of biological samples. Here, we develop a phase detecting cytometer based on quantitative interferometric microscopy with expanded principal component analysis phase retrieval method to obtain phase distributions of red blood cells with a spatial resolution ~1.5 ?m. Since expanded principal component analysis method is a time-domain phase retrieval algorithm, it could avoid disadvantages of traditional frequency-domain algorithms. Additionally, the phase retrieval method realizes high-speed phase imaging from multiple microscopic interferograms captured by CCD camera when the biological cells are scanned in the field of view. We believe this method can be a powerful tool to quantitatively measure the phase distributions of different biological samples in biological and medical fields.

  11. Machine learning methods for quantitative analysis of Raman spectroscopy data

    NASA Astrophysics Data System (ADS)

    Madden, Michael G.; Ryder, Alan G.

    2003-03-01

    The automated identification and quantification of illicit materials using Raman spectroscopy is of significant importance for law enforcement agencies. This paper explores the use of Machine Learning (ML) methods in comparison with standard statistical regression techniques for developing automated identification methods. In this work, the ML task is broken into two sub-tasks, data reduction and prediction. In well-conditioned data, the number of samples should be much larger than the number of attributes per sample, to limit the degrees of freedom in predictive models. In this spectroscopy data, the opposite is normally true. Predictive models based on such data have a high number of degrees of freedom, which increases the risk of models over-fitting to the sample data and having poor predictive power. In the work described here, an approach to data reduction based on Genetic Algorithms is described. For the prediction sub-task, the objective is to estimate the concentration of a component in a mixture, based on its Raman spectrum and the known concentrations of previously seen mixtures. Here, Neural Networks and k-Nearest Neighbours are used for prediction. Preliminary results are presented for the problem of estimating the concentration of cocaine in solid mixtures, and compared with previously published results in which statistical analysis of the same dataset was performed. Finally, this paper demonstrates how more accurate results may be achieved by using an ensemble of prediction techniques.

  12. Interlake production established using quantitative hydrocarbon well-log analysis

    SciTech Connect

    Lancaster, J.; Atkinson, A.

    1988-07-01

    Production was established in a new pay zone of the basal Interlake Formation adjacent to production in Midway field in Williams County, North Dakota. Hydrocarbon saturation, which was computed using hydrocarbon well-log (mud-log) data, and computed permeability encouraged the operator to run casing and test this zone. By use of drilling rig parameters, drilling mud properties, hydrocarbon-show data from the mud log, drilled rock and porosity descriptions, and wireline log porosity, this new technique computes oil saturation (percent of porosity) and permeability to the invading filtrate, using the Darcy equation. The Leonardo Fee well was drilled to test the Devonian Duperow, the Silurian upper Interlake, and the Ordovician Red River. The upper two objectives were penetrated downdip from Midway production and there were no hydrocarbon shows. It was determined that the Red River was tight, based on sample examination by well site personnel. The basal Interlake, however, liberated hydrocarbon shows that were analyzed by this new technology. The results of this evaluation accurately predicted this well would be a commercial success when placed in production. Where geophysical log analysis might be questionable, this new evaluation technique may provide answers to anticipated oil saturation and producibility. The encouraging results of hydrocarbon saturation and permeability, produced by this technique, may be largely responsible for the well being in production today.

  13. Quantitative safety analysis using fracture mechanics and ultrasonic stress measurements

    NASA Astrophysics Data System (ADS)

    Clark, Al V.; Anderson, Ted L.; Lozev, Margarit G.; Fuchs, P. A.

    1996-11-01

    Fracture mechanics can be applied to assess the safety of cracked bridge members. If crack length and stresses are known, the crack driving force (stress intensity factor, K) can be calculated. K was calculated for hot-rolled beams, as a function of crack length. K eventually becomes negative, indicating not further crack propagation. However a cracked girder will become compliant and 'shed' load to uncracked neighboring members. Our calculations show that the changes in both compliance and load-carrying capacity of the cracked girder are small until the girder is deeply cracked. A finite-element analysis of a cracked girder showed that by determining the bending stresses at about one beam depth from the crack it is possible to determine K. Measurement of these stresses was simulated in a field test. The method used small changes in sound speed to determine stress. The ultrasonic transducers used required no couplants and no surface preparation. They were also used to measure stresses in an integral backwall bridge.

  14. Segmentation and learning in the quantitative analysis of microscopy images

    NASA Astrophysics Data System (ADS)

    Ruggiero, Christy; Ross, Amy; Porter, Reid

    2015-02-01

    In material science and bio-medical domains the quantity and quality of microscopy images is rapidly increasing and there is a great need to automatically detect, delineate and quantify particles, grains, cells, neurons and other functional "objects" within these images. These are challenging problems for image processing because of the variability in object appearance that inevitably arises in real world image acquisition and analysis. One of the most promising (and practical) ways to address these challenges is interactive image segmentation. These algorithms are designed to incorporate input from a human operator to tailor the segmentation method to the image at hand. Interactive image segmentation is now a key tool in a wide range of applications in microscopy and elsewhere. Historically, interactive image segmentation algorithms have tailored segmentation on an image-by-image basis, and information derived from operator input is not transferred between images. But recently there has been increasing interest to use machine learning in segmentation to provide interactive tools that accumulate and learn from the operator input over longer periods of time. These new learning algorithms reduce the need for operator input over time, and can potentially provide a more dynamic balance between customization and automation for different applications. This paper reviews the state of the art in this area, provides a unified view of these algorithms, and compares the segmentation performance of various design choices.

  15. Direct Quantitative Analysis of Arsenic in Coal Fly Ash

    PubMed Central

    Hartuti, Sri; Kambara, Shinji; Takeyama, Akihiro; Kumabe, Kazuhiro; Moritomi, Hiroshi

    2012-01-01

    A rapid, simple method based on graphite furnace atomic absorption spectrometry is described for the direct determination of arsenic in coal fly ash. Solid samples were directly introduced into the atomizer without preliminary treatment. The direct analysis method was not always free of spectral matrix interference, but the stabilization of arsenic by adding palladium nitrate (chemical modifier) and the optimization of the parameters in the furnace program (temperature, rate of temperature increase, hold time, and argon gas flow) gave good results for the total arsenic determination. The optimal furnace program was determined by analyzing different concentrations of a reference material (NIST1633b), which showed the best linearity for calibration. The optimized parameters for the furnace programs for the ashing and atomization steps were as follows: temperatures of 500–1200 and 2150°C, heating rates of 100 and 500°C?s?1, hold times of 90 and 7?s, and medium then maximum and medium argon gas flows, respectively. The calibration plots were linear with a correlation coefficient of 0.9699. This method was validated using arsenic-containing raw coal samples in accordance with the requirements of the mass balance calculation; the distribution rate of As in the fly ashes ranged from 101 to 119%. PMID:23251836

  16. Quantitative Analysis with Heavy Ion E-TOF ERD

    SciTech Connect

    Banks, J.C.; Doyle, B.L.; Font, A. Climent

    1999-07-23

    Heavy ion TOF ERD combined with energy detection (E-TOF-ERD) is a powerful analytical technique taking advantage of the following facts: the scattering cross section is usually very high ({approximately}10{sup {minus}21} cm{sup 2}/sr) compared to regular He RBS ({approximately}10{sup {minus}25} cm{sup 2}/sr), contrary to what happens with the energy resolution in ordinary surface solid barrier detectors, time resolution is almost independent of the atomic mass of the detected element, and the detection in coincidence of time and energy signals allows for the mass separation of overlapping signals with the same energy (or time of flight). Measurements on several oxides have been performed with the E-TOF-ERD set up at Sandia National Laboratories using an incident beam of 10-15 MeV Au. The information on the composition of the sample is obtained from the time domain spectrum, which is converted to energy domain, and then, using existing software codes, the analysis is performed. During the quantification of the results, they have found problems related to the interaction of the beam with the sample and to the tabulated values of the stopping powers for heavy ions.

  17. Quantitative analysis of American woodcock nest and brood habitat

    USGS Publications Warehouse

    Bourgeois, A.

    1977-01-01

    Sixteen nest and 19 brood sites of American woodcock (Philohela minoI) were examined in northern lower Michigan between 15 April and 15 June 1974 to determine habitat structure associated with these sites. Woodcock hens utilized young, second-growth forest stands which were similar in species composition for both nesting and brood rearing. A multi-varIate discriminant function analysis revealed a significant (P< 0.05) difference, however, in habitat structure. Nest habitat was characterized by lower tree density (2176 trees/ha) and basal area (8.6 m2/ha), by being close to forest openings (7 m) and by being situated on dry, relatively well drained sites. In contrast, woodcock broods were located in sites that had nearly twice the tree density (3934 trees/hal and basal area (16.5 m2/ha), was located over twice as far from forest openings (18 m) and generally occurred on damp sites, near (8 m) standing water. Importance of the habitat features to the species and possible management implications are discussed.

  18. Quantitative analysis of the microscale of auxetic foams

    NASA Astrophysics Data System (ADS)

    Gaspar, N.; Smith, C. W.; Miller, E. A.; Seidler, G. T.; Evans, K. E.

    2005-03-01

    The auxetic foams first produced by Lakes have been modelled in a variety of ways, each model trying to reproduce some observed feature of the microscale of the foams. Such features include bent or broken ribs or inverted angles between ribs. These models can reproduce the Poisson's ratio or Poisson's function of auxetic foam if the model parameters are carefully chosen. However these model parameters may not actually reflect the internal structure of the foams. A big problem is that measurement of parameters such as lengths and angles is not straightforward within a 3-d sample. In this work a sample of auxetic foam has been imaged by 3-d X-ray computed tomography. The resulting image is translated to a form that emphasises the geometrical structure of connected ribs. This connected rib data are suitably analysed to describe both the microstructural construction of auxetic foams and the statistical spread of structure, that is, the heterogeneity of an auxetic foam. From the analysis of the microstructure, observations are made about the requirements for microstructural models and comparisons made to previous existing models. From the statistical data, measures of heterogeneity are made that will help with future modelling that includes the heterogeneous aspect of auxetic foams.

  19. Quantitative ultrasound texture analysis for clinical decision making support

    NASA Astrophysics Data System (ADS)

    Wu, Jie Ying; Beland, Michael; Konrad, Joseph; Tuomi, Adam; Glidden, David; Grand, David; Merck, Derek

    2015-03-01

    We propose a general ultrasound (US) texture-analysis and machine-learning framework for detecting the presence of disease that is suitable for clinical application across clinicians, disease types, devices, and operators. Its stages are image selection, image filtering, ROI selection, feature parameterization, and classification. Each stage is modular and can be replaced with alternate methods. Thus, this framework is adaptable to a wide range of tasks. Our two preliminary clinical targets are hepatic steatosis and adenomyosis diagnosis. For steatosis, we collected US images from 288 patients and their pathology-determined values of steatosis (%) from biopsies. Two radiologists independently reviewed all images and identified the region of interest (ROI) most representative of the hepatic echotexture for each patient. To parameterize the images into comparable quantities, we filter the US images at multiple scales for various texture responses. For each response, we collect a histogram of pixel features within the ROI, and parameterize it as a Gaussian function using its mean, standard deviation, kurtosis, and skew to create a 36-feature vector. Our algorithm uses a support vector machine (SVM) for classification. Using a threshold of 10%, we achieved 72.81% overall accuracy, 76.18% sensitivity, and 65.96% specificity in identifying steatosis with leave-ten-out cross-validation (p<0.0001). Extending this framework to adenomyosis, we identified 38 patients with MR-confirmed findings of adenomyosis and previous US studies and 50 controls. A single rater picked the best US-image and ROI for each case. Using the same processing pipeline, we obtained 76.14% accuracy, 86.00% sensitivity, and 63.16% specificity with leave-one-out cross-validation (p<0.0001).

  20. Quantitative flux analysis reveals folate-dependent NADPH production

    NASA Astrophysics Data System (ADS)

    Fan, Jing; Ye, Jiangbin; Kamphorst, Jurre J.; Shlomi, Tomer; Thompson, Craig B.; Rabinowitz, Joshua D.

    2014-06-01

    ATP is the dominant energy source in animals for mechanical and electrical work (for example, muscle contraction or neuronal firing). For chemical work, there is an equally important role for NADPH, which powers redox defence and reductive biosynthesis. The most direct route to produce NADPH from glucose is the oxidative pentose phosphate pathway, with malic enzyme sometimes also important. Although the relative contribution of glycolysis and oxidative phosphorylation to ATP production has been extensively analysed, similar analysis of NADPH metabolism has been lacking. Here we demonstrate the ability to directly track, by liquid chromatography-mass spectrometry, the passage of deuterium from labelled substrates into NADPH, and combine this approach with carbon labelling and mathematical modelling to measure NADPH fluxes. In proliferating cells, the largest contributor to cytosolic NADPH is the oxidative pentose phosphate pathway. Surprisingly, a nearly comparable contribution comes from serine-driven one-carbon metabolism, in which oxidation of methylene tetrahydrofolate to 10-formyl-tetrahydrofolate is coupled to reduction of NADP+ to NADPH. Moreover, tracing of mitochondrial one-carbon metabolism revealed complete oxidation of 10-formyl-tetrahydrofolate to make NADPH. As folate metabolism has not previously been considered an NADPH producer, confirmation of its functional significance was undertaken through knockdown of methylenetetrahydrofolate dehydrogenase (MTHFD) genes. Depletion of either the cytosolic or mitochondrial MTHFD isozyme resulted in decreased cellular NADPH/NADP+ and reduced/oxidized glutathione ratios (GSH/GSSG) and increased cell sensitivity to oxidative stress. Thus, although the importance of folate metabolism for proliferating cells has been long recognized and attributed to its function of producing one-carbon units for nucleic acid synthesis, another crucial function of this pathway is generating reducing power.

  1. Synthesis of quantitative and qualitative evidence for accident analysis in risk-based highway planning.

    PubMed

    Lambert, James H; Peterson, Kenneth D; Joshi, Nilesh N

    2006-09-01

    Accident analysis involves the use of both quantitative and qualitative data in decision-making. The aim of this paper is to demonstrate the synthesis of relevant quantitative and qualitative evidence for accident analysis and for planning a large and diverse portfolio of highway investment projects. The proposed analysis and visualization techniques along with traditional mathematical modeling serve as an aid to planners, engineers, and the public in comparing the benefits of current and proposed improvement projects. The analysis uses data on crash rates, average daily traffic, cost estimates from highway agency databases, and project portfolios for regions and localities. It also utilizes up to two motivations out of seven that are outlined in the Transportation Equity Act for the 21st Century (TEA-21). Three case studies demonstrate the risk-based approach to accident analysis for short- and long-range transportation plans. The approach is adaptable to other topics in accident analysis and prevention that involve the use of quantitative and qualitative evidence, risk analysis, and multi-criteria decision-making for project portfolio selection. PMID:16730627

  2. Whose American Government? A Quantitative Analysis of Gender and Authorship in American Politics Texts

    ERIC Educational Resources Information Center

    Cassese, Erin C.; Bos, Angela L.; Schneider, Monica C.

    2014-01-01

    American government textbooks signal to students the kinds of topics that are important and, by omission, the kinds of topics that are not important to the discipline of political science. This article examines portrayals of women in introductory American politics textbooks through a quantitative content analysis of 22 widely used texts. We find…

  3. Lemon-aid: using Lemon to aid quantitative historical linguistic analysis Steven Moran

    E-print Network

    Lemon-aid: using Lemon to aid quantitative historical linguistic analysis Steven Moran University the lexical data into an RDF model that is specified by Lemon. The resulting new Linked Data re- source, what specified in Lemon (McCrae et al., 2010; McCrae et al., 2011). The resulting resource allows users to query

  4. Dynamic ordering of nuclei in syncytial embryos: a quantitative analysis of the role of cytoskeletal networks

    E-print Network

    Schwarz, Ulrich

    Dynamic ordering of nuclei in syncytial embryos: a quantitative analysis of the role) before and after mitosis 13. Note that the plots for the individual embryos are not adjusted according to anaphase. SI2. Centrosomes organise the cytoskeletal networks. (A-C) Fluorescence images of a fixed embryo

  5. Journal of Quantitative Analysis in Volume 6, Issue 3 2010 Article 8

    E-print Network

    Jensen, Shane T.

    pitchers may have some ability to prevent hits on balls in play, the effect is small. And any ef- fectJournal of Quantitative Analysis in Sports Volume 6, Issue 3 2010 Article 8 A Point-Mass Mixture Random Effects Model for Pitching Metrics James Piette Alexander Braunstein Blakeley B. McShane Shane T

  6. Journal of Quantitative Analysis in Volume 3, Issue 3 2007 Article 2

    E-print Network

    Jensen, Shane T.

    Journal of Quantitative Analysis in Sports Volume 3, Issue 3 2007 Article 2 Evaluating Throwing of unsuccessful events. In addition, there is a more subtle effect of throwing ability that is not captured, 2007) but does not consider the influence of outfield ball-in-play location on these events. Research

  7. QUANTITATIVE PCR ANALYSIS OF MOLDS IN THE DUST FROM HOMES OF ASTHMATIC CHILDREN IN NORTH CAROLINA

    EPA Science Inventory

    The vacuum bag (VB) dust was analyzed by mold specific quantitative PCR. These results were compared to the analysis survey calculated for each of the homes. The mean and standard deviation (SD) of the ERMI values in the homes of the NC asthmatic children was 16.4 (6.77), compa...

  8. Quantitative Analysis of Sexual Dimorphism and Sex Ratio in Hyphydrus ovatus (Coleoptera: Dytiscidae)

    E-print Network

    Juliano, Steven A.

    : Dytiscidae) Steven A. Juliano Ecography, Vol. 15, No. 3. (Jul. - Sep., 1992), pp. 308-313. Stable URL: http dimorphism and sex ratio in Hyphydrus ovatus (Coleoptera:Dytiscidae) Steven A. Juliano Juliano, S. A. 1992. Quantitative analysis of sexual dimorphism and sex ratio in Hyphydrus ovatus (Coleoptera: Dytiscidae

  9. Universal Drag Tag for Direct Quantitative Analysis of Multiple David W. Wegman,

    E-print Network

    Krylov, Sergey

    Universal Drag Tag for Direct Quantitative Analysis of Multiple MicroRNAs David W. Wegman, Leonid T drag tags are built into the probes to introduce significant differential mobility between their respective hybrids. For the method to be practical it requires a universal extendable drag tag. Polymers

  10. Kinetic Analysis and Modeling of Firefly Luciferase as a Quantitative Reporter Gene

    E-print Network

    Kinetic Analysis and Modeling of Firefly Luciferase as a Quantitative Reporter Gene in Live.interscience.wiley.com). DOI: 10.1002/bit.20059 Abstract: Firefly luciferase has proven to be a highly sensitive effective metric of gene expression and cell behavior. B 2004 Wiley Periodicals, Inc. Keywords: firefly

  11. A Quantitative Discourse Analysis of Student-Initiated Checks of Understanding during Teacher-Fronted Lessons

    ERIC Educational Resources Information Center

    Shepherd, Michael A.

    2012-01-01

    Recent research highlights the paradoxical importance of students' being able to check their understanding with teachers and of teachers' constraining student participation. Using quantitative discourse analysis, this paper examines third graders' discursive strategies in initiating such checks and teachers' strategies in constraining them. The…

  12. Quantitative and Qualitative Analysis of Nutrition and Food Safety Information in School Science Textbooks of India

    ERIC Educational Resources Information Center

    Subba Rao, G. M.; Vijayapushapm, T.; Venkaiah, K.; Pavarala, V.

    2012-01-01

    Objective: To assess quantity and quality of nutrition and food safety information in science textbooks prescribed by the Central Board of Secondary Education (CBSE), India for grades I through X. Design: Content analysis. Methods: A coding scheme was developed for quantitative and qualitative analyses. Two investigators independently coded the…

  13. Quantitative analysis of sulfur functional groups in natural organic matter by XANES spectroscopy

    E-print Network

    Quantitative analysis of sulfur functional groups in natural organic matter by XANES spectroscopy sulfur functionalities in natural organic matter from S K-edge XANES spectroscopy are presented-induced errors, inherent to the choice of a particular curve, are typically lower than 5% of total sulfur

  14. Quantitative Analysis of Organic Compounds: A Simple and Rapid Method for Use in Schools

    ERIC Educational Resources Information Center

    Schmidt, Hans-Jurgen

    1973-01-01

    Describes the procedure for making a quantitative analysis of organic compounds suitable for secondary school chemistry classes. Using the Schoniger procedure, the organic compound, such as PVC, is decomposed in a conical flask with oxygen. The products are absorbed in a suitable liquid and analyzed by titration. (JR)

  15. Quantitative Intersectionality: A Critical Race Analysis of the Chicana/o Educational Pipeline

    ERIC Educational Resources Information Center

    Covarrubias, Alejandro

    2011-01-01

    Utilizing the critical race framework of intersectionality, this research reexamines the Chicana/o educational pipeline through a quantitative intersectional analysis. This approach disaggregates data along the intersection of race, class, gender, and citizenship status to provide a detailed portrait of the educational trajectory of Mexican-origin…

  16. Quantitative Analysis of Peristaltic and Segmental Motion In Vivo in the Rat Small Intestine Using Dynamic

    E-print Network

    Brasseur, James G.

    Quantitative Analysis of Peristaltic and Segmental Motion In Vivo in the Rat Small Intestine Using of nutrients that takes place within the small intestine. The normal processes of the small intestine are known been used extensively to study segments of the intestine that have been exteriorized from animals

  17. A Quantitative Features Analysis of Recommended No- and Low-Cost Preschool E-Books

    ERIC Educational Resources Information Center

    Parette, Howard P.; Blum, Craig; Luthin, Katie

    2015-01-01

    In recent years, recommended e-books have drawn increasing attention from early childhood education professionals. This study applied a quantitative descriptive features analysis of cost (n = 70) and no-cost (n = 60) e-books recommended by the Texas Computer Education Association. While t tests revealed no statistically significant differences…

  18. A Quantitative Analysis of Cognitive Strategy Usage in the Marking of Two GCSE Examinations

    ERIC Educational Resources Information Center

    Suto, W. M. Irenka; Greatorex, Jackie

    2008-01-01

    Diverse strategies for marking GCSE examinations have been identified, ranging from simple automatic judgements to complex cognitive operations requiring considerable expertise. However, little is known about patterns of strategy usage or how such information could be utilised by examiners. We conducted a quantitative analysis of previous verbal…

  19. Qualitative and quantitative analysis of mixtures of compounds containing both hydrogen and deuterium

    NASA Technical Reports Server (NTRS)

    Crespi, H. L.; Harkness, L.; Katz, J. J.; Norman, G.; Saur, W.

    1969-01-01

    Method allows qualitative and quantitative analysis of mixtures of partially deuterated compounds. Nuclear magnetic resonance spectroscopy determines location and amount of deuterium in organic compounds but not fully deuterated compounds. Mass spectroscopy can detect fully deuterated species but not the location.

  20. Clinical applications of a quantitative analysis of regional lift ventricular wall motion

    NASA Technical Reports Server (NTRS)

    Leighton, R. F.; Rich, J. M.; Pollack, M. E.; Altieri, P. I.

    1975-01-01

    Observations were summarized which may have clinical application. These were obtained from a quantitative analysis of wall motion that was used to detect both hypokinesis and tardokinesis in left ventricular cineangiograms. The method was based on statistical comparisons with normal values for regional wall motion derived from the cineangiograms of patients who were found not to have heart disease.

  1. PointTracked Quantitative Analysis of Left Ventricular Motion from 3D Image Sequences

    E-print Network

    Duncan, James S.

    in overestimation of true myocardial infarction. More sophisticated quantitative analysis of myocardial dynamics may of the remodeling process following myocardial infarction as it relates to the extent of myocardial injury motion parameters (path length and thickness changes) in detecting myocardial injury is tested

  2. Quantitative analysis of the eective inter-enzyme connectivity in glycolysis

    E-print Network

    Cortes, Jesus

    Quantitative analysis of the eective inter-enzyme connectivity in glycolysis Jesus M. Cortes1 Granada. Spain. E-mail: mtpmadei@ehu.es 4. Corresponding author Keywords: Glycolysis; Inter-Enzyme of glucose, the activity of enzymes can display either periodic, quasi-periodic or chaotic behavior. By means

  3. A Colorimetric Analysis Experiment Not Requiring a Spectrophotometer: Quantitative Determination of Albumin in Powdered Egg White

    ERIC Educational Resources Information Center

    Charlton, Amanda K.; Sevcik, Richard S.; Tucker, Dorie A.; Schultz, Linda D.

    2007-01-01

    A general science experiment for high school chemistry students might serve as an excellent review of the concepts of solution preparation, solubility, pH, and qualitative and quantitative analysis of a common food product. The students could learn to use safe laboratory techniques, collect and analyze data using proper scientific methodology and…

  4. Mapping and analysis of quantitative trait loci in Bos indicus x Bos Taurus cattle: chromosome 10 

    E-print Network

    Lutaaya, Emmanuel

    1996-01-01

    M or approximately 3.2% of the estimated 28OOcM genome length. The markers had heterozygosity values ranging from 0.36 to 0.87 and PIC values ranging from 0.39 to 0.83. An interval mapping analysis using regression methods was used to search for quantitative trait...

  5. Journal of Theoretical Biology 246 (2007) 260268 Quantitative analysis of the local structure of food webs

    E-print Network

    Stouffer, Daniel B.

    2007-01-01

    Journal of Theoretical Biology 246 (2007) 260­268 Quantitative analysis of the local structure of food webs J. Camachoa,b,Ã, D.B. Stoufferb , L.A.N. Amaralb a Departament de Fi´sica (Fi´sica Estadi analyze the local structure of model and empirical food webs through the statistics of three

  6. ANSI/ASHRAE/IES Standard 90.1-2013 Preliminary Determination: Quantitative Analysis

    SciTech Connect

    Halverson, Mark A.; Rosenberg, Michael I.; Wang, Weimin; Zhang, Jian; Mendon, Vrushali V.; Athalye, Rahul A.; Xie, YuLong; Hart, Reid; Goel, Supriya

    2014-03-01

    This report provides a preliminary quantitative analysis to assess whether buildings constructed according to the requirements of ANSI/ASHRAE/IES Standard 90.1-2013 would result in energy savings compared with buildings constructed to ANSI/ASHRAE/IES Standard 90.1-2010.

  7. Quantitative Analysis of Shoreline Erosion at Magnolia, Seattle David Kiehl, Department of Earth and Space Sciences

    E-print Network

    Winglee, Robert M.

    Quantitative Analysis of Shoreline Erosion at Magnolia, Seattle David Kiehl, Department of Earth and Space Sciences Dr. Terry Swanson and Dr. John Stone, Department of Earth and Space Sciences · granitic the Suzallo Maps Collection and georeferenced in ArcGIS. Control points for georeferencing were based

  8. Selenium and Lung Cancer: A Quantitative Analysis of Heterogeneity in the Current

    E-print Network

    California at Berkeley, University of

    Selenium and Lung Cancer: A Quantitative Analysis of Heterogeneity in the Current Epidemiological that selenium may have anticarcinogenic activity, the epidemiological data have been inconsistent combined, the summary relative risk (RR) for subjects with higher selenium exposures was 0.74 [95% con

  9. Forty Years of the "Journal of Librarianship and Information Science": A Quantitative Analysis, Part I

    ERIC Educational Resources Information Center

    Furner, Jonathan

    2009-01-01

    This paper reports on the first part of a two-part quantitative analysis of volume 1-40 (1969-2008) of the "Journal of Librarianship and Information Science" (formerly the "Journal of Librarianship"). It provides an overview of the current state of LIS research journal publishing in the UK; a review of the publication and printing history of…

  10. Quantitative orientational analysis of a polymeric material (Kevlar with x-ray microspectroscopy

    E-print Network

    Quantitative orientational analysis of a polymeric material (Kevlar® fibers) with x of Kevlar® fibers. © 1996 American Institute of Physics. S0003-6951 96 02951-8 Near edge x-ray absorption grades of poly p-phenylene terephthalamide Kevlar® fibers for chemical structure see inset of Fig. 1

  11. Evaluation of reference gene suitability for quantitative expression analysis by quantitative polymerase chain reaction in the mandibular condyle of sheep

    PubMed Central

    JIANG, XIN; XUE, YANG; ZHOU, HONGZHI; LI, SHOUHONG; ZHANG, ZONGMIN; HOU, RUI; DING, YUXIANG; HU, KAIJIN

    2015-01-01

    Reference genes are commonly used as a reliable approach to normalize the results of quantitative polymerase chain reaction (qPCR), and to reduce errors in the relative quantification of gene expression. Suitable reference genes belonging to numerous functional classes have been identified for various types of species and tissue. However, little is currently known regarding the most suitable reference genes for bone, specifically for the sheep mandibular condyle. Sheep are important for the study of human bone diseases, particularly for temporomandibular diseases. The present study aimed to identify a set of reference genes suitable for the normalization of qPCR data from the mandibular condyle of sheep. A total of 12 reference genes belonging to various functional classes were selected, and the expression stability of the reference genes was determined in both the normal and fractured area of the sheep mandibular condyle. RefFinder, which integrates the following currently available computational algorithms: geNorm, NormFinder, BestKeeper, and the comparative ?Ct method, was used to compare and rank the candidate reference genes. The results obtained from the four methods demonstrated a similar trend: RPL19, ACTB, and PGK1 were the most stably expressed reference genes in the sheep mandibular condyle. As determined by RefFinder comprehensive analysis, the results of the present study suggested that RPL19 is the most suitable reference gene for studies associated with the sheep mandibular condyle. In addition, ACTB and PGK1 may be considered suitable alternatives. PMID:26238421

  12. Quantitative analysis of bristle number in Drosophila mutants identifies genes involved in neural development

    NASA Technical Reports Server (NTRS)

    Norga, Koenraad K.; Gurganus, Marjorie C.; Dilda, Christy L.; Yamamoto, Akihiko; Lyman, Richard F.; Patel, Prajal H.; Rubin, Gerald M.; Hoskins, Roger A.; Mackay, Trudy F.; Bellen, Hugo J.

    2003-01-01

    BACKGROUND: The identification of the function of all genes that contribute to specific biological processes and complex traits is one of the major challenges in the postgenomic era. One approach is to employ forward genetic screens in genetically tractable model organisms. In Drosophila melanogaster, P element-mediated insertional mutagenesis is a versatile tool for the dissection of molecular pathways, and there is an ongoing effort to tag every gene with a P element insertion. However, the vast majority of P element insertion lines are viable and fertile as homozygotes and do not exhibit obvious phenotypic defects, perhaps because of the tendency for P elements to insert 5' of transcription units. Quantitative genetic analysis of subtle effects of P element mutations that have been induced in an isogenic background may be a highly efficient method for functional genome annotation. RESULTS: Here, we have tested the efficacy of this strategy by assessing the extent to which screening for quantitative effects of P elements on sensory bristle number can identify genes affecting neural development. We find that such quantitative screens uncover an unusually large number of genes that are known to function in neural development, as well as genes with yet uncharacterized effects on neural development, and novel loci. CONCLUSIONS: Our findings establish the use of quantitative trait analysis for functional genome annotation through forward genetics. Similar analyses of quantitative effects of P element insertions will facilitate our understanding of the genes affecting many other complex traits in Drosophila.

  13. Status of Terra and Aqua MODIS Instruments

    NASA Technical Reports Server (NTRS)

    Xiong, Xiaoxiong; Wenny, Brian N.; Kuyper, James; Salomonson, Vicent; Barmes. William

    2008-01-01

    Currently, two nearly identical MODIS instruments are operating in space: one on the Terra spacecraft launched in December 1999 and another on the Aqua spacecraft launched in May 2002. MODIS has 36 spectral bands with wavelengths covering from visible (VIS) to long-wave infrared (LWIR). Since launch, MODIS observations and data products have contributed significantly to studies of changes in the Earth system of land, oceans, and atmosphere. To maintain its on-orbit calibration and data product quality, MODIS was built with a comprehensive set of on-board calibrators, consisting of a solar diffuser (SD) and a solar diffuser stability monitor (SDSM) for the reflective solar bands (RSB) and an on-board blackbody (BB) for the thermal emissive bands (TEB). Both instruments have demonstrated good performance. The primary Level 1 B (LIB) data products are top of the atmosphere (TOA) reflectance for RSB and radiance for TEB This paper provides an overview of MODIS calibration methodologies, activities, lifetime on-orbit performance and challenging issues for each MODIS, the impact on LIB product quality, and lessons learned for future sensors such as the NPOESS VIIRS.

  14. A quantitative ratiometric sensor for time-resolved analysis of auxin dynamics

    PubMed Central

    Wend, Sabrina; Bosco, Cristina Dal; Kämpf, Michael M.; Ren, Fugang; Palme, Klaus; Weber, Wilfried; Dovzhenko, Alexander; Zurbriggen, Matias D.

    2013-01-01

    Time-resolved quantitative analysis of auxin-mediated processes in plant cells is as of yet limited. By applying a synergistic mammalian and plant synthetic biology approach, we have developed a novel ratiometric luminescent biosensor with wide applicability in the study of auxin metabolism, transport, and signalling. The sensitivity and kinetic properties of our genetically encoded biosensor open new perspectives for the analysis of highly complex auxin dynamics in plant growth and development. PMID:23787479

  15. [Application of calibration curve method and partial least squares regression analysis to quantitative analysis of nephrite samples using XRF].

    PubMed

    Liu, Song; Su, Bo-min; Li, Qing-hui; Gan, Fu-xi

    2015-01-01

    The authors tried to find a method for quantitative analysis using pXRF without solid bulk stone/jade reference samples. 24 nephrite samples were selected, 17 samples were calibration samples and the other 7 are test samples. All the nephrite samples were analyzed by Proton induced X-ray emission spectroscopy (PIXE) quantitatively. Based on the PIXE results of calibration samples, calibration curves were created for the interested components/elements and used to analyze the test samples quantitatively; then, the qualitative spectrum of all nephrite samples were obtained by pXRF. According to the PIXE results and qualitative spectrum of calibration samples, partial least square method (PLS) was used for quantitative analysis of test samples. Finally, the results of test samples obtained by calibration method, PLS method and PIXE were compared to each other. The accuracy of calibration curve method and PLS method was estimated. The result indicates that the PLS method is the alternate method for quantitative analysis of stone/jade samples. PMID:25993858

  16. Multispectral Cloud Retrievals from MODIS on Terra and Aqua

    NASA Technical Reports Server (NTRS)

    King, Michael D.; Platnick, Steven; Ackerman, Steven A.; Menzel, W. Paul; Gray, Mark A.; Moody, Eric G.

    2002-01-01

    The Moderate Resolution Imaging Spectroradiometer (MODIS) was developed by NASA and launched onboard the Terra spacecraft on December 18, 1999 and the Aqua spacecraft on April 26, 2002. MODIS scans a swath width sufficient to provide nearly complete global coverage every two days from each polar-orbiting, sun-synchronous, platform at an altitude of 705 km, and provides images in 36 spectral bands between 0.415 and 14.235 microns with spatial resolutions of 250 m (2 bands), 500 m (5 bands) and 1000 m (29 bands). In this paper we will describe the various methods being used for the remote sensing of cloud properties using MODIS data, focusing primarily on the MODIS cloud mask used to distinguish clouds, clear sky, heavy aerosol, and shadows on the ground, and on the remote sensing of cloud optical properties, especially cloud optical thickness and effective radius of water drops and ice crystals. Additional properties of clouds derived from multispectral thermal infrared measurements, especially cloud top pressure and emissivity, will also be described. Results will be presented of MODIS cloud properties both over the land and over the ocean, showing the consistency in cloud retrievals over various ecosystems used in the retrievals. The implications of this new observing system on global analysis of the Earth's environment will be discussed.

