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Sample records for gwas analyzer integrating

  1. Multispecies, Integrative GWAS for Focal Segmental Glomerulosclerosis

    Science.gov (United States)

    2017-09-01

    searching existing data sources, gathering and maintaining the data needed, and completing and reviewing the collection of information. Send comments...is a frequent cause of end-stage renal disease (ESRD. We investigated the genetic basis of FSGS and recruited a heterogeneous population of...understanding the complex genetic mechanisms of FSGS. 15. SUBJECT TERMS FSGS, MCD, GWAS, CNV  16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT uu

  2. Multispecies, Integrative GWAS for Focal Segmental Glomerulosclerosis

    Science.gov (United States)

    2017-09-01

    for the phenotypic analysis of the newly generated transgenic F1 hybrids. Serum will be analyzed for blood urea nitrogen, albumin , cholesterol...under a particular item, state “Nothing to Report.”  Publications, conference papers , and presentations Report only the major publication(s...resulting from the work under this award. Journal publications. List peer-reviewed articles or papers appearing in scientific, technical, or

  3. Integrating eQTL data with GWAS summary statistics in pathway-based analysis with application to schizophrenia.

    Science.gov (United States)

    Wu, Chong; Pan, Wei

    2018-04-01

    Many genetic variants affect complex traits through gene expression, which can be exploited to boost statistical power and enhance interpretation in genome-wide association studies (GWASs) as demonstrated by the transcriptome-wide association study (TWAS) approach. Furthermore, due to polygenic inheritance, a complex trait is often affected by multiple genes with similar functions as annotated in gene pathways. Here, we extend TWAS from gene-based analysis to pathway-based analysis: we integrate public pathway collections, expression quantitative trait locus (eQTL) data and GWAS summary association statistics (or GWAS individual-level data) to identify gene pathways associated with complex traits. The basic idea is to weight the SNPs of the genes in a pathway based on their estimated cis-effects on gene expression, then adaptively test for association of the pathway with a GWAS trait by effectively aggregating possibly weak association signals across the genes in the pathway. The P values can be calculated analytically and thus fast. We applied our proposed test with the KEGG and GO pathways to two schizophrenia (SCZ) GWAS summary association data sets, denoted by SCZ1 and SCZ2 with about 20,000 and 150,000 subjects, respectively. Most of the significant pathways identified by analyzing the SCZ1 data were reproduced by the SCZ2 data. Importantly, we identified 15 novel pathways associated with SCZ, such as GABA receptor complex (GO:1902710), which could not be uncovered by the standard single SNP-based analysis or gene-based TWAS. The newly identified pathways may help us gain insights into the biological mechanism underlying SCZ. Our results showcase the power of incorporating gene expression information and gene functional annotations into pathway-based association testing for GWAS. © 2018 WILEY PERIODICALS, INC.

  4. LocusTrack: Integrated visualization of GWAS results and genomic annotation.

    Science.gov (United States)

    Cuellar-Partida, Gabriel; Renteria, Miguel E; MacGregor, Stuart

    2015-01-01

    Genome-wide association studies (GWAS) are an important tool for the mapping of complex traits and diseases. Visual inspection of genomic annotations may be used to generate insights into the biological mechanisms underlying GWAS-identified loci. We developed LocusTrack, a web-based application that annotates and creates plots of regional GWAS results and incorporates user-specified tracks that display annotations such as linkage disequilibrium (LD), phylogenetic conservation, chromatin state, and other genomic and regulatory elements. Currently, LocusTrack can integrate annotation tracks from the UCSC genome-browser as well as from any tracks provided by the user. LocusTrack is an easy-to-use application and can be accessed at the following URL: http://gump.qimr.edu.au/general/gabrieC/LocusTrack/. Users can upload and manage GWAS results and select from and/or provide annotation tracks using simple and intuitive menus. LocusTrack scripts and associated data can be downloaded from the website and run locally.

  5. HiView: an integrative genome browser to leverage Hi-C results for the interpretation of GWAS variants.

    Science.gov (United States)

    Xu, Zheng; Zhang, Guosheng; Duan, Qing; Chai, Shengjie; Zhang, Baqun; Wu, Cong; Jin, Fulai; Yue, Feng; Li, Yun; Hu, Ming

    2016-03-11

    Genome-wide association studies (GWAS) have identified thousands of genetic variants associated with complex traits and diseases. However, most of them are located in the non-protein coding regions, and therefore it is challenging to hypothesize the functions of these non-coding GWAS variants. Recent large efforts such as the ENCODE and Roadmap Epigenomics projects have predicted a large number of regulatory elements. However, the target genes of these regulatory elements remain largely unknown. Chromatin conformation capture based technologies such as Hi-C can directly measure the chromatin interactions and have generated an increasingly comprehensive catalog of the interactome between the distal regulatory elements and their potential target genes. Leveraging such information revealed by Hi-C holds the promise of elucidating the functions of genetic variants in human diseases. In this work, we present HiView, the first integrative genome browser to leverage Hi-C results for the interpretation of GWAS variants. HiView is able to display Hi-C data and statistical evidence for chromatin interactions in genomic regions surrounding any given GWAS variant, enabling straightforward visualization and interpretation. We believe that as the first GWAS variants-centered Hi-C genome browser, HiView is a useful tool guiding post-GWAS functional genomics studies. HiView is freely accessible at: http://www.unc.edu/~yunmli/HiView .

  6. Integrated GWAS and Pathway profiling for feed efficiency traits in pigs leads to novel genes and their molecular pathways

    DEFF Research Database (Denmark)

    Do, Duy Ngoc; Ostersen, Tage; Strathe, Anders Bjerring

    2013-01-01

    Genome wide association studies (GWAS) are being extensively used in revealing genetic architecture of complex traits. However, GWAS offer limited understanding of the biological role of significant single nucleotide polymorphisms (SNPs) affecting complex traits. Pathway analysis using GWAS results...... is an important step where we firstly detect genes located near GWAS-detected SNPs and subsequently we detect enrichment of these genes in various biological processes and pathways. The objective of this study was to apply these steps to identify relevant pathways involved in residual feed intake (RFI) in pigs....... Residual feed intake is a feed efficiency measure and is highly economically important in animal production. In our study, a total of 596 Yorkshire boars had phenotypic and genotypic records. After quality control, 37,915 SNPs were available for GWAS which was implemented in the DMU software package...

  7. Simultaneous inference of phenotype-associated genes and relevant tissues from GWAS data via Bayesian integration of multiple tissue-specific gene networks.

    Science.gov (United States)

    Wu, Mengmeng; Lin, Zhixiang; Ma, Shining; Chen, Ting; Jiang, Rui; Wong, Wing Hung

    2017-12-01

    Although genome-wide association studies (GWAS) have successfully identified thousands of genomic loci associated with hundreds of complex traits in the past decade, the debate about such problems as missing heritability and weak interpretability has been appealing for effective computational methods to facilitate the advanced analysis of the vast volume of existing and anticipated genetic data. Towards this goal, gene-level integrative GWAS analysis with the assumption that genes associated with a phenotype tend to be enriched in biological gene sets or gene networks has recently attracted much attention, due to such advantages as straightforward interpretation, less multiple testing burdens, and robustness across studies. However, existing methods in this category usually exploit non-tissue-specific gene networks and thus lack the ability to utilize informative tissue-specific characteristics. To overcome this limitation, we proposed a Bayesian approach called SIGNET (Simultaneously Inference of GeNEs and Tissues) to integrate GWAS data and multiple tissue-specific gene networks for the simultaneous inference of phenotype-associated genes and relevant tissues. Through extensive simulation studies, we showed the effectiveness of our method in finding both associated genes and relevant tissues for a phenotype. In applications to real GWAS data of 14 complex phenotypes, we demonstrated the power of our method in both deciphering genetic basis and discovering biological insights of a phenotype. With this understanding, we expect to see SIGNET as a valuable tool for integrative GWAS analysis, thereby boosting the prevention, diagnosis, and treatment of human inherited diseases and eventually facilitating precision medicine.

  8. The Integration of Epistasis Network and Functional Interactions in a GWAS Implicates RXR Pathway Genes in the Immune Response to Smallpox Vaccine.

    Directory of Open Access Journals (Sweden)

    Brett A McKinney

    Full Text Available Although many diseases and traits show large heritability, few genetic variants have been found to strongly separate phenotype groups by genotype. Complex regulatory networks of variants and expression of multiple genes lead to small individual-variant effects and difficulty replicating the effect of any single variant in an affected pathway. Interaction network modeling of GWAS identifies effects ignored by univariate models, but population differences may still cause specific genes to not replicate. Integrative network models may help detect indirect effects of variants in the underlying biological pathway. In this study, we used gene-level functional interaction information from the Integrative Multi-species Prediction (IMP tool to reveal important genes associated with a complex phenotype through evidence from epistasis networks and pathway enrichment. We test this method for augmenting variant-based network analyses with functional interactions by applying it to a smallpox vaccine immune response GWAS. The integrative analysis spotlights the role of genes related to retinoid X receptor alpha (RXRA, which has been implicated in a previous epistasis network analysis of smallpox vaccine.

  9. A seal analyzer for testing container integrity

    International Nuclear Information System (INIS)

    McDaniel, P.; Jenkins, C.