  17. Analysis of focal adhesion turnover: A quantitative live cell imaging example

    PubMed Central

    Stehbens, Samantha

    2014-01-01

    Recent advances in optical and fluorescent protein technology have rapidly raised expectations in cell biology, allowing quantitative insights into dynamic intracellular processes like never before. However, quantitative live cell imaging comes with many challenges including how best to translate dynamic microscopy data into numerical outputs that can be used to make meaningful comparisons rather than relying on representative data sets. Here we use analysis of focal adhesion turnover dynamics as a straight-forward specific example on how to image, measure and analyze intracellular dynamics, but we believe this outlines a thought process and can provide guidance on how to understand dynamic microcopy data of other intracellular structures. PMID:24974036

  18. Quantitative analysis of the mixtures of illicit drugs using terahertz time-domain spectroscopy

    NASA Astrophysics Data System (ADS)

    Jiang, Dejun; Zhao, Shusen; Shen, Jingling

    2008-03-01

    A method was proposed to quantitatively inspect the mixtures of illicit drugs with terahertz time-domain spectroscopy technique. The mass percentages of all components in a mixture can be obtained by linear regression analysis, on the assumption that all components in the mixture and their absorption features be known. For illicit drugs were scarce and expensive, firstly we used common chemicals, Benzophenone, Anthraquinone, Pyridoxine hydrochloride and L-Ascorbic acid in the experiment. Then illicit drugs and a common adulterant, methamphetamine and flour, were selected for our experiment. Experimental results were in significant agreement with actual content, which suggested that it could be an effective method for quantitative identification of illicit drugs.

  19. Qualitative and quantitative analysis of stability and instability dynamics of positive lattice solitons

    NASA Astrophysics Data System (ADS)

    Sivan, Y.; Fibich, G.; Ilan, B.; Weinstein, M. I.

    2008-10-01

    We present a unified approach for qualitative and quantitative analysis of stability and instability dynamics of positive bright solitons in multidimensional focusing nonlinear media with a potential (lattice), which can be periodic, periodic with defects, quasiperiodic, single waveguide, etc. We show that when the soliton is unstable, the type of instability dynamic that develops depends on which of two stability conditions is violated. Specifically, violation of the slope condition leads to a focusing instability, whereas violation of the spectral condition leads to a drift instability. We also present a quantitative approach that allows one to predict the stability and instability strength.

  20. Compensation for Time-Dependent Star Tracker Thermal Deformation on the Aqua Spacecraft

    NASA Technical Reports Server (NTRS)

    Hashmall, Joseph A.; Natanson, Gregory; Glickman, Jonathan; Sedlak, Joseph

    2004-01-01

    Analysis of attitude sensor data from the Aqua mission showed small but systematic differences between batch least-squares and extended Kalman filter attitudes. These differences were also found to be correlated with star tracker residuals, gyro bias estimates, and star tracker baseplate temperatures. This paper describes the analysis that shows that these correlations are all consistent with a single cause: time-dependent thermal deformation of star tracker alignments. These varying alignments can be separated into relative and common components. The relative misalignments can be determined and compensated for. The common misalignments can only be determined in special cases.

  1. Quantitative Analysis of Pork and Chicken Products by Droplet Digital PCR

    PubMed Central

    Cai, Yicun; Li, Xiang; Lv, Rong; Yang, Jielin; Li, Jian; He, Yuping; Pan, Liangwen

    2014-01-01

    In this project, a highly precise quantitative method based on the digital polymerase chain reaction (dPCR) technique was developed to determine the weight of pork and chicken in meat products. Real-time quantitative polymerase chain reaction (qPCR) is currently used for quantitative molecular analysis of the presence of species-specific DNAs in meat products. However, it is limited in amplification efficiency and relies on standard curves based Ct values, detecting and quantifying low copy number target DNA, as in some complex mixture meat products. By using the dPCR method, we find the relationships between the raw meat weight and DNA weight and between the DNA weight and DNA copy number were both close to linear. This enabled us to establish formulae to calculate the raw meat weight based on the DNA copy number. The accuracy and applicability of this method were tested and verified using samples of pork and chicken powder mixed in known proportions. Quantitative analysis indicated that dPCR is highly precise in quantifying pork and chicken in meat products and therefore has the potential to be used in routine analysis by government regulators and quality control departments of commercial food and feed enterprises. PMID:25243184

  2. [A multivariate nonlinear model for quantitative analysis in laser-induced breakdown spectroscopy].

    PubMed

    Chen, Xing-Long; Fu, Hong-Bo; Wang, Jing-Ge; Ni, Zhi-Bo; He, Wen-Gan; Xu, Jun; Rao Rui-zhong; Dong, Rui-Zhong

    2014-11-01

    Most quantitative models used in laser-induced breakdown spectroscopy (LIBS) are based on the hypothesis that laser-induced plasma approaches the state of local thermal equilibrium (LTE). However, the local equilibrium is possible only at a specific time segment during the evolution. As the populations of each energy level does not follow Boltzmann distribution in non-LTE condition, those quantitative models using single spectral line would be inaccurate. A multivariate nonlinear model, in which the LTE is not required, was proposed in this article to reduce the signal fluctuation and improve the accuracy of quantitative analysis. This multivariate nonlinear model was compared with the internal calibration model which is based on the LTE condition. The content of Mn in steel samples was determined by using the two models, respectively. A minor error and a minor relative standard deviation (RSD) were observed in multivariate nonlinear model. This result demonstrates that multivariate nonlinear model can improve measurement accuracy and repeatability. PMID:25752066

  3. 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.

  4. Determinations of Carbon Dioxide by Titration: New Experiments for General, Physical, and Quantitative Analysis Courses

    NASA Astrophysics Data System (ADS)

    Crossno, S. K.; Kalbus, L. H.; Kalbus, G. E.

    1996-02-01

    The determination of mixtures containing NaOH and Na2CO3 or Na2CO3 and NaHCO3 by titration is a common experiment in a Quantitative Analysis course. This determination can be adapted for the analysis of CO2 within a sample. The CO2 is released and absorbed in a solution containing excess NaOH. Titration with standard HCl leads to the determination of CO2 present in the sample. A number of interesting experiments in Quantitative Analysis, General and/or Physical Chemistry have been developed. Among these are the following determinations: CO2 content in carbonated beverages, carbonate and bicarbonate in various real life samples, and the molecular weight of CO2.

  5. In situ sample processing approach (iSPA) for comprehensive quantitative phosphoproteome analysis.

    PubMed

    Huang, Junfeng; Qin, Hongqiang; Dong, Jing; Song, Chunxia; Bian, Yangyang; Dong, Mingming; Cheng, Kai; Wang, Fangjun; Sun, Deguang; Wang, Liming; Ye, Mingliang; Zou, Hanfa

    2014-09-01

    Current sample preparation protocols for quantitative phosphoproteome analysis are tedious and time-consuming. Here, a facile in situ sample processing approach (iSPA) is developed by using macroporous Ti(IV)-IMAC microspheres as the preparation "beds", where all sample preparation procedures including the enrichment of phosphoproteins, tryptic digestion of proteins, enrichment, and isotope labeling of phosphopeptides are performed in situ sequentially. As a result of the in situ processing design and the seamless procedures, extra steps for desalting and buffer exchanging, which are always required in conventional approaches, are avoided, and the sample loss and contamination could be greatly reduced. Thus, better sensitivity and accuracy for the quantitative phosphoproteome analysis were obtained. This strategy was further applied to differential phosphoproteome analysis of human liver tissues with or without hepatocellular carcinoma (HCC). In total, 8548 phosphorylation sites were confidently quantified from three replicate analyses of 0.5 mg of human liver protein extracts. PMID:25072903

  6. Quantitative trait locus analysis of susceptibility to diet-induced atherosclerosis in recombinant inbred mice

    SciTech Connect

    Hyman, R.W.; Frank, S.; Warden, C.H.

    1994-12-01

    Quantitative trait locus (QTL) analysis is a statistical method that can be applied to identify loci making a significant impact on a phenotype. For the phenotype of susceptibility to diet-induced atherosclerosis in the mouse, we have studied four quantitative traits: area of aortic fatty streaks and serum concentrations of high-density lipoprotein-bound cholesterol (HDL-cholesterol), apolipoprotein A-I, and apolipoprotein A-II (apo A-II). QTL analysis revealed a significant locus on chromosome 1 distal impacting serum apo A-II concentration on a high-fat diet and serum HDL-cholesterol concentration on a chow diet. This locus is presumably Apoa-2, the structural gene for apo A-II. QTL analysis of aortic fatty streaks failed to reveal a significant locus. 19 refs., 3 tabs.

  7. Metadata of the chapter that will be visualized online Chapter Title Quantitative Fluorescence Spectral Analysis of Protein Denaturation

    E-print Network

    van Stokkum, Ivo

    Spectral Analysis of Protein Denaturation Copyright Year 2013 Copyright Holder Springer Science measured with different concentrations of the denaturant to quantitatively study protein denaturation by "-") Global analysis - Protein denaturation - Singular value decomposition - Steady-state fluorescence #12

  8. HPTLC Hyphenated with FTIR: Principles, Instrumentation and Qualitative Analysis and Quantitation

    NASA Astrophysics Data System (ADS)

    Cimpoiu, Claudia

    In recent years, much effort has been devoted to the coupling of high-performance thin-layer chromatography (HPTLC) with spectrometric methods because of the robustness and simplicity of HPTLC and the need for detection techniques that provide identification and determination of sample constituents. IR is one of the spectroscopic methods that have been coupled with HPTLC. IR spectroscopy has a high potential for the elucidation of molecular structures, and the characteristic absorption bands can be used for compound-specific detection. HPTLC-FTIR coupled method has been widely used in the modern laboratories for the qualitative and quantitative analysis. The potential of this method is demonstrated by its application in different fields of analysis such as drug analysis, forensic analysis, food analysis, environmental analysis, biological analysis, etc. The hyphenated HPTLC-FTIR technique will be developed in the future with the aim of taking full advantage of this method.

  9. QARIP: a web server for quantitative proteomic analysis of regulated intramembrane proteolysis

    PubMed Central

    Ivankov, Dmitry N.; Bogatyreva, Natalya S.; Hönigschmid, Peter; Dislich, Bastian; Hogl, Sebastian; Kuhn, Peer-Hendrik; Frishman, Dmitrij; Lichtenthaler, Stefan F.

    2013-01-01

    Regulated intramembrane proteolysis (RIP) is a critical mechanism for intercellular communication and regulates the function of membrane proteins through sequential proteolysis. RIP typically starts with ectodomain shedding of membrane proteins by extracellular membrane-bound proteases followed by intramembrane proteolysis of the resulting membrane-tethered fragment. However, for the majority of RIP proteases the corresponding substrates and thus, their functions, remain unknown. Proteome-wide identification of RIP protease substrates is possible by mass spectrometry-based quantitative comparison of RIP substrates or their cleavage products between different biological states. However, this requires quantification of peptides from only the ectodomain or cytoplasmic domain. Current analysis software does not allow matching peptides to either domain. Here we present the QARIP (Quantitative Analysis of Regulated Intramembrane Proteolysis) web server which matches identified peptides to the protein transmembrane topology. QARIP allows determination of quantitative ratios separately for the topological domains (cytoplasmic, ectodomain) of a given protein and is thus a powerful tool for quality control, improvement of quantitative ratios and identification of novel substrates in proteomic RIP datasets. To our knowledge, the QARIP web server is the first tool directly addressing the phenomenon of RIP. The web server is available at http://webclu.bio.wzw.tum.de/qarip/. This website is free and open to all users and there is no login requirement. PMID:23729472

  10. Dynamic analysis of pathogen-infected host cells using quantitative phase microscopy

    NASA Astrophysics Data System (ADS)

    Lee, Seungrag; Kim, Young Ran; Lee, Ji Yong; Rhee, Joon Haeng; Park, Chang-Soo; Kim, Dug Young

    2011-03-01

    We present the real-time quantitative analysis of Vibrio vulnificus-infected host cells using quantitative phase microscopy (QPM) based on interferometric techniques. This provides the ability to retrieve the phase or optical path-length distribution over the cell with nanometer path-length sensitivity from a single interferogram image. We have used QPM to study dynamic cell morphologic changes and to noninvasively quantify the cell volumes of rat basophilic leukemia RBL-2H3 cells infected with V. vulnificus strains: wild type (MO6-24/O) and RtxA1 toxin mutant (CMM770). During the process of V. vulnificus infection in RBL-2H3 cells, the dynamic changes of quantitative phase images, cell volumes, and areas were observed in real time using QPM. In contrast, dramatic changes were not detected in RBL-2H3 cells infected with the noncytotoxic RtxA1 toxin mutant. The results showed good correlation between QPM analysis and biochemical assays, such as lactate dehydrogenase assay or ?-hexosaminidase release assay. We suggest that QPM is a powerful quantitative method to study the dynamic process of host cells infected with pathogens in a noninvasive manner.

  11. 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.

  12. AquaSMART: Water & Boating Safety, Grades K-2. Teacher's Guide.

    ERIC Educational Resources Information Center

    Texas State Dept. of Parks and Wildlife, Austin.

    This teacher's guide accompanies a program designed to teach water and boating safety to students in grades K-2. The written curriculum accompanies a video, AquaSMART K-2. The theme of the curriculum is AquaSMART. To become AquaSMART, students must learn 10 basic lessons for water and boating safety. The teacher's guide begins with an overview of…

  13. AquaSMART: Water & Boating Safety, Grades 3-5. Teacher's Guide.

    ERIC Educational Resources Information Center

    Texas State Dept. of Parks and Wildlife, Austin.

    This teacher's guide accompanies a program designed to teach water and boating safety to students in grades 3-5. The written curriculum accompanies a video, AquaSMART 3-5. The theme of the curriculum is AquaSMART. To become AquaSMART, students must learn 10 basic lessons for water and boating safety. The written curriculum begins with an overview…

  14. Ground ultra-low volume assessment of Aqua-Kontrol.

    PubMed

    Meisch, M V; Brown, James R; Dame, David A; Lewis, Carolyn N

    2006-12-01

    Against caged field-collected Anopheles quadrimaculatus Say adults, ultra-low volume (ULV) applications of 3.175 g a.i./0.40 ha (0.007 lb a.i.lac) of synergized permethrin (4% Aqua-Kontrol) gave excellent control (mean: 90%). Droplet collections on magnesium-oxide-coated (MGO) glass slides from 3 applications revealed mean deposition rate of 216 droplets/cm2 and 11-micron volume median diameter (VMD) (based on Aqua-Kontrol label spread factor of 0.61). PMID:17304947

  15. Corrections to the MODIS Aqua Calibration Derived From MODIS Aqua Ocean Color Products

    NASA Technical Reports Server (NTRS)

    Meister, Gerhard; Franz, Bryan Alden

    2013-01-01

    Ocean color products such as, e.g., chlorophyll-a concentration, can be derived from the top-of-atmosphere radiances measured by imaging sensors on earth-orbiting satellites. There are currently three National Aeronautics and Space Administration sensors in orbit capable of providing ocean color products. One of these sensors is the Moderate Resolution Imaging Spectroradiometer (MODIS) on the Aqua satellite, whose ocean color products are currently the most widely used of the three. A recent improvement to the MODIS calibration methodology has used land targets to improve the calibration accuracy. This study evaluates the new calibration methodology and describes further calibration improvements that are built upon the new methodology by including ocean measurements in the form of global temporally averaged water-leaving reflectance measurements. The calibration improvements presented here mainly modify the calibration at the scan edges, taking advantage of the good performance of the land target trending in the center of the scan.

  16. Quantitative analysis of saltwater-freshwater relationships in groundwater systems-A historical perspective

    USGS Publications Warehouse

    Reilly, T.E.; Goodman, A.S.

    1985-01-01

    Although much progress has been made toward the mathematical description of saltwater-freshwater relationships in groundwater systems since the late 19th century, the advective and dispersive mechanisms involved are still incompletely understood. This article documents the major historical advances in this subject and summarizes the major direction of current studies. From the time of Badon Ghyben and Herzberg, it has been recognized that density is important in mathematically describing saltwater-freshwater systems. Other mechanisms, such as hydrodynamic dispersion, were identified later and are still not fully understood. Quantitative analysis of a saltwater-freshwater system attempts to mathematically describe the physical system and the important mechanisms using reasonable simplifications and assumptions. This paper, in developing the history of quantitative analysis discusses many of these simplifications and assumptions and their effect on describing and understanding the phenomenon. ?? 1985.

  17. Quantitative analysis of terahertz spectra for illicit drugs using adaptive-range micro-genetic algorithm

    NASA Astrophysics Data System (ADS)

    Chen, Yi; Ma, Yong; Lu, Zheng; Peng, Bei; Chen, Qin

    2011-08-01

    In the field of anti-illicit drug applications, many suspicious mixture samples might consist of various drug components—for example, a mixture of methamphetamine, heroin, and amoxicillin—which makes spectral identification very difficult. A terahertz spectroscopic quantitative analysis method using an adaptive range micro-genetic algorithm with a variable internal population (ARVIP??GA) has been proposed. Five mixture cases are discussed using ARVIP??GA driven quantitative terahertz spectroscopic analysis in this paper. The devised simulation results show agreement with the previous experimental results, which suggested that the proposed technique has potential applications for terahertz spectral identifications of drug mixture components. The results show agreement with the results obtained using other experimental and numerical techniques.

  18. Quantitative Schlieren analysis applied to holograms of crystals grown on Spacelab 3

    NASA Technical Reports Server (NTRS)

    Brooks, Howard L.

    1986-01-01

    In order to extract additional information about crystals grown in the microgravity environment of Spacelab, a quantitative schlieren analysis technique was developed for use in a Holography Ground System of the Fluid Experiment System. Utilizing the Unidex position controller, it was possible to measure deviation angles produced by refractive index gradients of 0.5 milliradians. Additionally, refractive index gradient maps for any recorded time during the crystal growth were drawn and used to create solute concentration maps for the environment around the crystal. The technique was applied to flight holograms of Cell 204 of the Fluid Experiment System that were recorded during the Spacelab 3 mission on STS 51B. A triglycine sulfate crystal was grown under isothermal conditions in the cell and the data gathered with the quantitative schlieren analysis technique is consistent with a diffusion limited growth process.

  19. 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. PMID:26213072

  20. Genetic basis for systems of skeletal quantitative traits: Principal component analysis of the canid skeleton

    PubMed Central

    Chase, Kevin; Carrier, David R.; Adler, Frederick R.; Jarvik, Tyler; Ostrander, Elaine A.; Lorentzen, Travis D.; Lark, Karl G.

    2002-01-01

    Evolution of mammalian skeletal structure can be rapid and the changes profound, as illustrated by the morphological diversity of the domestic dog. Here we use principal component analysis of skeletal variation in a population of Portuguese Water Dogs to reveal systems of traits defining skeletal structures. This analysis classifies phenotypic variation into independent components that can be used to dissect genetic networks regulating complex biological systems. We show that unlinked quantitative trait loci associated with these principal components individually promote both correlations within structures (e.g., within the skull or among the limb bones) and inverse correlations between structures (e.g., skull vs. limb bones). These quantitative trait loci are consistent with regulatory genes that inhibit growth of some bones while enhancing growth of others. These systems of traits could explain the skeletal differences between divergent breeds such as Greyhounds and Pit Bulls, and even some of the skeletal transformations that characterize the evolution of hominids. PMID:12114542

  1. Quantitative Analysis for Monitoring Formulation of Lubricating Oil Using Terahertz Time-Domain Transmission Spectroscopy

    NASA Astrophysics Data System (ADS)

    Tian, Lu; Zhao, Kun; Zhou, Qing-Li; Shi, Yu-Lei; Zhang, Cun-Lin

    2012-04-01

    The quantitative analysis of zinc isopropyl-isooctyl-dithiophosphate (T204) mixed with lube base oil from Korea with viscosity index 70 (T204-Korea70) is presented by using terahertz time-domain spectroscopy (THz-TDS). Compared with the middle-infrared spectra of zinc n-butyl-isooctyl-dithiophosphate (T202) and T204, THz spectra of T202 and T204 show the weak broad absorption bands. Then, the absorption coefficients of the T204-Korea70 system follow Beer's law at the concentration from 0.124 to 4.024%. The experimental absorption spectra of T204-Korea70 agree with the calculated ones based on the standard absorption coefficients of T204 and Korea70. The quantitative analysis enables a strategy to monitor the formulation of lubricating oil in real time.

  2. [Study on the multicomponent quantitative analysis using near infrared spectroscopy based on building elman model].

    PubMed

    Liu, Bo-ping; Qin, Hua-jun; Luo, Xiang; Cao, Shu-wen; Wang, Jun-de

    2007-12-01

    The present paper introduces an application of near infrared spectroscopy (NIRS) multi-component quantitative analysis by building a kind of recurrent network (Elman) model. Elman prediction model for phenylalanine (Phe), lysine (Lys), tyrosine (Tyr) and cystine (Cys) in 45 feedstuff samples was established with good veracity. Twelve peak value data from 3 principal components straight forward compressed from the original data by PLS were taken as inputs of Elman, while 4 predictive targets as outputs. Forty seven nerve cells were taken as hidden nodes with the lowest error compared with taking 43 and 45 nerve cells. Its training iteration times was supposed to be 1000. Predictive correlation coefficients by the model are 0.960, 0.981, 0.979 and 0.952. The results show that Elman using in NIRS is a rapid, effective means for measuring Phe, Lys, Tyr and Cys in feedstuff powder, and can also be used in quantitative analysis of other samples. PMID:18330284

  3. Quantitative wake analysis of a freely swimming fish using 3D synthetic aperture PIV

    NASA Astrophysics Data System (ADS)

    Mendelson, Leah; Techet, Alexandra H.

    2015-07-01

    Synthetic aperture PIV (SAPIV) is used to quantitatively analyze the wake behind a giant danio ( Danio aequipinnatus) swimming freely in a seeded quiescent tank. The experiment is designed with minimal constraints on animal behavior to ensure that natural swimming occurs. The fish exhibits forward swimming and turning behaviors at speeds between 0.9 and 1.5 body lengths/second. Results show clearly isolated and linked vortex rings in the wake structure, as well as the thrust jet coming off of a visual hull reconstruction of the fish body. As a benchmark for quantitative analysis of volumetric PIV data, the vortex circulation and impulse are computed using methods consistent with those applied to planar PIV data. Volumetric momentum analysis frameworks are discussed for linked and asymmetric vortex structures, laying a foundation for further volumetric studies of swimming hydrodynamics with SAPIV. Additionally, a novel weighted refocusing method is presented as an improvement to SAPIV reconstruction.

  4. Exploratory data analysis groupware for qualitative and quantitative electrophoretic gel analysis over the Internet-WebGel.

    PubMed

    Lemkin, P F; Myrick, J M; Lakshmanan, Y; Shue, M J; Patrick, J L; Hornbeck, P V; Thornwal, G C; Partin, A W

    1999-12-01

    Many scientists use quantitative measurements to compare the presence and amount, of various proteins and nucleotides among series of one- and two-dimensional (1-D and 2-D) electrophoretic gels. These gels are often scanned into digital image files. Gel spots are then quantified using stand-alone analysis software. However, as more research collaborations take place over the Internet, it has become useful to share intermediate quantitative data between researchers. This allows research group members to investigate their data and share their work in progress. We developed a World Wide Web group-accessible software system, WebGel, for interactively exploring qualitative and quantitative differences between electrophoretic gels. Such Internet databases are useful for publishing quantitative data and allow other researchers to explore the data with respect to their own research. Because intermediate results of one user may be shared with their collaborators using WebGel, this form of active data-sharing constitutes a groupware method for enhancing collaborative research. Quantitative and image gel data from a stand-alone gel image processing system are copied to a database accessible on the WebGel Web server. These data are then available for analysis by the WebGel database program residing on that server. Visualization is critical for better understanding of the data. WebGel helps organize labeled gel images into montages of corresponding spots as seen in these different gels. Various views of multiple gel images, including sets of spots, normalization spots, labeled spots, segmented gels, etc. may also be displayed. These displays are active and may be used for performing database operations directly on individual protein spots by simply clicking on them. Corresponding regions between sets of gels may be visually analyzed using Flicker-comparison (Electrophoresis 1997, 18, 122-140) as one of the WebGel methods for qualitative analysis. Quantitative exploratory data analysis can be performed by comparing protein concentration values between corresponding spots for multiple samples run in separate gels. These data are then used to generate reports on statistical differences between sets of gels (e.g., between different disease states such as benign or metastatic cancers, etc.). Using combined visual and quantitative methods, WebGel can help bridge the analysis of dissimilar gels which are difficult to analyze with stand-alone systems and can serve as a collaborative Internet tool in a groupware setting. PMID:10612275

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

    PubMed

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

    2012-11-01

    Coronary artery atherosclerosis is a hugely prevalent condition in the Western World and is often encountered during autopsy. Atherosclerotic plaques can cause luminal stenosis: which, if over a significant level (75%), is said to contribute to cause of death. Estimation of stenosis can be macroscopically performed by the forensic pathologists at the time of autopsy or by microscopic examination. This study compares macroscopic estimation with quantitative microscopic image analysis with a particular focus on the assessment of significant stenosis (>75%). A total of 131 individuals were analysed. The sample consists of an atherosclerotic group (n=122) and a control group (n=9). The results of the two methods were significantly different from each other (p=0.001) and the macroscopic method gave a greater percentage stenosis by an average of 3.5%. Also, histological examination of coronary artery stenosis yielded a difference in significant stenosis in 11.5% of cases. The differences were attributed to either histological quantitative image analysis underestimation; gross examination overestimation; or, a combination of both. The underestimation may have come from tissue shrinkage during tissue processing for histological specimen. The overestimation from the macroscopic assessment can be attributed to the lumen shape, to the examiner observer error or to a possible bias to diagnose coronary disease when no other cause of death is apparent. The results indicate that the macroscopic estimation is open to more biases and that histological quantitative image analysis only gives a precise assessment of stenosis ex vivo. Once tissue shrinkage, if any, is accounted for then histological quantitative image analysis will yield a more accurate assessment of in vivo stenosis. It may then be considered a complementary tool for the examination of coronary stenosis. PMID:23084314

  6. Quantitative chemical analysis of ocular melanosomes in stained and non-stained tissues.

    PubMed

    Biesemeier, Antje; Schraermeyer, Ulrich; Eibl, Oliver

    2011-07-01

    Energy-filtered Analytical Electron Microscopy (AEM) was used to image the ultrastructure and determine quantitatively the chemical composition of rat melanosomes of the choroid and the Retinal Pigment Epithelium (RPE). For the first time, the effect of staining in elemental analysis of melanosomes was investigated. Detection limits and accuracies of the applied methods were determined. Compared to previous work applying only quantitative Energy Dispersive X-ray microanalysis (EDX) in the TEM (Eibl, O., et al., 2006. Micron 37, 262), here we present a combined quantitative EDX and Electron Energy Loss Spectroscopy (EELS) analysis, including N. This yields the fraction of eumelanin and pheomelanin in melanosomes by the S/N mole fraction ratio. Melanosomes of the sepia ink sac, used as eumelanin standard, showed an S/N mole fraction ratio of <0.004. Thus, they consist primarily of eumelanin as reported by degradation analysis. In contrast, melanosomes of the rats contained mixed melanin with significant amounts of pheomelanin (S/N 0.02) in the RPE and the choroid. Consistent with the previous publication, it was shown that oxygen mole fractions are especially large in melanosomes (7-10 at.%) compared to other cell compartments, e.g. 2-4 at.% oxygen in the cytoplasm. In the melanosomes of non-stained tissue, the oxygen mole fraction clearly correlated with the Ca mole fraction. EDX spectra used for quantitative analysis had about 15,000 net counts under the oxygen peak, which is necessary to obtain (i) a small statistical error for oxygen and (ii) optimum minimum detectable mole fractions for S, Ca and transition metals. The precise determination of the oxygen mole fraction in melanosomes is important for understanding metabolism. Therefore, a detailed analysis was carried out on the possible errors affecting quantification. While O, S, and N mole fractions yielded similar results in stained and non-stained ocular melanosomes of rats, transition metals can only be determined reliably in non-stained tissues. High-precision EDX analysis of melanosomes yielded minimum detectable mole fractions of less than 0.04 at.% for Cu and Zn, these elements were present in melanosomes with mole fractions of about 0.3 at.% and 0.1at.%, respectively. Zn is of great importance for metabolism and for age related macular degeneration. Its mole fraction in melanosomes of rats is large enough to be detected and to be quantitatively analyzed by EDX spectroscopy. Ultrastructural information can now be correlated to the elemental composition. This is important to better understand the physical and chemical properties of melanosomal metabolism and turnover. PMID:21330141

  7. Low-dose CT for quantitative analysis in acute respiratory distress syndrome

    PubMed Central

    2013-01-01

    Introduction The clinical use of serial quantitative computed tomography (CT) to characterize lung disease and guide the optimization of mechanical ventilation in patients with acute respiratory distress syndrome (ARDS) is limited by the risk of cumulative radiation exposure and by the difficulties and risks related to transferring patients to the CT room. We evaluated the effects of tube current-time product (mAs) variations on quantitative results in healthy lungs and in experimental ARDS in order to support the use of low-dose CT for quantitative analysis. Methods In 14 sheep chest CT was performed at baseline and after the induction of ARDS via intravenous oleic acid injection. For each CT session, two consecutive scans were obtained applying two different mAs: 60 mAs was paired with 140, 15 or 7.5 mAs. All other CT parameters were kept unaltered (tube voltage 120 kVp, collimation 32 × 0.5 mm, pitch 0.85, matrix 512 × 512, pixel size 0.625 × 0.625 mm). Quantitative results obtained at different mAs were compared via Bland-Altman analysis. Results Good agreement was observed between 60 mAs and 140 mAs and between 60 mAs and 15 mAs (all biases less than 1%). A further reduction of mAs to 7.5 mAs caused an increase in the bias of poorly aerated and nonaerated tissue (-2.9% and 2.4%, respectively) and determined a significant widening of the limits of agreement for the same compartments (-10.5% to 4.8% for poorly aerated tissue and -5.9% to 10.8% for nonaerated tissue). Estimated mean effective dose at 140, 60, 15 and 7.5 mAs corresponded to 17.8, 7.4, 2.0 and 0.9 mSv, respectively. Image noise of scans performed at 140, 60, 15 and 7.5 mAs corresponded to 10, 16, 38 and 74 Hounsfield units, respectively. Conclusions A reduction of effective dose up to 70% has been achieved with minimal effects on lung quantitative results. Low-dose computed tomography provides accurate quantitative results and could be used to characterize lung compartment distribution and possibly monitor time-course of ARDS with a lower risk of exposure to ionizing radiation. A further radiation dose reduction is associated with lower accuracy in quantitative results. PMID:24004842

  8. Quantitative analysis of wet-heat inactivation in bovine spongiform encephalopathy

    SciTech Connect

    Matsuura, Yuichi; Ishikawa, Yukiko; Bo, Xiao; Murayama, Yuichi; Yokoyama, Takashi; Somerville, Robert A.; Kitamoto, Tetsuyuki; Mohri, Shirou

    2013-03-01

    Highlights: ? We quantitatively analyzed wet-heat inactivation of the BSE agent. ? Infectivity of the BSE macerate did not survive 155 °C wet-heat treatment. ? Once the sample was dehydrated, infectivity was observed even at 170 °C. ? A quantitative PMCA assay was used to evaluate the degree of BSE inactivation. - Abstract: The bovine spongiform encephalopathy (BSE) agent is resistant to conventional microbial inactivation procedures and thus threatens the safety of cattle products and by-products. To obtain information necessary to assess BSE inactivation, we performed quantitative analysis of wet-heat inactivation of infectivity in BSE-infected cattle spinal cords. Using a highly sensitive bioassay, we found that infectivity in BSE cattle macerates fell with increase in temperatures from 133 °C to 150 °C and was not detected in the samples subjected to temperatures above 155 °C. In dry cattle tissues, infectivity was detected even at 170 °C. Thus, BSE infectivity reduces with increase in wet-heat temperatures but is less affected when tissues are dehydrated prior to the wet-heat treatment. The results of the quantitative protein misfolding cyclic amplification assay also demonstrated that the level of the protease-resistant prion protein fell below the bioassay detection limit by wet-heat at 155 °C and higher and could help assess BSE inactivation. Our results show that BSE infectivity is strongly resistant to wet-heat inactivation and that it is necessary to pay attention to BSE decontamination in recycled cattle by-products.

  9. Quantitative analysis of powder mixtures by Raman spectrometry: the influence of particle size and its correction.

    PubMed

    Chen, Zeng-Ping; Li, Li-Mei; Jin, Jing-Wen; Nordon, Alison; Littlejohn, David; Yang, Jing; Zhang, Juan; Yu, Ru-Qin

    2012-05-01

    Particle size distribution and compactness have significant confounding effects on Raman signals of powder mixtures, which cannot be effectively modeled or corrected by traditional multivariate linear calibration methods such as partial least-squares (PLS), and therefore greatly deteriorate the predictive abilities of Raman calibration models for powder mixtures. The ability to obtain directly quantitative information from Raman signals of powder mixtures with varying particle size distribution and compactness is, therefore, of considerable interest. In this study, an advanced quantitative Raman calibration model was developed to explicitly account for the confounding effects of particle size distribution and compactness on Raman signals of powder mixtures. Under the theoretical guidance of the proposed Raman calibration model, an advanced dual calibration strategy was adopted to separate the Raman contributions caused by the changes in mass fractions of the constituents in powder mixtures from those induced by the variations in the physical properties of samples, and hence achieve accurate quantitative determination for powder mixture samples. The proposed Raman calibration model was applied to the quantitative analysis of backscatter Raman measurements of a proof-of-concept model system of powder mixtures consisting of barium nitrate and potassium chromate. The average relative prediction error of prediction obtained by the proposed Raman calibration model was less than one-third of the corresponding value of the best performing PLS model for mass fractions of barium nitrate in powder mixtures with variations in particle size distribution, as well as compactness. PMID:22468859

  10. Inhibition of Bacterial Conjugation by Phage M13 and Its Protein g3p: Quantitative Analysis and Model

    E-print Network

    Liu, David R.

    of Bacterial Conjugation by Phage M13 and Its Protein g3p: Quantitative Analysis and Model. PLoS ONE 6(5): e://www.sysbio.harvard.edu/csb). The funders had no role in study design, data collection and analysis, decision to publish, or preparationInhibition of Bacterial Conjugation by Phage M13 and Its Protein g3p: Quantitative Analysis

  11. Quantitative analysis of reptation of partially extended DNA in sub-30 nm nanoslits

    E-print Network

    Yeh, Jia-Wei; Taloni, Alessandro; Chen, Yeng-Long; Chou, Chia-Fu

    2015-01-01

    We observed reptation of single DNA molecules in fused silica nanoslits of sub-30 nm height. The reptation behavior and the effect of confinement are quantitatively characterized using orientation correlation and transverse fluctuation analysis. We show tube-like polymer motion arises for a tense polymer under strong quasi-2D confinement and interaction with surface- passivating polyvinylpyrrolidone (PVP) molecules in nanoslits, while etching- induced device surface roughness, chip bonding materials and DNA-intercalated dye-surface interaction, play minor roles. These findings have strong implications for the effect of surface modification in nanofluidic systems with potential applications for single molecule DNA analysis.

  12. Quantitative analysis of reptation of partially extended DNA in sub-30 nm nanoslits

    E-print Network

    Jia-Wei Yeh; K. K. Sriram; Alessandro Taloni; Yeng-Long Chen; Chia-Fu Chou

    2015-02-18

    We observed reptation of single DNA molecules in fused silica nanoslits of sub-30 nm height. The reptation behavior and the effect of confinement are quantitatively characterized using orientation correlation and transverse fluctuation analysis. We show tube-like polymer motion arises for a tense polymer under strong quasi-2D confinement and interaction with surface- passivating polyvinylpyrrolidone (PVP) molecules in nanoslits, while etching- induced device surface roughness, chip bonding materials and DNA-intercalated dye-surface interaction, play minor roles. These findings have strong implications for the effect of surface modification in nanofluidic systems with potential applications for single molecule DNA analysis.

  13. Quantitative analysis of tin alloy combined with artificial neural network prediction

    SciTech Connect

    Oh, Seong Y.; Yueh, Fang-Yu; Singh, Jagdish P.

    2010-05-01

    Laser-induced breakdown spectroscopy was applied to quantitative analysis of three impurities in Sn alloy. The impurities analysis was based on the internal standard method using the Sn I 333.062-nm line as the reference line to achieve the best reproducible results. Minor-element concentrations (Ag, Cu, Pb) in the alloy were comparatively evaluated by artificial neural networks (ANNs) and calibration curves. ANN was found to effectively predict elemental concentrations with a trend of nonlinear growth due to self-absorption. The limits of detection for Ag, Cu, and Pb in Sn alloy were determined to be 29, 197, and 213 ppm, respectively.

  14. Quantitative X-ray diffraction analysis of oxides formed on superalloys

    NASA Technical Reports Server (NTRS)

    Garlick, R. G.

    1972-01-01

    Methods were developed for quantitative analysis by X-ray diffraction of the oxides Al2O3, NiO, Cr2O3, CoO, and CoCr2O4 within a standard deviation of about 10 percent of the weight fraction reported or within 1 percent absolute. These error limits assume that the sample oxides are well characterized and that the physiochemical structure of the oxides in the samples are identical with those in the synthesized standards. Results are given for the use of one of the techniques in the analysis of spalls from a series of oxidation tests of the cobalt base alloy WI-52.

  15. Complex Politics: A Quantitative Semantic and Topological Analysis of UK House of Commons Debates

    E-print Network

    Gurciullo, Stefano; Pereda, María; Battiston, Federico; Patania, Alice; Poledna, Sebastian; Hedblom, Daniel; Oztan, Bahattin Tolga; Herzog, Alexander; John, Peter; Mikhaylov, Slava

    2015-01-01

    This study is a first, exploratory attempt to use quantitative semantics techniques and topological analysis to analyze systemic patterns arising in a complex political system. In particular, we use a rich data set covering all speeches and debates in the UK House of Commons between 1975 and 2014. By the use of dynamic topic modeling (DTM) and topological data analysis (TDA) we show that both members and parties feature specific roles within the system, consistent over time, and extract global patterns indicating levels of political cohesion. Our results provide a wide array of novel hypotheses about the complex dynamics of political systems, with valuable policy applications.

  16. High Throughput Quantitative Analysis of Serum Proteins using Glycopeptide Capture and Liquid Chromatography Mass Spectrometry

    SciTech Connect

    Zhang, Hui; Yi, Eugene C.; Li, Xiao-jun; Mallick, Parag; Kelly-Spratt, Karen S.; Masselon, Christophe D.; Camp, David G.; Smith, Richard D.; Kemp, Christopher; Aebersold, Ruedi

    2005-02-01

    It is expected that the composition of the serum proteome can provide valuable information about the state of the human body in health and disease, and that this information can be extracted via quantitative proteomic measurements. Suitable proteomic techniques need to be sensitive, reproducible and robust to detect potential biomarkers below the level of highly expressed proteins, to generate data sets that are comparable between experiments and laboratories, and have high throughput to support statistical studies. In this paper, we report a method for high throughput quantitative analysis of serum proteins. It consists of the selective isolation of peptides that are N-linked glycosylated in the intact protein, the analysis of these, no de-glycosylated peptides by LC-ESI-MS, and the comparative analysis of the resulting patterns. By focusing selectively on a few formerly N-linked glycopeptides per serum protein, the complexity of the analyte sample is significantly reduced and the sensitivity and throughput of serum proteome analysis are increased compared with the analysis of total tryptic peptides from unfractionated samples. We provide data that document the performance of the method and show that sera from untreated normal mice and genetically identical mice with carcinogen induced skin cancer can be unambiguously discriminated using unsupervised clustering of the resulting peptide patterns. We further identify, by tandem mass spectrometry, some of the peptides that were consistently elevated in cancer mice compared to their control littermates.

  17. High Throughput Quantitative Analysis of Serum Proteins Using Glycopeptide Capture and Liquid Chromatography Mass Spectrometry

    SciTech Connect

    Zhang, Hui; Yi, Eugene C.; Li, Xiao-jun; Mallick, Parag; Kelly-Spratt, Karen S.; Masselon, Christophe D.; Camp, David G.; Smith, Richard D.; Kemp, Christopher J.; Aebersold, Reudi

    2005-02-01

    It is expected that the composition of the serum proteome can provide valuable information about the state of the human body in health and disease and that this information can be extracted via quantitative proteomic measurements. Suitable proteomic techniques need to be sensitive, reproducible, and robust to detect potential biomarkers below the level of highly expressed proteins, generate data sets that are comparable between experiments and laboratories, and have high throughput to support statistical studies. Here we report a method for high throughput quantitative analysis of serum proteins. It consists of the selective isolation of peptides that are N-linked glycosylated in the intact protein, the analysis of these now deglycosylated peptides by liquid chromatography electrospray ionization mass spectrometry, and the comparative analysis of the resulting patterns. By focusing selectively on a few formerly N-linked glycopeptides per serum protein, the complexity of the analyte sample is significantly reduced and the sensitivity and throughput of serum proteome analysis are increased compared with the analysis of total tryptic peptides from unfractionated samples. We provide data that document the performance of the method and show that sera from untreated normal mice and genetically identical mice with carcinogen-induced skin cancer can be unambiguously discriminated using unsupervised clustering of the resulting peptide patterns. We further identify, by tandem mass spectrometry, some of the peptides that were consistently elevated in cancer mice compared with their control littermates.

  18. Investigating reference genes for quantitative real-time PCR analysis across four chicken tissues.

    PubMed

    Bagés, S; Estany, J; Tor, M; Pena, R N

    2015-04-25

    Accurate normalization of data is required to correct for different efficiencies and errors during the processing of samples in reverse transcription PCR analysis. The chicken is one of the main livestock species and its genome was one of the first reported and used in large scale transcriptomic analysis. Despite this, the chicken has not been investigated regarding the identification of reference genes suitable for the quantitative PCR analysis of growth and fattening genes. In this study, five candidate reference genes (B2M, RPL32, SDHA, TBP and YWHAZ) were evaluated to determine the most stable internal reference for quantitative PCR normalization in the two main commercial muscles (pectoralis major (breast) and biceps femoris (thigh)), liver and abdominal fat. Four statistical methods (geNorm, NormFinder, CV and BestKeeper) were used in the evaluation of the most suitable combination of reference genes. Additionally, a comprehensive ranking was established with the RefFinder tool. This analysis identified YWHAZ and TBP as the recommended combination for the analysis of biceps femoris and liver, YWHAZ and RPL32 for pectoralis major and RPL32 and B2M for abdominal fat and across-tissue studies. The final ranking for each tool changed slightly but overall the results, and most particularly the ability to discard the least robust candidates, were consistent between tools. The selection and number of reference genes were validated using SCD, a target gene related to fat metabolism. Overall, the results can be directly used to quantitate target gene expression in different tissues or in validation studies from larger transcriptomic experiments. PMID:25680290

  19. 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. PMID:25529686

  20. Power Analysis of Artificial Selection Experiments Using Efficient Whole Genome Simulation of Quantitative Traits

    PubMed Central

    Kessner, Darren; Novembre, John

    2015-01-01

    Evolve and resequence studies combine artificial selection experiments with massively parallel sequencing technology to study the genetic basis for complex traits. In these experiments, individuals are selected for extreme values of a trait, causing alleles at quantitative trait loci (QTL) to increase or decrease in frequency in the experimental population. We present a new analysis of the power of artificial selection experiments to detect and localize quantitative trait loci. This analysis uses a simulation framework that explicitly models whole genomes of individuals, quantitative traits, and selection based on individual trait values. We find that explicitly modeling QTL provides qualitatively different insights than considering independent loci with constant selection coefficients. Specifically, we observe how interference between QTL under selection affects the trajectories and lengthens the fixation times of selected alleles. We also show that a substantial portion of the genetic variance of the trait (50–100%) can be explained by detected QTL in as little as 20 generations of selection, depending on the trait architecture and experimental design. Furthermore, we show that power depends crucially on the opportunity for recombination during the experiment. Finally, we show that an increase in power is obtained by leveraging founder haplotype information to obtain allele frequency estimates. PMID:25672748

  1. Quantitative analysis of suspicious thyroid nodules by contrast-enhanced ultrasonography

    PubMed Central

    Hu, Yizhou; Li, Ping; Jiang, Shufei; Li, Fenghua

    2015-01-01

    Objective: This study aimed to investigate the characteristics of suspicious thyroid nodules of different pathological types on contrast-enhanced ultrasound (CEUS) with quantitative analysis software (Qlab). Methods: A total of 101 suspicious thyroid nodules were recruited from 90 adult patients undergoing ultrasound (US), CEUS and fine-needle aspiration cytology (FNCA). The CEUS characteristics were quantitatively analyzed by investigators blind to the pathological information. Results: In 68 benign thyroid nodules, the proportion of single nodules was higher (54.4%) than that of miliary nodules (n = 2-4), and most of them were identical-in, slow-out and hypoenhancement as compared to adjacent normal tissues. In 17 malignant thyroid nodules, most of them were slow-in, identical-out and more hypoenhancement as compared to adjacent normal tissues on CEUS. Conclusion: Benign thyroid nodules show identical-in, slow-out and hypoenhancement while malignant thyroid nodules have slow-in, identical-out and more hypoenhancement as compared to adjacent normal tissues on CEUS. Quantitative analysis of thyroid nodules on CEUS may help to identify suspicious nodules and select a proper treatment. PMID:26380019

  2. Quantitative scintigraphy with deconvolutional analysis for the dynamic measurement of hepatic function

    SciTech Connect

    Tagge, E.P.; Campbell, D.A. Jr.; Reichle, R.; Averill, D.R. Jr.; Merion, R.M.; Dafoe, D.C.; Turcotte, J.G.; Juni, J.E.

    1987-06-01

    A mathematical technique known as deconvolutional analysis was used to provide a critical and previously missing element in the computations required to quantitate hepatic function scintigraphically. This computer-assisted technique allowed for the determination of the time required, in minutes, of a labeled bilirubin analog (/sup 99m/Tc-disofenin) to enter the liver via blood and exit via bile. This interval was referred to as the mean transit time (MTT). The critical process provided for by deconvolution is the mathematical simulation of a bolus injection of tracer directly into the afferent blood supply of the liver. The raw data required for this simulation are obtained from the intravenous injection of labeled disofenin, a member of the HIDA family of radiopharmaceuticals. In this study, we perform experiments which document that the simulation process itself is accurate. We then calculate the MTT under a variety of experimental conditions involving progressive hepatic ischemia/reperfusion injury and correlate these results with the results of simultaneously performed BSP determinations and hepatic histology. The experimental group with the most pronounced histologic findings (necrosis, vacuolization, disorganization of hepatic cords) also have the most prolonged MTT and BSP half-life. However, both quantitative imaging and BSP testing are able to identify milder degrees of hepatic ischemic injury not reflected in the histologic evaluation. Quantitative imaging with deconvolutional analysis is a technique easily adaptable to the standard nuclear medicine minicomputer. It provides rapid results and appears to be a sensitive monitor of hepatic functional disturbances resulting from ischemia and reperfusion.

  3. Quantitative analysis of phytosterols in edible oils using APCI liquid chromatography-tandem mass spectrometry

    PubMed Central

    Mo, Shunyan; Dong, Linlin; Hurst, W. Jeffrey; van Breemen, Richard B.

    2014-01-01

    Previous methods for the quantitative analysis of phytosterols have usually used GC-MS and require elaborate sample preparation including chemical derivatization. Other common methods such as HPLC with absorbance detection do not provide information regarding the identity of the analytes. To address the need for an assay that utilizes mass selectivity while avoiding derivatization, a quantitative method based on LC-tandem mass spectrometry (LC-MS-MS) was developed and validated for the measurement of six abundant dietary phytosterols and structurally related triterpene alcohols including brassicasterol, campesterol, cycloartenol, ?-sitosterol, stigmasterol, and lupeol in edible oils. Samples were saponified, extracted with hexane and then analyzed using reversed phase HPLC with positive ion atmospheric pressure chemical ionization tandem mass spectrometry and selected reaction monitoring. The utility of the LC-MS-MS method was demonstrated by analyzing 14 edible oils. All six compounds were present in at least some of the edible oils. The most abundant phytosterol in all samples was ?-sitosterol, which was highest in corn oil at 4.35 ± 0.03 mg/g, followed by campesterol in canola oil at 1.84 ± 0.01 mg/g. The new LC-MS-MS method for the quantitative analysis of phytosterols provides a combination of speed, selectivity and sensitivity that exceed those of previous assays. PMID:23884629

  4. Quantitative Analysis in the General Chemistry Laboratory: Training Students to Analyze Individual Results in the Context of Collective Data

    ERIC Educational Resources Information Center

    Ling, Chris D.; Bridgeman, Adam J.

    2011-01-01

    Titration experiments are ideal for generating large data sets for use in quantitative-analysis activities that are meaningful and transparent to general chemistry students. We report the successful implementation of a sophisticated quantitative exercise in which the students identify a series of unknown acids by determining their molar masses…

  5. Analysis of nuclear organization with TANGO, software for high-throughput quantitative analysis of 3D fluorescence microscopy images.

    PubMed

    Ollion, Jean; Cochennec, Julien; Loll, François; Escudé, Christophe; Boudier, Thomas

    2015-01-01

    The cell nucleus is a highly organized cellular organelle that contains the genome. An important step to understand the relationships between genome positioning and genome functions is to extract quantitative data from three-dimensional (3D) fluorescence imaging. However, such approaches are limited by the requirement for processing and analyzing large sets of images. Here we present a practical approach using TANGO (Tools for Analysis of Nuclear Genome Organization), an image analysis tool dedicated to the study of nuclear architecture. TANGO is a generic tool able to process large sets of images, allowing quantitative study of nuclear organization. In this chapter a practical description of the software is drawn in order to give an overview of its different concepts and functionalities. This description is illustrated with a precise example that can be performed step-by-step on experimental data provided on the website http://biophysique.mnhn.fr/tango/HomePage. PMID:25311132

  6. Quantitative Reverse Transcription-qPCR-Based Gene Expression Analysis in Plants.

    PubMed

    Abdallah, Heithem Ben; Bauer, Petra

    2016-01-01

    The investigation of gene expression is an initial and essential step to understand the function of a gene in a physiological context. Reverse transcription-quantitative real-time PCR (RT-qPCR) assays are reproducible, quantitative, and fast. They can be adapted to study model and non-model plant species without the need to have whole genome or transcriptome sequence data available. Here, we provide a protocol for a reliable RT-qPCR assay, which can be easily adapted to any plant species of interest. We describe the design of the qPCR strategy and primer design, considerations for plant material generation, RNA preparation and cDNA synthesis, qPCR setup and run, and qPCR data analysis, interpretation, and final presentation. PMID:26577777

  7. Fourier transform infrared spectroscopy quantitative analysis of SF6 partial discharge decomposition components

    NASA Astrophysics Data System (ADS)

    Zhang, Xiaoxing; Liu, Heng; Ren, Jiangbo; Li, Jian; Li, Xin

    2015-02-01

    Gas-insulated switchgear (GIS) internal SF6 gas produces specific decomposition components under partial discharge (PD). By detecting these characteristic decomposition components, such information as the type and level of GIS internal insulation deterioration can be obtained effectively, and the status of GIS internal insulation can be evaluated. SF6 was selected as the background gas for Fourier transform infrared spectroscopy (FTIR) detection in this study. SOF2, SO2F2, SO2, and CO were selected as the characteristic decomposition components for system analysis. The standard infrared absorption spectroscopy of the four characteristic components was measured, the optimal absorption peaks were recorded and the corresponding absorption coefficient was calculated. Quantitative detection experiments on the four characteristic components were conducted. The volume fraction variation trend of four characteristic components at different PD time were analyzed. And under five different PD quantity, the quantitative relationships among gas production rate, PD time, and PD quantity were studied.

  8. Fourier transform infrared spectroscopy quantitative analysis of SF6 partial discharge decomposition components.

    PubMed

    Zhang, Xiaoxing; Liu, Heng; Ren, Jiangbo; Li, Jian; Li, Xin

    2015-02-01

    Gas-insulated switchgear (GIS) internal SF6 gas produces specific decomposition components under partial discharge (PD). By detecting these characteristic decomposition components, such information as the type and level of GIS internal insulation deterioration can be obtained effectively, and the status of GIS internal insulation can be evaluated. SF6 was selected as the background gas for Fourier transform infrared spectroscopy (FTIR) detection in this study. SOF2, SO2F2, SO2, and CO were selected as the characteristic decomposition components for system analysis. The standard infrared absorption spectroscopy of the four characteristic components was measured, the optimal absorption peaks were recorded and the corresponding absorption coefficient was calculated. Quantitative detection experiments on the four characteristic components were conducted. The volume fraction variation trend of four characteristic components at different PD time were analyzed. And under five different PD quantity, the quantitative relationships among gas production rate, PD time, and PD quantity were studied. PMID:25459612

  9. TOPICAL REVIEW Quantitative strain analysis of surfaces and interfaces using extremely asymmetric x-ray diffraction

    NASA Astrophysics Data System (ADS)

    Akimoto, Koichi; Emoto, Takashi

    2010-12-01

    Strain can reduce carrier mobility and the reliability of electronic devices and affect the growth mode of thin films and the stability of nanometer-scale crystals. To control lattice strain, a technique for measuring the minute lattice strain at surfaces and interfaces is needed. Recently, an extremely asymmetric x-ray diffraction method has been developed for this purpose. By employing Darwin's dynamical x-ray diffraction theory, quantitative evaluation of strain at surfaces and interfaces becomes possible. In this paper, we review our quantitative strain analysis studies on native SiO2/Si interfaces, reconstructed Si surfaces, Ni/Si(111)-H interfaces, sputtered III-V compound semiconductor surfaces, high-k/Si interfaces, and Au ion-implanted Si.

  10. Mechanical Model Analysis for Quantitative Evaluation of Liver Fibrosis Based on Ultrasound Tissue Elasticity Imaging

    NASA Astrophysics Data System (ADS)

    Shiina, Tsuyoshi; Maki, Tomonori; Yamakawa, Makoto; Mitake, Tsuyoshi; Kudo, Masatoshi; Fujimoto, Kenji

    2012-07-01

    Precise evaluation of the stage of chronic hepatitis C with respect to fibrosis has become an important issue to prevent the occurrence of cirrhosis and to initiate appropriate therapeutic intervention such as viral eradication using interferon. Ultrasound tissue elasticity imaging, i.e., elastography can visualize tissue hardness/softness, and its clinical usefulness has been studied to detect and evaluate tumors. We have recently reported that the texture of elasticity image changes as fibrosis progresses. To evaluate fibrosis progression quantitatively on the basis of ultrasound tissue elasticity imaging, we introduced a mechanical model of fibrosis progression and simulated the process by which hepatic fibrosis affects elasticity images and compared the results with those clinical data analysis. As a result, it was confirmed that even in diffuse diseases like chronic hepatitis, the patterns of elasticity images are related to fibrous structural changes caused by hepatic disease and can be used to derive features for quantitative evaluation of fibrosis stage.

  11. A voxel-map quantitative analysis approach for atherosclerotic noncalcified plaques of the coronary artery tree.

    PubMed

    Li, Ying; Chen, Wei; Liu, Kaijun; Wu, Yi; Chen, Yonglin; Chu, Chun; Fang, Bingji; Tan, Liwen; Zhang, Shaoxiang

    2013-01-01

    Noncalcified plaques (NCPs) are associated with the presence of lipid-core plaques that are prone to rupture. Thus, it is important to detect and monitor the development of NCPs. Contrast-enhanced coronary Computed Tomography Angiography (CTA) is a potential imaging technique to identify atherosclerotic plaques in the whole coronary tree, but it fails to provide information about vessel walls. In order to overcome the limitations of coronary CTA and provide more meaningful quantitative information for percutaneous coronary intervention (PCI), we proposed a Voxel-Map based on mathematical morphology to quantitatively analyze the noncalcified plaques on a three-dimensional coronary artery wall model (3D-CAWM). This approach is a combination of Voxel-Map analysis techniques, plaque locating, and anatomical location related labeling, which show more detailed and comprehensive coronary tree wall visualization. PMID:24348749

  12. Quantitative Analysis of Snake Venoms Using Soluble Polymer-based Isotope Labeling*S?

    PubMed Central

    Galan, Jacob A.; Guo, Minjie; Sanchez, Elda E.; Cantu, Esteban; Rodriguez-Acosta, Alexis; Perez, John C.; Tao, W. Andy

    2008-01-01

    We present the design and synthesis of a new quantitative strategy termed soluble polymer-based isotope labeling (SoPIL) and its application as a novel and inclusive method for the identification and relative quantification of individual proteins in complex snake venoms. The SoPIL reagent selectively captures and isolates cysteine-containing peptides, and the subsequent tagged peptides are released and analyzed using nanoflow liquid chromatography-tandem mass spectrometry. The SoPIL strategy was used to quantify venom proteins from two pairs of venomous snakes: Crotalus scutulatus scutulatus type A, C. scutulatus scutulatus type B, Crotalus oreganus helleri, and Bothrops colombiensis. The hemorrhagic, hemolytic, clotting ability, and fibrinogenolytic activities of crude venoms were measured and correlated with difference in protein abundance determined by the SoPIL analysis. The SoPIL approach could provide an efficient and widely applicable tool for quantitative proteomics. PMID:18089550

  13. Kinetics analysis and quantitative calculations for the successive radioactive decay process

    NASA Astrophysics Data System (ADS)

    Zhou, Zhiping; Yan, Deyue; Zhao, Yuliang; Chai, Zhifang

    2015-01-01

    The general radioactive decay kinetics equations with branching were developed and the analytical solutions were derived by Laplace transform method. The time dependence of all the nuclide concentrations can be easily obtained by applying the equations to any known radioactive decay series. Taking the example of thorium radioactive decay series, the concentration evolution over time of various nuclide members in the family has been given by the quantitative numerical calculations with a computer. The method can be applied to the quantitative prediction and analysis for the daughter nuclides in the successive decay with branching of the complicated radioactive processes, such as the natural radioactive decay series, nuclear reactor, nuclear waste disposal, nuclear spallation, synthesis and identification of superheavy nuclides, radioactive ion beam physics and chemistry, etc.

  14. Noninvasive Characterization of Locally Advanced Breast Cancer Using Textural Analysis of Quantitative Ultrasound Parametric Images

    PubMed Central

    Tadayyon, Hadi; Sadeghi-Naini, Ali; Czarnota, Gregory J.

    2014-01-01

    PURPOSE: The identification of tumor pathologic characteristics is an important part of breast cancer diagnosis, prognosis, and treatment planning but currently requires biopsy as its standard. Here, we investigated a noninvasive quantitative ultrasound method for the characterization of breast tumors in terms of their histologic grade, which can be used with clinical diagnostic ultrasound data. METHODS: Tumors of 57 locally advanced breast cancer patients were analyzed as part of this study. Seven quantitative ultrasound parameters were determined from each tumor region from the radiofrequency data, including mid-band fit, spectral slope, 0-MHz intercept, scatterer spacing, attenuation coefficient estimate, average scatterer diameter, and average acoustic concentration. Parametric maps were generated corresponding to the region of interest, from which four textural features, including contrast, energy, homogeneity, and correlation, were determined as further tumor characterization parameters. Data were examined on the basis of tumor subtypes based on histologic grade (grade I versus grade II to III). RESULTS: Linear discriminant analysis of the means of the parametric maps resulted in classification accuracy of 79%. On the other hand, the linear combination of the texture features of the parametric maps resulted in classification accuracy of 82%. Finally, when both the means and textures of the parametric maps were combined, the best classification accuracy was obtained (86%). CONCLUSIONS: Textural characteristics of quantitative ultrasound spectral parametric maps provided discriminant information about different types of breast tumors. The use of texture features significantly improved the results of ultrasonic tumor characterization compared to conventional mean values. Thus, this study suggests that texture-based quantitative ultrasound analysis of in vivo breast tumors can provide complementary diagnostic information about tumor histologic characteristics. PMID:25500086

  15. Quantitative and Qualitative Analysis of the Quality of Life of Individuals With Eating Disorders

    PubMed Central

    McCune, Ashley M.; Mandal, Konoy; Lundgren, Jennifer D.

    2015-01-01

    Objective: To examine the quality of a broad range of life domains using both quantitative and qualitative methodologies. Method: Forty-eight individuals seeking inpatient treatment for an eating disorder (mean age = 29.8 years, female = 100%, white = 96.4%) from 2007 to 2009 completed the Quality of Life Inventory (QOLI) and the Eating Disorder Examination Questionnaire; a medical chart review confirmed diagnosis and treatment history. Patients diagnosed with anorexia nervosa (n = 24) and bulimia nervosa (n = 24) were compared. Body mass index (kg/m2), treatment history, number of comorbid psychiatric conditions, and eating disorder severity were used to predict quality of life. Finally, an inductive content analysis was performed on qualitative QOLI responses to contextualize the quantitative findings. Results: Participants with anorexia nervosa, compared to those with bulimia nervosa, reported significantly less satisfaction with the domain of relatives (F1,46 = 5.35; P = .025); no other significant group differences were found. The only significant predictor of QOLI global score was number of previous treatments (F1,41 = 8.67; P = .005; R2 = 0.175). Content analysis of qualitative data yielded complementary findings to the quantitative data; interesting group differences emerged for satisfaction with health with implications for measuring quality of life domains. Conclusions: Across several life domains, individuals seeking treatment for anorexia nervosa and bulimia nervosa appear to have similar levels of satisfaction, as evidenced by numeric and descriptive responses. Satisfaction with relatives, however, appears to differ between groups and suggests a specific target for intervention among patients in treatment for anorexia nervosa (eg, a family-based intervention such as the Maudsley approach). The use of quantitative and qualitative assessments, such as the QOLI, provides more clinically meaningful, contextualized information about quality of life than traditional self-report assessments alone. PMID:26445689

  16. Aqua-planet simulations of the formation of the South Atlantic convergence zone

    NASA Technical Reports Server (NTRS)

    Nieto Ferreira, Rosana; Chao, Winston C.

    2013-01-01

    The impact of Amazon Basin convection and cold fronts on the formation and maintenance of the South Atlantic convergence zone (SACZ) is studied using aqua-planet simulations with a general circulation model. In the model, a circular patch of warm sea-surface temperature (SST) is used to mimic the effect of the Amazon Basin on South American monsoon convection. The aqua-planet simulations were designed to study the effect of the strength and latitude of Amazon Basin convection on the formation of the SACZ. The simulations indicate that the strength of the SACZ increases as the Amazon convection intensifies and is moved away from the equator. Of the two controls studied here, the latitude of the Amazon convection exerts the strongest effect on the strength of the SACZ. An analysis of the synoptic-scale variability in the simulations shows the importance of frontal systems in the formation of the aqua-planet SACZ. Composite time series of frontal systems that occurred in the simulations show that a robust SACZ occurs when fronts penetrate into the subtropics and become stationary there as they cross eastward of the longitude of the Amazon Basin. Moisture convergence associated with these frontal systems produces rainfall not along the model SACZ region and along a large portion of the northern model Amazon Basin. Simulations in which the warm SST patch was too weak or too close to the equator did not produce frontal systems that extended into the tropics and became stationary, and did not form a SACZ. In the model, the SACZ forms as Amazon Basin convection strengthens and migrates far enough southward to allow frontal systems to penetrate into the tropics and stall over South America. This result is in agreement with observations that the SACZ tends to form after the onset of the monsoon season in the Amazon Basin.

  17. Qualitative and quantitative analysis of calcium-based microfillers using terahertz spectroscopy and imaging.

    PubMed

    Abina, Andreja; Puc, Uroš; Jegli?, Anton; Prah, Jana; Venckevi?ius, Rimvydas; Kašalynas, Irmantas; Valušis, Gintaras; Zidanšek, Aleksander

    2015-10-01

    In different industrial applications, several strictly defined parameters of calcium-based microfillers such as average particle size, particle size distribution, morphology, specific surface area, polymorphism and chemical purity, play a key role in the determination of its usefulness and effectiveness. Therefore, an analytical tool is required for rapid and non-destructive characterization of calcium-based microfillers during the synthesis process or before its use in a further manufacturing process. Since spectroscopic techniques are preferred over microscopy and thermogravimetry, particularly due to its non-destructive nature and short analysis time, we applied terahertz (THz) spectroscopy to analyse calcite microfillers concentration in polymer matrix, its granulation and chemical treatment. Based on the analysis of peak absorbance amplitude, peak frequency position, and the appearance of additional spectral features, quantitative and qualitative analysis was successfully achieved. In addition, THz imaging was also applied for both quantitative and qualitative analysis of calcium-based microfillers. By using spatial distribution map, the inhomogeneity in concentration of calcium carbonate in polymer matrix was characterized. Moreover, by THz spectroscopy and imaging different calcium compounds were detected in binary mixtures. Finally, we demonstrated that the applied spectroscopic technique offers valuable results and can be, in combination with other spectroscopic and microscopic techniques, converted to a powerful rapid analytical tool. PMID:26078145

  18. Acousto-Optic Tunable Filter Spectroscopic Instrumentation for Quantitative Near-Ir Analysis of Organic Materials.

    NASA Astrophysics Data System (ADS)

    Eilert, Arnold James

    1995-01-01

    The utility of near-IR spectroscopy for routine quantitative analyses of a wide variety of compositional, chemical, or physical parameters of organic materials is well understood. It can be used for relatively fast and inexpensive non-destructive bulk material analysis before, during, and after processing. It has been demonstrated as being a particularly useful technique for numerous analytical applications in cereal (food and feed) science and industry. Further fulfillment of the potential of near-IR spectroscopic analysis, both in the process and laboratory environment, is reliant upon the development of instrumentation that is capable of meeting the challenges of increasingly difficult applications. One approach to the development of near-IR spectroscopic instrumentation that holds a great deal of promise is acousto-optic tunable filter (AOTF) technology. A combination of attributes offered by AOTF spectrometry, including speed, optical throughput, wavelength reproducibility, ruggedness (no -moving-parts operation) and flexibility, make it particularly desirable for numerous applications. A series of prototype (research model) acousto -optic tunable filter instruments were developed and tested in order to investigate the feasibility of the technology for quantitative near-IR spectrometry. Development included design, component procurement, assembly and/or configuration of the optical and electronic subsystems of which each functional spectrometer arrangement was comprised, as well as computer interfacing and acquisition/control software development. Investigation of this technology involved an evolution of several operational spectrometer systems, each of which offered improvements over its predecessor. Appropriate testing was conducted at various stages of development. Demonstrations of the potential applicability of our AOTF spectrometer to quantitative process monitoring or laboratory analysis of numerous organic substances, including food materials, were performed. Lipid determination in foods by spectroscopic analysis of a solvent used after cold batch extraction and simulated supercritical fluid extraction monitoring were among the applications tested. The ultimate performance specifications of our instrument included full-range wavelength coverage from 1250 to 2400 nm (with random, segmented range, or continuous range wavelength access capability), real -time quantitative analysis rates in excess of 150 determinations per second, and full range (2 nm increment) scanning speeds of 200 milliseconds.

  19. EXTRACTION AND QUANTITATIVE ANALYSIS OF ELEMENTAL SULFUR FROM SULFIDE MINERAL SURFACES BY HIGH-PERFORMANCE LIQUID CHROMATOGRAPHY. (R826189)

    EPA Science Inventory

    A simple method for the quantitative determination of elemental sulfur on oxidized sulfide minerals is described. Extraction of elemental sulfur in perchloroethylene and subsequent analysis with high-performance liquid chromatography were used to ascertain the total elemental ...

  20. Benchtop testing of polyethylene passive sampling towards a quantitative analysis of volatile organic compounds (VOCs) in soil vapours

    E-print Network

    Soo, Yu Xiang Jaren

    2015-01-01

    The feasibility of polyethylene (PE) as a passive sampler for quantitative analysis of volatile organic compounds (VOCs) was analysed in this work by means of a benchtop testing. A benchtop physical model was setup, which ...

  1. Development of a computer-aided fault tree synthesis methodology for quantitative risk analysis in the chemical process industry 

    E-print Network

    Wang, Yanjun

    2005-02-17

    -1 DEVELOPMENT OF A COMPUTER-AIDED FAULT TREE SYNTHESIS METHODOLOGY FOR QUANTITATIVE RISK ANALYSIS IN THE CHEMICAL PROCESS INDUSTRY A Dissertation by YANJUN WANG Submitted to the Office of Graduate Studies of Texas A&M University in partial... fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY December 2004 Major Subject: Chemical Engineering DEVELOPMENT OF A COMPUTER-AIDED FAULT TREE SYNTHESIS METHODOLOGY FOR QUANTITATIVE RISK ANALYSIS...

  2. Biomonitoring and risk assessment on earth and during exploratory missions using AquaHab ®

    NASA Astrophysics Data System (ADS)

    Slenzka, K.; Dünne, M.; Jastorff, B.