    1988-01-01

    This paper reports on the development of laboratory and production seal analyzer that offers a rapid, nondestructive method of assuring the seal integrity of virtually any type of single or double sealed container. The system can test a broad range of metal cans, drums and trays, membrane-lidded vessels, flexible pouches, aerosol containers, and glass or metal containers with twist-top lids that are used in the chemical/pesticide (hazardous materials/waste), beverage, food, medical and pharmaceutical industries

  10. Network-Based Integration of GWAS and Gene Expression Identifies a HOX-Centric Network Associated with Serous Ovarian Cancer Risk.

    Science.gov (United States)

    Kar, Siddhartha P; Tyrer, Jonathan P; Li, Qiyuan; Lawrenson, Kate; Aben, Katja K H; Anton-Culver, Hoda; Antonenkova, Natalia; Chenevix-Trench, Georgia; Baker, Helen; Bandera, Elisa V; Bean, Yukie T; Beckmann, Matthias W; Berchuck, Andrew; Bisogna, Maria; Bjørge, Line; Bogdanova, Natalia; Brinton, Louise; Brooks-Wilson, Angela; Butzow, Ralf; Campbell, Ian; Carty, Karen; Chang-Claude, Jenny; Chen, Yian Ann; Chen, Zhihua; Cook, Linda S; Cramer, Daniel; Cunningham, Julie M; Cybulski, Cezary; Dansonka-Mieszkowska, Agnieszka; Dennis, Joe; Dicks, Ed; Doherty, Jennifer A; Dörk, Thilo; du Bois, Andreas; Dürst, Matthias; Eccles, Diana; Easton, Douglas F; Edwards, Robert P; Ekici, Arif B; Fasching, Peter A; Fridley, Brooke L; Gao, Yu-Tang; Gentry-Maharaj, Aleksandra; Giles, Graham G; Glasspool, Rosalind; Goode, Ellen L; Goodman, Marc T; Grownwald, Jacek; Harrington, Patricia; Harter, Philipp; Hein, Alexander; Heitz, Florian; Hildebrandt, Michelle A T; Hillemanns, Peter; Hogdall, Estrid; Hogdall, Claus K; Hosono, Satoyo; Iversen, Edwin S; Jakubowska, Anna; Paul, James; Jensen, Allan; Ji, Bu-Tian; Karlan, Beth Y; Kjaer, Susanne K; Kelemen, Linda E; Kellar, Melissa; Kelley, Joseph; Kiemeney, Lambertus A; Krakstad, Camilla; Kupryjanczyk, Jolanta; Lambrechts, Diether; Lambrechts, Sandrina; Le, Nhu D; Lee, Alice W; Lele, Shashi; Leminen, Arto; Lester, Jenny; Levine, Douglas A; Liang, Dong; Lissowska, Jolanta; Lu, Karen; Lubinski, Jan; Lundvall, Lene; Massuger, Leon; Matsuo, Keitaro; McGuire, Valerie; McLaughlin, John R; McNeish, Iain A; Menon, Usha; Modugno, Francesmary; Moysich, Kirsten B; Narod, Steven A; Nedergaard, Lotte; Ness, Roberta B; Nevanlinna, Heli; Odunsi, Kunle; Olson, Sara H; Orlow, Irene; Orsulic, Sandra; Weber, Rachel Palmieri; Pearce, Celeste Leigh; Pejovic, Tanja; Pelttari, Liisa M; Permuth-Wey, Jennifer; Phelan, Catherine M; Pike, Malcolm C; Poole, Elizabeth M; Ramus, Susan J; Risch, Harvey A; Rosen, Barry; Rossing, Mary Anne; Rothstein, Joseph H; Rudolph, Anja; Runnebaum, Ingo B; Rzepecka, Iwona K; Salvesen, Helga B; Schildkraut, Joellen M; Schwaab, Ira; Shu, Xiao-Ou; Shvetsov, Yurii B; Siddiqui, Nadeem; Sieh, Weiva; Song, Honglin; Southey, Melissa C; Sucheston-Campbell, Lara E; Tangen, Ingvild L; Teo, Soo-Hwang; Terry, Kathryn L; Thompson, Pamela J; Timorek, Agnieszka; Tsai, Ya-Yu; Tworoger, Shelley S; van Altena, Anne M; Van Nieuwenhuysen, Els; Vergote, Ignace; Vierkant, Robert A; Wang-Gohrke, Shan; Walsh, Christine; Wentzensen, Nicolas; Whittemore, Alice S; Wicklund, Kristine G; Wilkens, Lynne R; Woo, Yin-Ling; Wu, Xifeng; Wu, Anna; Yang, Hannah; Zheng, Wei; Ziogas, Argyrios; Sellers, Thomas A; Monteiro, Alvaro N A; Freedman, Matthew L; Gayther, Simon A; Pharoah, Paul D P

    2015-10-01

    Genome-wide association studies (GWAS) have so far reported 12 loci associated with serous epithelial ovarian cancer (EOC) risk. We hypothesized that some of these loci function through nearby transcription factor (TF) genes and that putative target genes of these TFs as identified by coexpression may also be enriched for additional EOC risk associations. We selected TF genes within 1 Mb of the top signal at the 12 genome-wide significant risk loci. Mutual information, a form of correlation, was used to build networks of genes strongly coexpressed with each selected TF gene in the unified microarray dataset of 489 serous EOC tumors from The Cancer Genome Atlas. Genes represented in this dataset were subsequently ranked using a gene-level test based on results for germline SNPs from a serous EOC GWAS meta-analysis (2,196 cases/4,396 controls). Gene set enrichment analysis identified six networks centered on TF genes (HOXB2, HOXB5, HOXB6, HOXB7 at 17q21.32 and HOXD1, HOXD3 at 2q31) that were significantly enriched for genes from the risk-associated end of the ranked list (P < 0.05 and FDR < 0.05). These results were replicated (P < 0.05) using an independent association study (7,035 cases/21,693 controls). Genes underlying enrichment in the six networks were pooled into a combined network. We identified a HOX-centric network associated with serous EOC risk containing several genes with known or emerging roles in serous EOC development. Network analysis integrating large, context-specific datasets has the potential to offer mechanistic insights into cancer susceptibility and prioritize genes for experimental characterization. ©2015 American Association for Cancer Research.

  11. Integration of human adipocyte chromosomal interactions with adipose gene expression prioritizes obesity-related genes from GWAS.

    Science.gov (United States)

    Pan, David Z; Garske, Kristina M; Alvarez, Marcus; Bhagat, Yash V; Boocock, James; Nikkola, Elina; Miao, Zong; Raulerson, Chelsea K; Cantor, Rita M; Civelek, Mete; Glastonbury, Craig A; Small, Kerrin S; Boehnke, Michael; Lusis, Aldons J; Sinsheimer, Janet S; Mohlke, Karen L; Laakso, Markku; Pajukanta, Päivi; Ko, Arthur

    2018-04-17

    Increased adiposity is a hallmark of obesity and overweight, which affect 2.2 billion people world-wide. Understanding the genetic and molecular mechanisms that underlie obesity-related phenotypes can help to improve treatment options and drug development. Here we perform promoter Capture Hi-C in human adipocytes to investigate interactions between gene promoters and distal elements as a transcription-regulating mechanism contributing to these phenotypes. We find that promoter-interacting elements in human adipocytes are enriched for adipose-related transcription factor motifs, such as PPARG and CEBPB, and contribute to heritability of cis-regulated gene expression. We further intersect these data with published genome-wide association studies for BMI and BMI-related metabolic traits to identify the genes that are under genetic cis regulation in human adipocytes via chromosomal interactions. This integrative genomics approach identifies four cis-eQTL-eGene relationships associated with BMI or obesity-related traits, including rs4776984 and MAP2K5, which we further confirm by EMSA, and highlights 38 additional candidate genes.

  12. Network-Based Integration of GWAS and Gene Expression Identifies a HOX-Centric Network Associated with Serous Ovarian Cancer Risk

    DEFF Research Database (Denmark)

    Kar, Siddhartha P; Tyrer, Jonathan P; Li, Qiyuan

    2015-01-01

    BACKGROUND: Genome-wide association studies (GWAS) have so far reported 12 loci associated with serous epithelial ovarian cancer (EOC) risk. We hypothesized that some of these loci function through nearby transcription factor (TF) genes and that putative target genes of these TFs as identified...... in the unified microarray dataset of 489 serous EOC tumors from The Cancer Genome Atlas. Genes represented in this dataset were subsequently ranked using a gene-level test based on results for germline SNPs from a serous EOC GWAS meta-analysis (2,196 cases/4,396 controls). RESULTS: Gene set enrichment analysis...

  13. easyGWAS: A Cloud-Based Platform for Comparing the Results of Genome-Wide Association Studies.