    2008-12-01

    Bioregenerative closed ecological life support systems (CELSS) will be necessary in the exploration context revitalizing atmosphere, waste water and producing food for the human CELSS mates. During these long-term space travels and stays far away from Earth in an hostile environment as well as far for example from any hospital and surgery potential, it will be necessary to know much more about chemical and drug contamination in the special sense and by human's themselves in detail. Additionally, there is a strong need on Earth for more relevant standardized test systems including aquatic ones for the prospective risk assessment of chemicals and drugs in general on a laboratory scale. Current standardized test systems are mono species tests, and thus do not represent system aspects and have reduced environmental relevance. The experience gained during the last years in our research group lead to the development of a self-sustaining closed aquatic habitat/facility, called AquaHab ® which can serve regarding space exploration and Earth application. The AquaHab ® module can be the home of several fish species, snails, plants, amphipods and bacteria. The possibility to use different effect endpoints with certain beneficial characteristics is the basis for the application of AquaHab ® in different fields. Influence of drugs and chemicals can be tested on several trophic levels and ecosystem levels; guaranteeing a high relevance for aquatic systems in the real environment. Analyses of effect parameters of different complexity (e.g. general biological and water chemical parameters, activity of biotransforming enzymes) result in broad spectra of sensitivity. Combined with residual analyses (including all metabolites), this leads to an extended prospective risk assessment of a chemical on Earth and in a closed Life Support System. The possibility to measure also sensitive "online" parameters (e.g. behavior, respiration/photosynthetic activity) enables a quick and sensitive effect analysis of water contaminants in respective environments. AquaHab ® is currently under development to an early warning biomonitoring system using genetically modified fish and green algae. The implementation of biosensors/biochip in addition is also discussed.

  3. Qualitative and quantitative analysis of environmental samples by laser-induced breakdown spectrometry

    NASA Astrophysics Data System (ADS)

    Zorov, N. B.; Popov, A. M.; Zaytsev, S. M.; Labutin, T. A.

    2015-10-01

    The key achievements in the determination of trace amounts of components in environmental samples (soils, ores, natural waters, etc.) by laser-induced breakdown spectrometry are considered. Unique capabilities of this method make it suitable for rapid analysis of metals and alloys, glasses, polymers, objects of cultural heritage, archaeological and various environmental samples. The key advantages of the method that account for its high efficiency are demonstrated, in particular, a small amount of analyzed material, the absence of sample preparation, the possibility of local and remote analysis of either one or several elements. The use of chemometrics in laser-induced breakdown spectrometry for qualitative sample classification is described in detail. Various approaches to improving the figures of merit of quantitative analysis of environmental samples are discussed. The achieved limits of detection for most elements in geochemical samples are critically evaluated. The bibliography includes 302 references.

  4. Quantitative analysis of Si/SiGeC superlattices using atom probe tomography.

    PubMed

    Estivill, Robert; Grenier, Adeline; Duguay, Sébastien; Vurpillot, François; Terlier, Tanguy; Barnes, Jean-Paul; Hartmann, Jean-Michel; Blavette, Didier

    2015-12-01

    SiGe and its alloys are used as key materials in innovative electronic devices. The analysis of these materials together with the localisation of dopants and impurities on a very fine scale is of crucial importance for better understanding their electronic properties. The quantification of carbon and germanium in an as-grown Si/SiGeC superlattice has been investigated using Atom Probe Tomography as a function of analysis conditions and sample anneal temperature. The mass spectrum is heavily influenced by the analysis conditions and chemical identification is needed. It was found that quantitative results are obtained using a intermediate electric field. The evaporation of carbon ions shows a strong spatial and temporal correlation. A series of annealed samples have been analysed, presenting an inhomogeneous carbon distribution, appearing in the shape of small clusters. These findings confirm previous results and give a better understanding of the processes occurring in these technologically important materials. PMID:25814020

  5. Quantitative LC-MS/MS Analysis of Proteins Involved in Metastasis of Breast Cancer.

    PubMed

    Goto, Rieko; Nakamura, Yasushi; Takami, Tomonori; Sanke, Tokio; Tozuka, Zenzaburo

    2015-01-01

    The purpose of this study was to develop quantitative liquid chromatography-tandem mass spectrometry (LC-MS/MS) methods for the analysis of proteins involved in metastasis of breast cancer for diagnosis and determining disease prognosis, as well as to further our understand of metastatic mechanisms. We have previously demonstrated that the protein type XIV collagen may be specifically expressed in metastatic tissues by two dimensional LC-MS/MS. In this study, we developed quantitative LC-MS/MS methods for type XIV collagen. Type XIV collagen was quantified by analyzing 2 peptides generated by digesting type XIV collagen using stable isotope-labeled peptides. The individual concentrations were equivalent between 2 different peptides of type XIV collagen by evaluation of imprecise transitions and using the best transition for the peptide concentration. The results indicated that type XIV collagen is highly expressed in metastatic tissues of patients with massive lymph node involvement compared to non-metastatic tissues. These findings were validated by quantitative real-time RT-PCR. Further studies on type XIV collagen are desired to verify its role as a prognostic factor and diagnosis marker for metastasis. PMID:26176947

  6. Quantitative proteomic analysis for high-throughput screening of differential glycoproteins in hepatocellular carcinoma serum

    PubMed Central

    Gao, Hua-Jun; Chen, Ya-Jing; Zuo, Duo; Xiao, Ming-Ming; Li, Ying; Guo, Hua; Zhang, Ning; Chen, Rui-Bing

    2015-01-01

    Objective Hepatocellular carcinoma (HCC) is a leading cause of cancer-related deaths. Novel serum biomarkers are required to increase the sensitivity and specificity of serum screening for early HCC diagnosis. This study employed a quantitative proteomic strategy to analyze the differential expression of serum glycoproteins between HCC and normal control serum samples. Methods Lectin affinity chromatography (LAC) was used to enrich glycoproteins from the serum samples. Quantitative mass spectrometric analysis combined with stable isotope dimethyl labeling and 2D liquid chromatography (LC) separations were performed to examine the differential levels of the detected proteins between HCC and control serum samples. Western blot was used to analyze the differential expression levels of the three serum proteins. Results A total of 2,280 protein groups were identified in the serum samples from HCC patients by using the 2D LC-MS/MS method. Up to 36 proteins were up-regulated in the HCC serum, whereas 19 proteins were down-regulated. Three differential glycoproteins, namely, fibrinogen gamma chain (FGG), FOS-like antigen 2 (FOSL2), and ?-1,6-mannosylglycoprotein 6-?-N-acetylglucosaminyltransferase B (MGAT5B) were validated by Western blot. All these three proteins were up-regulated in the HCC serum samples. Conclusion A quantitative glycoproteomic method was established and proven useful to determine potential novel biomarkers for HCC. PMID:26487969

  7. Qualitative and quantitative environmental analysis by capillary column gas chromatography/lightpipe Fourier transform infrared spectrometry

    SciTech Connect

    Gurka, D.F.; Pyle, S.M.

    1988-08-01

    A new state-of-art commercial gas chromatography/Fourier transform infrared (GC/FT-IR) lightpipe-containing system has been evaluated for its applicability to qualitative and quantitative environmental analysis of typical environmental contaminants. This system exhibited minimum identifiable quantities, for many compounds, in the 10-50-ng range. On a wide-bore capillary column, quantitation curves generated from chromatogram peak areas were linear over the 10-250-ng range. The mean correlation coefficient for 38 quantitation calibration curves on 24 standards was 0.976. The selectivity of the new system was evaluated with standards, soil, and still-bottom samples. It was demonstrated with 27 standards that no discernible loss in identification selectivity occurred when a narrow-band infrared detector (spectral cutoff 750 cm/sup -1/) was used in place of a midband detector (cutoff 700 cm/sup -1/). This allows the meaningful utilization of the extra sensitivity associated with narrower frequency range infrared detectors.

  8. High-throughput pesticide residue quantitative analysis achieved by tandem mass spectrometry with automated flow injection.

    PubMed

    Nanita, Sergio C; Pentz, Anne M; Bramble, Frederick Q

    2009-04-15

    The use of automated flow injection with MS/MS detection for fast quantitation of agrochemicals in food and water samples was demonstrated in this study. Active ingredients from the sulfonylurea herbicide and carbamate insecticide classes were selected as model systems. Samples were prepared using typical procedures from residue methods, placed in an autosampler, and injected directly into a triple quadrupole instrument without chromatographic separation. The technique allows data acquisition in 15 s per injection, with samples being injected every 65 s, representing a significant improvement from the 15-30 min needed in typical HPLC/MS/MS methods. The availability of HPLC systems is an advantage since they can be used in flow-injection mode (bypassing the column compartment). Adequate accuracy, linearity, and precision (R(2) > 0.99 and RSD < 20%) were obtained using external standards prepared in each control matrix. The limit of quantitation (LOQ) achieved for all analytes was 0.01 mg/kg in food samples and 0.1 ng/mL in water; while limits of detection (LOD) were estimated to be about 0.003 mg/kg and 0.03 ng/mL in food and water, respectively. The advantages and limitations of flow injection MS/MS for ultratrace-level quantitative analysis in complex matrixes are discussed. PMID:19296591

  9. Structured Qualitative Research: Organizing “Mountains of Words” for Data Analysis, both Qualitative and Quantitative

    PubMed Central

    Johnson, Bruce D.; Dunlap, Eloise; Benoit, Ellen

    2008-01-01

    Qualitative research creates mountains of words. U.S. federal funding supports mostly structured qualitative research, which is designed to test hypotheses using semi-quantitative coding and analysis. The authors have 30 years of experience in designing and completing major qualitative research projects, mainly funded by the US National Institute on Drug Abuse [NIDA]. This article reports on strategies for planning, organizing, collecting, managing, storing, retrieving, analyzing, and writing about qualitative data so as to most efficiently manage the mountains of words collected in large-scale ethnographic projects. Multiple benefits accrue from this approach. Several different staff members can contribute to the data collection, even when working from remote locations. Field expenditures are linked to units of work so productivity is measured, many staff in various locations have access to use and analyze the data, quantitative data can be derived from data that is primarily qualitative, and improved efficiencies of resources are developed. The major difficulties involve a need for staff who can program and manage large databases, and who can be skillful analysts of both qualitative and quantitative data. PMID:20222777

  10. Quantitative LC-MS/MS Analysis of Proteins Involved in Metastasis of Breast Cancer

    PubMed Central

    Goto, Rieko; Nakamura, Yasushi; Takami, Tomonori; Sanke, Tokio; Tozuka, Zenzaburo

    2015-01-01

    The purpose of this study was to develop quantitative liquid chromatography-tandem mass spectrometry (LC-MS/MS) methods for the analysis of proteins involved in metastasis of breast cancer for diagnosis and determining disease prognosis, as well as to further our understand of metastatic mechanisms. We have previously demonstrated that the protein type XIV collagen may be specifically expressed in metastatic tissues by two dimensional LC-MS/MS. In this study, we developed quantitative LC-MS/MS methods for type XIV collagen. Type XIV collagen was quantified by analyzing 2 peptides generated by digesting type XIV collagen using stable isotope-labeled peptides. The individual concentrations were equivalent between 2 different peptides of type XIV collagen by evaluation of imprecise transitions and using the best transition for the peptide concentration. The results indicated that type XIV collagen is highly expressed in metastatic tissues of patients with massive lymph node involvement compared to non-metastatic tissues. These findings were validated by quantitative real-time RT-PCR. Further studies on type XIV collagen are desired to verify its role as a prognostic factor and diagnosis marker for metastasis. PMID:26176947

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

    PubMed

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

    2015-01-01

    There is an emerging demand for the use of molecular profiling to facilitate biomarker identification and development, and to stratify patients for more efficient treatment decisions with reduced adverse effects. In the past decade, great strides have been made to advance genomic, transcriptomic and proteomic approaches to address these demands. While there has been much progress with these large scale approaches, profiling at the protein level still faces challenges due to limitations in clinical sample size, poor reproducibility, unreliable quantitation, and lack of assay robustness. A novel automated capillary nano-immunoassay (CNIA) technology has been developed. This technology offers precise and accurate measurement of proteins and their post-translational modifications using either charge-based or size-based separation formats. The system not only uses ultralow nanogram levels of protein but also allows multi-analyte analysis using a parallel single-analyte format for increased sensitivity and specificity. The high sensitivity and excellent reproducibility of this technology make it particularly powerful for analysis of clinical samples. Furthermore, the system can distinguish and detect specific protein post-translational modifications that conventional Western blot and other immunoassays cannot easily capture. This review will summarize and evaluate the latest progress to optimize the CNIA system for comprehensive, quantitative protein and signaling event characterization. It will also discuss how the technology has been successfully applied in both discovery research and clinical studies, for signaling pathway dissection, proteomic biomarker assessment, targeted treatment evaluation and quantitative proteomic analysis. Lastly, a comparison of this novel system with other conventional immuno-assay platforms is performed. PMID:26048678

  12. ED-XRF analysis for Cultural Heritage: is quantitative evaluation always essential?

    NASA Astrophysics Data System (ADS)

    Bonizzoni, L.

    2015-07-01

    Energy Dispersive X-Ray Fluorescence (ED-XRF) is a very suitable tool for examination of Cultural Heritage materials because of its simplicity, with no requirement for any sample preparation and the possibility of operating with portable instruments, and it can probably be considered the most useful non-destructive analytical technique for ancient valuable objects of archaeological, historical or artistic interest. As regards the possibility of getting quantitative analysis in archaeometric applications, the problems arising from the limited sensitivity in detecting low Z elements, the irregular shape or the non-homogeneous composition of the sample have generated a widespread opinion that only semi-quantitative analyses are possible in XRF applications to archaeometry. In fact, this is always true for non-homogeneous samples as, typically, painting layers. On the contrary, the problems deriving from limited sensitivity in detecting matrix light elements as well as from irregular surface under analysis can be solved in most cases. Notwithstanding, working on unique and not standardized objects requires to pay attention on details and to know how to choose correct parameters and calculation algorithms to obtain reliable results. Indeed opportunities to deal with these objects are very limited and results have implication in other fields, so that each information about materials and production technique is of great interest. Two typical materials of archaeological interest showing particular features are considered - namely high corroded metallic artefacts and ceramics - revealing that, even if in cultural heritage field detailed quantitative analysis is the goal, it is not always necessary as also qualitative information by XRF spectra increase the knowledge of artefact.

  13. Portland Cement (KS and API Class G) and Relative Quantitative Analysis

    NASA Astrophysics Data System (ADS)

    LEE, Seung-Woo; CHAE, Gi-Tak; KIM, Taehee

    2015-04-01

    Portland cement is a common component consisting of a sealing material for wellbores for geological carbon storage to prevent vertical fluid migration and provide mechanical support. Portland cement was reacted with carbon dioxide (CO2) in supercritical, gaseous, and aqueous phases at various pressure and temperature conditions to simulate a cement-CO2 reaction along the wellbore from the carbon injection depth to the near surface. The reaction of the cement phase with CO2 can lead to important changes in its structure and properties. In this study, two types of cement were used: KS Portland cement and API Class G Portland cement. The hydrated cement sample columns (14 mm diameter X 90 mm long; water-to-cement ratio = 0.5) were reacted with CO2 in the saturated and the unsaturated condition. Fly-ash was used as additives to promote carbonation. These conditions were maintained under high pressure (8 MPa) and temperature (40 degree Celsius) for 10 and 100 days. To analyze the degree of carbonation after cement carbonation, relative quantitative analysis was proposed. And Rietveld method were conducted to evaluate a relative quantitative analysis (RQA) with an aragonite-calcite equation. This method can be an alternative to the general quantitative analysis method to identify the state of cement carbonation between Portland cement and CO2. Based on an understanding of cement carbonation and its relative quantification, we propose that our method should be used to select the optimized cement for CO2 storage. Using our method, KS (Korea Standard) Portland cement (type I) and API Class G Portland cement have been compared with respect to the characterization of each cement and to the cement carbonation of each cement.

  14. Quantitative Analysis of Food and Feed Samples with Droplet Digital PCR

    PubMed Central

    Morisset, Dany; Štebih, Dejan; Milavec, Mojca; Gruden, Kristina; Žel, Jana

    2013-01-01

    In this study, the applicability of droplet digital PCR (ddPCR) for routine analysis in food and feed samples was demonstrated with the quantification of genetically modified organisms (GMOs). Real-time quantitative polymerase chain reaction (qPCR) is currently used for quantitative molecular analysis of the presence of GMOs in products. However, its use is limited for detecting and quantifying very small numbers of DNA targets, as in some complex food and feed matrices. Using ddPCR duplex assay, we have measured the absolute numbers of MON810 transgene and hmg maize reference gene copies in DNA samples. Key performance parameters of the assay were determined. The ddPCR system is shown to offer precise absolute and relative quantification of targets, without the need for calibration curves. The sensitivity (five target DNA copies) of the ddPCR assay compares well with those of individual qPCR assays and of the chamber digital PCR (cdPCR) approach. It offers a dynamic range over four orders of magnitude, greater than that of cdPCR. Moreover, when compared to qPCR, the ddPCR assay showed better repeatability at low target concentrations and a greater tolerance to inhibitors. Finally, ddPCR throughput and cost are advantageous relative to those of qPCR for routine GMO quantification. It is thus concluded that ddPCR technology can be applied for routine quantification of GMOs, or any other domain where quantitative analysis of food and feed samples is needed. PMID:23658750

  15. Quantitative analysis of food and feed samples with droplet digital PCR.

    PubMed

    Morisset, Dany; Štebih, Dejan; Milavec, Mojca; Gruden, Kristina; Žel, Jana

    2013-01-01

    In this study, the applicability of droplet digital PCR (ddPCR) for routine analysis in food and feed samples was demonstrated with the quantification of genetically modified organisms (GMOs). Real-time quantitative polymerase chain reaction (qPCR) is currently used for quantitative molecular analysis of the presence of GMOs in products. However, its use is limited for detecting and quantifying very small numbers of DNA targets, as in some complex food and feed matrices. Using ddPCR duplex assay, we have measured the absolute numbers of MON810 transgene and hmg maize reference gene copies in DNA samples. Key performance parameters of the assay were determined. The ddPCR system is shown to offer precise absolute and relative quantification of targets, without the need for calibration curves. The sensitivity (five target DNA copies) of the ddPCR assay compares well with those of individual qPCR assays and of the chamber digital PCR (cdPCR) approach. It offers a dynamic range over four orders of magnitude, greater than that of cdPCR. Moreover, when compared to qPCR, the ddPCR assay showed better repeatability at low target concentrations and a greater tolerance to inhibitors. Finally, ddPCR throughput and cost are advantageous relative to those of qPCR for routine GMO quantification. It is thus concluded that ddPCR technology can be applied for routine quantification of GMOs, or any other domain where quantitative analysis of food and feed samples is needed. PMID:23658750

  16. iTRAQ-Based Quantitative Proteomic Analysis of the Initiation of Head Regeneration in Planarians.

    PubMed

    Geng, Xiaofang; Wang, Gaiping; Qin, Yanli; Zang, Xiayan; Li, Pengfei; Geng, Zhi; Xue, Deming; Dong, Zimei; Ma, Kexue; Chen, Guangwen; Xu, Cunshuan

    2015-01-01

    The planarian Dugesia japonica has amazing ability to regenerate a head from the anterior ends of the amputated stump with maintenance of the original anterior-posterior polarity. Although planarians present an attractive system for molecular investigation of regeneration and research has focused on clarifying the molecular mechanism of regeneration initiation in planarians at transcriptional level, but the initiation mechanism of planarian head regeneration (PHR) remains unclear at the protein level. Here, a global analysis of proteome dynamics during the early stage of PHR was performed using isobaric tags for relative and absolute quantitation (iTRAQ)-based quantitative proteomics strategy, and our data are available via ProteomeXchange with identifier PXD002100. The results showed that 162 proteins were differentially expressed at 2 h and 6 h following amputation. Furthermore, the analysis of expression patterns and functional enrichment of the differentially expressed proteins showed that proteins involved in muscle contraction, oxidation reduction and protein synthesis were up-regulated in the initiation of PHR. Moreover, ingenuity pathway analysis showed that predominant signaling pathways such as ILK, calcium, EIF2 and mTOR signaling which were associated with cell migration, cell proliferation and protein synthesis were likely to be involved in the initiation of PHR. The results for the first time demonstrated that muscle contraction and ILK signaling might played important roles in the initiation of PHR at the global protein level. The findings of this research provide a molecular basis for further unraveling the mechanism of head regeneration initiation in planarians. PMID:26131905

  17. iTRAQ-Based Quantitative Proteomic Analysis of the Initiation of Head Regeneration in Planarians

    PubMed Central

    Geng, Xiaofang; Wang, Gaiping; Qin, Yanli; Zang, Xiayan; Li, Pengfei; Geng, Zhi; Xue, Deming; Dong, Zimei; Ma, Kexue; Chen, Guangwen; Xu, Cunshuan

    2015-01-01

    The planarian Dugesia japonica has amazing ability to regenerate a head from the anterior ends of the amputated stump with maintenance of the original anterior-posterior polarity. Although planarians present an attractive system for molecular investigation of regeneration and research has focused on clarifying the molecular mechanism of regeneration initiation in planarians at transcriptional level, but the initiation mechanism of planarian head regeneration (PHR) remains unclear at the protein level. Here, a global analysis of proteome dynamics during the early stage of PHR was performed using isobaric tags for relative and absolute quantitation (iTRAQ)-based quantitative proteomics strategy, and our data are available via ProteomeXchange with identifier PXD002100. The results showed that 162 proteins were differentially expressed at 2 h and 6 h following amputation. Furthermore, the analysis of expression patterns and functional enrichment of the differentially expressed proteins showed that proteins involved in muscle contraction, oxidation reduction and protein synthesis were up-regulated in the initiation of PHR. Moreover, ingenuity pathway analysis showed that predominant signaling pathways such as ILK, calcium, EIF2 and mTOR signaling which were associated with cell migration, cell proliferation and protein synthesis were likely to be involved in the initiation of PHR. The results for the first time demonstrated that muscle contraction and ILK signaling might played important roles in the initiation of PHR at the global protein level. The findings of this research provide a molecular basis for further unraveling the mechanism of head regeneration initiation in planarians. PMID:26131905

  18. Qualitative and Quantitative Analysis for Facial Complexion in Traditional Chinese Medicine

    PubMed Central

    Zhao, Changbo; Li, Guo-zheng; Li, Fufeng; Wang, Zhi; Liu, Chang

    2014-01-01

    Facial diagnosis is an important and very intuitive diagnostic method in Traditional Chinese Medicine (TCM). However, due to its qualitative and experience-based subjective property, traditional facial diagnosis has a certain limitation in clinical medicine. The computerized inspection method provides classification models to recognize facial complexion (including color and gloss). However, the previous works only study the classification problems of facial complexion, which is considered as qualitative analysis in our perspective. For quantitative analysis expectation, the severity or degree of facial complexion has not been reported yet. This paper aims to make both qualitative and quantitative analysis for facial complexion. We propose a novel feature representation of facial complexion from the whole face of patients. The features are established with four chromaticity bases splitting up by luminance distribution on CIELAB color space. Chromaticity bases are constructed from facial dominant color using two-level clustering; the optimal luminance distribution is simply implemented with experimental comparisons. The features are proved to be more distinctive than the previous facial complexion feature representation. Complexion recognition proceeds by training an SVM classifier with the optimal model parameters. In addition, further improved features are more developed by the weighted fusion of five local regions. Extensive experimental results show that the proposed features achieve highest facial color recognition performance with a total accuracy of 86.89%. And, furthermore, the proposed recognition framework could analyze both color and gloss degrees of facial complexion by learning a ranking function. PMID:24967342

  19. Quantitative Analysis of Surface Plasma Membrane Proteins of Primary and Metastatic Melanoma Cells

    PubMed Central

    Qiu, Haibo; Wang, Yinsheng

    2016-01-01

    Plasma membrane proteins play critical roles in cell-to-cell recognition, signal transduction and material transport. Because of their accessibility, membrane proteins constitute the major targets for protein-based drugs. Here, we described an approach, which included stable isotope labeling by amino acids in cell culture (SILAC), cell surface biotinylation, affinity peptide purification and LC-MS/MS for the identification and quantification of cell surface membrane proteins. We applied the strategy for the quantitative analysis of membrane proteins expressed by a pair of human melanoma cell lines, WM-115 and WM-266-4, which were derived initially from the primary and metastatic tumor sites of the same individual. We were able to identify more than 100 membrane and membrane-associated proteins from these two cell lines, including cell surface histones. We further confirmed the surface localization of histone H2B and three other proteins by immunocytochemical analysis with confocal microscopy. The contamination from cytoplasmic and other nonmembrane-related sources is greatly reduced by using cell surface biotinylation and affinity purification of biotinylated peptides. We also quantified the relative expression of 62 identified proteins in the two types of melanoma cells. The application to quantitative analysis of membrane proteins of primary and metastatic melanoma cells revealed great potential of the method in the comprehensive identification of tumor progression markers as well as in the discovery of new protein-based therapeutic targets. PMID:18410138

  20. Qualitative and quantitative analysis for facial complexion in traditional Chinese medicine.

    PubMed

    Zhao, Changbo; Li, Guo-zheng; Li, Fufeng; Wang, Zhi; Liu, Chang

    2014-01-01

    Facial diagnosis is an important and very intuitive diagnostic method in Traditional Chinese Medicine (TCM). However, due to its qualitative and experience-based subjective property, traditional facial diagnosis has a certain limitation in clinical medicine. The computerized inspection method provides classification models to recognize facial complexion (including color and gloss). However, the previous works only study the classification problems of facial complexion, which is considered as qualitative analysis in our perspective. For quantitative analysis expectation, the severity or degree of facial complexion has not been reported yet. This paper aims to make both qualitative and quantitative analysis for facial complexion. We propose a novel feature representation of facial complexion from the whole face of patients. The features are established with four chromaticity bases splitting up by luminance distribution on CIELAB color space. Chromaticity bases are constructed from facial dominant color using two-level clustering; the optimal luminance distribution is simply implemented with experimental comparisons. The features are proved to be more distinctive than the previous facial complexion feature representation. Complexion recognition proceeds by training an SVM classifier with the optimal model parameters. In addition, further improved features are more developed by the weighted fusion of five local regions. Extensive experimental results show that the proposed features achieve highest facial color recognition performance with a total accuracy of 86.89%. And, furthermore, the proposed recognition framework could analyze both color and gloss degrees of facial complexion by learning a ranking function. PMID:24967342

  1. [Quantitative analysis of thiram by surface-enhanced raman spectroscopy combined with feature extraction Algorithms].

    PubMed

    Zhang, Bao-hua; Jiang, Yong-cheng; Sha, Wen; Zhang, Xian-yi; Cui, Zhi-feng

    2015-02-01

    Three feature extraction algorithms, such as the principal component analysis (PCA), the discrete cosine transform (DCT) and the non-negative factorization (NMF), were used to extract the main information of the spectral data in order to weaken the influence of the spectral fluctuation on the subsequent quantitative analysis results based on the SERS spectra of the pesticide thiram. Then the extracted components were respectively combined with the linear regression algorithm--the partial least square regression (PLSR) and the non-linear regression algorithm--the support vector machine regression (SVR) to develop the quantitative analysis models. Finally, the effect of the different feature extraction algorithms on the different kinds of the regression algorithms was evaluated by using 5-fold cross-validation method. The experiments demonstrate that the analysis results of SVR are better than PLSR for the non-linear relationship between the intensity of the SERS spectrum and the concentration of the analyte. Further, the feature extraction algorithms can significantly improve the analysis results regardless of the regression algorithms which mainly due to extracting the main information of the source spectral data and eliminating the fluctuation. Additionally, PCA performs best on the linear regression model and NMF is best on the non-linear model, and the predictive error can be reduced nearly three times in the best case. The root mean square error of cross-validation of the best regression model (NMF+SVR) is 0.0455 micormol x L(-1) (10(-6) mol x L(-1)), and it attains the national detection limit of thiram, so the method in this study provides a novel method for the fast detection of thiram. In conclusion, the study provides the experimental references the selecting the feature extraction algorithms on the analysis of the SERS spectrum, and some common findings of feature extraction can also help processing of other kinds of spectroscopy. PMID:25970898

  2. Modular Isotopomer Synthesis of ?-Hydroxybutyric Acid for a Quantitative Analysis of Metabolic Fates

    PubMed Central

    2015-01-01

    Herein we report a study combining metabolomics and mass isotopomer analysis used for investigation of the biochemical fate of ?-hydroxybutyric acid (GHB). Using various 13C incorporation labeling patterns into GHB, we have discovered that GHB is catabolized by previously unknown processes that include (i) direct ?-oxidation to acetyl-CoA and glycolate, (ii) ?-oxidation to 3-hydroxypropionyl-CoA and formate, and (iii) cleavage of C-4 to yield 3-hydroxypropionate and CO2. We further utilized the unique attributes of our labeling patterns and the resultant isotopomers to quantitate relative flux down the identified pathways. PMID:24933109

  3. DAnTE: a statistical tool for quantitative analysis of –omics data

    SciTech Connect

    Polpitiya, Ashoka D.; Qian, Weijun; Jaitly, Navdeep; Petyuk, Vladislav A.; Adkins, Joshua N.; Camp, David G.; Anderson, Gordon A.; Smith, Richard D.

    2008-05-03

    DAnTE (Data Analysis Tool Extension) is a statistical tool designed to address challenges unique to quantitative bottom-up, shotgun proteomics data. This tool has also been demonstrated for microarray data and can easily be extended to other high-throughput data types. DAnTE features selected normalization methods, missing value imputation algorithms, peptide to protein rollup methods, an extensive array of plotting functions, and a comprehensive ANOVA scheme that can handle unbalanced data and random effects. The Graphical User Interface (GUI) is designed to be very intuitive and user friendly.

  4. The impact of quantitative optimization of hybridization conditions on gene expression analysis

    E-print Network

    Sykacek, Peter; Kreil, David P.; Meadows, Lisa A.; Auburn, Richard P.; Fischer, Bettina; Russell, Steven R.; Micklem, Gos

    2011-03-14

    The impact of quantitative optimization of hybridization conditions on gene expression analysis Peter Sykacek1*†, David P Kreil1†, Lisa A Meadows2,3, Richard P Auburn2,3, Bettina Fischer2,3, Steven Russell2,3, Gos Micklem2,3,4 Abstract Background... ://www.biomedcentral.com/1471-2105/12/73 © 2011 Sykacek et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use...

  5. Quantitative determination of electric field strengths within dynamically operated devices using EBIC analysis in the SEM.

    PubMed

    Pugatschow, Anton; Heiderhoff, Ralf; Balk, Ludwig J

    2008-01-01

    Although electron beam-induced current (EBIC) technique was invented in the seventies, it is still a powerful technique for failure analysis and reliability investigations of modern materials and devices. Time-resolved and stroboscopic microanalyses using sampling Fourier components decomposed by modulated charge carrier excitation are introduced. Quantitative determination of electric field strengths within dynamically operated devices in the scanning electron microscope (SEM) will be demonstrated. This technique allows investigations of diffusion and drift processes and of variations of electric field distributions inside active devices. PMID:18523959

  6. The Government Finance Database: A Common Resource for Quantitative Research in Public Financial Analysis

    PubMed Central

    Pierson, Kawika; Hand, Michael L.; Thompson, Fred

    2015-01-01

    Quantitative public financial management research focused on local governments is limited by the absence of a common database for empirical analysis. While the U.S. Census Bureau distributes government finance data that some scholars have utilized, the arduous process of collecting, interpreting, and organizing the data has led its adoption to be prohibitive and inconsistent. In this article we offer a single, coherent resource that contains all of the government financial data from 1967-2012, uses easy to understand natural-language variable names, and will be extended when new data is available. PMID:26107821

  7. The Government Finance Database: A Common Resource for Quantitative Research in Public Financial Analysis.

    PubMed

    Pierson, Kawika; Hand, Michael L; Thompson, Fred

    2015-01-01

    Quantitative public financial management research focused on local governments is limited by the absence of a common database for empirical analysis. While the U.S. Census Bureau distributes government finance data that some scholars have utilized, the arduous process of collecting, interpreting, and organizing the data has led its adoption to be prohibitive and inconsistent. In this article we offer a single, coherent resource that contains all of the government financial data from 1967-2012, uses easy to understand natural-language variable names, and will be extended when new data is available. PMID:26107821

  8. Characterizing Aging in the Human Brainstem Using Quantitative Multimodal MRI Analysis

    PubMed Central

    Lambert, Christian; Chowdhury, Rumana; FitzGerald, Thomas H. B.; Fleming, Stephen M.; Lutti, Antoine; Hutton, Chloe; Draganski, Bogdan; Frackowiak, Richard; Ashburner, John

    2013-01-01

    Aging is ubiquitous to the human condition. The MRI correlates of healthy aging have been extensively investigated using a range of modalities, including volumetric MRI, quantitative MRI (qMRI), and diffusion tensor imaging. Despite this, the reported brainstem related changes remain sparse. This is, in part, due to the technical and methodological limitations in quantitatively assessing and statistically analyzing this region. By utilizing a new method of brainstem segmentation, a large cohort of 100 healthy adults were assessed in this study for the effects of aging within the human brainstem in vivo. Using qMRI, tensor-based morphometry (TBM), and voxel-based quantification (VBQ), the volumetric and quantitative changes across healthy adults between 19 and 75?years were characterized. In addition to the increased R2* in substantia nigra corresponding to increasing iron deposition with age, several novel findings were reported in the current study. These include selective volumetric loss of the brachium conjunctivum, with a corresponding decrease in magnetization transfer and increase in proton density (PD), accounting for the previously described “midbrain shrinkage.” Additionally, we found increases in R1 and PD in several pontine and medullary structures. We consider these changes in the context of well-characterized, functional age-related changes, and propose potential biophysical mechanisms. This study provides detailed quantitative analysis of the internal architecture of the brainstem and provides a baseline for further studies of neurodegenerative diseases that are characterized by early, pre-clinical involvement of the brainstem, such as Parkinson’s and Alzheimer’s diseases. PMID:23970860

  9. Pleiotropy Analysis of Quantitative Traits at Gene Level by Multivariate Functional Linear Models

    PubMed Central

    Wang, Yifan; Liu, Aiyi; Mills, James L.; Boehnke, Michael; Wilson, Alexander F.; Bailey-Wilson, Joan E.; Xiong, Momiao; Wu, Colin O.; Fan, Ruzong

    2015-01-01

    In genetics, pleiotropy describes the genetic effect of a single gene on multiple phenotypic traits. A common approach is to analyze the phenotypic traits separately using univariate analyses and combine the test results through multiple comparisons. This approach may lead to low power. Multivariate functional linear models are developed to connect genetic variant data to multiple quantitative traits adjusting for covariates for a unified analysis. Three types of approximate F-distribution tests based on Pillai–Bartlett trace, Hotelling–Lawley trace, and Wilks’s Lambda are introduced to test for association between multiple quantitative traits and multiple genetic variants in one genetic region. The approximate F-distribution tests provide much more significant results than those of F-tests of univariate analysis and optimal sequence kernel association test (SKAT-O). Extensive simulations were performed to evaluate the false positive rates and power performance of the proposed models and tests. We show that the approximate F-distribution tests control the type I error rates very well. Overall, simultaneous analysis of multiple traits can increase power performance compared to an individual test of each trait. The proposed methods were applied to analyze (1) four lipid traits in eight European cohorts, and (2) three biochemical traits in the Trinity Students Study. The approximate F-distribution tests provide much more significant results than those of F-tests of univariate analysis and SKAT-O for the three biochemical traits. The approximate F-distribution tests of the proposed functional linear models are more sensitive than those of the traditional multivariate linear models that in turn are more sensitive than SKAT-O in the univariate case. The analysis of the four lipid traits and the three biochemical traits detects more association than SKAT-O in the univariate case. PMID:25809955

  10. Quantitative Microbial Community Analysis of Three Different Sulfidic Mine Tailing Dumps Generating Acid Mine Drainage?

    PubMed Central

    Kock, Dagmar; Schippers, Axel

    2008-01-01

    The microbial communities of three different sulfidic and acidic mine waste tailing dumps located in Botswana, Germany, and Sweden were quantitatively analyzed using quantitative real-time PCR (Q-PCR), fluorescence in situ hybridization (FISH), catalyzed reporter deposition-FISH (CARD-FISH), Sybr green II direct counting, and the most probable number (MPN) cultivation technique. Depth profiles of cell numbers showed that the compositions of the microbial communities are greatly different at the three sites and also strongly varied between zones of oxidized and unoxidized tailings. Maximum cell numbers of up to 109 cells g?1 dry weight were determined in the pyrite or pyrrhotite oxidation zones, whereas cell numbers in unoxidized tailings were significantly lower. Bacteria dominated over Archaea and Eukarya at all tailing sites. The acidophilic Fe(II)- and/or sulfur-oxidizing Acidithiobacillus spp. dominated over the acidophilic Fe(II)-oxidizing Leptospirillum spp. among the Bacteria at two sites. The two genera were equally abundant at the third site. The acidophilic Fe(II)- and sulfur-oxidizing Sulfobacillus spp. were generally less abundant. The acidophilic Fe(III)-reducing Acidiphilium spp. could be found at only one site. The neutrophilic Fe(III)-reducing Geobacteraceae as well as the dsrA gene of sulfate reducers were quantifiable at all three sites. FISH analysis provided reliable data only for tailing zones with high microbial activity, whereas CARD-FISH, Q-PCR, Sybr green II staining, and MPN were suitable methods for a quantitative microbial community analysis of tailings in general. PMID:18586975

  11. Quantitative neuroanatomy of all Purkinje cells with light sheet microscopy and high-throughput image analysis.

    PubMed

    Silvestri, Ludovico; Paciscopi, Marco; Soda, Paolo; Biamonte, Filippo; Iannello, Giulio; Frasconi, Paolo; Pavone, Francesco S

    2015-01-01

    Characterizing the cytoarchitecture of mammalian central nervous system on a brain-wide scale is becoming a compelling need in neuroscience. For example, realistic modeling of brain activity requires the definition of quantitative features of large neuronal populations in the whole brain. Quantitative anatomical maps will also be crucial to classify the cytoarchtitectonic abnormalities associated with neuronal pathologies in a high reproducible and reliable manner. In this paper, we apply recent advances in optical microscopy and image analysis to characterize the spatial distribution of Purkinje cells (PCs) across the whole cerebellum. Light sheet microscopy was used to image with micron-scale resolution a fixed and cleared cerebellum of an L7-GFP transgenic mouse, in which all PCs are fluorescently labeled. A fast and scalable algorithm for fully automated cell identification was applied on the image to extract the position of all the fluorescent PCs. This vectorized representation of the cell population allows a thorough characterization of the complex three-dimensional distribution of the neurons, highlighting the presence of gaps inside the lamellar organization of PCs, whose density is believed to play a significant role in autism spectrum disorders. Furthermore, clustering analysis of the localized somata permits dividing the whole cerebellum in groups of PCs with high spatial correlation, suggesting new possibilities of anatomical partition. The quantitative approach presented here can be extended to study the distribution of different types of cell in many brain regions and across the whole encephalon, providing a robust base for building realistic computational models of the brain, and for unbiased morphological tissue screening in presence of pathologies and/or drug treatments. PMID:26074783

  12. Quantitative Analysis of Localized Sources Identified by Focal Impulse and Rotor Modulation Mapping in Atrial Fibrillation

    PubMed Central

    Benharash, Peyman; Buch, Eric; Frank, Paul; Share, Michael; Tung, Roderick; Shivkumar, Kalyanam; Mandapati, Ravi

    2015-01-01

    Background New approaches to ablation of atrial fibrillation (AF) include focal impulse and rotor modulation (FIRM) mapping, and initial results reported with this technique have been favorable. We sought to independently evaluate the approach by analyzing quantitative characteristics of atrial electrograms used to identify rotors and describe acute procedural outcomes of FIRM-guided ablation. Methods and Results All FIRM-guided ablation procedures (n=24; 50% paroxysmal) at University of California, Los Angeles Medical Center were included for analysis. During AF, unipolar atrial electrograms collected from a 64-pole basket catheter were used to construct phase maps and identify putative AF sources. These sites were targeted for ablation, in conjunction with pulmonary vein isolation in most patients (n=19; 79%). All patients had rotors identified (mean, 2.3±0.9 per patient; 72% in left atrium). Prespecified acute procedural end point was achieved in 12 of 24 (50%) patients: AF termination (n=1), organization (n=3), or >10% slowing of AF cycle length (n=8). Basket electrodes were within 1 cm of 54% of left atrial surface area, and a mean of 31 electrodes per patient showed interpretable atrial electrograms. Offline analysis revealed no differences between rotor and distant sites in dominant frequency or Shannon entropy. Electroanatomic mapping showed no rotational activation at FIRM-identified rotor sites in 23 of 24 patients (96%). Conclusions FIRM-identified rotor sites did not exhibit quantitative atrial electrogram characteristics expected from rotors and did not differ quantitatively from surrounding tissue. Catheter ablation at these sites, in conjunction with pulmonary vein isolation, resulted in AF termination or organization in a minority of patients (4/24; 17%). Further validation of this approach is necessary. PMID:25873718

  13. Quantitative neuroanatomy of all Purkinje cells with light sheet microscopy and high-throughput image analysis

    PubMed Central

    Silvestri, Ludovico; Paciscopi, Marco; Soda, Paolo; Biamonte, Filippo; Iannello, Giulio; Frasconi, Paolo; Pavone, Francesco S.

    2015-01-01

    Characterizing the cytoarchitecture of mammalian central nervous system on a brain-wide scale is becoming a compelling need in neuroscience. For example, realistic modeling of brain activity requires the definition of quantitative features of large neuronal populations in the whole brain. Quantitative anatomical maps will also be crucial to classify the cytoarchtitectonic abnormalities associated with neuronal pathologies in a high reproducible and reliable manner. In this paper, we apply recent advances in optical microscopy and image analysis to characterize the spatial distribution of Purkinje cells (PCs) across the whole cerebellum. Light sheet microscopy was used to image with micron-scale resolution a fixed and cleared cerebellum of an L7-GFP transgenic mouse, in which all PCs are fluorescently labeled. A fast and scalable algorithm for fully automated cell identification was applied on the image to extract the position of all the fluorescent PCs. This vectorized representation of the cell population allows a thorough characterization of the complex three-dimensional distribution of the neurons, highlighting the presence of gaps inside the lamellar organization of PCs, whose density is believed to play a significant role in autism spectrum disorders. Furthermore, clustering analysis of the localized somata permits dividing the whole cerebellum in groups of PCs with high spatial correlation, suggesting new possibilities of anatomical partition. The quantitative approach presented here can be extended to study the distribution of different types of cell in many brain regions and across the whole encephalon, providing a robust base for building realistic computational models of the brain, and for unbiased morphological tissue screening in presence of pathologies and/or drug treatments. PMID:26074783

  14. Quantitative analysis of cotton-polyester textile blends from near-infrared spectra.

    PubMed

    Ruckebusch, C; Orhan, F; Durand, A; Boubellouta, T; Huvenne, J P

    2006-05-01

    Quantitative analysis of textile blends and textile fabrics is currently of particular interest in the industrial context. In this frame, this work investigates whether the use of Fourier transform (FT) near-infrared (NIR) spectroscopy and chemometrics is powerful for rapid and accurate quantitative analysis of cotton-polyester content in blend products. As samples of the same composition have many sources of variability that affect NIR spectra, indirect prediction is particularly challenging and a large sample population is required to design robust calibration models. Thus, a total of more than three-hundred cotton-polyester samples were selected covering the range from the 0% to 100% cotton and the corresponding NIR reflectance spectra were measured on raw fabrics. The data set obtained was used to develop multivariate models for quantitative prediction from reference measurements. A successful approach was found to rely on partial least squares (PLS) regression combined with genetic algorithms (GAs) for wavelength selection. It involved evaluating a set of calibration models considering different spectral regions. The results obtained considering 27.5% of the original variables yielded a prediction error (RMSEP) of 2.3 in percent cotton content. It demonstrates that FT-NIR spectroscopy has the potential to be used in the textile industry for the prediction of the composition of cotton-polyester blends. As a further consequence, it was observed that the spectral preprocessing and the complexity of the model are simplified compared to the full-spectrum approach. Also, the relevancy of the spectral intervals retained after variable selection can be discussed. PMID:16756705

  15. Quantitative characterisation of historic paper using THz spectroscopy and multivariate data analysis

    NASA Astrophysics Data System (ADS)

    Trafela, Tanja; Mizuno, Maya; Fukunaga, Kaori; Strli?, Matija

    2013-04-01

    THz spectroscopy in the time domain was explored in combination with multivariate data analysis, for quantitative determination of chemical and mechanical properties of historic paper, such as lignin content, tensile strength, and ash content. Using partial least squares (PLS) regression, it was shown that quantitative prediction of the material properties is possible, which indicates the potential of THz spectroscopy for chemical characterisation of complex organic materials of natural origin. In addition, the results demonstrate that THz spectra and PLS loading weights for lignin content differ significantly, which leads to the conclusion that THz spectra of composite macromolecular materials do not represent sums of spectra of the individual components. This supports the premise that THz spectra reflect intermolecular interactions. The study was carried out using 250 historical paper samples from the sixteenth century to present. Although the measurements were performed in vacuum to improve the quality of spectra, THz spectroscopy is in principle non-destructive. This research therefore reinforces the role of THz spectroscopy in characterisation of valuable historic materials, where invasive analysis is often not possible.

  16. Simultaneous quantitative analysis of metabolites using ion-pair liquid chromatography-electrospray ionization mass spectrometry.

    PubMed

    Coulier, Leon; Bas, Richard; Jespersen, Sonja; Verheij, Elwin; van der Werf, Mariët J; Hankemeier, Thomas

    2006-09-15

    We have developed an analytical method, consisting of ion-pair liquid chromatography coupled to electrospray ionization mass spectrometry (IP-LC-ESI-MS), for the simultaneous quantitative analysis of several key classes of polar metabolites, like nucleotides, coenzyme A esters, sugar nucleotides, and sugar bisphosphates. The use of the ion-pair agent hexylamine and optimization of the pH of the mobile phases were critical parameters in obtaining good retention and peak shapes of many of the above-mentioned polar and acidic metabolites that are impossible to analyze using standard reversed-phase LC/MS. Optimum conditions were found when using a gradient from 5 mM hexylamine in water (pH 6.3) to 90% methanol/10% 10 mM ammonium acetate (pH 8.5). The IP-LC-ESI-MS method was extensively validated by determining the linearity (R2 > 0.995), sensitivity (limit of detection 0.1-1 ng), repeatability, and reproducibility (relative standard deviation <10%). The IP-LC-ESI-MS method was shown to be a useful tool for microbial metabolomics, i.e., the comprehensive quantitative analysis of metabolites in extracts of microorganisms, and for the determination of the energy charge, i.e., the cellular energy status, as an overall quality measure for the sample workup and analytical protocols. PMID:16970336

  17. Quantitative analysis of perfumes in talcum powder by using headspace sorptive extraction.

    PubMed

    Ng, Khim Hui; Heng, Audrey; Osborne, Murray

    2012-03-01

    Quantitative analysis of perfume dosage in talcum powder has been a challenge due to interference of the matrix and has so far not been widely reported. In this study, headspace sorptive extraction (HSSE) was validated as a solventless sample preparation method for the extraction and enrichment of perfume raw materials from talcum powder. Sample enrichment is performed on a thick film of poly(dimethylsiloxane) (PDMS) coated onto a magnetic stir bar incorporated in a glass jacket. Sampling is done by placing the PDMS stir bar in the headspace vial by using a holder. The stir bar is then thermally desorbed online with capillary gas chromatography-mass spectrometry. The HSSE method is based on the same principles as headspace solid-phase microextraction (HS-SPME). Nevertheless, a relatively larger amount of extracting phase is coated on the stir bar as compared to SPME. Sample amount and extraction time were optimized in this study. The method has shown good repeatability (with relative standard deviation no higher than 12.5%) and excellent linearity with correlation coefficients above 0.99 for all analytes. The method was also successfully applied in the quantitative analysis of talcum powder spiked with perfume at different dosages. PMID:22318774

  18. Dissecting eukaryotic cells by coherent phase microscopy: quantitative analysis of quiescent and activated T lymphocytes

    NASA Astrophysics Data System (ADS)

    Tychinsky, Vladimir P.; Kretushev, Alexander V.; Vyshenskaya, Tatiana V.; Shtil, Alexander A.

    2012-07-01

    We present a concept for quantitative characterization of a functional state of an individual eukaryotic cell based on interference imaging. The informative parameters of the phase images of quiescent and mitogen-activated T lymphocytes included the phase thickness, phase volume, the area, and the size of organelles. These parameters were obtained without a special hypothesis about cell structure. Combinations of these parameters generated a ``phase portrait'' of the cell. A simplified spherical multilayer optic model of a T lymphocyte was used to calculate the refractivity profile, to identify structural elements of the image with the organelles, and to interpret the parameters of the phase portrait. The values of phase image parameters underwent characteristic changes in the course of mitogenic stimulation of T cells; thereby, the functional state of individual cells can be described using these parameters. Because the values of the components of the phase portrait are measured in absolute units, it is possible to compare the parameters of images obtained with different interference microscopes. Thus, the analysis of phase portraits provides a new and perspective approach for quantitative, real-time analysis of subcellular structure and physiologic state of an individual cell.

  19. Quantitative analysis of diffusion tensor imaging (DTI) using statistical parametric mapping (SPM) for brain disorders

    NASA Astrophysics Data System (ADS)

    Lee, Jae-Seung; Im, In-Chul; Kang, Su-Man; Goo, Eun-Hoe; Kwak, Byung-Joon

    2013-07-01

    This study aimed to quantitatively analyze data from diffusion tensor imaging (DTI) using statistical parametric mapping (SPM) in patients with brain disorders and to assess its potential utility for analyzing brain function. DTI was obtained by performing 3.0-T magnetic resonance imaging for patients with Alzheimer's disease (AD) and vascular dementia (VD), and the data were analyzed using Matlab-based SPM software. The two-sample t-test was used for error analysis of the location of the activated pixels. We compared regions of white matter where the fractional anisotropy (FA) values were low and the apparent diffusion coefficients (ADCs) were increased. In the AD group, the FA values were low in the right superior temporal gyrus, right inferior temporal gyrus, right sub-lobar insula, and right occipital lingual gyrus whereas the ADCs were significantly increased in the right inferior frontal gyrus and right middle frontal gyrus. In the VD group, the FA values were low in the right superior temporal gyrus, right inferior temporal gyrus, right limbic cingulate gyrus, and right sub-lobar caudate tail whereas the ADCs were significantly increased in the left lateral globus pallidus and left medial globus pallidus. In conclusion by using DTI and SPM analysis, we were able to not only determine the structural state of the regions affected by brain disorders but also quantitatively analyze and assess brain function.

  20. Chromosome mechanics in vivo: quantitative analysis of nonrigid 3D chromosome motion in Drosophila embryos

    NASA Astrophysics Data System (ADS)

    Marshall, Wallace F.; Agard, David A.; Sedat, John W.

    1996-05-01

    Chromosomes are often arranged into specific configurations. One example is the metaphase plate of the Drosophila embryo in which chromosomes are arranged into a parallel bundle. How is this configuration established and maintained? Quantitative analysis of chromosomes motion in vivo should help answer this question by providing a measure of the relevant mechanical properties of the chromosomes themselves. In addition, motion analysis will allow us to study interactions of chromosomes with the mitotic spindle. In order to analyze moving mitotic chromosomes, we acquire time-lapse 3D images of chromosomes in living Drosophila embryos, and then interactively model the chromosome configuration at each time point. A model-based motion estimation algorithm is then applied. From the motion estimate, we can visualize trajectories of different regions on the chromosomes, such as centromeres and telomeres, during metaphase and during prometaphase congression. In addition, quantitative estimates of mechanical properties such as mobility and flexibility can be computed. In this preliminary report we describe computational tools for tracking and visualizing 3D chromosome motion, and for detecting oscillations in position along the mitotic spindle.

  1. Quantitative CMMI Assessment for Offshoring through the Analysis of Project Management Repositories

    NASA Astrophysics Data System (ADS)

    Sunetnanta, Thanwadee; Nobprapai, Ni-On; Gotel, Olly

    The nature of distributed teams and the existence of multiple sites in offshore software development projects pose a challenging setting for software process improvement. Often, the improvement and appraisal of software processes is achieved through a turnkey solution where best practices are imposed or transferred from a company’s headquarters to its offshore units. In so doing, successful project health checks and monitoring for quality on software processes requires strong project management skills, well-built onshore-offshore coordination, and often needs regular onsite visits by software process improvement consultants from the headquarters’ team. This paper focuses on software process improvement as guided by the Capability Maturity Model Integration (CMMI) and proposes a model to evaluate the status of such improvement efforts in the context of distributed multi-site projects without some of this overhead. The paper discusses the application of quantitative CMMI assessment through the collection and analysis of project data gathered directly from project repositories to facilitate CMMI implementation and reduce the cost of such implementation for offshore-outsourced software development projects. We exemplify this approach to quantitative CMMI assessment through the analysis of project management data and discuss the future directions of this work in progress.

  2. Quantitative Image Analysis of Ni-P Coatings Deposited on Carbon Fibers

    NASA Astrophysics Data System (ADS)

    Kozera, R.; Bucki, J. J.; Sa?aci?ska, A.; Bieli?ski, J.; Boczkowska, A.

    2015-09-01

    In this work, polyacrylonitrile (PAN)-based carbon fibers coated with different thicknesses of Ni-P coatings were studied. The coatings were deposited by electroless metallization lasting from 3 to 22 min and consisted of approximately 3 wt.% phosphorous. Computer quantitative image analysis was used to characterize the surface features and thickness of the coatings as a function of the time of metallization. The results showed that quantitative image analysis is a useful technique for the measurement of the coating thickness and can be used as a tool for obtaining an innovative description of the Ni-P coating morphology. The morphology of the coatings and their thicknesses were investigated by scanning electron microscopy. The image analyses were performed using the proprietary software Micrometer, developed at the Faculty of Materials Science and Engineering, Warsaw University of Technology. The observations revealed that a specific feature of the coating topography is the hemispherical bulge of a diameter ranging from 0.1 to 10 ?m. The thickness of the coatings increases linearly with the metallization time. The obtained results indicated that the methodology proposed in the present work can be successfully applied and possesses several advantages over the traditionally used weight measurements technique.

  3. Quantitative texture analysis of metal sheets and polymer foils by neutron diffraction

    NASA Astrophysics Data System (ADS)

    Vratislav, Stanislav; Dlouhá, Maja; Kalvoda, Ladislav; Grishin, Alexander

    2006-11-01

    Experimental and calculation techniques for quantitative texture analysis based on the ODF combined with the diffraction of thermal neutrons were developed and tested. In our work the texture of the oriented steel sheets was investigated after different stages of their processing. The texture experiments were carried out on the KSN-2 diffractometer (installed by the LVR-15 reactor in Rez near Prague) which is equipped with the TG-1 texture goniometer-supplied automatic data collection for transmission and reflection geometry. The TODF-N package was used and the ODF values were obtained together with all texture characteristics. Although most of our texture studies performed until recently concentrated on metallic materials, now we have extended research field to texture investigation of semi-crystalline polymer materials (rigid PVC foils) finding an extensive industrial application. Results achieved in our study confirm that the quantitative texture analysis in connection with neutron diffraction can help to improve the technology of the preparation of oriented magnetic steel sheets and to determine the final functional properties of polymer foils.

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

    PubMed Central

    2015-01-01

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

  5. Digital Holographic Microscopy: Quantitative Phase Imaging and Applications in Live Cell Analysis

    NASA Astrophysics Data System (ADS)

    Kemper, Björn; Langehanenberg, Patrik; Kosmeier, Sebastian; Schlichthaber, Frank; Remmersmann, Christian; von Bally, Gert; Rommel, Christina; Dierker, Christian; Schnekenburger, Jürgen

    The analysis of complex processes in living cells creates a high demand for fast and label-free methods for online monitoring. Widely used fluorescence methods require specific labeling and are often restricted to chemically fixated samples. Thus, methods that offer label-free and minimally invasive detection of live cell processes and cell state alterations are of particular interest. In combination with light microscopy, digital holography provides label-free, multi-focus quantitative phase imaging of living cells. In overview, several methods for digital holographic microscopy (DHM) are presented. First, different experimental setups for the recording of digital holograms and the modular integration of DHM into common microscopes are described. Then the numerical processing of digitally captured holograms is explained. This includes the description of spatial and temporal phase shifting techniques, spatial filtering based reconstruction, holographic autofocusing, and the evaluation of self-interference holograms. Furthermore, the usage of partial coherent light and multi-wavelength approaches is discussed. Finally, potentials of digital holographic microscopy for quantitative cell imaging are illustrated by results from selected applications. It is shown that DHM can be used for automated tracking of migrating cells and cell thickness monitoring as well as for refractive index determination of cells and particles. Moreover, the use of DHM for label-free analysis in fluidics and micro-injection monitoring is demonstrated. The results show that DHM is a highly relevant method that allows novel insights in dynamic cell biology, with applications in cancer research and for drugs and toxicity testing.

  6. Quantitative analysis of brain nuclear phosphoproteins identifies developmentally regulated phosphorylation events

    PubMed Central

    Liao, Lujian; McClatchy, Daniel B.; Park, Sung Kyu; Xu, Tao; Lu, Bingwen; Yates, John R.

    2009-01-01

    Protein phosphorylation is a globally adopted and tightly controlled post-translational modification, and represents one of the most important molecular switching mechanisms that govern the entire spectrum of biological processes. In the central nervous system, it has been demonstrated that phosphorylation of key proteins mediating chromatin remodeling and gene transcription plays an important role controlling brain development, synaptogenesis, learning and memory. Many studies have focused on large scale identification of phosphopeptides in brain tissue. These studies have identified phosphorylation site specific motifs useful for predicting protein kinases substrates. In this study, we applied a previously developed quantitative approach, stable isotope labeling of amino acids in mammals (SILAM), to quantify changes in the phosphorylation of nuclear proteins between a postnatal day one (p1) and a p45 rat brain cortex. Using a 15N labeled rat brain as an internal standard, we quantified 705 phosphopeptides in the p1 cortex and 1477 phosphopeptides in the p45 cortex, which translates to 380 and 585 phosphoproteins in p1 and p45 cortex, respectively. Bioinformatic analysis of the differentially modified phosphoproteins revealed that phosphorylation is upregulated on multiple components of chromatin remodeling complexes in the p1 cortex. Taken together, we demonstrated for the first time the usefulness of employing stable isotope labeled rat tissue for global quantitative phosphorylation analysis. PMID:18823140

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

    NASA Astrophysics Data System (ADS)

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

    2011-09-01

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

  8. Quantitative chemical imaging and unsupervised analysis using hyperspectral coherent anti-Stokes Raman scattering microscopy.

    PubMed

    Masia, Francesco; Glen, Adam; Stephens, Phil; Borri, Paola; Langbein, Wolfgang

    2013-11-19

    In this work, we report a method to acquire and analyze hyperspectral coherent anti-Stokes Raman scattering (CARS) microscopy images of organic materials and biological samples resulting in an unbiased quantitative chemical analysis. The method employs singular value decomposition on the square root of the CARS intensity, providing an automatic determination of the components above noise, which are retained. Complex CARS susceptibility spectra, which are linear in the chemical composition, are retrieved from the CARS intensity spectra using the causality of the susceptibility by two methods, and their performance is evaluated by comparison with Raman spectra. We use non-negative matrix factorization applied to the imaginary part and the nonresonant real part of the susceptibility with an additional concentration constraint to obtain absolute susceptibility spectra of independently varying chemical components and their absolute concentration. We demonstrate the ability of the method to provide quantitative chemical analysis on known lipid mixtures. We then show the relevance of the method by imaging lipid-rich stem-cell-derived mouse adipocytes as well as differentiated embryonic stem cells with a low density of lipids. We retrieve and visualize the most significant chemical components with spectra given by water, lipid, and proteins segmenting the image into the cell surrounding, lipid droplets, cytosol, and the nucleus, and we reveal the chemical structure of the cells, with details visualized by the projection of the chemical contrast into a few relevant channels. PMID:24099603

  9. Quantitative Analysis of Differential Proteome Expression in Bladder Cancer vs. Normal Bladder Cells Using SILAC Method

    PubMed Central

    Yang, Ganglong; Xu, Zhipeng; Lu, Wei; Li, Xiang; Sun, Chengwen; Guo, Jia; Xue, Peng; Guan, Feng

    2015-01-01

    The best way to increase patient survival rate is to identify patients who are likely to progress to muscle-invasive or metastatic disease upfront and treat them more aggressively. The human cell lines HCV29 (normal bladder epithelia), KK47 (low grade nonmuscle invasive bladder cancer, NMIBC), and YTS1 (metastatic bladder cancer) have been widely used in studies of molecular mechanisms and cell signaling during bladder cancer (BC) progression. However, little attention has been paid to global quantitative proteome analysis of these three cell lines. We labeled HCV29, KK47, and YTS1 cells by the SILAC method using three stable isotopes each of arginine and lysine. Labeled proteins were analyzed by 2D ultrahigh-resolution liquid chromatography LTQ Orbitrap mass spectrometry. Among 3721 unique identified and annotated proteins in KK47 and YTS1 cells, 36 were significantly upregulated and 74 were significantly downregulated with >95% confidence. Differential expression of these proteins was confirmed by western blotting, quantitative RT-PCR, and cell staining with specific antibodies. Gene ontology (GO) term and pathway analysis indicated that the differentially regulated proteins were involved in DNA replication and molecular transport, cell growth and proliferation, cellular movement, immune cell trafficking, and cell death and survival. These proteins and the advanced proteome techniques described here will be useful for further elucidation of molecular mechanisms in BC and other types of cancer. PMID:26230496

  10. [Multicomponent quantitative analysis using near infrared spectroscopy by building PLS-GRNN model].

    PubMed

    Liu, Bo-Ping; Qin, Hua-Jun; Luo, Xiang; Cao, Shu-Wen; Wang, Jun-De

    2007-11-01

    The present paper introduces an application of near infrared spectroscopy(NIRS) multi-component quantitative analysis by building partial least squares (PLS)-generalized regression neural networks (GRNN) model. The PLS-GRNN prediction model for chlorine, fibre and fat in 45 feedstuff samples was established with good veracity and recurrence. Eight peak values in principal components compressed from original data by PLS and four in original spectra were taken as inputs of GRNN while 4 predictive targets as outputs. 0.1 was chosen as smoothing factor for its good approximation and prediction with the lowest error compared with 0.2, 0.3, 0.4 and 0.5. Predictive correlation coefficient and Standard error of the estimate of three components by the model are 0.984 0, 0.987 0 and 0.983 0, and 0.015 89, 0.154 1 and 0.115 1, while the Standard deviations of an unknown sample scanned 8 times are 0.003 26, 0.065 5 and 0.031 4. The results show that PLS-GRNN used in NIRS is a rapid, effective means for measuring chlorine, fibre in the fat in feedstuff powder, and can also be used in quantitative analysis of other samples. A settlement in the high error of prediction of other samples with lower contents was also shown. PMID:18260398

  11. Quantitative PCR Analysis of Molds in the Dust from Homes of Asthmatic Children in North Carolina

    SciTech Connect

    Vesper, Stephen J.; McKinstry, Craig A.; Ashley, Peter; Haugland, Richard A.; Yeatts, Karin; Bradham, Karen; Svendsen, Eric

    2007-07-10

    The vacuum cleaner bag (VCB) dust from the homes of 19 asthmatic children in North Carolina (NC) was analyzed by mold specific quantitative PCR. These results were compared to the analysis of the VCB dust from 157 homes in the HUD “American Healthy Home Survey” of homes in the US. The American Relative Moldiness Index (ARMI) was calculated for each of the homes. The mean and standard deviation (SD) of the ARMI values in the homes of the NC asthmatic children was 11.0 (5.3), compared to the HUD survey VCB ARMI value mean and SD of 6.6 (4.4). The median ARMI value was significantly higher(p < 0.001) in the asthmatic childrens’s homes. The molds Chaetomium globosum and Eurotium amsterdameli were the primary species in the NC homes making the ARMI values higher. Vacuum cleaner bag dust samples may be a less expensive but still useful method of home mold analysis.

  12. DanteR: an extensible R-based tool for quantitative analysis of -omics data

    SciTech Connect

    Taverner, Thomas; Karpievitch, Yuliya; Polpitiya, Ashoka D.; Brown, Joseph N.; Dabney, Alan R.; Anderson, Gordon A.; Smith, Richard D.

    2012-09-15

    Motivation: The size and complex nature of LC-MS proteomics data sets motivates development of specialized software for statistical data analysis and exploration. We present DanteR, a graphical R package that features extensive statistical and diagnostic functions for quantitative proteomics data analysis, including normalization, imputation, hypothesis testing, interactive visualization and peptide-to-protein rollup. More importantly, users can easily extend the existing functionality by including their own algorithms under the Add-On tab. Availability: DanteR and its associated user guide are available for download at http://omics.pnl.gov/software/. For Windows, a single click automatically installs DanteR along with the R programming environment. For Linux and Mac OS X, users must first install R and then follow instructions on the DanteR web site for package installation.

  13. The Recent Progress in Quantitative Medical Image Analysis for Computer Aided Diagnosis Systems

    PubMed Central

    Kim, Tae-Yun; Son, Jaebum

    2011-01-01

    Computer-aided diagnosis (CAD) has become one of the major research subjects in medical imaging and diagnostic radiology. Many different CAD schemes are being developed for use in the detection and/or characterization of various lesions found through various types of medical imaging. These imaging technologies employ conventional projection radiography, computed tomography, magnetic resonance imaging, ultrasonography, etc. In order to achieve a high performance level for a computerized diagnosis, it is important to employ effective image analysis techniques in the major steps of a CAD scheme. The main objective of this review is to attempt to introduce the diverse methods used for quantitative image analysis, and to provide a guide for clinicians. PMID:22084808

  14. Chemical fingerprint and quantitative analysis for quality control of polyphenols extracted from pomegranate peel by HPLC.

    PubMed

    Li, Jianke; He, Xiaoye; Li, Mengying; Zhao, Wei; Liu, Liu; Kong, Xianghong

    2015-06-01

    A simple and efficient HPLC fingerprint method was developed and validated for quality control of the polyphenols extracted from pomegranate peel (PPPs). Ten batches of pomegranate collected from different orchards in Shaanxi Lintong of China were used to establish the fingerprint. For the fingerprint analysis, 15 characteristic peaks were selected to evaluate the similarities of 10 batches of the PPPs. The similarities of the PPPs samples were all more than 0.968, indicating that the samples from different areas of Lintong were consistent. Additionally, simultaneous quantification of eight monophenols (including gallic acid, punicalagin, catechin, chlorogenic acid, caffeic acid, epicatechin, rutin, and ellagic acid) in the PPPs was conducted to interpret the consistency of the quality test. The results demonstrated that the HPLC fingerprint as a characteristic distinguishing method combining similarity evaluation and quantitative analysis can be successfully used to assess the quality and to identify the authenticity of the PPPs. PMID:25624199

  15. Identification and quantitative analysis of genes encoding odorant binding proteins in Aedes albopictus (Diptera: Culicidae).

    PubMed

    Li, Chunxiao; Yan, Ting; Dong, Yande; Zhao, Tongyan

    2012-05-01

    Odorant binding proteins (OBPs) play a critical role in mediating mosquito behaviors. In the current study, four AealOBP genes were cloned and sequenced. Basic Local Alignment Search Tool Program and phylogenetic analysis of the deduced amino acid sequences identified a unique putative ortholog in Aedes aegypti (L.) for each Aedes albopictus (Skuse) OBP. Quantitative analysis showed some AealOBPs with a strong female/male expression ratio, which we proposed to be involved in the host seeking of female mosquitoes. Other OBPs are expressed at higher levels in male antennae and are considered candidates for the detection of floral volatiles. The current study provides basis for further detailed molecular characterization of Ae. albopictus olfactory systems. PMID:22679864

  16. The existence of amorphous phase in Portland cements: Physical factors affecting Rietveld quantitative phase analysis

    SciTech Connect

    Snellings, Ruben Bazzoni, Amélie Scrivener, Karen

    2014-05-01

    Rietveld quantitative phase analysis has become a widespread tool for the characterization of Portland cement, both for research and production control purposes. One of the major remaining points of debate is whether Portland cements contain amorphous content or not. This paper presents detailed analyses of the amorphous phase contents in a set of commercial Portland cements, clinker, synthetic alite and limestone by Rietveld refinement of X-ray powder diffraction measurements using both external and internal standard methods. A systematic study showed that the sample preparation and comminution procedure is closely linked to the calculated amorphous contents. Particle size reduction by wet-grinding lowered the calculated amorphous contents to insignificant quantities for all materials studied. No amorphous content was identified in the final analysis of the Portland cements under investigation.

  17. ANSI/ASHRAE/IES Standard 90.1-2013 Determination of Energy Savings: Quantitative Analysis

    SciTech Connect

    Halverson, Mark A.; Athalye, Rahul A.; Rosenberg, Michael I.; Xie, YuLong; Wang, Weimin; Hart, Philip R.; Zhang, Jian; Goel, Supriya; Mendon, Vrushali V.

    2014-09-04

    This report provides a final quantitative analysis to assess whether buildings constructed according to the requirements of ANSI/ASHRAE/IES Standard 90.1-2013 would result in improved energy efficiency in commercial buildings. The final analysis considered each of the 110 addenda to Standard 90.1-2010 that were included in Standard 90.1-2013. PNNL reviewed all addenda included by ASHRAE in creating Standard 90.1-2013 from Standard 90.1-2010, and considered their combined impact on a suite of prototype building models across all U.S. climate zones. Most addenda were deemed to have little quantifiable impact on building efficiency for the purpose of DOE’s final determination. However, out of the 110 total addenda, 30 were identified as having a measureable and quantifiable impact.

  18. Screening hypochromism (sieve effect) in red blood cells: a quantitative analysis.

    PubMed

    Razi Naqvi, K

    2014-04-01

    Multiwavelength UV-visible spectroscopy, Kramers-Kronig analysis, and several other experimental and theoretical tools have been applied over the last several decades to fathom absorption and scattering of light by suspensions of micron-sized pigmented particles, including red blood cells, but a satisfactory quantitative analysis of the difference between the absorption spectra of suspension of intact and lysed red blood cells is still lacking. It is stressed that such a comparison is meaningful only if the pertinent spectra are free from, or have been corrected for, scattering losses, and it is shown that Duysens' theory can, whereas that of Vekshin cannot, account satisfactorily for the observed hypochromism of suspensions of red blood cells. PMID:24761307

  19. Screening hypochromism (sieve effect) in red blood cells: a quantitative analysis

    PubMed Central

    Razi Naqvi, K.