    Science.gov (United States)

    Grimm, Dominik G; Roqueiro, Damian; Salomé, Patrice A; Kleeberger, Stefan; Greshake, Bastian; Zhu, Wangsheng; Liu, Chang; Lippert, Christoph; Stegle, Oliver; Schölkopf, Bernhard; Weigel, Detlef; Borgwardt, Karsten M

    2017-01-01

    The ever-growing availability of high-quality genotypes for a multitude of species has enabled researchers to explore the underlying genetic architecture of complex phenotypes at an unprecedented level of detail using genome-wide association studies (GWAS). The systematic comparison of results obtained from GWAS of different traits opens up new possibilities, including the analysis of pleiotropic effects. Other advantages that result from the integration of multiple GWAS are the ability to replicate GWAS signals and to increase statistical power to detect such signals through meta-analyses. In order to facilitate the simple comparison of GWAS results, we present easyGWAS, a powerful, species-independent online resource for computing, storing, sharing, annotating, and comparing GWAS. The easyGWAS tool supports multiple species, the uploading of private genotype data and summary statistics of existing GWAS, as well as advanced methods for comparing GWAS results across different experiments and data sets in an interactive and user-friendly interface. easyGWAS is also a public data repository for GWAS data and summary statistics and already includes published data and results from several major GWAS. We demonstrate the potential of easyGWAS with a case study of the model organism Arabidopsis thaliana , using flowering and growth-related traits. © 2016 American Society of Plant Biologists. All rights reserved.

  14. Integration of liver gene co-expression networks and eGWAs analyses highlighted candidate regulators implicated in lipid metabolism in pigs.

    Science.gov (United States)

    Ballester, Maria; Ramayo-Caldas, Yuliaxis; Revilla, Manuel; Corominas, Jordi; Castelló, Anna; Estellé, Jordi; Fernández, Ana I; Folch, Josep M

    2017-04-19

    In the present study, liver co-expression networks and expression Genome Wide Association Study (eGWAS) were performed to identify DNA variants and molecular pathways implicated in the functional regulatory mechanisms of meat quality traits in pigs. With this purpose, the liver mRNA expression of 44 candidates genes related with lipid metabolism was analysed in 111 Iberian x Landrace backcross animals. The eGWAS identified 92 eSNPs located in seven chromosomal regions and associated with eight genes: CROT, CYP2U1, DGAT1, EGF, FABP1, FABP5, PLA2G12A, and PPARA. Remarkably, cis-eSNPs associated with FABP1 gene expression which may be determining the C18:2(n-6)/C18:3(n-3) ratio in backfat through the multiple interaction of DNA variants and genes were identified. Furthermore, a hotspot on SSC8 associated with the gene expression of eight genes was identified and the TBCK gene was pointed out as candidate gene regulating it. Our results also suggested that the PI3K-Akt-mTOR pathway plays an important role in the control of the analysed genes highlighting nuclear receptors as the NR3C1 or PPARA. Finally, sex-dimorphism associated with hepatic lipid metabolism was identified with over-representation of female-biased genes. These results increase our knowledge of the genetic architecture underlying fat composition traits.

  15. Differentiation and Integration: Guiding Principles for Analyzing Cognitive Change

    Science.gov (United States)

    Siegler, Robert S.; Chen, Zhe

    2008-01-01

    Differentiation and integration played large roles within classic developmental theories but have been relegated to obscurity within contemporary theories. However, they may have a useful role to play in modern theories as well, if conceptualized as guiding principles for analyzing change rather than as real-time mechanisms. In the present study,…

  16. UPDG: Utilities package for data analysis of Pooled DNA GWAS

    Directory of Open Access Journals (Sweden)

    Ho Daniel WH

    2012-01-01

    Full Text Available Abstract Background Despite being a well-established strategy for cost reduction in disease gene mapping, pooled DNA association study is much less popular than the individual DNA approach. This situation is especially true for pooled DNA genomewide association study (GWAS, for which very few computer resources have been developed for its data analysis. This motivates the development of UPDG (Utilities package for data analysis of Pooled DNA GWAS. Results UPDG represents a generalized framework for data analysis of pooled DNA GWAS with the integration of Unix/Linux shell operations, Perl programs and R scripts. With the input of raw intensity data from GWAS, UPDG performs the following tasks in a stepwise manner: raw data manipulation, correction for allelic preferential amplification, normalization, nested analysis of variance for genetic association testing, and summarization of analysis results. Detailed instructions, procedures and commands are provided in the comprehensive user manual describing the whole process from preliminary preparation of software installation to final outcome acquisition. An example dataset (input files and sample output files is also included in the package so that users can easily familiarize themselves with the data file formats, working procedures and expected output. Therefore, UPDG is especially useful for users with some computer knowledge, but without a sophisticated programming background. Conclusions UPDG provides a free, simple and platform-independent one-stop service to scientists working on pooled DNA GWAS data analysis, but with less advanced programming knowledge. It is our vision and mission to reduce the hindrance for performing data analysis of pooled DNA GWAS through our contribution of UPDG. More importantly, we hope to promote the popularity of pooled DNA GWAS, which is a very useful research strategy.

  17. Controlling the Rate of GWAS False Discoveries.

    Science.gov (United States)

    Brzyski, Damian; Peterson, Christine B; Sobczyk, Piotr; Candès, Emmanuel J; Bogdan, Malgorzata; Sabatti, Chiara

    2017-01-01

    With the rise of both the number and the complexity of traits of interest, control of the false discovery rate (FDR) in genetic association studies has become an increasingly appealing and accepted target for multiple comparison adjustment. While a number of robust FDR-controlling strategies exist, the nature of this error rate is intimately tied to the precise way in which discoveries are counted, and the performance of FDR-controlling procedures is satisfactory only if there is a one-to-one correspondence between what scientists describe as unique discoveries and the number of rejected hypotheses. The presence of linkage disequilibrium between markers in genome-wide association studies (GWAS) often leads researchers to consider the signal associated to multiple neighboring SNPs as indicating the existence of a single genomic locus with possible influence on the phenotype. This a posteriori aggregation of rejected hypotheses results in inflation of the relevant FDR. We propose a novel approach to FDR control that is based on prescreening to identify the level of resolution of distinct hypotheses. We show how FDR-controlling strategies can be adapted to account for this initial selection both with theoretical results and simulations that mimic the dependence structure to be expected in GWAS. We demonstrate that our approach is versatile and useful when the data are analyzed using both tests based on single markers and multiple regression. We provide an R package that allows practitioners to apply our procedure on standard GWAS format data, and illustrate its performance on lipid traits in the North Finland Birth Cohort 66 cohort study. Copyright © 2017 by the Genetics Society of America.

  18. Molecular pathological epidemiology of epigenetics: emerging integrative science to analyze environment, host, and disease.

    Science.gov (United States)

    Ogino, Shuji; Lochhead, Paul; Chan, Andrew T; Nishihara, Reiko; Cho, Eunyoung; Wolpin, Brian M; Meyerhardt, Jeffrey A; Meissner, Alexander; Schernhammer, Eva S; Fuchs, Charles S; Giovannucci, Edward

    2013-04-01

    Epigenetics acts as an interface between environmental/exogenous factors, cellular responses, and pathological processes. Aberrant epigenetic signatures are a hallmark of complex multifactorial diseases (including neoplasms and malignancies such as leukemias, lymphomas, sarcomas, and breast, lung, prostate, liver, and colorectal cancers). Epigenetic signatures (DNA methylation, mRNA and microRNA expression, etc) may serve as biomarkers for risk stratification, early detection, and disease classification, as well as targets for therapy and chemoprevention. In particular, DNA methylation assays are widely applied to formalin-fixed, paraffin-embedded archival tissue specimens as clinical pathology tests. To better understand the interplay between etiological factors, cellular molecular characteristics, and disease evolution, the field of 'molecular pathological epidemiology (MPE)' has emerged as an interdisciplinary integration of 'molecular pathology' and 'epidemiology'. In contrast to traditional epidemiological research including genome-wide association studies (GWAS), MPE is founded on the unique disease principle, that is, each disease process results from unique profiles of exposomes, epigenomes, transcriptomes, proteomes, metabolomes, microbiomes, and interactomes in relation to the macroenvironment and tissue microenvironment. MPE may represent a logical evolution of GWAS, termed 'GWAS-MPE approach'. Although epigenome-wide association study attracts increasing attention, currently, it has a fundamental problem in that each cell within one individual has a unique, time-varying epigenome. Having a similar conceptual framework to systems biology, the holistic MPE approach enables us to link potential etiological factors to specific molecular pathology, and gain novel pathogenic insights on causality. The widespread application of epigenome (eg, methylome) analyses will enhance our understanding of disease heterogeneity, epigenotypes (CpG island methylator

  19. A fully integrated standalone portable cavity ringdown breath acetone analyzer

    Science.gov (United States)

    Sun, Meixiu; Jiang, Chenyu; Gong, Zhiyong; Zhao, Xiaomeng; Chen, Zhuying; Wang, Zhennan; Kang, Meiling; Li, Yingxin; Wang, Chuji

    2015-09-01

    Breath analysis is a promising new technique for nonintrusive disease diagnosis and metabolic status monitoring. One challenging issue in using a breath biomarker for potential particular disease screening is to find a quantitative relationship between the concentration of the breath biomarker and clinical diagnostic parameters of the specific disease. In order to address this issue, we need a new instrument that is capable of conducting real-time, online breath analysis with high data throughput, so that a large scale of clinical test (more subjects) can be achieved in a short period of time. In this work, we report a fully integrated, standalone, portable analyzer based on the cavity ringdown spectroscopy technique for near-real time, online breath acetone measurements. The performance of the portable analyzer in measurements of breath acetone was interrogated and validated by using the certificated gas chromatography-mass spectrometry. The results show that this new analyzer is useful for reliable online (online introduction of a breath sample without pre-treatment) breath acetone analysis with high sensitivity (57 ppb) and high data throughput (one data per second). Subsequently, the validated breath analyzer was employed for acetone measurements in 119 human subjects under various situations. The instrument design, packaging, specifications, and future improvements were also described. From an optical ringdown cavity operated by the lab-set electronics reported previously to this fully integrated standalone new instrument, we have enabled a new scientific tool suited for large scales of breath acetone analysis and created an instrument platform that can even be adopted for study of other breath biomarkers by using different lasers and ringdown mirrors covering corresponding spectral fingerprints.

  20. A fully integrated standalone portable cavity ringdown breath acetone analyzer.

    Science.gov (United States)

    Sun, Meixiu; Jiang, Chenyu; Gong, Zhiyong; Zhao, Xiaomeng; Chen, Zhuying; Wang, Zhennan; Kang, Meiling; Li, Yingxin; Wang, Chuji

    2015-09-01

    Breath analysis is a promising new technique for nonintrusive disease diagnosis and metabolic status monitoring. One challenging issue in using a breath biomarker for potential particular disease screening is to find a quantitative relationship between the concentration of the breath biomarker and clinical diagnostic parameters of the specific disease. In order to address this issue, we need a new instrument that is capable of conducting real-time, online breath analysis with high data throughput, so that a large scale of clinical test (more subjects) can be achieved in a short period of time. In this work, we report a fully integrated, standalone, portable analyzer based on the cavity ringdown spectroscopy technique for near-real time, online breath acetone measurements. The performance of the portable analyzer in measurements of breath acetone was interrogated and validated by using the certificated gas chromatography-mass spectrometry. The results show that this new analyzer is useful for reliable online (online introduction of a breath sample without pre-treatment) breath acetone analysis with high sensitivity (57 ppb) and high data throughput (one data per second). Subsequently, the validated breath analyzer was employed for acetone measurements in 119 human subjects under various situations. The instrument design, packaging, specifications, and future improvements were also described. From an optical ringdown cavity operated by the lab-set electronics reported previously to this fully integrated standalone new instrument, we have enabled a new scientific tool suited for large scales of breath acetone analysis and created an instrument platform that can even be adopted for study of other breath biomarkers by using different lasers and ringdown mirrors covering corresponding spectral fingerprints.

  1. AnalyzeHOLE: An Integrated Wellbore Flow Analysis Tool

    Energy Technology Data Exchange (ETDEWEB)

    Keith J. Halford

    2009-10-01

    Conventional interpretation of flow logs assumes that hydraulic conductivity is directly proportional to flow change with depth. However, well construction can significantly alter the expected relation between changes in fluid velocity and hydraulic conductivity. Strong hydraulic conductivity contrasts between lithologic intervals can be masked in continuously screened wells. Alternating intervals of screen and blank casing also can greatly complicate the relation between flow and hydraulic properties. More permeable units are not necessarily associated with rapid fluid-velocity increases. Thin, highly permeable units can be misinterpreted as thick and less permeable intervals or not identified at all. These conditions compromise standard flow-log interpretation because vertical flow fields are induced near the wellbore. AnalyzeHOLE, an integrated wellbore analysis tool for simulating flow and transport in wells and aquifer systems, provides a better alternative for simulating and evaluating complex well-aquifer system interaction. A pumping well and adjacent aquifer system are simulated with an axisymmetric, radial geometry in a two-dimensional MODFLOW model. Hydraulic conductivities are distributed by depth and estimated with PEST by minimizing squared differences between simulated and measured flows and drawdowns. Hydraulic conductivity can vary within a lithology but variance is limited with regularization. Transmissivity of the simulated system also can be constrained to estimates from single-well, pumping tests. Water-quality changes in the pumping well are simulated with simple mixing models between zones of differing water quality. These zones are differentiated by backtracking thousands of particles from the well screens with MODPATH. An Excel spreadsheet is used to interface the various components of AnalyzeHOLE by (1) creating model input files, (2) executing MODFLOW, MODPATH, PEST, and supporting FORTRAN routines, and (3) importing and graphically

  2. Genes Linked to Endometriosis by GWAS Are Integral to Cytoskeleton Regulation and Suggests That Mesothelial Barrier Homeostasis Is a Factor in the Pathogenesis of Endometriosis.

    Science.gov (United States)

    Albertsen, Hans M; Ward, Kenneth

    2017-06-01

    Endometriosis, defined by the presence of ectopic endometrial lesions, is a common disease in reproductive-age women that profoundly affects patients' quality of life. Various pathogenic models have been proposed, but the origin of endometriosis remains elusive. In this article, we propose that the mesothelial barrier, which protects the underlying stroma from endometrial transplants present in retrograde menstrual fluid, can be compromised by activation of the epithelial to mesenchymal transition (EMT) repair mechanism that lead to temporary loss of barrier integrity. Absent of the mesothelial barrier, endometrial cells can more readily adhere to the underlying peritoneal stroma and establish endometrial lesions. The hypothesis is based on the clinical and experimental observations that correlate the location of endometrial lesions with areas of mesothelial damage, together with genetic evidence that 4 genes associated with endometriosis are direct regulators of the actin-cytoskeleton, which coordinates mesothelial barrier integrity. It supports past observations that implicate the peritoneum in the pathogenesis of endometriosis and unifies previously disparate theories that endometriosis may be triggered by infection, mechanical damage, and inflammation since each of these mechanisms can induce EMT in the mesothelium. If the hypothesis is correct, inhibition of EMT in the mesothelial barrier provides a novel paradigm for the prevention and treatment of endometriosis.

  3. Port supply chain integration : analyzing biofuel supply chains

    NARCIS (Netherlands)

    Stevens, Leonie C. E.; Vis, Iris F. A.

    2016-01-01

    This paper focuses on port supply chain integration to strengthen operational and business performance. We provide a structured and comprehensive method to enable port supply chain integration and demonstrate its applicability to the biofuel supply chain. We define the value proposition, role,

  4. Integrative methods for analyzing big data in precision medicine.

    Science.gov (United States)

    Gligorijević, Vladimir; Malod-Dognin, Noël; Pržulj, Nataša

    2016-03-01

    We provide an overview of recent developments in big data analyses in the context of precision medicine and health informatics. With the advance in technologies capturing molecular and medical data, we entered the area of "Big Data" in biology and medicine. These data offer many opportunities to advance precision medicine. We outline key challenges in precision medicine and present recent advances in data integration-based methods to uncover personalized information from big data produced by various omics studies. We survey recent integrative methods for disease subtyping, biomarkers discovery, and drug repurposing, and list the tools that are available to domain scientists. Given the ever-growing nature of these big data, we highlight key issues that big data integration methods will face. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Analyzing inflation in Nigeria: a fractionally integrated ARFIMA ...

    African Journals Online (AJOL)

    The study looked into the stochastic properties of CPI-inflation rate for Nigeria from 1995Q1 to 2016Q4. The study employed an autoregressive fractionally integrated moving average and a general autoregressive conditional heteroskedasticity (ARFIMA-GARCH) methodology as well as ADF/KPSS to investigate the ...

  6. [Integrated Development of Full-automatic Fluorescence Analyzer].

    Science.gov (United States)

    Zhang, Mei; Lin, Zhibo; Yuan, Peng; Yao, Zhifeng; Hu, Yueming

    2015-10-01

    In view of the fact that medical inspection equipment sold in the domestic market is mainly imported from abroad and very expensive, we developed a full-automatic fluorescence analyzer in our center, presented in this paper. The present paper introduces the hardware architecture design of FPGA/DSP motion controlling card+PC+ STM32 embedded micro processing unit, software system based on C# multi thread, design and implementation of double-unit communication in detail. By simplifying the hardware structure, selecting hardware legitimately and adopting control system software to object-oriented technology, we have improved the precision and velocity of the control system significantly. Finally, the performance test showed that the control system could meet the needs of automated fluorescence analyzer on the functionality, performance and cost.

  7. The AraGWAS Catalog: a curated and standardized Arabidopsis thaliana GWAS catalog

    Science.gov (United States)

    Togninalli, Matteo; Seren, Ümit; Meng, Dazhe; Fitz, Joffrey; Nordborg, Magnus; Weigel, Detlef

    2018-01-01

    Abstract The abundance of high-quality genotype and phenotype data for the model organism Arabidopsis thaliana enables scientists to study the genetic architecture of many complex traits at an unprecedented level of detail using genome-wide association studies (GWAS). GWAS have been a great success in A. thaliana and many SNP-trait associations have been published. With the AraGWAS Catalog (https://aragwas.1001genomes.org) we provide a publicly available, manually curated and standardized GWAS catalog for all publicly available phenotypes from the central A. thaliana phenotype repository, AraPheno. All GWAS have been recomputed on the latest imputed genotype release of the 1001 Genomes Consortium using a standardized GWAS pipeline to ensure comparability between results. The catalog includes currently 167 phenotypes and more than 222 000 SNP-trait associations with P < 10−4, of which 3887 are significantly associated using permutation-based thresholds. The AraGWAS Catalog can be accessed via a modern web-interface and provides various features to easily access, download and visualize the results and summary statistics across GWAS. PMID:29059333

  8. Microbial genome-wide association studies: lessons from human GWAS.

    Science.gov (United States)

    Power, Robert A; Parkhill, Julian; de Oliveira, Tulio

    2017-01-01

    The reduced costs of sequencing have led to whole-genome sequences for a large number of microorganisms, enabling the application of microbial genome-wide association studies (GWAS). Given the successes of human GWAS in understanding disease aetiology and identifying potential drug targets, microbial GWAS are likely to further advance our understanding of infectious diseases. These advances include insights into pressing global health problems, such as antibiotic resistance and disease transmission. In this Review, we outline the methodologies of GWAS, the current state of the field of microbial GWAS, and how lessons from human GWAS can direct the future of the field.