    2014-01-01

    Multiwavelength UV-visible spectroscopy, Kramers-Kronig analysis, and several other experimental and theoretical tools have been applied over the last several decades to fathom absorption and scattering of light by suspensions of micron-sized pigmented particles, including red blood cells, but a satisfactory quantitative analysis of the difference between the absorption spectra of suspension of intact and lysed red blood cells is still lacking. It is stressed that such a comparison is meaningful only if the pertinent spectra are free from, or have been corrected for, scattering losses, and it is shown that Duysens’ theory can, whereas that of Vekshin cannot, account satisfactorily for the observed hypochromism of suspensions of red blood cells. PMID:24761307

  20. A philosophy of science perspective on the quantitative analysis of behavior.

    PubMed

    Smith, Terry L

    2015-05-01

    B.F. Skinner argued that the science of behavior would progress more rapidly without appealing to theories of learning. He also suggested that theories in a quite different sense were possible, but that the science of behavior as of 1950 was not ready for them. The following analysis distinguishes between Skinner's two concepts of theory. It argues that theory in the second sense has arisen in the quantitative analysis of behavior. The attempt to give a dynamic account of the static regularities of this theory, however, has produced a theory in the first sense. Within its limited domain, this theory offers a rigorous alternative to cognitive accounts of behavior. Rather than distracting attention from actual behavior, it has now led to novel predictions about it. This article is part of a Special Issue entitled 'SQAB 2014'. PMID:25680330

  1. Quantitative RT-PCR gene expression analysis of laser microdissected tissue samples

    PubMed Central

    Erickson, Heidi S.; Albert, Paul S.; Gillespie, John W.; Rodriguez-Canales, Jaime; Linehan, W. Marston; Pinto, Peter A.; Chuaqui, Rodrigo F.; Emmert-Buck, Michael R.

    2009-01-01

    Quantitative reverse transcription polymerase chain reaction (qRT-PCR) is a valuable tool for measuring gene expression in biological samples. However, unique challenges are encountered when studies are performed on cells microdissected from tissues derived from animal models or the clinic, including specimen related issues, variability of RNA template quality and quantity, and normalization. qRT-PCR using small amounts of mRNA derived from dissected cell populations requires adaptation of standard methods to allow meaningful comparisons across sample sets. The protocol described here presents the rationale, technical steps, normalization strategy, and data analysis necessary to generate reliable gene expression measurements of transcripts from dissected samples. The entire protocol from tissue microdissection through qRT-PCR analysis requires approximately 16 hours. PMID:19478806

  2. Probabilistic partial least squares regression for quantitative analysis of Raman spectra.

    PubMed

    Li, Shuo; Nyagilo, James O; Dave, Digant P; Wang, Wei; Zhang, Baoju; Gao, Jean

    2015-01-01

    With the latest development of Surface-Enhanced Raman Scattering (SERS) technique, quantitative analysis of Raman spectra has shown the potential and promising trend of development in vivo molecular imaging. Partial Least Squares Regression (PLSR) is state-of-the-art method. But it only relies on training samples, which makes it difficult to incorporate complex domain knowledge. Based on probabilistic Principal Component Analysis (PCA) and probabilistic curve fitting idea, we propose a probabilistic PLSR (PPLSR) model and an Estimation Maximisation (EM) algorithm for estimating parameters. This model explains PLSR from a probabilistic viewpoint, describes its essential meaning and provides a foundation to develop future Bayesian nonparametrics models. Two real Raman spectra datasets were used to evaluate this model, and experimental results show its effectiveness. PMID:26255384

  3. Quantitative high-pressure pair distribution function analysis of nanocrystalline gold

    NASA Astrophysics Data System (ADS)

    Martin, C. David; Antao, Sytle M.; Chupas, Peter J.; Lee, Peter L.; Shastri, Sarvjit D.; Parise, John B.

    2005-02-01

    Using a diamond anvil cell with high-energy monochromatic x rays, we have studied the total scattering of nanocrystalline gold to 20Å-1 at pressures up to 10GPa in a hydrostatic alcohol pressure-medium. Through direct Fourier transformation of the structure function [S(Q)], pair distribution functions (PDFs) [G(r)] are calculated without Kaplow-type iterative corrections. Quantitative high-pressure PDF (QHP-PDF) analysis is performed via full-profile least-squares modeling and confirmed through comparison of Rietveld analysis of Bragg diffraction. The quality of the high pressure PDFs obtained demonstrates the integrity of our technique and suggests the feasibility of future QHP-PDF studies of liquids, disordered solids, and materials at phase transition under pressure.

  4. Summary of Terra and Aqua MODIS Long-Term Performance

    NASA Technical Reports Server (NTRS)

    Xiong, Xiaoxiong (Jack); Wenny, Brian N.; Angal, Amit; Barnes, William; Salomonson, Vincent

    2011-01-01

    Since launch in December 1999, the MODIS ProtoFlight Model (PFM) onboard the Terra spacecraft has successfully operated for more than 11 years. Its Flight Model (FM) onboard the Aqua spacecraft, launched in May 2002, has also successfully operated for over 9 years. MODIS observations are made in 36 spectral bands at three nadir spatial resolutions and are calibrated and characterized regularly by a set of on-board calibrators (OBC). Nearly 40 science products, supporting a variety of land, ocean, and atmospheric applications, are continuously derived from the calibrated reflectances and radiances of each MODIS instrument and widely distributed to the world-wide user community. Following an overview of MODIS instrument operation and calibration activities, this paper provides a summary of both Terra and Aqua MODIS long-term performance. Special considerations that are critical to maintaining MODIS data quality and beneficial for future missions are also discussed.

  5. Simple preparation of plant epidermal tissue for laser microdissection and downstream quantitative proteome and carbohydrate analysis

    PubMed Central

    Falter, Christian; Ellinger, Dorothea; von Hülsen, Behrend; Heim, René; Voigt, Christian A.

    2015-01-01

    The outwardly directed cell wall and associated plasma membrane of epidermal cells represent the first layers of plant defense against intruding pathogens. Cell wall modifications and the formation of defense structures at sites of attempted pathogen penetration are decisive for plant defense. A precise isolation of these stress-induced structures would allow a specific analysis of regulatory mechanism and cell wall adaption. However, methods for large-scale epidermal tissue preparation from the model plant Arabidopsis thaliana, which would allow proteome and cell wall analysis of complete, laser-microdissected epidermal defense structures, have not been provided. We developed the adhesive tape – liquid cover glass technique (ACT) for simple leaf epidermis preparation from A. thaliana, which is also applicable on grass leaves. This method is compatible with subsequent staining techniques to visualize stress-related cell wall structures, which were precisely isolated from the epidermal tissue layer by laser microdissection (LM) coupled to laser pressure catapulting. We successfully demonstrated that these specific epidermal tissue samples could be used for quantitative downstream proteome and cell wall analysis. The development of the ACT for simple leaf epidermis preparation and the compatibility to LM and downstream quantitative analysis opens new possibilities in the precise examination of stress- and pathogen-related cell wall structures in epidermal cells. Because the developed tissue processing is also applicable on A. thaliana, well-established, model pathosystems that include the interaction with powdery mildews can be studied to determine principal regulatory mechanisms in plant–microbe interaction with their potential outreach into crop breeding. PMID:25870605

  6. MODIS Collection 6 aerosol products: Comparison between Aqua's e-Deep Blue, Dark Target, and "merged" data sets, and usage recommendations

    NASA Astrophysics Data System (ADS)

    Sayer, A. M.; Munchak, L. A.; Hsu, N. C.; Levy, R. C.; Bettenhausen, C.; Jeong, M.-J.

    2014-12-01

    The Moderate Resolution Imaging Spectroradiometer (MODIS) Atmospheres data product suite includes three algorithms applied to retrieve midvisible aerosol optical depth (AOD): the Enhanced Deep Blue (DB) and Dark Target (DT) algorithms over land, and a DT over-water algorithm. All three have been refined in the recent "Collection 6" (C6) MODIS reprocessing. In particular, DB has been expanded to cover vegetated land surfaces as well as brighter desert/urban areas. Additionally, a new "merged" data set which draws from all three algorithms is included in the C6 products. This study is intended to act as a point of reference for new and experienced MODIS data users with which to understand the global and regional characteristics of the C6 DB, DT, and merged data sets, based on MODIS Aqua data. This includes validation against Aerosol Robotic Network (AERONET) observations at 111 sites, focused toward regional and categorical (surface/aerosol type) analysis. Neither algorithm consistently outperforms the other, although in many cases the retrieved AOD and the level of its agreement with AERONET are very similar. In many regions the DB, DT, and merged data sets are all suitable for quantitative applications, bearing in mind that they cannot be considered independent, while in other cases one algorithm does consistently outperform the other. Usage recommendations and caveats are thus somewhat complicated and regionally dependent.

  7. Inter-Comparison of Terra and Aqua MODIS

    NASA Technical Reports Server (NTRS)

    Xiong, X.; Salomonson, V. V.; Sun, J.; Wu, A.; Barnes, W.; Guenther, B.

    2004-01-01

    Nearly identical copies of the Moderate Resolution Imaging Spectroradiometer (MODIS) have been operating on-board the NASA's Earth Observing System (EOS) Terra and Aqua satellites since their launches in December 1999 and May 2002, respectively. Each MODIS has 20 reflective solar bands (RSB) with center wavelengths ranging from 0.41 to 2.1 micrometers and 16 thermal emissive bands (TEB) from 3.7 to 14.4 micrometers. The absolute radiometric accuracy requirements (1 sigma) at the typical spectral radiance levels are plus or minus 2% for the RSB for the RSB reflectance factors and plus or minus 5% for the RSB radiance products. With few exceptions, the TEB requirements are plus or minus 1%. The sensor's on-orbit radiometric calibration is performed by the on-board calibrators, including a solar diffuser (SD) and a solar diffuser stability monitor (SDSM) system for the RSB and a V-groove flat panel blackbody (BB) for the TEB. In addition, the Moon has been extensively used by both Terra and Aqua MODIS to support their on-orbit calibration and characterization. This paper presents MODIS lunar calibration methodology and inter-comparison of Terra and Aqua MODIS in the VIS/NIR spectral regions. Current results from lunar observations show that the calibration difference between the two sensors is less than plus or minus 1%. Also discussed in this paper are the approaches and results of inter-comparison of Terra and Aqua MODIS in the TEB using closely matched thermal infrared (TIR) channels on the Advanced Very High Resolution Radiometer (AVHRR) at 11 and 12 micrometers.

  8. Surface Albedo/BRDF Parameters (Terra/Aqua MODIS)

    DOE Data Explorer

    Trishchenko, Alexander

    2008-01-15

    Spatially and temporally complete surface spectral albedo/BRDF products over the ARM SGP area were generated using data from two Moderate Resolution Imaging Spectroradiometer (MODIS) sensors on Terra and Aqua satellites. A landcover-based fitting (LBF) algorithm is developed to derive the BRDF model parameters and albedo product (Luo et al., 2004a). The approach employs a landcover map and multi-day clearsky composites of directional surface reflectance. The landcover map is derived from the Landsat TM 30-meter data set (Trishchenko et al., 2004a), and the surface reflectances are from MODIS 500m-resolution 8-day composite products (MOD09/MYD09). The MOD09/MYD09 data are re-arranged into 10-day intervals for compatibility with other satellite products, such as those from the NOVA/AVHRR and SPOT/VGT sensors. The LBF method increases the success rate of the BRDF fitting process and enables more accurate monitoring of surface temporal changes during periods of rapid spring vegetation green-up and autumn leaf-fall, as well as changes due to agricultural practices and snowcover variations (Luo et al., 2004b, Trishchenko et al., 2004b). Albedo/BRDF products for MODIS on Terra and MODIS on Aqua, as well as for Terra/Aqua combined dataset, are generated at 500m spatial resolution and every 10-day since March 2000 (Terra) and July 2002 (Aqua and combined), respectively. The purpose for the latter product is to obtain a more comprehensive dataset that takes advantages of multi-sensor observations (Trishchenko et al., 2002). To fill data gaps due to cloud presence, various interpolation procedures are applied based on a multi-year observation database and referring to results from other locations with similar landcover property. Special seasonal smoothing procedure is also applied to further remove outliers and artifacts in data series.

  9. Comparison of Different Time of Flight-Mass Spectrometry Modes for Small Molecule Quantitative Analysis.

    PubMed

    Chindarkar, Nandkishor S; Park, Hyung-Doo; Stone, Judith A; Fitzgerald, Robert L

    2015-11-01

    Currently, the use of time of flight (TOF)-mass spectrometry (MS) in quantitative analysis of small molecules is rare. Recently, the quantitative performance of TOF mass analyzers has improved due to the advancements in TOF technology. We evaluated a Q-TOF-MS in different modes, i.e., Q-TOF-full scan (Q-TOF-FS), Q-TOF-enhanced-full scan (Q-TOF-En-FS), MS(E), Q-TOF-targeted (Q-TOF-TGT), Q-TOF-enhanced-targeted (Q-TOF-En-TGT), and compared their quantitative performance against a unit resolution LC-MS-MS (tandem quadrupole) platform. The five modes were investigated for sensitivity, linearity, signal-to-noise ratio, recovery and precision using 11-nor-9-carboxy-?(9)-tetrahydrocannabinol (THC-COOH) as a model compound in electrospray ionization (ESI) with negative polarity. Preliminary studies indicated that Q-TOF-FS mode was the least linear and precise; hence, it was eliminated from further investigation. Total imprecision in remaining four modes was <10%. The Q-TOF-En-FS and Q-TOF-En-TGT showed better signal intensity than their respective modes without enhancement. Overall, peak signal intensity was the highest in MS(E) mode, whereas the signal-to-noise ratio was the best in the Q-TOF-En-TGT mode. Relatively, MS(E) and Q-TOF-En-TGT modes were the best overall performers compared with the other modes. Both MS(E) and Q-TOF-En-TGT modes showed excellent precision (coefficient of variation <6%), patient correlation (r > 0.99) and linearity (range, 5-455 ng/mL) for THC-COOH analysis when compared with LC-MS-MS. We also investigated the performance of the same four modes using methamphetamine in positive ESI. Quantitative data obtained by Q-TOF-En-TGT and MS(E), using both positive and negative ESI, suggest that these modes performed better than the other modes. While unit resolution LC-MS-MS remains the optimal technique for quantification, our data showed that Q-TOF-MS can also be used to quantify small molecules in complex biological specimens. PMID:26239972

  10. Simulation of realistic abnormal SPECT brain perfusion images: application in semi-quantitative analysis

    NASA Astrophysics Data System (ADS)

    Ward, T.; Fleming, J. S.; Hoffmann, S. M. A.; Kemp, P. M.

    2005-11-01

    Simulation is useful in the validation of functional image analysis methods, particularly when considering the number of analysis techniques currently available lacking thorough validation. Problems exist with current simulation methods due to long run times or unrealistic results making it problematic to generate complete datasets. A method is presented for simulating known abnormalities within normal brain SPECT images using a measured point spread function (PSF), and incorporating a stereotactic atlas of the brain for anatomical positioning. This allows for the simulation of realistic images through the use of prior information regarding disease progression. SPECT images of cerebral perfusion have been generated consisting of a control database and a group of simulated abnormal subjects that are to be used in a UK audit of analysis methods. The abnormality is defined in the stereotactic space, then transformed to the individual subject space, convolved with a measured PSF and removed from the normal subject image. The dataset was analysed using SPM99 (Wellcome Department of Imaging Neuroscience, University College, London) and the MarsBaR volume of interest (VOI) analysis toolbox. The results were evaluated by comparison with the known ground truth. The analysis showed improvement when using a smoothing kernel equal to system resolution over the slightly larger kernel used routinely. Significant correlation was found between effective volume of a simulated abnormality and the detected size using SPM99. Improvements in VOI analysis sensitivity were found when using the region median over the region mean. The method and dataset provide an efficient methodology for use in the comparison and cross validation of semi-quantitative analysis methods in brain SPECT, and allow the optimization of analysis parameters.

  11. Quantitative inverse modelling of a cylindrical object in the laboratory using ERT: An error analysis

    NASA Astrophysics Data System (ADS)

    Korteland, Suze-Anne; Heimovaara, Timo

    2015-03-01

    Electrical resistivity tomography (ERT) is a geophysical technique that can be used to obtain three-dimensional images of the bulk electrical conductivity of the subsurface. Because the electrical conductivity is strongly related to properties of the subsurface and the flow of water it has become a valuable tool for visualization in many hydrogeological and environmental applications. In recent years, ERT is increasingly being used for quantitative characterization, which requires more detailed prior information than a conventional geophysical inversion for qualitative purposes. In addition, the careful interpretation of measurement and modelling errors is critical if ERT measurements are to be used in a quantitative way. This paper explores the quantitative determination of the electrical conductivity distribution of a cylindrical object placed in a water bath in a laboratory-scale tank. Because of the sharp conductivity contrast between the object and the water, a standard geophysical inversion using a smoothness constraint could not reproduce this target accurately. Better results were obtained by using the ERT measurements to constrain a model describing the geometry of the system. The posterior probability distributions of the parameters describing the geometry were estimated with the Markov chain Monte Carlo method DREAM(ZS). Using the ERT measurements this way, accurate estimates of the parameters could be obtained. The information quality of the measurements was assessed by a detailed analysis of the errors. Even for the uncomplicated laboratory setup used in this paper, errors in the modelling of the shape and position of the electrodes and the shape of the domain could be identified. The results indicate that the ERT measurements have a high information content which can be accessed by the inclusion of prior information and the consideration of measurement and modelling errors.

  12. Early quantitative CT analysis of oleic acid induced acute respiratory distress syndrome in a canine model

    PubMed Central

    Chen, Huai; Zeng, Qing-Si; Chen, Rong-Chang; Li, Wen; Zhou, Jia-Xuan; Liu, Qin; Dai, Wang-Chun

    2015-01-01

    Background: Although quantitative computed tomography (CT) has been used to analyze the lungs of patients with confirmed diagnoses of acute respiratory distress syndrome (ARDS), there are few reports to show the diagnosis during the early stage of ARDS. Using a canine model and quantitative CT, we aimed to develop an oleic acid (OA) induced ARDS regarding the early stage of ARDS that could improve in the early diagnosis of ARDS. Methods: Fourteen healthy beagle dogs underwent CT. Their lung tissue was manually partitioned into four compartments, i.e., non-aerated, poorly aerated, normally aerated, and hyper-aerated lung compartments. The mean CT attenuation value Hounsfield unit (HU), tissue mass (g), residual volume (ml), and percentage of lung area were automatically determined for each lung compartment and compared between groups by receiver operating characteristic curve (ROC) analyses using area under curve (AUC). The optimized cut-off point for each parameter was determined by Youden’s index. Results: Regarding lung compartments during the expiratory phase, the percentage of non-aerated lung area in the ARDS group was higher vs. controls at all time points (T1 to T6). CT attenuation values for the ARDS group increased with time during both respiratory phases compared with controls. During both respiratory phases, tissue mass within the ARDS group significantly increased compared with controls at T3-T6. Conclusions: Quantitative CT analysis can detect ARDS at an early stage with high sensitivity and specificity, providing a minimum of assistance in the early diagnosis of ARDS. PMID:26221239

  13. A subject-specific framework for in vivo myeloarchitectonic analysis using high resolution quantitative MRI.

    PubMed

    Waehnert, Miriam D; Dinse, Juliane; Schäfer, Andreas; Geyer, Stefan; Bazin, Pierre-Louis; Turner, Robert; Tardif, Christine Lucas

    2016-01-15

    Structural magnetic resonance imaging can now resolve laminar features within the cerebral cortex in vivo. A variety of intracortical contrasts have been used to study the cortical myeloarchitecture with the purpose of mapping cortical areas in individual subjects. In this article, we first briefly review recent advances in MRI analysis of cortical microstructure to portray the potential and limitations of the current state-of-the-art. We then present an integrated framework for the analysis of intracortical structure, composed of novel image processing tools designed for high resolution cortical images. The main features of our framework are the segmentation of quantitative T1 maps to delineate the cortical boundaries (Bazin et al., 2014), and the use of an equivolume layering model to define an intracortical coordinate system that follows the anatomical layers of the cortex (Waehnert et al., 2014). We evaluate the framework with 150?m isotropic post mortem T2(?)-weighted images and 0.5mm isotropic in vivo T1 maps, a quantitative index of myelin content. We study the laminar structure of the primary visual cortex (Brodmann area 17) in the post mortem and in vivo data, as well as the central sulcus region in vivo, in particular Brodmann areas 1, 3b and 4. We also investigate the impact of the layering models on the relationship between T1 and cortical curvature. Our experiments demonstrate that the equivolume intracortical surfaces and transcortical profiles best reflect the laminar structure of the cortex in areas of curvature in comparison to the state-of-the-art equidistant and Laplace implementations. This framework generates a subject specific intracortical coordinate system, the basis for subsequent architectonic analyses of the cortex. Any structural or functional contrast co-registered to the T1 maps, used to segment the cortex, can be sampled on the curved grid for analysis. This work represents an important step towards in vivo structural brain mapping of individual subjects. PMID:26455795

  14. Quantitative proteomic analysis reveals potential diagnostic markers and pathways involved in pathogenesis of renal cell carcinoma.

    PubMed

    White, Nicole M A; Masui, Olena; Desouza, Leroi V; Krakovska, Olga; Metias, Shereen; Romaschin, Alexander D; Honey, R John; Stewart, Robert; Pace, Kenneth; Lee, Jason; Jewett, Michael As; Bjarnason, Georg A; Siu, K W Michael; Yousef, George M

    2014-01-30

    There are no serum biomarkers for the accurate diagnosis of clear cell renal cell carcinoma (ccRCC). Diagnosis and decision of nephrectomy rely on imaging which is not always accurate. Non-invasive diagnostic biomarkers are urgently required. In this study, we preformed quantitative proteomics analysis on a total of 199 patients including 30 matched pairs of normal kidney and ccRCC using isobaric tags for relative and absolute quantitation (iTRAQ) labeling and LC-MS/MS analysis to identify differentially expressed proteins. We found 55 proteins significantly dysregulated in ccRCC compared to normal kidney tissue. 54 were previously reported to play a role in carcinogenesis, and 39 are secreted proteins. Dysregulation of alpha-enolase (ENO1), L-lactate dehydrogenase A chain (LDHA), heat shock protein beta-1 (HSPB1/Hsp27), and 10 kDa heat shock protein, mitochondrial (HSPE1) was confirmed in two independent sets of patients by western blot and immunohistochemistry. Pathway analysis, validated by PCR, showed glucose metabolism is altered in ccRCC compared to normal kidney tissue. In addition, we examined the utility of Hsp27 as biomarker in serum and urine. In ccRCC patients, Hsp27 was elevated in the urine and serum and high serum Hsp27 was associated with high grade (Grade 3-4) tumors. These data together identify potential diagnostic biomarkers for ccRCC and shed new light on the molecular mechanisms that are dysregulated and contribute to the pathogenesis of ccRCC. Hsp27 is a promising diagnostic marker for ccRCC although further large-scale studies are required. Also, molecular profiling may help pave the road to the discovery of new therapies. PMID:24504108

  15. Quantitative proteomic analysis reveals potential diagnostic markers and pathways involved in pathogenesis of renal cell carcinoma

    PubMed Central

    DeSouza, Leroi V.; Krakovska-Yutz, Olga; Metias, Shereen; Romaschin, Alexander D.; Honey, R. John; Stewart, Robert; Pace, Kenneth; Lee, Jason; Jewett, Michael AS; Bjarnason, Georg A.; Siu, K.W. Michael; Yousef, George M.

    2014-01-01

    There are no serum biomarkers for the accurate diagnosis of clear cell renal cell carcinoma (ccRCC). Diagnosis and decision of nephrectomy rely on imaging which is not always accurate. Non-invasive diagnostic biomarkers are urgently required. In this study, we preformed quantitative proteomics analysis on a total of 199 patients including 30 matched pairs of normal kidney and ccRCC using isobaric tags for relative and absolute quantitation (iTRAQ) labeling and LC-MS/MS analysis to identify differentially expressed proteins. We found 55 proteins significantly dysregulated in ccRCC compared to normal kidney tissue. 54 were previously reported to play a role in carcinogenesis, and 39 are secreted proteins. Dysregulation of alpha-enolase (ENO1), L-lactate dehydrogenase A chain (LDHA), heat shock protein beta-1 (HSPB1/Hsp27), and 10 kDa heat shock protein, mitochondrial (HSPE1) was confirmed in two independent sets of patients by western blot and immunohistochemistry. Pathway analysis, validated by PCR, showed glucose metabolism is altered in ccRCC compared to normal kidney tissue. In addition, we examined the utility of Hsp27 as biomarker in serum and urine. In ccRCC patients, Hsp27 was elevated in the urine and serum and high serum Hsp27 was associated with high grade (Grade 3–4) tumors. These data together identify potential diagnostic biomarkers for ccRCC and shed new light on the molecular mechanisms that are dysregulated and contribute to the pathogenesis of ccRCC. Hsp27 is a promising diagnostic marker for ccRCC although further large-scale studies are required. Also, molecular profiling may help pave the road to the discovery of new therapies. PMID:24504108

  16. A quantitative analysis of municipal solid waste disposal charges in China.

    PubMed

    Wu, Jian; Zhang, Weiqian; Xu, Jiaxuan; Che, Yue

    2015-03-01

    Rapid industrialization and economic development have caused a tremendous increase in municipal solid waste (MSW) generation in China. China began implementing a policy of MSW disposal fees for household waste management at the end of last century. Three charging methods were implemented throughout the country: a fixed disposal fee, a potable water-based disposal fee, and a plastic bag-based disposal fee. To date, there has been little qualitative or quantitative analysis on the effectiveness of this relatively new policy. This paper provides a general overview of MSW fee policy in China, attempts to verify whether the policy is successful in reducing general waste collected, and proposes an improved charging system to address current problems. The paper presents an empirical statistical analysis of policy effectiveness derived from an environmental Kuznets curve (EKC) test on panel data of China. EKC tests on different kinds of MSW charge systems were then examined for individual provinces or cities. A comparison of existing charging systems was conducted using environmental and economic criteria. The results indicate the following: (1) the MSW policies implemented over the study period were effective in the reduction of waste generation, (2) the household waste discharge fee policy did not act as a strong driver in terms of waste prevention and reduction, and (3) the plastic bag-based disposal fee appeared to be performing well according to qualitative and quantitative analysis. Based on current situation of waste discharging management in China, a three-stage transitional charging scheme is proposed and both advantages and drawbacks discussed. Evidence suggests that a transition from a fixed disposal fee to a plastic bag-based disposal fee involving various stakeholders should be the next objective of waste reduction efforts. PMID:25647799

  17. Quantitation of protein–protein interactions by thermal stability shift analysis

    PubMed Central

    Layton, Curtis J; Hellinga, Homme W

    2011-01-01

    Thermal stability shift analysis is a powerful method for examining binding interactions in proteins. We demonstrate that under certain circumstances, protein–protein interactions can be quantitated by monitoring shifts in thermal stability using thermodynamic models and data analysis methods presented in this work. This method relies on the determination of protein stabilities from thermal unfolding experiments using fluorescent dyes such as SYPRO Orange that report on protein denaturation. Data collection is rapid and straightforward using readily available real-time polymerase chain reaction instrumentation. We present an approach for the analysis of the unfolding transitions corresponding to each partner to extract the affinity of the interaction between the proteins. This method does not require the construction of a titration series that brackets the dissociation constant. In thermal shift experiments, protein stability data are obtained at different temperatures according to the affinity- and concentration-dependent shifts in unfolding transition midpoints. Treatment of the temperature dependence of affinity is, therefore, intrinsic to this method and is developed in this study. We used the interaction between maltose-binding protein (MBP) and a thermostable synthetic ankyrin repeat protein (Off7) as an experimental test case because their unfolding transitions overlap minimally. We found that MBP is significantly stabilized by Off7. High experimental throughput is enabled by sample parallelization, and the ability to extract quantitative binding information at a single partner concentration. In a single experiment, we were able to quantify the affinities of a series of alanine mutants, covering a wide range of affinities (? 100 nM to ? 100 ?M). PMID:21674662

  18. A novel benzene quantitative analysis method using miniaturized metal ionization gas sensor and non-linear bistable dynamic system.

    PubMed

    Tang, Xuxiang; Liu, Fuqi

    2015-09-01

    In this paper, a novel benzene quantitative analysis method utilizing miniaturized metal ionization gas sensor and non-linear bistable dynamic system was investigated. Al plate anodic gas-ionization sensor was installed for electrical current-voltage data measurement. Measurement data was analyzed by non-linear bistable dynamics system. Results demonstrated that this method realized benzene concentration quantitative determination. This method is promising in laboratory safety management in benzene leak detection. PMID:26218927

  19. The Aqua-Planet Experiment (APE): CONTROL SST Simulation

    NASA Technical Reports Server (NTRS)

    Blackburn, Michael; Williamson, David L.; Nakajima, Kensuke; Ohfuchi, Wataru; Takahashi, Yoshiyuki O.; Hayashi, Yoshi-Yuki; Nakamura, Hisashi; Ishiwatari, Masaki; Mcgregor, John L.; Borth, Hartmut; Wirth, Volkmar; Frank, Helmut; Bechtold, Peter; Wedi, Nils P.; Tomita, Hirofumi; Satoh, Masaki; Zhao, Ming; Held, Isaac M.; Suarez, Max J.; Lee, Myong-In; Watanabe, Masahiro; Kimoto, Masahide; Liu, Yimin; Wang, Zaizhi; Molod, Andrea M.; Rajendran, Kavirajan; Kotoh, Akio; Stratton, Rachel

    2013-01-01

    Climate simulations by 16 atmospheric general circulation models (AGCMs) are compared on an aqua-planet, a water-covered Earth with prescribed sea surface temperature varying only in latitude. The idealised configuration is designed to expose differences in the circulation simulated by different models. Basic features of the aqua-planet climate are characterised by comparison with Earth. The models display a wide range of behaviour. The balanced component of the tropospheric mean flow, and mid-latitude eddy covariances subject to budget constraints, vary relatively little among the models. In contrast, differences in damping in the dynamical core strongly influence transient eddy amplitudes. Historical uncertainty in modelled lower stratospheric temperatures persists in APE.Aspects of the circulation generated more directly by interactions between the resolved fluid dynamics and parameterized moist processes vary greatly. The tropical Hadley circulation forms either a single or double inter-tropical convergence zone (ITCZ) at the equator, with large variations in mean precipitation. The equatorial wave spectrum shows a wide range of precipitation intensity and propagation characteristics. Kelvin mode-like eastward propagation with remarkably constant phase speed dominates in most models. Westward propagation, less dispersive than the equatorial Rossby modes, dominates in a few models or occurs within an eastward propagating envelope in others. The mean structure of the ITCZ is related to precipitation variability, consistent with previous studies.The aqua-planet global energy balance is unknown but the models produce a surprisingly large range of top of atmosphere global net flux, dominated by differences in shortwave reflection by clouds. A number of newly developed models, not optimised for Earth climate, contribute to this. Possible reasons for differences in the optimised models are discussed.The aqua-planet configuration is intended as one component of an experimental hierarchy used to evaluate AGCMs. This comparison does suggest that the range of model behaviour could be better understood and reduced in conjunction with Earth climate simulations. Controlled experimentation is required to explore individual model behavior and investigate convergence of the aqua-planet climate with increasing resolution.

  20. [Qualitative-Quantitative Analysis of Rice Bran Oil Adulteration Based on Laser Near Infrared Spectroscopy].

    PubMed

    Tu, Bin; Song, Zhi-qiang; Zheng, Xiao; Zeng, Lu-lu; Yin, Cheng; He, Dong-ping; Qi, Pei-shi

    2015-06-01

    The purpose of this study is mainly to have qualitative-quantitative analysis on the adulteration in rice bran oil by near-infrared spectroscopy analytical technology combined with chemo metrics methods. The author configured 189 adulterated oil samples according to the different mass ratios by selecting rice bran oil as base oil and choosing soybean oil, corn oil, colza oil, and waste oil of catering industry as adulterated oil. Then, the spectral data of samples was collected by using near-infrared spectrometer, and it was pre-processed through the following methods, including without processing, Multiplicative Scatter Correction(MSC), Orthogonal Signal Correction(OSC), Standard Normal Variate and Standard Normal Variate transformation DeTrending(SNV_DT). Furthermore, this article extracted characteristic wavelengths of the spectral datum from the pre-processed date by Successive Projections Algorithm(SPA), established qualitatively classified calibration methods of adulterated oil through classification method of Support Vector Machine(SVM), optimized model parameters(C, g) by Mesh Search Algorithm and determined the optimal process condition. In extracting characteristic wavelengths of the spectral datum from pretreatment by Backward interval Partial Least Squares(BiPLS) and SPA, quantitatively classified calibration models of adulterated oil through Partial Least Squares(PLS) and Support Vector Machine Regression(SVR) was established respectively. In the end, the author optimized the combination of model parameters(C, g) by Mesh Search Algorithm and determined the optimal parameter model. According to the analysis, the accuracy of prediction set and calibration set for SVC model reached 95% and 100% respectively. Compared with the prediction of the adulteration oil content of rice bran oil which was established by the PLS model, the SVR model is the better one, although both of them could implement the content prediction. Furthermore, the correlation coefficient R is above 0.99 and the Root Mean Square Error (MSE) is below 5.55 x 10(-4). The results show that the near-infrared spectroscopy technology is effective in qualitative-quantitative analysis on the adulteration of rice bran oil. And the method is applicable to analyze adulteration in other oils. PMID:26601363

  1. Blind Analysis of Fortified Pesticide Residues in Carrot Extracts using GC-MS to Evaluate Qualitative and Quantitative Performance

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Unlike quantitative analysis, the quality of the qualitative results in the analysis of pesticide residues in food are generally ignored in practice. Instead, chemists tend to rely on advanced mass spectrometric techniques and general subjective guidelines or fixed acceptability criteria when makin...