  9. Pseudocode Interpreter (Pseudocode Integrated Development Environment with Lexical Analyzer and Syntax Analyzer using Recursive Descent Parsing Algorithm

    Directory of Open Access Journals (Sweden)

    Christian Lester D. Gimeno

    2017-11-01

    Full Text Available –This research study focused on the development of a software that helps students design, write, validate and run their pseudocode in a semi Integrated Development Environment (IDE instead of manually writing it on a piece of paper.Specifically, the study aimed to develop lexical analyzer or lexer, syntax analyzer or parser using recursive descent parsing algorithm and an interpreter. The lexical analyzer reads pseudocodesource in a sequence of symbols or characters as lexemes.The lexemes are then analyzed by the lexer that matches a pattern for valid tokens and passes to the syntax analyzer or parser. The syntax analyzer or parser takes those valid tokens and builds meaningful commands using recursive descent parsing algorithm in a form of an abstract syntax tree. The generation of an abstract syntax tree is based on the specified grammar rule created by the researcher expressed in Extended Backus-Naur Form. The Interpreter takes the generated abstract syntax tree and starts the evaluation or interpretation to produce pseudocode output. The software was evaluated using white-box testing by several ICT professionals and black-box testing by several computer science students based on the International Organization for Standardization (ISO 9126 software quality standards. The overall results of the evaluation both for white-box and black-box were described as “Excellent in terms of functionality, reliability, usability, efficiency, maintainability and portability”.

  10. In-silico analysis of inflammatory bowel disease (IBD GWAS loci to novel connections.

    Directory of Open Access Journals (Sweden)

    Md Mesbah-Uddin

    Full Text Available Genome-wide association studies (GWASs for many complex diseases, including inflammatory bowel disease (IBD, produced hundreds of disease-associated loci-the majority of which are noncoding. The number of GWAS loci is increasing very rapidly, but the process of translating single nucleotide polymorphisms (SNPs from these loci to genomic medicine is lagging. In this study, we investigated 4,734 variants from 152 IBD associated GWAS loci (IBD associated 152 lead noncoding SNPs identified from pooled GWAS results + 4,582 variants in strong linkage-disequilibrium (LD (r2 ≥0.8 for EUR population of 1K Genomes Project using four publicly available bioinformatics tools, e.g. dbPSHP, CADD, GWAVA, and RegulomeDB, to annotate and prioritize putative regulatory variants. Of the 152 lead noncoding SNPs, around 11% are under strong negative selection (GERP++ RS ≥2; and ~30% are under balancing selection (Tajima's D score >2 in CEU population (1K Genomes Project--though these regions are positively selected (GERP++ RS <0 in mammalian evolution. The analysis of 4,734 variants using three integrative annotation tools produced 929 putative functional SNPs, of which 18 SNPs (from 15 GWAS loci are in concordance with all three classifiers. These prioritized noncoding SNPs may contribute to IBD pathogenesis by dysregulating the expression of nearby genes. This study showed the usefulness of integrative annotation for prioritizing fewer functional variants from a large number of GWAS markers.

  11. Analyzing the Feasibility of Using Secure Application Integration Methodology (SAIM) for Integrating DON Enterprise Resource Planning (ERP) Applications

    National Research Council Canada - National Science Library

    Marin, Ramon

    2004-01-01

    ...) would provide useful information about a beneficial methodology. SAIM is analyzed, by accessing its step by step directions, for suitability in the integration of the Enterprise Resource Planning (ERP...

  12. Time-domain single-source integral equations for analyzing scattering from homogeneous penetrable objects

    KAUST Repository

    Valdé s, Felipe; Andriulli, Francesco P.; Bagci, Hakan; Michielssen, Eric

    2013-01-01

    Single-source time-domain electric-and magnetic-field integral equations for analyzing scattering from homogeneous penetrable objects are presented. Their temporal discretization is effected by using shifted piecewise polynomial temporal basis

  13. Analyzing Developing Country Market Integration using Incomplete Price Data and Cluster Analysis

    NARCIS (Netherlands)

    Ansah, I.G.; Gardebroek, Koos; Ihle, R.; Jaletac, M.

    2015-01-01

    Recent global food price developments have spurred renewed interest in analyzing integration of local markets to global markets. A popular approach to quantify market integration is cointegration analysis. However, local market price data often has missing values, outliers, or short and incomplete

  14. Gene set analysis of GWAS data for human longevity highlights the relevance of the insulin/IGF-1 signaling and telomere maintenance pathways

    NARCIS (Netherlands)

    J. Deelen (Joris); H.-W. Uh; R. Monajemi (Ramin); D. van Heemst (Diana); P.E. Thijssen (Peter); S. Böhringer (Stefan); E.B. van den Akker (Erik); A.J.M. de Craen (Anton J.M.); F. Rivadeneira Ramirez (Fernando); R.G.J. Westendorp (Rudi); A.G. Uitterlinden (André); J.J. Goeman (Jelle); P.E. Slagboom (Eline); J.J. Houwing-Duistermaat (Jeanine); M. Beekman (Marian)

    2013-01-01

    textabstractIn genome-wide association studies (GWAS) of complex traits, single SNP analysis is still the most applied approach. However, the identified SNPs have small effects and provide limited biological insight. A more appropriate approach to interpret GWAS data of complex traits is to analyze

  15. Analysis and visualization of Arabidopsis thaliana GWAS using web 2.0 technologies.

    Science.gov (United States)

    Huang, Yu S; Horton, Matthew; Vilhjálmsson, Bjarni J; Seren, Umit; Meng, Dazhe; Meyer, Christopher; Ali Amer, Muhammad; Borevitz, Justin O; Bergelson, Joy; Nordborg, Magnus

    2011-01-01

    With large-scale genomic data becoming the norm in biological studies, the storing, integrating, viewing and searching of such data have become a major challenge. In this article, we describe the development of an Arabidopsis thaliana database that hosts the geographic information and genetic polymorphism data for over 6000 accessions and genome-wide association study (GWAS) results for 107 phenotypes representing the largest collection of Arabidopsis polymorphism data and GWAS results to date. Taking advantage of a series of the latest web 2.0 technologies, such as Ajax (Asynchronous JavaScript and XML), GWT (Google-Web-Toolkit), MVC (Model-View-Controller) web framework and Object Relationship Mapper, we have created a web-based application (web app) for the database, that offers an integrated and dynamic view of geographic information, genetic polymorphism and GWAS results. Essential search functionalities are incorporated into the web app to aid reverse genetics research. The database and its web app have proven to be a valuable resource to the Arabidopsis community. The whole framework serves as an example of how biological data, especially GWAS, can be presented and accessed through the web. In the end, we illustrate the potential to gain new insights through the web app by two examples, showcasing how it can be used to facilitate forward and reverse genetics research. Database URL: http://arabidopsis.usc.edu/

  16. Integrated analyzing method for the progress event based on subjects and predicates in events

    International Nuclear Information System (INIS)

    Minowa, Hirotsugu; Munesawa, Yoshiomi

    2014-01-01

    It is expected to make use of the knowledge that was extracted by analyzing the mistakes of the past to prevent recurrence of accidents. Currently main analytic style is an analytic style that experts decipher deeply the accident cases, but cross-analysis has come to an end with extracting the common factors in the accident cases. We propose an integrated analyzing method for progress events to analyze among accidents in this study. Our method realized the integration of many accident cases by the integration connecting the common keyword called as 'Subject' or 'Predicate' that are extracted from each progress event in accident cases or near-miss cases. Our method can analyze and visualize the partial risk identification and the frequency to cause accidents and the risk assessment from the data integrated accident cases. The result of applying our method to PEC-SAFER accident cases identified 8 hazardous factors which can be caused from tank again, and visualized the high frequent factors that the first factor was damage of tank 26% and the second factor was the corrosion 21%, and visualized the high risks that the first risk was the damage 3.3 x 10 -2 [risk rank / year] and the second risk was the destroy 2.5 x 10 -2 [risk rank / year]. (author)

  17. Using crosscorrelation to mitigate analog/RF impairments for integrated spectrum analyzers

    NARCIS (Netherlands)

    Oude Alink, M.S.; Klumperink, Eric A.M.; Kokkeler, Andre B.J.; Ru, Z.; Cheng, W.; Nauta, Bram

    2013-01-01

    An integrated spectrum analyzer is useful for built-in self-test purposes, software-defined radios, or dynamic spectrum access in cognitive radio. The analog/RF performance is impaired by a number of factors, including thermal noise, phase noise, and nonlinearity. In this paper, we present an

  18. Tiny Integrated Network Analyzer for Noninvasive Measurements of Electrically Small Antennas

    DEFF Research Database (Denmark)

    Buskgaard, Emil Feldborg; Krøyer, Ben; Tatomirescu, Alexandru

    2016-01-01

    the system. The tiny integrated network analyzer is a stand-alone Arduino-based measurement system that utilizes the transmit signal of the system under test as its reference. It features a power meter with triggering ability, on-board memory, universal serial bus, and easy extendibility with general...

  19. Analyzing Integrated Cost-Schedule Risk for Complex Product Systems R&D Projects

    Directory of Open Access Journals (Sweden)

    Zhe Xu

    2014-01-01

    Full Text Available The vast majority of the research efforts in project risk management tend to assess cost risk and schedule risk independently. However, project cost and time are related in reality and the relationship between them should be analyzed directly. We propose an integrated cost and schedule risk assessment model for complex product systems R&D projects. Graphical evaluation review technique (GERT, Monte Carlo simulation, and probability distribution theory are utilized to establish the model. In addition, statistical analysis and regression analysis techniques are employed to analyze simulation outputs. Finally, a complex product systems R&D project as an example is modeled by the proposed approach and the simulation outputs are analyzed to illustrate the effectiveness of the risk assessment model. It seems that integrating cost and schedule risk assessment can provide more reliable risk estimation results.

  20. Analyzing the effects of information technology on supply chain integration: The role of ERP success mediator

    Directory of Open Access Journals (Sweden)

    Samaneh Alimohamadian

    2014-04-01

    Full Text Available This research analyzes the effects of Information Technology (IT on Supply Chain Integration (SCI through ERP mediator by proposing a conceptual model among these components. We also hypothesize that three constructs of IT influence on enterprise resource planning (ERP success and one construct of ERP success influences on SCI. To clarify the relationships among the constructs, structural equation model (SEM is conducted to examine the model fit and seven hypotheses. The data was collected from three Iranian firms through questionnaire with 23 questions adopted by past researches. The results confirmed that top management support of IT and employees’ general IT skills factors of IT enhance ERP success, and ERP success positively influences on Supply Chain Integration, so these two IT factors influence Supply Chain Integration through ERP success. Our data unsupported negative impact of satisfaction with legacy IT system on ERP success.

  1. SU-D-204-06: Integration of Machine Learning and Bioinformatics Methods to Analyze Genome-Wide Association Study Data for Rectal Bleeding and Erectile Dysfunction Following Radiotherapy in Prostate Cancer

    Energy Technology Data Exchange (ETDEWEB)

    Oh, J; Deasy, J [Memorial Sloan Kettering Cancer Center, New York, NY (United States); Kerns, S [University of Rochester Medical Center, Rochester, NY (United States); Ostrer, H [Albert Einstein College of Medicine, Bronx, NY (United States); Rosenstein, B [Mount Sinai School of Medicine, New York, NY (United States)

    2016-06-15

    Purpose: We investigated whether integration of machine learning and bioinformatics techniques on genome-wide association study (GWAS) data can improve the performance of predictive models in predicting the risk of developing radiation-induced late rectal bleeding and erectile dysfunction in prostate cancer patients. Methods: We analyzed a GWAS dataset generated from 385 prostate cancer patients treated with radiotherapy. Using genotype information from these patients, we designed a machine learning-based predictive model of late radiation-induced toxicities: rectal bleeding and erectile dysfunction. The model building process was performed using 2/3 of samples (training) and the predictive model was tested with 1/3 of samples (validation). To identify important single nucleotide polymorphisms (SNPs), we computed the SNP importance score, resulting from our random forest regression model. We performed gene ontology (GO) enrichment analysis for nearby genes of the important SNPs. Results: After univariate analysis on the training dataset, we filtered out many SNPs with p>0.001, resulting in 749 and 367 SNPs that were used in the model building process for rectal bleeding and erectile dysfunction, respectively. On the validation dataset, our random forest regression model achieved the area under the curve (AUC)=0.70 and 0.62 for rectal bleeding and erectile dysfunction, respectively. We performed GO enrichment analysis for the top 25%, 50%, 75%, and 100% SNPs out of the select SNPs in the univariate analysis. When we used the top 50% SNPs, more plausible biological processes were obtained for both toxicities. An additional test with the top 50% SNPs improved predictive power with AUC=0.71 and 0.65 for rectal bleeding and erectile dysfunction. A better performance was achieved with AUC=0.67 when age and androgen deprivation therapy were added to the model for erectile dysfunction. Conclusion: Our approach that combines machine learning and bioinformatics techniques

  2. SU-D-204-06: Integration of Machine Learning and Bioinformatics Methods to Analyze Genome-Wide Association Study Data for Rectal Bleeding and Erectile Dysfunction Following Radiotherapy in Prostate Cancer

    International Nuclear Information System (INIS)

    Oh, J; Deasy, J; Kerns, S; Ostrer, H; Rosenstein, B

    2016-01-01

    Purpose: We investigated whether integration of machine learning and bioinformatics techniques on genome-wide association study (GWAS) data can improve the performance of predictive models in predicting the risk of developing radiation-induced late rectal bleeding and erectile dysfunction in prostate cancer patients. Methods: We analyzed a GWAS dataset generated from 385 prostate cancer patients treated with radiotherapy. Using genotype information from these patients, we designed a machine learning-based predictive model of late radiation-induced toxicities: rectal bleeding and erectile dysfunction. The model building process was performed using 2/3 of samples (training) and the predictive model was tested with 1/3 of samples (validation). To identify important single nucleotide polymorphisms (SNPs), we computed the SNP importance score, resulting from our random forest regression model. We performed gene ontology (GO) enrichment analysis for nearby genes of the important SNPs. Results: After univariate analysis on the training dataset, we filtered out many SNPs with p>0.001, resulting in 749 and 367 SNPs that were used in the model building process for rectal bleeding and erectile dysfunction, respectively. On the validation dataset, our random forest regression model achieved the area under the curve (AUC)=0.70 and 0.62 for rectal bleeding and erectile dysfunction, respectively. We performed GO enrichment analysis for the top 25%, 50%, 75%, and 100% SNPs out of the select SNPs in the univariate analysis. When we used the top 50% SNPs, more plausible biological processes were obtained for both toxicities. An additional test with the top 50% SNPs improved predictive power with AUC=0.71 and 0.65 for rectal bleeding and erectile dysfunction. A better performance was achieved with AUC=0.67 when age and androgen deprivation therapy were added to the model for erectile dysfunction. Conclusion: Our approach that combines machine learning and bioinformatics techniques

  3. High-frequency acoustic spectrum analyzer based on polymer integrated optics

    Science.gov (United States)

    Yacoubian, Araz

    This dissertation presents an acoustic spectrum analyzer based on nonlinear polymer-integrated optics. The device is used in a scanning heterodyne geometry by zero biasing a Michelson interferometer. It is capable of detecting vibrations from DC to the GHz range. Initial low frequency experiments show that the device is an effective tool for analyzing an acoustic spectrum even in noisy environments. Three generations of integrated sensors are presented, starting with a very lossy (86 dB total insertion loss) initial device that detects vibrations as low as λ/10, and second and third generation improvements with a final device of 44 dB total insertion loss. The sensor was further tested for detecting a pulsed laser-excited vibration and resonances due to the structure of the sample. The data are compared to the acoustic spectrum measured using a low loss passive fiber interferometer detection scheme which utilizes a high speed detector. The peaks present in the passive detection scheme are clearly visible with our sensor data, which have a lower noise floor. Hybrid integration of GHz electronics is also investigated in this dissertation. A voltage controlled oscillator (VCO) is integrated on a polymer device using a new approach. The VCO is shown to operate as specified by the manufacturer, and the RF signal is efficiently launched onto the micro-strip line used for EO modulation. In the future this technology can be used in conjunction with the presented sensor to produce a fully integrated device containing high frequency drive electronics controlled by low DC voltage. Issues related to device fabrication, loss analysis, RF power delivery to drive circuitry, efficient poling of large area samples, and optimizing poling conditions are also discussed throughout the text.

  4. ANALYZING THE CONSUMER PROFILING FOR IMPROVING EFFORTS OF INTEGRATED MARKETING COMMUNICATION

    Directory of Open Access Journals (Sweden)

    Olimpia OANCEA

    2014-06-01

    Full Text Available In an economy with a strong concurential character, organizations must capitalize the integrated marketing communication in the most effective way, to ensure the creation and maintenance of long-term relationships with current and potential customers. Building and managing the relationships with customers can have a direct and favourable effect on the efficiency of an organization's communication efforts. The integrated marketing communication identifies with the nowadays market dynamics and learns the organizations how easy can be to prosper in an environment where changes occur in an alarming way. Therefore, the purpose of this paper is to analyze the socio-demographic profile of the consumers of bread in Arges County, as well as the preferences and purchasing behaviour at the level of the market segments identified using the K-Means Cluster Analysis method.

  5. Digital pulse-shape analyzer based on fast sampling of an integrated charge pulse

    International Nuclear Information System (INIS)

    Jordanov, V.T.; Knoll, G.F.