  2. Quantitative morphologic analysis of boulder shape and surface texture to infer environmental history: A case study of rock

    E-print Network

    Bourke, Mary C.

    morphologic analysis of boulder shape and surface texture to infer environmental history: A case study of rock applications to planetary environmental histories as well as those on Earth. Landed planetary missionsQuantitative morphologic analysis of boulder shape and surface texture to infer environmental

  3. A semi-quantitative approach to GMO risk-benefit analysis.

    PubMed

    Morris, E Jane

    2011-10-01

    In many countries there are increasing calls for the benefits of genetically modified organisms (GMOs) to be considered as well as the risks, and for a risk-benefit analysis to form an integral part of GMO regulatory frameworks. This trend represents a shift away from the strict emphasis on risks, which is encapsulated in the Precautionary Principle that forms the basis for the Cartagena Protocol on Biosafety, and which is reflected in the national legislation of many countries. The introduction of risk-benefit analysis of GMOs would be facilitated if clear methodologies were available to support the analysis. Up to now, methodologies for risk-benefit analysis that would be applicable to the introduction of GMOs have not been well defined. This paper describes a relatively simple semi-quantitative methodology that could be easily applied as a decision support tool, giving particular consideration to the needs of regulators in developing countries where there are limited resources and experience. The application of the methodology is demonstrated using the release of an insect resistant maize variety in South Africa as a case study. The applicability of the method in the South African regulatory system is also discussed, as an example of what might be involved in introducing changes into an existing regulatory process. PMID:21197601

  4. Oqtans: the RNA-seq workbench in the cloud for complete and reproducible quantitative transcriptome analysis.

    PubMed

    Sreedharan, Vipin T; Schultheiss, Sebastian J; Jean, Géraldine; Kahles, André; Bohnert, Regina; Drewe, Philipp; Mudrakarta, Pramod; Görnitz, Nico; Zeller, Georg; Rätsch, Gunnar

    2014-05-01

    We present Oqtans, an open-source workbench for quantitative transcriptome analysis, that is integrated in Galaxy. Its distinguishing features include customizable computational workflows and a modular pipeline architecture that facilitates comparative assessment of tool and data quality. Oqtans integrates an assortment of machine learning-powered tools into Galaxy, which show superior or equal performance to state-of-the-art tools. Implemented tools comprise a complete transcriptome analysis workflow: short-read alignment, transcript identification/quantification and differential expression analysis. Oqtans and Galaxy facilitate persistent storage, data exchange and documentation of intermediate results and analysis workflows. We illustrate how Oqtans aids the interpretation of data from different experiments in easy to understand use cases. Users can easily create their own workflows and extend Oqtans by integrating specific tools. Oqtans is available as (i) a cloud machine image with a demo instance at cloud.oqtans.org, (ii) a public Galaxy instance at galaxy.cbio.mskcc.org, (iii) a git repository containing all installed software (oqtans.org/git); most of which is also available from (iv) the Galaxy Toolshed and (v) a share string to use along with Galaxy CloudMan. PMID:24413671

  5. 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.

  6. Quantitative analysis of metformin in antidiabetic tablets by laser-induced breakdown spectroscopy

    NASA Astrophysics Data System (ADS)

    Contreras, U.; Ornelas-Soto, N.; Meneses-Nava, M. A.; Barbosa-García, O.; López-de-Alba, P. L.; López-Martínez, L.

    2011-09-01

    Nowadays the production of counterfeit and low quality drugs affects human health and generates losses to pharmaceutical industries and tax revenue losses to government. Currently there are several methods for pharmaceutical product analysis; nevertheless, most of them depend on complex and time consuming steps such as sample preparation. In contrast to conventional methods, Laser-induced breakdown spectroscopy (LIBS) is evaluated as a potential analytical technique for the rapid screening and quality control of anti-diabetic solid formulations. In this paper authors propose a simple method to analyze qualitatively and quantitatively Active Pharmaceutical Ingredients (APIs) such as Metformin hydrochloride. The authors used ten nanosecond duration pulses (FWHM) from a Nd:YAG laser produces the induced breakdown for the analysis. Light is collected and focused into a Cerny-Turner spectrograph and dispersed into an ICCD camera for its detection. We used atomic emissions from Chlorine atoms present only in APIs as analyte signal. The analysis was improved using Bromine as internal standard. Linear calibration curves from synthetic samples were prepared achieving linearity higher than 99%. Our results were compared with HPLC results and validation was performed by statistical methods. The validation analysis suggests that both methods have no significant differences i.e., the proposed method can be implemented for monitoring the pharmaceutical production process in-situ in real time or for inspection and recognition of authenticity.

  7. 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.

  8. Accuracy and Precision of Silicon Based Impression Media for Quantitative Areal Texture Analysis

    PubMed Central

    Goodall, Robert H.; Darras, Laurent P.; Purnell, Mark A.

    2015-01-01

    Areal surface texture analysis is becoming widespread across a diverse range of applications, from engineering to ecology. In many studies silicon based impression media are used to replicate surfaces, and the fidelity of replication defines the quality of data collected. However, while different investigators have used different impression media, the fidelity of surface replication has not been subjected to quantitative analysis based on areal texture data. Here we present the results of an analysis of the accuracy and precision with which different silicon based impression media of varying composition and viscosity replicate rough and smooth surfaces. Both accuracy and precision vary greatly between different media. High viscosity media tested show very low accuracy and precision, and most other compounds showed either the same pattern, or low accuracy and high precision, or low precision and high accuracy. Of the media tested, mid viscosity President Jet Regular Body and low viscosity President Jet Light Body (Coltène Whaledent) are the only compounds to show high levels of accuracy and precision on both surface types. Our results show that data acquired from different impression media are not comparable, supporting calls for greater standardisation of methods in areal texture analysis. PMID:25991505

  9. Quantitative Analysis of Respiration-Related Movement for Abdominal Artery in Multiphase Hepatic CT

    PubMed Central

    Lin, Yang-Hsien; Huang, Shih-Min; Huang, Chin-Yi; Tu, Yun-Niang; Liu, Shing-Hong; Huang, Tzung-Chi

    2014-01-01

    Objectives Respiration-induced motion in the liver causes potential errors on the measurement of contrast medium in abdominal artery from multiphase hepatic CT scans. In this study, we investigated the use of hepatic CT images to quantitatively estimate the abdominal artery motion due to respiration by optical flow method. Materials and Methods A total of 132 consecutive patients were included in our patient cohort. We apply the optical flow method to compute the motion of the abdominal artery due to respiration. Results The minimum and maximum displacements of the abdominal artery motion were 0.02 and 30.87 mm by manual delineation, 0.03 and 40.75 mm calculated by optical flow method, respectively. Both high consistency and correlation between the present method and the physicians’ manual delineations were acquired with the regression equation of movement, y = 0.81x+0.25, r = 0.95, p<0.001. Conclusion We estimated the motion of abdominal artery due to respiration using the optical flow method in multiphase hepatic CT scans and the motion estimations were validated with the visualization of physicians. The quantitative analysis of respiration-related movement of abdominal artery could be used for motion correction in the measurement of contrast medium passing though abdominal artery in multiphase CT liver scans. PMID:25536144

  10. 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.

  11. Recombinant expression of aryl hydrocarbon receptor for quantitative ligand-binding analysis.

    PubMed

    Fan, Ming Qi; Bell, Alex R; Bell, David R; Clode, Sally; Fernandes, Alwyn; Foster, Paul M D; Fry, Jeffrey R; Jiang, Tao; Loizou, George; MacNicoll, Alan; Miller, Brian G; Rose, Martin; Shaikh-Omar, Osama; Tran, Lang; White, Shaun

    2009-01-15

    Recombinant expression of the aryl hydrocarbon receptor (AhR) yields small amounts of ligand-binding-competent AhR. Therefore, Spodoptera frugiperda (Sf9) cells and baculovirus have been evaluated for high-level and functional expression of AhR. Rat and human AhR were expressed as soluble protein in significant amounts. Expression of ligand-binding-competent AhR was sensitive to the protein concentration of Sf9 extract, and coexpression of the chaperone p23 failed to affect the yield of functional ligand-binding AhR. The expression system yielded high levels of functional protein, with the ligand-binding capacity (Bmax) typically 20-fold higher than that obtained with rat liver cytosol. Quantitative estimates of the ligand-binding affinity of human and rat AhR were obtained; the Kd for recombinant rat AhR was indistinguishable from that of native rat AhR, thereby validating the expression system as a faithful model for native AhR. The human AhR bound TCDD with significantly lower affinity than the rat AhR. These findings demonstrate high-level expression of ligand-binding-competent AhR, and sufficient AhR for quantitative analysis of ligand binding. PMID:18938125

  12. Recombinant expression of Aryl Hydrocarbon Receptor for quantitative ligand-binding analysis

    PubMed Central

    Fan, Ming Qi; Bell, Alex R.; Bell, David R; Clode, Sally; Fernandes, Alwyn; Foster, Paul M D; Fry, Jeffrey R; Jiang, Tao; Loizou, George; MacNicoll, Alan; Miller, Brian G.; Rose, Martin; Shaikh-Omar, Osama; Tran, Lang; White, Shaun

    2009-01-01

    Recombinant expression of the Aryl Hydrocarbon Receptor (AhR) yields small amounts of ligand-binding competent AhR. Therefore, Spodoptera frugiperda (Sf9) cells and baculovirus have been evaluated for high level and functional expression of AhR. Rat and human AhR were expressed as soluble protein in significant amounts. Expression of ligand-binding competent AhR was sensitive to the protein concentration of Sf9 extract, and co-expression of the chaperone p23 failed to affect the yield of functional ligand-binding AhR. The expression system yielded high levels of functional protein, with the ligand-binding capacity (Bmax) typically 20-fold higher than that obtained with rat liver cytosol. Quantitative estimates of the ligand-binding affinity of human and rat AhR were obtained; the Kd for recombinant rat AhR was indistinguishable from that of native rat AhR, thereby validating the expression system as a faithful model for native AhR. The human AhR bound TCDD with significantly lower affinity than the rat AhR. These findings demonstrate high-level expression of ligand-binding competent AhR, and sufficient AhR for quantitative analysis of ligand-binding. PMID:18938125

  13. 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.

  14. Radioisotopic neutron transmission spectrometry: Quantitative analysis by using partial least-squares method.

    PubMed

    Kim, Jong-Yun; Choi, Yong Suk; Park, Yong Joon; Jung, Sung-Hee

    2009-01-01

    Neutron spectrometry, based on the scattering of high energy fast neutrons from a radioisotope and slowing-down by the light hydrogen atoms, is a useful technique for non-destructive, quantitative measurement of hydrogen content because it has a large measuring volume, and is not affected by temperature, pressure, pH value and color. The most common choice for radioisotope neutron source is (252)Cf or (241)Am-Be. In this study, (252)Cf with a neutron flux of 6.3x10(6)n/s has been used as an attractive neutron source because of its high flux neutron and weak radioactivity. Pulse-height neutron spectra have been obtained by using in-house built radioisotopic neutron spectrometric system equipped with (3)He detector and multi-channel analyzer, including a neutron shield. As a preliminary study, polyethylene block (density of approximately 0.947g/cc and area of 40cmx25cm) was used for the determination of hydrogen content by using multivariate calibration models, depending on the thickness of the block. Compared with the results obtained from a simple linear calibration model, partial least-squares regression (PLSR) method offered a better performance in a quantitative data analysis. It also revealed that the PLSR method in a neutron spectrometric system can be promising in the real-time, online monitoring of the powder process to determine the content of any type of molecules containing hydrogen nuclei. PMID:19285419

  15. Quantitative Proteomics Analysis of Herbaceous Peony in Response to Paclobutrazol Inhibition of Lateral Branching.

    PubMed

    Zhao, Daqiu; Gong, Saijie; Hao, Zhaojun; Meng, Jiasong; Tao, Jun

    2015-01-01

    Herbaceous peony (Paeonia lactiflora Pall.) is an emerging high-grade cut flower worldwide, which is usually used in wedding bouquets and known as the "wedding flower". However, abundant lateral branches appear frequently in some excellent cultivars, and a lack of a method to remove Paeonia lactiflora lateral branches other than inefficient artificial methods is an obstacle for improving the quality of its cut flowers. In this study, paclobutrazol (PBZ) application was found to inhibit the growth of lateral branches in Paeonia lactiflora for the first time, including 96.82% decreased lateral bud number per branch, 77.79% and 42.31% decreased length and diameter of lateral branches, respectively, declined cell wall materials and changed microstructures. Subsequently, isobaric tag for relative and absolute quantitation (iTRAQ) technology was used for quantitative proteomics analysis of lateral branches under PBZ application and control. The results indicated that 178 differentially expressed proteins (DEPs) successfully obtained, 98 DEPs were up-regulated and 80 DEPs were down-regulated. Thereafter, 34 candidate DEPs associated with the inhibited growth of lateral branches were screened according to their function and classification. These PBZ-stress responsive candidate DEPs were involved in eight biological processes, which played a very important role in the growth and development of lateral branches together with the response to PBZ stress. These results provide a better understanding of the molecular theoretical basis for removing Paeonia lactiflora lateral branches using PBZ application. PMID:26473855

  16. Quantitative analysis on PUVA-induced skin photodamages using optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Zhai, Juan; Guo, Zhouyi; Liu, Zhiming; Xiong, Honglian; Zeng, Changchun; Jin, Ying

    2009-08-01

    Psoralen plus ultraviolet A radiation (PUVA) therapy is a very important clinical treatment of skin diseases such as vitiligo and psoriasis, but associated with an increased risk of skin photodamages especially photoaging. Since skin biopsy alters the original skin morphology and always requires an iatrogenic trauma, optical coherence tomography (OCT) appears to be a promising technique to study skin damage in vivo. In this study, the Balb/c mice had 8-methoxypsralen (8-MOP) treatment prior to UVA radiation was used as PUVA-induced photo-damaged modal. The OCT imaging of photo-damaged group (modal) and normal group (control) in vivo was obtained of mice dorsal skin at 0, 24, 48, 72 hours after irradiation respectively. And then the results were quantitatively analyzed combined with histological information. The experimental results showed that, PUVA-induced photo-damaged skin had an increase in epidermal thickness (ET), a reduction of attenuation coefficient in OCT images signal, and an increase in brightness of the epidermis layer compared with the control group. In conclusion, noninvasive high-resolution imaging techniques such as OCT may be a promising tool for photobiological studies aimed at assessing photo-damage and repair processes in vivo. It can be used to quantitative analysis of changes in photo-damaged skin, such as the ET and collagen in dermis, provides a theoretical basis for treatment and prevention of skin photodamages.

  17. Development of qualitative and quantitative PCR analysis for meat adulteration from RNA samples.

    PubMed

    Cheng, Jai-Hong; Chou, Hsiao-Ting; Lee, Meng-Shiou; Sheu, Shyang-Chwen

    2016-02-01

    Total RNA samples were used to establish qualitative and quantitative PCR-based methods for assessing meat adulteration. The primers were designed based on the mRNA sequences of troponin I (TnI), mitochondrial ribosomal protein (MRP) and tropomodulin genes to distinguish chicken, pork, goat, beef and ostrich. There was no cross reaction between the primers, and the detection limit of the cDNA template was 0.01 and 20 ng in simplex PCR and multiplex PCR, respectively. In the low temperature storage test, the detection limits of cDNA template with 10 and 1 ng were determined at 4 °C and -80 °C. In quantitative assay, the precision of real-time PCR analysis expressed as a coefficient of variation (CV) ranged from 0.25% to 5.24% and the trueness, expressed as an error, ranged from 0.28% to 6.98% for adulteration. Thus, herein, we provided alternative tools for the assessment of meat adulteration using mRNA-based PCR methods. PMID:26304356

  18. Quantitative and trajectory analysis of movement trajectories in supplementary motor area seizures of frontal lobe epilepsy.

    PubMed

    Chen, Lei; Yang, Xuhong; Liu, Yonghong; Zeng, Dong; Tang, Yufeng; Yan, Bo; Lin, Xu; Liu, Ling; Xu, Hongru; Zhou, Dong

    2009-02-01

    The objectives of this study were to quantitatively analyze the movement trajectories of four types of supplementary motor area (SMA) seizures (hyperkinetic, tonic posturing, fencing posture, tonic head turning), and to compare the movement trajectories of SMA seizures with those of temporal lobe seizures and psychogenic nonepileptic seizures. Ten video/EEG recordings of each type of seizure were obtained. Imaging data collected by video/EEG monitoring were transformed into a digital matrix with image processing software and then transformed into a movement trajectory curve with MATLAB 6.5 software. From these movement trajectories, amplitude, frequency, proximal/distal limb amplitude ratios, and shoulder/abdominal amplitude ratios measurements were calculated. One-way ANOVA revealed statistically significant differences in average amplitude, as well as proximal/distal limb amplitude ratios, in SMA seizures when compared with those of temporal lobe seizures and psychogenic nonepileptic seizures. This study proved the feasibility of quantitative analysis of SMA seizures and suggests it should be further evaluated for its capability to distinguish different seizure semiologies for the diagnosis of epilepsy. PMID:19100340

  19. Quantitative laser-induced breakdown spectroscopy analysis of calcified tissue samples

    NASA Astrophysics Data System (ADS)

    Samek, O.; Beddows, D. C. S.; Telle, H. H.; Kaiser, J.; Liška, M.; Cáceres, J. O.; Gonzáles Ureña, A.

    2001-06-01

    We report on the application of laser-induced breakdown spectroscopy (LIBS) to the analysis of important minerals and the accumulation of potentially toxic elements in calcified tissue, to trace e.g. the influence of environmental exposure, and other medical or biological factors. This theme was exemplified for quantitative detection and mapping of Al, Pb and Sr in representative samples, including teeth (first teeth of infants, second teeth of children and teeth of adults) and bones (tibia and femur). In addition to identifying and quantifying major and trace elements in the tissues, one- and two-dimensional profiles and maps were generated. Such maps (a) provide time/concentration relations, (b) allow to follow mineralisation of the hydroxyapatite matrix and the migration of the elements within it and (c) enable to identify disease states, such as caries in teeth. In order to obtain quantitative calibration, reference samples in the form of pressed pellets with calcified tissue-equivalent material (majority compound of pellets is CaCO 3) were used whose physical properties closely resembled hydroxyapatite. Compounds of Al, Sr and Pb were added to the pellets, containing atomic concentrations in the range 100-10 000 ppm relative to the Ca content of the matrix. Analytical results based on this calibration against artificial samples for the trace elements under investigation agree with literature values, and with our atomic absorption spectroscopy (AAS) cross-validation measurements.

  20. On the quantitative method for measurement and analysis of the fine structure of Fraunhofer line profiles

    NASA Astrophysics Data System (ADS)

    Kuli-Zade, D. M.

    The methods of measurement and analysis of the fine structure of weak and moderate Fraunhofer line profiles are considered. The digital spectral materials were obtained using rapid scanning high dispersion and high resolution double monochromators. The methods of asymmetry coefficient, bisector method and new quantitative method pro- posed by the author are discussed. The new physical values of differential, integral, residual and relative asymmetries are first introduced. These quantitative values permit us to investigate the dependence of asymmetry on microscopic (atomic) and macro- scopic (photospheric) values. It is shown that the integral profile asymmetries grow appreciably with increase in line equivalent width. The average effective depths of the formation of used Fraunhofer lines in the photosphere of the Sun are determined. It is shown that with the increasing of the effective formation depths of the lines integral and residual asymmetries of the lines profiles noticeably decrease. It is in fine agree- ment with the results of intensity dependence of asymmetry. The above-mentioned methods are critically compared and the advantages of author's method are shown. The computer program of calculation of the line-profile asymmetry parameters has been worked out.

  1. Quantitative analysis of intrinsic skin aging in dermal papillae by in vivo harmonic generation microscopy

    PubMed Central

    Liao, Yi-Hua; Kuo, Wei-Cheng; Chou, Sin-Yo; Tsai, Cheng-Shiun; Lin, Guan-Liang; Tsai, Ming-Rung; Shih, Yuan-Ta; Lee, Gwo-Giun; Sun, Chi-Kuang

    2014-01-01

    Chronological skin aging is associated with flattening of the dermal-epidermal junction (DEJ), but to date no quantitative analysis focusing on the aging changes in the dermal papillae (DP) has been performed. The aim of the study is to determine the architectural changes and the collagen density related to chronological aging in the dermal papilla zone (DPZ) by in vivo harmonic generation microscopy (HGM) with a sub-femtoliter spatial resolution. We recruited 48 Asian subjects and obtained in vivo images on the sun-protected volar forearm. Six parameters were defined to quantify 3D morphological changes of the DPZ, which we analyzed both manually and computationally to study their correlation with age. The depth of DPZ, the average height of isolated DP, and the 3D interdigitation index decreased with age, while DP number density, DP volume, and the collagen density in DP remained constant over time. In vivo high-resolution HGM technology has uncovered chronological aging-related variations in DP, and sheds light on real-time quantitative skin fragility assessment and disease diagnostics based on collagen density and morphology. PMID:25401037

  2. [Quantitative proteomics analysis of ClpS-mediated rifampicin resistance in Mycobacterium].

    PubMed

    Adilijiang, Gulishana; Feng, Shan; Mi, Kaixia; Deng, Haiteng

    2014-07-01

    Adaptor protein ClpS is an essential regulator of prokaryotic ATP-dependent protease ClpAP, which delivers certain protein substrates with specific amino acid sequences to ClpAP for degradation. However, ClpS also functions as the inhibitor of the ClpAP-mediated protein degradation for other proteins. Here, we constructed the clpS-overexpression Mycobacterium smegmatis strain, and showed for the first time that overexpression of ClpS increased the resistance of M. smegmatis to rifampicin that is one of most widely used antibiotic drugs in treatment of tuberculosis. Using quantitative proteomic technology, we systematically analyzed effects of ClpS overexpression on changes in M. smegmatis proteome, and proposed that the increased rifampicin resistance was caused by ClpS-regulated drug sedimentation and drug metabolism. Our results indicate that the changes in degradation related proteins enhanced drug resistance and quantitative proteomic analysis is an important tool for understanding molecular mechanisms responsible for bacteria drug resistance. PMID:25345012

  3. Ultrasensitive, self-calibrated cavity ring-down spectrometer for quantitative trace gas analysis.

    PubMed

    Chen, Bing; Sun, Yu R; Zhou, Ze-Yi; Chen, Jian; Liu, An-Wen; Hu, Shui-Ming

    2014-11-10

    A cavity ring-down spectrometer is built for trace gas detection using telecom distributed feedback (DFB) diode lasers. The longitudinal modes of the ring-down cavity are used as frequency markers without active-locking either the laser or the high-finesse cavity. A control scheme is applied to scan the DFB laser frequency, matching the cavity modes one by one in sequence and resulting in a correct index at each recorded spectral data point, which allows us to calibrate the spectrum with a relative frequency precision of 0.06 MHz. Besides the frequency precision of the spectrometer, a sensitivity (noise-equivalent absorption) of 4×10-11??cm-1??Hz-1/2 has also been demonstrated. A minimum detectable absorption coefficient of 5×10-12??cm-1 has been obtained by averaging about 100 spectra recorded in 2  h. The quantitative accuracy is tested by measuring the CO2 concentrations in N2 samples prepared by the gravimetric method, and the relative deviation is less than 0.3%. The trace detection capability is demonstrated by detecting CO2 of ppbv-level concentrations in a high-purity nitrogen gas sample. Simple structure, high sensitivity, and good accuracy make the instrument very suitable for quantitative trace gas analysis. PMID:25402995

  4. Quantitative toxicoproteomic analysis of zebrafish embryos exposed to a retinoid X receptor antagonist UVI3003.

    PubMed

    Zheng, Liang; Yu, Jianlan; Shi, Huahong; Xia, Liang; Xin, Qi; Zhang, Qiang; Zhao, Heng; Luo, Ji; Jin, Wenhai; Li, Daoji; Zhou, Junliang

    2015-09-01

    Retinoid X receptor (RXR) antagonists, including some environmental endocrine disruptors, have a teratogenic effect on vertebrate embryos. To investigate the toxicological mechanism on the protein expression level, a quantitative proteomic study was conducted to analyze the proteome alterations of zebrafish (Danio rerio) embryos exposed to gradient concentrations of a representative RXR antagonist UVI3003. Using isobaric Tags for Relative and Absolute Quantitation (iTRAQ) labeling coupled nano high-performance liquid chromatography-tandem mass spectrometry (nano HPLC-MS/MS), in total 6592 proteins were identified, among which 195 proteins were found to be differentially expressed by more than a two-fold change in exposed groups compared with the control. Gene ontology analysis showed that these differential proteins were mostly involved in anatomical structure development, biosynthetic process, ion binding and oxidoreductase activity. Moreover, the biological pathways of translation, lipoprotein metabolism, cell survival and gluconeogenesis were intensively inhibited after exposure. Some significantly downregulated proteins such as apolipoprotein A-I and vitellogenin and upregulated proteins such as calcium activated nucleotidase 1b, glutathione S-transferase and glucose 6-dehydrogenases showed a strong dose-dependent response. The results provided new insight into the molecular details of RXR antagonist-induced teratogenicity and added novel information of pathways and potential biomarkers for evaluation of RXR interfering activity. PMID:25581642

  5. Quantitative Proteomics Analysis of Herbaceous Peony in Response to Paclobutrazol Inhibition of Lateral Branching

    PubMed Central

    Zhao, Daqiu; Gong, Saijie; Hao, Zhaojun; Meng, Jiasong; Tao, Jun

    2015-01-01

    Herbaceous peony (Paeonia lactiflora Pall.) is an emerging high-grade cut flower worldwide, which is usually used in wedding bouquets and known as the “wedding flower”. However, abundant lateral branches appear frequently in some excellent cultivars, and a lack of a method to remove Paeonia lactiflora lateral branches other than inefficient artificial methods is an obstacle for improving the quality of its cut flowers. In this study, paclobutrazol (PBZ) application was found to inhibit the growth of lateral branches in Paeonia lactiflora for the first time, including 96.82% decreased lateral bud number per branch, 77.79% and 42.31% decreased length and diameter of lateral branches, respectively, declined cell wall materials and changed microstructures. Subsequently, isobaric tag for relative and absolute quantitation (iTRAQ) technology was used for quantitative proteomics analysis of lateral branches under PBZ application and control. The results indicated that 178 differentially expressed proteins (DEPs) successfully obtained, 98 DEPs were up-regulated and 80 DEPs were down-regulated. Thereafter, 34 candidate DEPs associated with the inhibited growth of lateral branches were screened according to their function and classification. These PBZ-stress responsive candidate DEPs were involved in eight biological processes, which played a very important role in the growth and development of lateral branches together with the response to PBZ stress. These results provide a better understanding of the molecular theoretical basis for removing Paeonia lactiflora lateral branches using PBZ application. PMID:26473855

  6. Quantitative analysis of paracetamol polymorphs in powder mixtures by FT-Raman spectroscopy and PLS regression.

    PubMed

    Kachrimanis, Kyriakos; Braun, Doris E; Griesser, Ulrich J

    2007-01-17

    A fast and simple method for the quantitative analysis of monoclinic (form I) and orthorhombic (form II) paracetamol was developed, based on FT-Raman spectroscopy and PLS regression. Three different preprocessing algorithms, namely orthogonal signal correction (OSC), standard normal variate transformation (SNV) and multiplicative scatter correction (MSC), were applied in order to eliminate effects caused by sample preparation and sample inhomogeneities. Subsequently, PLS regression models were fitted and their predictive performance was evaluated on the basis of the root mean squared error of cross-validation (RMSECV) over the complete data set. Furthermore, the data were split into two equal-sized training and test subsets by the Kennard-Stone design and the errors of calibration (RMSEC) and prediction (RMSEP) were calculated. It was found that the OSC preprocessing contributes to a significant increase in the predictive performance of the PLS regression model (RMSECV=0.500%, RMSEC=0.842% and RMSEP=0.538%) in the overall concentration range of form I, compared to the SNV (RMSECV=2.398%, RMSEC=0.911% and RMSEP=7.177%) and MSC (RMSECV=2.7648%, RMSEC=1.572% and RMSEP=4.838%). In addition, the model developed on OSC preprocessed data is more parsimonious, requiring a single latent variable, compared to three latent variables required by the models fitted to the SNV and MSC preprocessed data. The proposed multivariate calibration presents a significant improvement over existing methods for the quantitation of paracetamol polymorphs. PMID:16935450

  7. Quantitative Spectral Morphology Analysis of Unusually Red and Blue L Dwarfs

    NASA Astrophysics Data System (ADS)

    Camnasio, Sara; Khalida Alam, Munazza; Rice, Emily L.; Cruz, Kelle L.; Faherty, Jacqueline K.; Mace, Gregory N.; Martin, Emily; Logsdon, Sarah E.; McLean, Ian S.; Brown Dwarfs in New York City (BDNYC)

    2016-01-01

    In an effort to constrain the properties of photometric color outliers, we present a quantitative spectral morphology analysis of medium-resolution NIRSPEC (R~2,000), SpeX cross-dispersed (R~2,000), Palomar TripleSpec (R~2600), and Magellan FIRE (R~6000) J-band spectra for a sample of unusually red and blue L dwarfs. Some red L dwarfs are low surface gravity, young objects whose spectra present weak Na I doublets and FeH absorption bands, but strong VO features (Cruz et al. 2009). Some blue L dwarfs are subdwarfs with low metallicity spectral features such as greater H2 absorption, stronger metal hydride bands, and enhanced TiO absorption (Burgasser et al 2008c). We fit 3rd order polynomials to the pseudo-continuum in order to provide a quantitative comparison of spectral morphology with other peculiar L dwarfs, field standards, young L dwarfs, and L subdwarf. The results indicated that the coefficients of the fit correlate with spectral type, but are independent of color. This newly found trend provides a parameter which can be utilized as an additional tool in characterizing quantifiable differences in the spectra of brown dwarfs. Furthermore, this method can be applied in studying the atmospheric properties of exoplanets, given their similarities with brown dwarfs in mass and photospheric properties.

  8. Quantitative proteomic analysis of microdissected oral epithelium for cancer biomarker discovery.

    PubMed

    Xiao, Hua; Langerman, Alexander; Zhang, Yan; Khalid, Omar; Hu, Shen; Cao, Cheng-Xi; Lingen, Mark W; Wong, David T W

    2015-11-01

    Specific biomarkers are urgently needed for the detection and progression of oral cancer. The objective of this study was to discover cancer biomarkers from oral epithelium through utilizing high throughput quantitative proteomics approaches. Morphologically malignant, epithelial dysplasia, and adjacent normal epithelial tissues were laser capture microdissected (LCM) from 19 patients and used for proteomics analysis. Total proteins from each group were extracted, digested and then labelled with corresponding isobaric tags for relative and absolute quantitation (iTRAQ). Labelled peptides from each sample were combined and analyzed by liquid chromatography-mass spectrometry (LC-MS/MS) for protein identification and quantification. In total, 500 proteins were identified and 425 of them were quantified. When compared with adjacent normal oral epithelium, 17 and 15 proteins were consistently up-regulated or down-regulated in malignant and epithelial dysplasia, respectively. Half of these candidate biomarkers were discovered for oral cancer for the first time. Cornulin was initially confirmed in tissue protein extracts and was further validated in tissue microarray. Its presence in the saliva of oral cancer patients was also explored. Myoglobin and S100A8 were pre-validated by tissue microarray. These data demonstrated that the proteomic biomarkers discovered through this strategy are potential targets for oral cancer detection and salivary diagnostics. PMID:26321370

  9. Normalization and statistical analysis of quantitative proteomics data generated by metabolic labeling.

    PubMed

    Ting, Lily; Cowley, Mark J; Hoon, Seah Lay; Guilhaus, Michael; Raftery, Mark J; Cavicchioli, Ricardo

    2009-10-01

    Comparative proteomics is a powerful analytical method for learning about the responses of biological systems to changes in growth parameters. To make confident inferences about biological responses, proteomics approaches must incorporate appropriate statistical measures of quantitative data. In the present work we applied microarray-based normalization and statistical analysis (significance testing) methods to analyze quantitative proteomics data generated from the metabolic labeling of a marine bacterium (Sphingopyxis alaskensis). Quantitative data were generated for 1,172 proteins, representing 1,736 high confidence protein identifications (54% genome coverage). To test approaches for normalization, cells were grown at a single temperature, metabolically labeled with (14)N or (15)N, and combined in different ratios to give an artificially skewed data set. Inspection of ratio versus average (MA) plots determined that a fixed value median normalization was most suitable for the data. To determine an appropriate statistical method for assessing differential abundance, a -fold change approach, Student's t test, unmoderated t test, and empirical Bayes moderated t test were applied to proteomics data from cells grown at two temperatures. Inverse metabolic labeling was used with multiple technical and biological replicates, and proteomics was performed on cells that were combined based on equal optical density of cultures (providing skewed data) or on cell extracts that were combined to give equal amounts of protein (no skew). To account for arbitrarily complex experiment-specific parameters, a linear modeling approach was used to analyze the data using the limma package in R/Bioconductor. A high quality list of statistically significant differentially abundant proteins was obtained by using lowess normalization (after inspection of MA plots) and applying the empirical Bayes moderated t test. The approach also effectively controlled for the number of false discoveries and corrected for the multiple testing problem using the Storey-Tibshirani false discovery rate (Storey, J. D., and Tibshirani, R. (2003) Statistical significance for genomewide studies. Proc. Natl. Acad. Sci. U.S.A. 100, 9440-9445). The approach we have developed is generally applicable to quantitative proteomics analyses of diverse biological systems. PMID:19605365

  10. A new technique for quantitative analysis of hair loss in mice using grayscale analysis.

    PubMed

    Ponnapakkam, Tulasi; Katikaneni, Ranjitha; Gulati, Rohan; Gensure, Robert

    2015-01-01

    Alopecia is a common form of hair loss which can occur in many different conditions, including male-pattern hair loss, polycystic ovarian syndrome, and alopecia areata. Alopecia can also occur as a side effect of chemotherapy in cancer patients. In this study, our goal was to develop a consistent and reliable method to quantify hair loss in mice, which will allow investigators to accurately assess and compare new therapeutic approaches for these various forms of alopecia. The method utilizes a standard gel imager to obtain and process images of mice, measuring the light absorption, which occurs in rough proportion to the amount of black (or gray) hair on the mouse. Data that has been quantified in this fashion can then be analyzed using standard statistical techniques (i.e., ANOVA, T-test). This methodology was tested in mouse models of chemotherapy-induced alopecia, alopecia areata and alopecia from waxing. In this report, the detailed protocol is presented for performing these measurements, including validation data from C57BL/6 and C3H/HeJ strains of mice. This new technique offers a number of advantages, including relative simplicity of application, reliance on equipment which is readily available in most research laboratories, and applying an objective, quantitative assessment which is more robust than subjective evaluations. Improvements in quantification of hair growth in mice will improve study of alopecia models and facilitate evaluation of promising new therapies in preclinical studies. PMID:25867252

  11. Assessment of ERCC1 and XPF Protein Expression Using Quantitative Immunohistochemistry in Nasopharyngeal Carcinoma Patients Undergoing Curative Intent Treatment

    SciTech Connect

    Jagdis, Amanda; Phan, Tien; Faculty of Medicine, University of Calgary, Calgary, Alberta ; Klimowicz, Alexander C.; Faculty of Medicine, University of Calgary, Calgary, Alberta ; Laskin, Janessa J.; Faculty of Medicine, University of British Columbia, Vancouver, British Columbia ; Lau, Harold Y.; Faculty of Medicine, University of Calgary, Calgary, Alberta ; Petrillo, Stephanie K.; Siever, Jodi E.; Thomson, Thomas A.; Faculty of Medicine, University of British Columbia, Vancouver, British Columbia ; Magliocco, Anthony M.; Faculty of Medicine, University of Calgary, Calgary, Alberta ; Hao, Desirée; Faculty of Medicine, University of Calgary, Calgary, Alberta

    2013-04-01

    Purpose: We sought to evaluate the prognostic/predictive value of ERCC1 and XPF in patients with nonmetastatic nasopharyngeal carcinoma (NPC) treated with curative intent. Methods and Materials: ERCC1 and XPF protein expression was evaluated by immunofluorescence combined with automated quantitative analysis (AQUA) using the FL297 and 3F2 antibodies, respectively. ERCC1 and XPF protein expression levels were correlated with clinical outcomes. Results: Patient characteristics were as follows: mean age 52 years (range, 18-85 years), 67% male, 72% Karnofsky performance status (KPS) ?90%, World Health Organization (WHO) type 1/2/3 = 12%/28%/60%, stage III/IV 65%. With a median follow-up time of 50 months (range, 2.9 to 120 months), the 5-year overall survival (OS) was 70.8%. Median standardized nuclear AQUA scores were used as cutpoints for ERCC1 (n=138) and XPF (n=130) protein expression. Agreement between dichotomized ERCC1 and XPF scores was high at 79.4% (kappa = 0.587, P<.001). Neither biomarker predicted locoregional recurrence, DFS, or OS after adjustment for age and KPS, irrespective of stratification by stage, WHO type, or treatment. Conclusions: Neither ERCC1 nor XPF, analyzed by quantitative immunohistochemistry using the FL297 and 3F2 antibodies, was prognostic or predictive in this cohort of NPC patients.