    1995-01-01

    A novel configuration for pulse-shape analysis and discrimination has been developed. The current pulse from detector is sent to a gated integrator and then sampled by a flash analog-to-digital converter (ADC). The sampled data are processed digitally, thus allowing implementation of a near-optimum weighting function and elimination some of the instabilities associated with the gated integrator. The analyzer incorporates pileup rejection circuit that reduces the pileup effects at high counting rates. The system was tested liquid scintillator. Figures of merit for neutron-gamma pulse-shape discrimination were found to be: 0.78 for 25 keV (electron equivalent energy) and 3.5 for 500 keV. The technique described in this paper was developed to be used in a near tissue-equivalent neutron-gamma dosimeter which employs a liquid scintillator detector

  6. An integrative conceptual framework for analyzing customer satisfaction with shopping trip experiences in grocery retailing

    DEFF Research Database (Denmark)

    Esbjerg, Lars; Jensen, Birger Boutrup; Bech-Larsen, Tino

    2012-01-01

    Grocery retailers aim to satisfy customers, and because grocery shopping trips are frequently recurring, they must do socontinuously. Surprisingly, little research has addressed satisfaction with individual grocery shopping trips. This article therefore develops a conceptual framework for analyzing...... customer satisfaction with individual grocery shopping trip experiences within a overall ‘disconfirmation of expectations model’ of customer satisfaction. The contribution of the framework is twofold. First, by focusing on satisfaction with individual grocery shopping trips, previous research...... on satisfaction in the retailing literature. Second, the framework synthesizes and integrates multiple central concepts from different research streams into a common framework for analyzing shopping trip satisfaction. Propositions are derived regarding the relationships among the different concepts...

  7. Genome-wide association study (GWAS) for molar-incisor hypomineralization (MIH).

    Science.gov (United States)

    Kühnisch, Jan; Thiering, Elisabeth; Heitmüller, Daniela; Tiesler, Carla M T; Grallert, Harald; Heinrich-Weltzien, Roswitha; Hickel, Reinhard; Heinrich, Joachim

    2014-01-01

    This genome-wide association study (GWAS) investigated the relationship between molar-incisor hypomineralization (MIH) and possible genetic loci. Clinical and genetic data from the 10-year follow-up of 668 children from the Munich GINI-plus and LISA-plus birth cohort studies were analyzed. The dental examinations included the diagnosis of MIH according to the criteria of the European Academy of Paediatric Dentistry (EAPD). Children with MIH were categorized as those with a minimum of one hypomineralized first permanent molar. A GWAS was implemented following a quality-control step and an additive genetic effect was assumed. A total of 2,013,491 single-nucleotide polymorphisms (SNPs) were available for analysis. Rs13058467, which is located near the SCUBE1 gene on chromosome 22 (p MIH when using a threshold of p value MIH.

  8. Effect of sample stratification on dairy GWAS results

    Directory of Open Access Journals (Sweden)

    Ma Li

    2012-10-01

    Full Text Available Abstract Background Artificial insemination and genetic selection are major factors contributing to population stratification in dairy cattle. In this study, we analyzed the effect of sample stratification and the effect of stratification correction on results of a dairy genome-wide association study (GWAS. Three methods for stratification correction were used: the efficient mixed-model association expedited (EMMAX method accounting for correlation among all individuals, a generalized least squares (GLS method based on half-sib intraclass correlation, and a principal component analysis (PCA approach. Results Historical pedigree data revealed that the 1,654 contemporary cows in the GWAS were all related when traced through approximately 10–15 generations of ancestors. Genome and phenotype stratifications had a striking overlap with the half-sib structure. A large elite half-sib family of cows contributed to the detection of favorable alleles that had low frequencies in the general population and high frequencies in the elite cows and contributed to the detection of X chromosome effects. All three methods for stratification correction reduced the number of significant effects. EMMAX method had the most severe reduction in the number of significant effects, and the PCA method using 20 principal components and GLS had similar significance levels. Removal of the elite cows from the analysis without using stratification correction removed many effects that were also removed by the three methods for stratification correction, indicating that stratification correction could have removed some true effects due to the elite cows. SNP effects with good consensus between different methods and effect size distributions from USDA’s Holstein genomic evaluation included the DGAT1-NIBP region of BTA14 for production traits, a SNP 45kb upstream from PIGY on BTA6 and two SNPs in NIBP on BTA14 for protein percentage. However, most of these consensus effects had

  9. ITHNA.SYS: An Integrated Thermal Hydraulic and Neutronic Analyzer SYStem for NUR research reactor

    Energy Technology Data Exchange (ETDEWEB)

    Mazidi, S., E-mail: samirmazidi@gmail.com [Division Physique et Applications Nucléaires, Centre de Recherche Nucléaire de Draria (CRND), BP 43 Sebala, Draria, Alger (Algeria); Meftah, B., E-mail: b_meftah@yahoo.com [Division Physique et Applications Nucléaires, Centre de Recherche Nucléaire de Draria (CRND), BP 43 Sebala, Draria, Alger (Algeria); Belgaid, M., E-mail: belgaidm@yahoo.com [Faculté de Physique, Université Houari Boumediene, USTHB, BP 31, Bab Ezzouar, Alger (Algeria); Letaim, F., E-mail: fletaim@yahoo.fr [Faculté des Sciences et Technologies, Université d’El-oued, PO Box 789, El-oued (Algeria); Halilou, A., E-mail: hal_rane@yahoo.fr [Division Réacteur NUR, Centre de Recherche Nucléaire de Draria, BP 43 Sebala, Draria, Alger (Algeria)

    2015-08-15

    Highlights: • We develop a neutronic and thermal hydraulic MTR reactor analyzer. • The analyzer allows a rapid determination of the reactor core parameters. • Some NUR reactor parameters have been analyzed. - Abstract: This paper introduces the Integrated Thermal Hydraulic and Neutronic Analyzer SYStem (ITHNA.SYS) that has been developed for the Algerian research reactor NUR. It is used both as an operating aid tool and as a core physics engineering analysis tool. The system embeds three modules of the MTR-PC software package developed by INVAP SE: the cell calculation code WIMSD, the core calculation code CITVAP and the program TERMIC for thermal hydraulic analysis of a material testing reactor (MTR) core in forced convection. ITHNA.SYS operates both in on-line and off-line modes. In the on-line mode, the system is linked, via the computer parallel port, to the data acquisition console of the reactor control room and allows a real time monitoring of major physical and safety parameters of the NUR core. PC-based ITHNA.SYS provides a viable and convenient way of using an accumulated and often complex reactor physics stock of knowledge and frees the user from the intricacy of adequate reactor core modeling. This guaranties an accurate, though rapid, determination of a variety of neutronic and thermal hydraulic parameters of importance for the operation and safety analysis of the NUR research reactor. Instead of the several hours usually required, the processing time for the determination of such parameters is now reduced to few seconds. Validation of the system was performed with respect to experimental measurements and to calculations using reference codes. ITHNA.SYS can be easily adapted to accommodate other kinds of MTR reactors.

  10. GWAS meta-analysis and replication identifies three new susceptibility loci for ovarian cancer

    Science.gov (United States)

    Pharoah, Paul D. P.; Tsai, Ya-Yu; Ramus, Susan J.; Phelan, Catherine M.; Goode, Ellen L.; Lawrenson, Kate; Price, Melissa; Fridley, Brooke L.; Tyrer, Jonathan P.; Shen, Howard; Weber, Rachel; Karevan, Rod; Larson, Melissa C.; Song, Honglin; Tessier, Daniel C.; Bacot, François; Vincent, Daniel; Cunningham, Julie M.; Dennis, Joe; Dicks, Ed; Aben, Katja K.; Anton-Culver, Hoda; Antonenkova, Natalia; Armasu, Sebastian M.; Baglietto, Laura; Bandera, Elisa V.; Beckmann, Matthias W.; Birrer, Michael J.; Bloom, Greg; Bogdanova, Natalia; Brenton, James D.; Brinton, Louise A.; Brooks-Wilson, Angela; Brown, Robert; Butzow, Ralf; Campbell, Ian; Carney, Michael E; Carvalho, Renato S.; Chang-Claude, Jenny; Chen, Y. Anne; Chen, Zhihua; Chow, Wong-Ho; Cicek, Mine S.; Coetzee, Gerhard; Cook, Linda S.; Cramer, Daniel W.; Cybulski, Cezary; Dansonka-Mieszkowska, Agnieszka; Despierre, Evelyn; Doherty, Jennifer A; Dörk, Thilo; du Bois, Andreas; Dürst, Matthias; Eccles, Diana; Edwards, Robert; Ekici, Arif B.; Fasching, Peter A.; Fenstermacher, David; Flanagan, James; Gao, Yu-Tang; Garcia-Closas, Montserrat; Gentry-Maharaj, Aleksandra; Giles, Graham; Gjyshi, Anxhela; Gore, Martin; Gronwald, Jacek; Guo, Qi; Halle, Mari K; Harter, Philipp; Hein, Alexander; Heitz, Florian; Hillemanns, Peter; Hoatlin, Maureen; Høgdall, Estrid; Høgdall, Claus K.; Hosono, Satoyo; Jakubowska, Anna; Jensen, Allan; Kalli, Kimberly R.; Karlan, Beth Y.; Kelemen, Linda E.; Kiemeney, Lambertus A.; Kjaer, Susanne Krüger; Konecny, Gottfried E.; Krakstad, Camilla; Kupryjanczyk, Jolanta; Lambrechts, Diether; Lambrechts, Sandrina; Le, Nhu D.; Lee, Nathan; Lee, Janet; Leminen, Arto; Lim, Boon Kiong; Lissowska, Jolanta; Lubiński, Jan; Lundvall, Lene; Lurie, Galina; Massuger, Leon F.A.G.; Matsuo, Keitaro; McGuire, Valerie; McLaughlin, John R; Menon, Usha; Modugno, Francesmary; Moysich, Kirsten B.; Nakanishi, Toru; Narod, Steven A.; Ness, Roberta B.; Nevanlinna, Heli; Nickels, Stefan; Noushmehr, Houtan; Odunsi, Kunle; Olson, Sara; Orlow, Irene; Paul, James; Pejovic, Tanja; Pelttari, Liisa M; Permuth-Wey, Jenny; Pike, Malcolm C; Poole, Elizabeth M; Qu, Xiaotao; Risch, Harvey A.; Rodriguez-Rodriguez, Lorna; Rossing, Mary Anne; Rudolph, Anja; Runnebaum, Ingo; Rzepecka, Iwona K; Salvesen, Helga B.; Schwaab, Ira; Severi, Gianluca; Shen, Hui; Shridhar, Vijayalakshmi; Shu, Xiao-Ou; Sieh, Weiva; Southey, Melissa C.; Spellman, Paul; Tajima, Kazuo; Teo, Soo-Hwang; Terry, Kathryn L.; Thompson, Pamela J; Timorek, Agnieszka; Tworoger, Shelley S.; van Altena, Anne M.; Berg, David Van Den; Vergote, Ignace; Vierkant, Robert A.; Vitonis, Allison F.; Wang-Gohrke, Shan; Wentzensen, Nicolas; Whittemore, Alice S.; Wik, Elisabeth; Winterhoff, Boris; Woo, Yin Ling; Wu, Anna H; Yang, Hannah P.; Zheng, Wei; Ziogas, Argyrios; Zulkifli, Famida; Goodman, Marc T.; Hall, Per; Easton, Douglas F; Pearce, Celeste L; Berchuck, Andrew; Chenevix-Trench, Georgia; Iversen, Edwin; Monteiro, Alvaro N.A.; Gayther, Simon A.; Schildkraut, Joellen M.; Sellers, Thomas A.