  12. Mesoscopic dynamics of fermionic cold atoms: Exact quantitative analysis of transport coefficients and relaxation times

    E-print Network

    Kikuchi, Yuta; Kunihiro, Teiji

    2015-01-01

    We give a quantitative analysis of the shear viscosity, heat conductivity, and viscous relaxation times, using the novel microscopic expressions derived by the renormalization group (RG) method, where the Boltzmann equation is faithfully solved to extract the hydrodynamics without recourse to any ansatz. We examine the quantum statistical effects, temperature dependence, and scattering-length dependence of the transport coefficients and the viscous relaxation times. The numerical calculation shows that the relation $\\tau_\\pi=\\eta/P$, which is derived in the relaxation-time approximation (RTA) and is used in the most literature, turns out to be satisfied quite well, while the similar relation for the viscous relaxation time $\\tau_J$ of the heat conductivity is satisfied only approximately with a considerable error.

  13. Quantitative analysis of individual motor unit potentials: a proposition for standardized terminology and criteria for measurement.

    PubMed

    Stålberg, E; Andreassen, S; Falck, B; Lang, H; Rosenfalck, A; Trojaborg, W

    1986-10-01

    The physiology of the motor unit potential (MUP) is reviewed. The aim is to identify the electrophysiological events in the motor unit that generate the individual parts of the MUP. This is based on insight gained from new experimental techniques, such as single-fiber electromyography (EMG), scanning EMG, and simulation studies of the MUP. A terminology for the different parts of the MUP is also suggested, and nine parameters used to describe different features of the MUP are delineated: duration, spike duration, amplitude, area, spike area, phases, turns, satellites, and variability. Technical aspects, such as electrode type, filtering, and sampling rate of the computers, are discussed as well. In Appendix A, different manual and computer-aided methods for quantitative MUP analysis are described. Despite minor systematic differences between the methods, MUP durations measured by different methods correlate highly with each other (Appendix B). The manual and computer-aided methods have comparable variability between repeated measurements. PMID:3332279

  14. Full quantitative phase analysis of hydrated lime using the Rietveld method

    SciTech Connect

    Lassinantti Gualtieri, Magdalena

    2012-09-15

    Full quantitative phase analysis (FQPA) using X-ray powder diffraction and Rietveld refinements is a well-established method for the characterization of various hydraulic binders such as Portland cement and hydraulic limes. In this paper, the Rietveld method is applied to hydrated lime, a non-hydraulic traditional binder. The potential presence of an amorphous phase in this material is generally ignored. Both synchrotron radiation and a conventional X-ray source were used for data collection. The applicability of the developed control file for the Rietveld refinements was investigated using samples spiked with glass. The results were cross-checked by other independent methods such as thermal and chemical analyses. The sample microstructure was observed by transmission electron microscopy. It was found that the consistency between the different methods was satisfactory, supporting the validity of FQPA for this material. For the samples studied in this work, the amount of amorphous material was in the range 2-15 wt.%.

  15. Mesoscopic dynamics of fermionic cold atoms: Exact quantitative analysis of transport coefficients and relaxation times

    E-print Network

    Yuta Kikuchi; Kyosuke Tsumura; Teiji Kunihiro

    2015-11-15

    We give a quantitative analysis of the shear viscosity, heat conductivity, and viscous relaxation times, using the novel microscopic expressions derived by the renormalization group (RG) method, where the Boltzmann equation is faithfully solved to extract the hydrodynamics without recourse to any ansatz. We examine the quantum statistical effects, temperature dependence, and scattering-length dependence of the transport coefficients and the viscous relaxation times. The numerical calculation shows that the relation $\\tau_\\pi=\\eta/P$, which is derived in the relaxation-time approximation (RTA) and is used in the most literature, turns out to be satisfied quite well, while the similar relation for the viscous relaxation time $\\tau_J$ of the heat conductivity is satisfied only approximately with a considerable error.

  16. Dynamics of Natural Killer cell receptor revealed by quantitative analysis of photoswitchable protein

    E-print Network

    Pageon, Sophie V; Lagrue, Kathryn; Köhler, Karsten; Endres, Robert G; Davis, Daniel M

    2013-01-01

    Natural Killer (NK) cell activation is dynamically regulated by numerous activating and inhibitory surface receptors that accumulate at the immune synapse. Quantitative analysis of receptor dynamics has been limited by methodologies which rely on indirect measurements such as fluorescence recovery after photobleaching. Here, we report a novel approach to study how proteins traffic to and from the immune synapse using NK cell receptors tagged with the photoswitchable fluorescent protein tdEosFP, which can be irreversibly photoswitched from a green to red fluorescent state by ultraviolet light. Thus, following a localized switching event, the movement of the photoswitched molecules can be temporally and spatially resolved by monitoring fluorescence in two regions of interest. By comparing images with mathematical models, we evaluated the diffusion coefficient of the receptor KIR2DL1 (0.23 +- 0.06 micron^2/s) and assessed how synapse formation affects receptor dynamics. Our data conclude that the inhibitory NK c...

  17. Quantitative analysis of sesquiterpene lactones in extract of Arnica montana L. by 1H NMR spectroscopy.

    PubMed

    Staneva, Jordanka; Denkova, Pavletta; Todorova, Milka; Evstatieva, Ljuba

    2011-01-01

    (1)H NMR spectroscopy was used as a method for quantitative analysis of sesquiterpene lactones present in a crude lactone fraction isolated from Arnica montana. Eight main components - tigloyl-, methacryloyl-, isobutyryl- and 2-methylbutyryl-esters of helenalin (H) and 11?,13-dihydrohelenalin (DH) were identified in the studied sample. The method allows the determination of the total amount of sesquiterpene lactones and the quantity of both type helenalin and 11?,13-dihydrohelenalin esters separately. Furthermore, 6-O-tigloylhelenalin (HT, 1), 6-O-methacryloylhelenalin (HM, 2), 6-O-tigloyl-11?,13-dihydrohelenalin (DHT, 5), and 6-O-methacryloyl-11?,13-dihydrohelenalin (DHM, 6) were quantified as individual components. PMID:20837387

  18. Quantitative analysis of volatile organic compounds using ion mobility spectra and cascade correlation neural networks

    NASA Technical Reports Server (NTRS)

    Harrington, Peter DEB.; Zheng, Peng

    1995-01-01

    Ion Mobility Spectrometry (IMS) is a powerful technique for trace organic analysis in the gas phase. Quantitative measurements are difficult, because IMS has a limited linear range. Factors that may affect the instrument response are pressure, temperature, and humidity. Nonlinear calibration methods, such as neural networks, may be ideally suited for IMS. Neural networks have the capability of modeling complex systems. Many neural networks suffer from long training times and overfitting. Cascade correlation neural networks train at very fast rates. They also build their own topology, that is a number of layers and number of units in each layer. By controlling the decay parameter in training neural networks, reproducible and general models may be obtained.

  19. Investigating Cellular Responses During Photohydrogen Production by the Marine Microalga Tetraselmis subcordiformis by Quantitative Proteome Analysis.

    PubMed

    Ji, Chaofan; Cao, Xupeng; Liu, Hongwei; Qu, Junge; Yao, Changhong; Zou, Hanfa; Xue, Song

    2015-10-01

    The marine microalga Tetraselmis subcordiformis could photoproduce hydrogen under the regulation of carbonyl cyanide m-chlorophenylhydrazone (CCCP), and a hydrogen production process kinetic analysis was characterized by two peaks, suggesting that two distinct mechanisms might exist in this alga. Therefore, 2D nanoliquid chromatography-tandem mass spectrometry (LC-MS/MS) was introduced to analyze the proteome of samples from different time points. A total of 912 proteins were identified, providing a global view of the cellular responses at the proteomic level. These proteins can be divided into multiple functional groups including stress responses, energy metabolism and redox homeostasis. The quantitative proteomic data provided more details on the electron donors for hydrogen production. During the first stage, photosystem II produced electrons for hydrogen production; during the second stage, metabolites were the major electron donors via nonphotochemical plastoquinone reduction by NADH dehydrogenase. PMID:26234437

  20. Quantitative analysis of cyclic dimer fatty acid content in the dimerization product by proton NMR spectroscopy.

    PubMed

    Park, Kyun Joo; Kim, Minyoung; Seok, Seunghwan; Kim, Young-Wun; Kim, Do Hyun

    2015-10-01

    In this work, (1)H NMR is utilized for the quantitative analysis of a specific cyclic dimer fatty acid in a dimer acid mixture using the pseudo-standard material of mesitylene on the basis of its structural similarity. Mesitylene and cyclic dimer acid levels were determined using the signal of the proton on the cyclic ring (?=6.8) referenced to the signal of maleic acid (?=6.2). The content of the cyclic dimer fatty acid was successfully determined through the standard curve of mesitylene and the reported equation. Using the linearity of the mesitylene curve, the cyclic dimer fatty acid in the oil mixture was quantified. The results suggest that the proposed method can be used to quantify cyclic compounds in mixtures to optimize the dimerization process. PMID:25974673

  1. A hybrid calibration-free/artificial neural networks approach to the quantitative analysis of LIBS spectra

    NASA Astrophysics Data System (ADS)

    D'Andrea, Eleonora; Pagnotta, Stefano; Grifoni, Emanuela; Legnaioli, Stefano; Lorenzetti, Giulia; Palleschi, Vincenzo; Lazzerini, Beatrice

    2015-03-01

    A `hybrid' method is proposed for the quantitative analysis of materials by LIBS, combining the precision of the calibration-free LIBS (CF-LIBS) algorithm with the quickness of artificial neural networks. The method allows the precise determination of the samples' composition even in the presence of relatively large laser fluctuations and matrix effects. To show the strength and robustness of this approach, a number of synthetic LIBS spectra of Cu-Ni binary alloys with different composition were computer-simulated, in correspondence of different plasma temperatures, electron number densities and ablated mass. The CF-LIBS/ANN approach here proposed demonstrated to be capable, after appropriate training, of `learning' the basic physical relations between the experimentally measured line intensities and the plasma parameters. Because of that the composition of the sample can be correctly determined, as in CF-LIBS measurements, but in a much shorter time.

  2. Quantitative analysis of the multifunctional finishing of cotton fabric with non-formaldehyde agents.

    PubMed

    Popescu, Vasilica; Vasluianu, Ecaterina; Popescu, Gabriel

    2014-10-13

    Realization of simultaneous hydrophilizing and wrinkle-proofing effects on a cotton fabric is not impossible. This work proves that these objectives can be reached by using adequate multifunctional compounds: Tetronic 701 (T), chitosan (CS) and monochlorotriazine-?-cyclodextrin (MCT-?-CD). These were applied by means of three pad-dry-cure type treatments. We have studied, at first, the influences resulted after each stage in order to establish the optimum working fields. The results of the FTIR, XPS, XRD, DSC and TGA analyses confirmed the proposed mechanism. By applying the multiple linear regression as a statistical analysis of the data produced after the third treatment stage, one could determine the quantitative influences produced by the concentrations of the three multifunctional agents on the following parameters: taking-in degree, wrinkle recovery angles (WRA), breaking strength, durability test, immersion time, contact angle, and capillarity. PMID:25037427

  3. Quantitative Analysis of Chiari-Like Malformation and Syringomyelia in the Griffon Bruxellois Dog

    PubMed Central

    Knowler, Susan P.; McFadyen, Angus K.; Freeman, Courtenay; Kent, Marc; Platt, Simon R.; Kibar, Zoha; Rusbridge, Clare

    2014-01-01

    This study aimed to develop a system of quantitative analysis of canine Chiari-like malformation and syringomyelia on variable quality MRI. We made a series of measurements from magnetic resonance DICOM images from Griffon Bruxellois dogs with and without Chiari-like malformation and syringomyelia and identified several significant variables. We found that in the Griffon Bruxellois dog, Chiari-like malformation is characterized by an apparent shortening of the entire cranial base and possibly by increased proximity of the atlas to the occiput. As a compensatory change, there appears to be an increased height of the rostral cranial cavity with lengthening of the dorsal cranial vault and considerable reorganization of the brain parenchyma including ventral deviation of the olfactory bulbs and rostral invagination of the cerebellum under the occipital lobes. PMID:24533070

  4. Quantitative measurement of phase variation amplitude of ultrasonic diffraction grating based on diffraction spectral analysis

    SciTech Connect

    Pan, Meiyan Zeng, Yingzhi; Huang, Zuohua

    2014-09-15

    A new method based on diffraction spectral analysis is proposed for the quantitative measurement of the phase variation amplitude of an ultrasonic diffraction grating. For a traveling wave, the phase variation amplitude of the grating depends on the intensity of the zeroth- and first-order diffraction waves. By contrast, for a standing wave, this amplitude depends on the intensity of the zeroth-, first-, and second-order diffraction waves. The proposed method is verified experimentally. The measured phase variation amplitude ranges from 0 to 2?, with a relative error of approximately 5%. A nearly linear relation exists between the phase variation amplitude and driving voltage. Our proposed method can also be applied to ordinary sinusoidal phase grating.

  5. Quantitative analysis of shadow x-ray magnetic circular dichroism photoemission electron microscopy

    NASA Astrophysics Data System (ADS)

    Jamet, S.; Da, S., Col; Rougemaille, N.; Wartelle, A.; Locatelli, A.; Mente?, T. O.; Santos Burgos, B.; Afid, R.; Cagnon, L.; Bochmann, S.; Bachmann, J.; Fruchart, O.; Toussaint, J. C.

    2015-10-01

    Shadow x-ray magnetic circular dichroism photoemission electron microscopy is a recent technique, in which the photon intensity in the shadow of an object lying on a surface may be used to gather information about the three-dimensional magnetization texture inside the object. Our purpose here is to lay the basis of a quantitative analysis of this technique. We first discuss the principle and implementation of a method to simulate the contrast expected from an arbitrary micromagnetic state. Textbook examples and successful comparison with experiments are then given. Instrumental settings are finally discussed, having an impact on the contrast and spatial resolution: photon energy, microscope extraction voltage and plane of focus, microscope background level, electric-field related distortion of three-dimensional objects, Fresnel diffraction, or photon scattering.

  6. Quantitative agent-based firm dynamics simulation with parameters estimated by financial and transaction data analysis

    NASA Astrophysics Data System (ADS)

    Ikeda, Yuichi; Souma, Wataru; Aoyama, Hideaki; Iyetomi, Hiroshi; Fujiwara, Yoshi; Kaizoji, Taisei

    2007-03-01

    Firm dynamics on a transaction network is considered from the standpoint of econophysics, agent-based simulations, and game theory. In this model, interacting firms rationally invest in a production facility to maximize net present value. We estimate parameters used in the model through empirical analysis of financial and transaction data. We propose two different methods ( analytical method and regression method) to obtain an interaction matrix of firms. On a subset of a real transaction network, we simulate firm's revenue, cost, and fixed asset, which is the accumulated investment for the production facility. The simulation reproduces the quantitative behavior of past revenues and costs within a standard error when we use the interaction matrix estimated by the regression method, in which only transaction pairs are taken into account. Furthermore, the simulation qualitatively reproduces past data of fixed assets.

  7. Data set for the proteomic inventory and quantitative analysis of chicken uterine fluid during eggshell biomineralization

    PubMed Central

    Marie, Pauline; Labas, Valérie; Brionne, Aurélien; Harichaux, Grégoire; Hennequet-Antier, Christelle; Nys, Yves; Gautron, Joël

    2014-01-01

    Chicken eggshell is the protective barrier of the egg. It is a biomineral composed of 95% calcium carbonate on calcitic form and 3.5% organic matrix proteins. Mineralization process occurs in uterus into the uterine fluid. This acellular fluid contains ions and organic matrix proteins precursors which are interacting with the mineral phase and control crystal growth, eggshell structure and mechanical properties. We performed a proteomic approach and identified 308 uterine fluid proteins. Gene Ontology terms enrichments were determined to investigate their potential functions. Mass spectrometry analyses were also combined to label free quantitative analysis to determine the relative abundance of 96 proteins at initiation, rapid growth phase and termination of shell calcification. Sixty four showed differential abundance according to the mineralization stage. Their potential functions have been annotated. The complete proteomic, bioinformatic and functional analyses are reported in Marie et al., J. Proteomics (2015) [1]. PMID:26217689

  8. Quantitative Analysis of Multivalent Ligand Presentation on Gold Glyconanoparticles and Their Effects on Protein Binding

    NASA Astrophysics Data System (ADS)

    Wang, Xin; Ramström, Olof; Yan, Mingdi

    2010-03-01

    Bio-functionalized nanomaterials, which combine functions of biological ligands and unique properties of nano-sized building blocks, have exhibited increased potential applications in biosensing, therapeutics, and diagnostics. Glyconanoparitcles carrying a monolayer of carbohydrate ligands on nanoparticles provide an excellent platform for sensitive protein recognitions. Using Au nanoparticles as the scaffold, multivalent interactions between glycan ligands and proteins have been demonstrated. However, quantitative analysis especially the binding affinity of the resulting glyconanoparticles is challenging to determine. Here we present a new characterization technique, based on fluorescent competition binding assays, for measuring dissociation constants for glyconanoparticles-protein interactions. Au nanoparticles coupled with a series of un-derivatized carbohydrates were prepared by a photocoupling chemistry. Dramatic binding affinity enhancement was observed due to the high ligand density on nanoparticles, which was highly relevant to ligand display, controlled by the linker type, chain length, ligand size and density.

  9. On quantitative analysis of interband recombination dynamics: Theory and application to bulk ZnO

    SciTech Connect

    Lettieri, S.; Capello, V.; Santamaria, L.; Maddalena, P.; Physics Department, University of Naples “Federico II,” Via Cintia I-80126 Napoli

    2013-12-09

    The issue of the quantitative analysis of time-resolved photoluminescence experiments is addressed by developing and describing two approaches for determination of unimolecular lifetime, bimolecular recombination coefficient, and equilibrium free-carrier concentration, based on a quite general second-order expression of the electron-hole recombination rate. Application to the case of band-edge emission of ZnO single crystals is reported, evidencing the signature of sub-nanosecond second-order recombination dynamics for optical transitions close to the interband excitation edge. The resulting findings are in good agreement with the model prediction and further confirm the presence, formerly evidenced in literature by non-optical methods, of near-surface conductive layers in ZnO crystals with sheet charge densities of about 3–5×10{sup 13} cm{sup ?2}.

  10. Chemometric study of excitation-emission matrix fluorescence data: quantitative analysis of petrol-kerosene mixtures.

    PubMed

    Divya, O; Mishra, Ashok K

    2008-07-01

    Products of petroleum crude are multifluorophoric in nature due to the presence of a mixture of a variety polycyclic aromatic hydrocarbons (PAHs). The use of excitation-emission matrix fluorescence (EEMF) spectroscopy for the analysis of such multifluorophoric samples is gaining progressive acceptance. In this work, EEMF spectroscopic data is processed using chemometric multivariate methods to develop a reliable calibration model for the quantitative determination of kerosene fraction present in petrol. The application of the N-way partial least squares regression (N-PLS) method was found to be very efficient for the estimation of kerosene fraction. A very good degree of accuracy of prediction, expressed in terms of root mean square error of prediction (RMSEP), was achieved at a kerosene fraction of 2.05%. PMID:18935824

  11. Calibration Phantom for Quantitative Tomography Analysis of Biodistribution of Magnetic Nanoparticles

    NASA Astrophysics Data System (ADS)

    Rahn, Helen; Kettering, Melanie; Richter, Heike; Hilger, Ingrid; Trahms, Lutz; Odenbach, Stefan

    2010-12-01

    Ferrofluids are being investigated for cancer treatments such as magnetic drug targeting (MDT) and magnetic heating treatments with the aim of treating the cancer locally, since magnetic nanoparticles with attached drugs are concentrated within the target region. Thus, the side effects are considerably reduced. One of the crucial factors for the success of these therapies is the magnetic nanoparticle distribution. Microcomputed X-ray tomography (X?CT) has been introduced as adequate technique for non-destructive three-dimensional analysis of biological samples enriched with magnetic nanoparticles. The biological tissue specimens, in this case tumor bearing mice after intra-tumoral magnetic nanoparticle injection, have been analyzed by means of X?CT. Complementary measurements have been performed by magnetorelaxometry (MRX). This technique enables a sensitive quantification of magnetic nanoparticles down to few nanograms. For multi-phase samples, such as biological tissue enriched with magnetic nanoparticles the polychromasy and beam hardening artifacts occurring in X?CT with conventional X-ray tubes cause severe problems for quantitative density determination. This problem requires an appropriate calibration of the polychromatic tomography equipment enabling a semi-quantitative analysis of the data. For this purpose a phantom system has been implemented. These phantoms consist of a tissue substitute containing different amounts of magnetic nanoparticles. Since the attenuation of the beam also depends on the thickness i.e. the path length of the beam transmitting the object, the reference sample has been defined to a cone shape. Thus, with one phantom the information about the magnetic nanoparticle concentration as well as the attenuation in dependence of the path length can be determined. Two phantom systems will be presented, one based on agarose-gel and one based on soap.

  12. Quantitative Proteomic Analysis of the Hfq-Regulon in Sinorhizobium meliloti 2011

    PubMed Central

    Sobrero, Patricio; Schlüter, Jan-Philip; Lanner, Ulrike; Schlosser, Andreas; Becker, Anke; Valverde, Claudio

    2012-01-01

    Riboregulation stands for RNA-based control of gene expression. In bacteria, small non-coding RNAs (sRNAs) are a major class of riboregulatory elements, most of which act at the post-transcriptional level by base-pairing target mRNA genes. The RNA chaperone Hfq facilitates antisense interactions between target mRNAs and regulatory sRNAs, thus influencing mRNA stability and/or translation rate. In the ?-proteobacterium Sinorhizobium meliloti strain 2011, the identification and detection of multiple sRNAs genes and the broadly pleitropic phenotype associated to the absence of a functional Hfq protein both support the existence of riboregulatory circuits controlling gene expression to ensure the fitness of this bacterium in both free living and symbiotic conditions. In order to identify target mRNAs subject to Hfq-dependent riboregulation, we have compared the proteome of an hfq mutant and the wild type S. meliloti by quantitative proteomics following protein labelling with 15N. Among 2139 univocally identified proteins, a total of 195 proteins showed a differential abundance between the Hfq mutant and the wild type strain; 65 proteins accumulated ?2-fold whereas 130 were downregulated (?0.5-fold) in the absence of Hfq. This profound proteomic impact implies a major role for Hfq on regulation of diverse physiological processes in S. meliloti, from transport of small molecules to homeostasis of iron and nitrogen. Changes in the cellular levels of proteins involved in transport of nucleotides, peptides and amino acids, and in iron homeostasis, were confirmed with phenotypic assays. These results represent the first quantitative proteomic analysis in S. meliloti. The comparative analysis of the hfq mutant proteome allowed identification of novel strongly Hfq-regulated genes in S. meliloti. PMID:23119037

  13. Fully automated quantitative analysis of breast cancer risk in DCE-MR images

    NASA Astrophysics Data System (ADS)

    Jiang, Luan; Hu, Xiaoxin; Gu, Yajia; Li, Qiang

    2015-03-01

    Amount of fibroglandular tissue (FGT) and background parenchymal enhancement (BPE) in dynamic contrast enhanced magnetic resonance (DCE-MR) images are two important indices for breast cancer risk assessment in the clinical practice. The purpose of this study is to develop and evaluate a fully automated scheme for quantitative analysis of FGT and BPE in DCE-MR images. Our fully automated method consists of three steps, i.e., segmentation of whole breast, fibroglandular tissues, and enhanced fibroglandular tissues. Based on the volume of interest extracted automatically, dynamic programming method was applied in each 2-D slice of a 3-D MR scan to delineate the chest wall and breast skin line for segmenting the whole breast. This step took advantages of the continuity of chest wall and breast skin line across adjacent slices. We then further used fuzzy c-means clustering method with automatic selection of cluster number for segmenting the fibroglandular tissues within the segmented whole breast area. Finally, a statistical method was used to set a threshold based on the estimated noise level for segmenting the enhanced fibroglandular tissues in the subtraction images of pre- and post-contrast MR scans. Based on the segmented whole breast, fibroglandular tissues, and enhanced fibroglandular tissues, FGT and BPE were automatically computed. Preliminary results of technical evaluation and clinical validation showed that our fully automated scheme could obtain good segmentation of the whole breast, fibroglandular tissues, and enhanced fibroglandular tissues to achieve accurate assessment of FGT and BPE for quantitative analysis of breast cancer risk.

  14. Linkage Analysis of Quantitative Refraction and Refractive Errors in the Beaver Dam Eye Study

    PubMed Central

    Duggal, Priya; Lee, Kristine E.; Cheng, Ching-Yu; Klein, Ronald; Bailey-Wilson, Joan E.; Klein, Barbara E. K.

    2011-01-01

    Purpose. Refraction, as measured by spherical equivalent, is the need for an external lens to focus images on the retina. While genetic factors play an important role in the development of refractive errors, few susceptibility genes have been identified. However, several regions of linkage have been reported for myopia (2q, 4q, 7q, 12q, 17q, 18p, 22q, and Xq) and for quantitative refraction (1p, 3q, 4q, 7p, 8p, and 11p). To replicate previously identified linkage peaks and to identify novel loci that influence quantitative refraction and refractive errors, linkage analysis of spherical equivalent, myopia, and hyperopia in the Beaver Dam Eye Study was performed. Methods. Nonparametric, sibling-pair, genome-wide linkage analyses of refraction (spherical equivalent adjusted for age, education, and nuclear sclerosis), myopia and hyperopia in 834 sibling pairs within 486 extended pedigrees were performed. Results. Suggestive evidence of linkage was found for hyperopia on chromosome 3, region q26 (empiric P = 5.34 × 10?4), a region that had shown significant genome-wide evidence of linkage to refraction and some evidence of linkage to hyperopia. In addition, the analysis replicated previously reported genome-wide significant linkages to 22q11 of adjusted refraction and myopia (empiric P = 4.43 × 10?3 and 1.48 × 10?3, respectively) and to 7p15 of refraction (empiric P = 9.43 × 10?4). Evidence was also found of linkage to refraction on 7q36 (empiric P = 2.32 × 10?3), a region previously linked to high myopia. Conclusions. The findings provide further evidence that genes controlling refractive errors are located on 3q26, 7p15, 7p36, and 22q11. PMID:21571680

  15. A comparative phosphoproteomic analysis of a human tumor metastasis model using a label free quantitative approach

    PubMed Central

    Xie, Xiaolei; Feng, Shun; Vuong, Huy; Liu, Yashu; Goodison, Steve; Lubman, David M

    2010-01-01

    Alterations in cellular phosphorylation patterns have been implicated in a number of diseases, including cancer, through multiple mechanisms. Herein we present a survey of the phosphorylation profiles of an isogenic pair of human cancer cell lines with opposite metastatic phenotype. Phosphopeptides were enriched from tumor cell lysates with titanium dioxide and zirconium dioxide, and identified with nano-LC-MS/MS using an automatic cross-validation of MS/MS and MS/MS/MS (MS2 + MS3) data-dependent neutral loss method. A spectral counting quantitative strategy was applied to the two cell line samples on the MS2-only scan which was implemented successively after each MS2 + MS3 scan in the same sample. For all regulated phosphopeptides reported by spectral counting analysis, sequence and phosphorylation site assignments were validated by a MS2 + MS3 data-dependent neutral loss method. With this approach, we identified over 70 phosphorylated sites on 27 phosphoproteins as being differentially expressed with respect to tumor cell phenotype. The altered expression levels of proteins identified by LC-MS/MS were validated using Western blotting. Using network pathway analysis, we observed that the majority of the differentially expressed proteins were highly interconnected and belong to two major intracellular signaling pathways. Our findings suggest that the phosphorylation of isoform A of lamin A/C and GTPase activating protein binding protein 1 is associated with metastatic propensity. The study demonstrates a quantitative and comparative proteomics strategy to identify differential phosphorylation patterns in complex biological samples. PMID:20446291

  16. From "weight of evidence" to quantitative data integration using multicriteria decision analysis and Bayesian methods.

    PubMed

    Linkov, Igor; Massey, Olivia; Keisler, Jeff; Rusyn, Ivan; Hartung, Thomas

    2015-01-01

    "Weighing" available evidence in the process of decision-making is unavoidable, yet it is one step that routinely raises suspicions: what evidence should be used, how much does it weigh, and whose thumb may be tipping the scales? This commentary aims to evaluate the current state and future roles of various types of evidence for hazard assessment as it applies to environmental health. In its recent evaluation of the US Environmental Protection Agency's Integrated Risk Information System assessment process, the National Research Council committee singled out the term "weight of evidence" (WoE) for critique, deeming the process too vague and detractive to the practice of evaluating human health risks of chemicals. Moving the methodology away from qualitative, vague and controversial methods towards generalizable, quantitative and transparent methods for appropriately managing diverse lines of evidence is paramount for both regulatory and public acceptance of the hazard assessments. The choice of terminology notwithstanding, a number of recent Bayesian WoE-based methods, the emergence of multi criteria decision analysis for WoE applications, as well as the general principles behind the foundational concepts of WoE, show promise in how to move forward and regain trust in the data integration step of the assessments. We offer our thoughts on the current state of WoE as a whole and while we acknowledge that many WoE applications have been largely qualitative and subjective in nature, we see this as an opportunity to turn WoE towards a quantitative direction that includes Bayesian and multi criteria decision analysis. PMID:25592482

  17. Quantitative electron spin resonance (ESR) analysis of antioxidative properties using the acetaldehyde/xanthine oxidase system

    NASA Astrophysics Data System (ADS)

    Souchard, J.-P.; Nepveu, F.

    1998-05-01

    We present a method for the quantitative ESR analysis of the antioxidant properties of drugs using the acetaldhehyde/xanthine oxidase (AC/XOD) superoxide generating system and 5,5-dimethyl-l-pyrroline-N-oxide (DMPO) as spin trap. In stoichiometric conditions (AC/XOD, 60 mM/0.018 U), the resulting paramagnetic DMPO adduct disappeared with superoxide dismutase and remained when catalase or DMSO were used. That adduct was dependent only on superoxide and resulted from the trapping of a carboxyl radical by DMPO (aN = 15.2 G, aH = 18.9 G). Similar results were obtained using 4-pyridyl-l-oxide-N-t-butyl nitrone (POBN) as spin trap. The ESR signal of the DMPO-CO2- adduct was very stable and allowed quantitative analysis of the antioxidative activity of redox molecules from an IC{50} value representing the concentration causing 50% inhibition of its intensity. Among the tested compounds, manganese(II), complexes were the most effective, 25 times as active as ascorbic acid or (+)catechin and 500-fold more antioxidative than Trolox^R. Nous présentons une méthode d'analyse quantitative de l'activité antioxydante de composés d'intérêt pharmaceutique basée sur le système acétaldéhyde/xanthine oxydase (AC/XOD), l'utilisation de la RPE et du piégeage de spin avec le 5,5-diméthyl-l-pyrroline-N-oxyde (DMPO). Dans les conditions stoechiométriques {AC/XOD, 60 mM/0,018 U/ml}, l'adduit radicalaire résultant de ce système disparaît en présence de superoxyde dismutase et persiste en présence de catalase ou de DMSO. Cet adduit ne dépend que de la présence de l'anion superoxyde et provient du piégeage d'un radical carboxyle CO2- sur le DMPO (aN = 15.2 G, aH = 18.9 G). Des résultats similaires ont été obtenus avec le piégeur de spin 4-pyridyl-l-oxyde-N-t-butyl nitrone (POBN). Le signal RPE de l'adduit DMPO-CO2- est très stable et permet la quantification de l'activité antioxydante de pharmacophores redox par la détermination de la CI{50}, concentration qui diminue de 50 % son intensité. Parmi les composés testés, les complexes du manganèse sont les plus antioxydants, 25 fois plus actifs que la vitamine C ou la catéchine(+), 500 fois plus antioxydants que le Trolox^R.

  18. Misconceived Relationships between Logical Positivism and Quantitative Research: An Analysis in the Framework of Ian Hacking.

    ERIC Educational Resources Information Center

    Yu, Chong Ho

    Although quantitative research methodology is widely applied by psychological researchers, there is a common misconception that quantitative research is based on logical positivism. This paper examines the relationship between quantitative research and eight major notions of logical positivism: (1) verification; (2) pro-observation; (3)…

  19. Obtaining of Ni/NiO nanopowder from aqua solutions of Ni(CH3COO)2 ammonia complexes

    NASA Astrophysics Data System (ADS)

    Dulina, Iryna; Lobunets, Tetyana; Klochkov, Leonid; Ragulya, Andrey

    2015-03-01

    Ni/NiO nanopowders have been prepared by using thermal decomposition of aqua solutions of nickel acetate ammine complexes in air at the annealing temperature range of 300°C to 500°C, time of decomposition from 30 to 180 min, and ammonia content in initial complex 3.6 to 9.55 mol/mol Ni2+. Chemical composition of obtained powders has been characterized by chemical and thermal analysis. Phase analysis and particle size of powders have been investigated by X-ray diffraction method, transmission electron microscopy (TEM), and scanning electron microscopy (SEM). The powders' pore structure has been determinated by low-temperature nitrogen adsorption method.

  20. Quantitative and qualitative analysis of urine component in the toilet set using Raman spectroscopy

    NASA Astrophysics Data System (ADS)

    Chung, So Hyun; Park, Kwang Suk; Choi, Jong Min; Lee, Won Jin

    2004-07-01

    As a part of non-invasive and unaware measurement of physiological signal in the house of live-alone person, Raman spectroscopy was applied for urine component analysis in the toilet set. 785nm, 250-300mW output solid state diode laser and 2048 element linear silicon TE cooled CCD array were incorporated for this system. Several tests were performed for setting up Raman spectroscopy in non-constrained situation: toilet set in the house. The effect of dark current, integration time, warming up time of laser, property of probe and interference of water in the toilet were tested and controlled for appropriate measurement in this environment. The spectra were obtained immediately when the subject uses the toilet set, and they can be transmitted to the server though Bluetooth. Those spectra were pre-processed for removing or correcting the effect of undesired light scattering, sample path-length difference and baseline-effect. The preprocessed data were enhanced for more exact result of multivariate analysis. The training data was prepared for predicting unknown component and its concentration by using multivariate methods. Several kinds of multivariate methods: PCA, PCR, PLS were performed to validate what is the fittest method in this environment. Through quantitative and qualitative analysis of Raman spectroscopy"s spectra obtained in the house's toilet set, we could know the component and its concentration of urine which can be index of disease.