    2013-01-01

    Genome wide association studies (GWAS) have identified four susceptibility loci for epithelial ovarian cancer (EOC) with another two loci being close to genome-wide significance. We pooled data from a GWAS conducted in North America with another GWAS from the United Kingdom. We selected the top 24,551 SNPs for inclusion on the iCOGS custom genotyping array. Follow-up genotyping was carried out in 18,174 cases and 26,134 controls from 43 studies from the Ovarian Cancer Association Consortium. We validated the two loci at 3q25 and 17q21 previously near genome-wide significance and identified three novel loci associated with risk; two loci associated with all EOC subtypes, at 8q21 (rs11782652, P=5.5×10-9) and 10p12 (rs1243180; P=1.8×10-8), and another locus specific to the serous subtype at 17q12 (rs757210; P=8.1×10-10). An integrated molecular analysis of genes and regulatory regions at these loci provided evidence for functional mechanisms underlying susceptibility that implicates CHMP4C in the pathogenesis of ovarian cancer. PMID:23535730

  11. Time-domain single-source integral equations for analyzing scattering from homogeneous penetrable objects

    KAUST Repository

    Valdés, Felipe

    2013-03-01

    Single-source time-domain electric-and magnetic-field integral equations for analyzing scattering from homogeneous penetrable objects are presented. Their temporal discretization is effected by using shifted piecewise polynomial temporal basis functions and a collocation testing procedure, thus allowing for a marching-on-in-time (MOT) solution scheme. Unlike dual-source formulations, single-source equations involve space-time domain operator products, for which spatial discretization techniques developed for standalone operators do not apply. Here, the spatial discretization of the single-source time-domain integral equations is achieved by using the high-order divergence-conforming basis functions developed by Graglia alongside the high-order divergence-and quasi curl-conforming (DQCC) basis functions of Valdés The combination of these two sets allows for a well-conditioned mapping from div-to curl-conforming function spaces that fully respects the space-mapping properties of the space-time operators involved. Numerical results corroborate the fact that the proposed procedure guarantees accuracy and stability of the MOT scheme. © 2012 IEEE.

  12. Ion-beam apparatus and method for analyzing and controlling integrated circuits

    Science.gov (United States)

    Campbell, Ann N.; Soden, Jerry M.

    1998-01-01

    An ion-beam apparatus and method for analyzing and controlling integrated circuits. The ion-beam apparatus comprises a stage for holding one or more integrated circuits (ICs); a source means for producing a focused ion beam; and a beam-directing means for directing the focused ion beam to irradiate a predetermined portion of the IC for sufficient time to provide an ion-beam-generated electrical input signal to a predetermined element of the IC. The apparatus and method have applications to failure analysis and developmental analysis of ICs and permit an alteration, control, or programming of logic states or device parameters within the IC either separate from or in combination with applied electrical stimulus to the IC for analysis thereof. Preferred embodiments of the present invention including a secondary particle detector and an electron floodgun further permit imaging of the IC by secondary ions or electrons, and allow at least a partial removal or erasure of the ion-beam-generated electrical input signal.

  13. Education and leisure: analyzing the Integrated School Program in Belo Horizonte

    Directory of Open Access Journals (Sweden)

    Marcília de Sousa Silva

    2015-01-01

    Full Text Available This article aims to analyze the concepts of leisure and education that permeate the documents in the Integrated School Program in Belo Horizonte. The analysis was based on the Policy cycle approach and emphasized the contexts of influence and the policy text production. Thus, the formation of the political agenda, the Political Pedagogical Project Program and the Strategic Plan 2010-2030 BH were investigated. The policy context is not organized in a linear fashion; it is a process of groups of interest interaction. With the discourse of coping with school failure, revealed by the students’ yield and flow evaluation indices (approval, repetition and dropout, the Integrated School education documents announce education and leisure as forms of production, strengthening links between public and private. The right to education is restricted to children’s and youth’s access and permanence in school without creating a perspective of universalization and quality. The documents address the leisure with a simplistic view of construction and maintenance of equipment and the idea of activity

  14. Improved Use of Small Reference Panels for Conditional and Joint Analysis with GWAS Summary Statistics.

    Science.gov (United States)

    Deng, Yangqing; Pan, Wei

    2018-06-01

    Due to issues of practicality and confidentiality of genomic data sharing on a large scale, typically only meta- or mega-analyzed genome-wide association study (GWAS) summary data, not individual-level data, are publicly available. Reanalyses of such GWAS summary data for a wide range of applications have become more and more common and useful, which often require the use of an external reference panel with individual-level genotypic data to infer linkage disequilibrium (LD) among genetic variants. However, with a small sample size in only hundreds, as for the most popular 1000 Genomes Project European sample, estimation errors for LD are not negligible, leading to often dramatically increased numbers of false positives in subsequent analyses of GWAS summary data. To alleviate the problem in the context of association testing for a group of SNPs, we propose an alternative estimator of the covariance matrix with an idea similar to multiple imputation. We use numerical examples based on both simulated and real data to demonstrate the severe problem with the use of the 1000 Genomes Project reference panels, and the improved performance of our new approach. Copyright © 2018 by the Genetics Society of America.

  15. Simulation Tools and Techniques for Analyzing the Impacts of Photovoltaic System Integration

    Science.gov (United States)

    Hariri, Ali

    Solar photovoltaic (PV) energy integration in distribution networks is one of the fastest growing sectors of distributed energy integration. The growth in solar PV integration is incentivized by various clean power policies, global interest in solar energy, and reduction in manufacturing and installation costs of solar energy systems. The increase in solar PV integration has raised a number of concerns regarding the potential impacts that might arise as a result of high PV penetration. Some impacts have already been recorded in networks with high PV penetration such as in China, Germany, and USA (Hawaii and California). Therefore, network planning is becoming more intricate as new technologies are integrated into the existing electric grid. The integrated new technologies pose certain compatibility concerns regarding the existing electric grid infrastructure. Therefore, PV integration impact studies are becoming more essential in order to have a better understanding of how to advance the solar PV integration efforts without introducing adverse impacts into the network. PV impact studies are important for understanding the nature of the new introduced phenomena. Understanding the nature of the potential impacts is a key factor for mitigating and accommodating for said impacts. Traditionally, electric power utilities relied on phasor-based power flow simulations for planning their electric networks. However, the conventional, commercially available, phasor-based simulation tools do not provide proper visibility across a wide spectrum of electric phenomena. Moreover, different types of simulation approaches are suitable for specific types of studies. For instance, power flow software cannot be used for studying time varying phenomena. At the same time, it is not practical to use electromagnetic transient (EMT) tools to perform power flow solutions. Therefore, some electric phenomena caused by the variability of PV generation are not visible using the conventional

  16. Analyzing the concept of disruptive behavior in healthcare work: an integrative review*

    Directory of Open Access Journals (Sweden)

    Roberta Meneses Oliveira

    Full Text Available Abstract OBJECTIVE To analyze the concept of disruptive behavior in healthcare work. METHOD An integrative review carried out in the theoretical phase of a qualitative research substantiated by the theoretical framework of the Hybrid Model of Concept Development. The search for articles was conducted in the CINAHL, LILACS, PsycINFO, PubMed and SciVerse Scopus databases in 2013. RESULTS 70 scientific articles answered the guiding question and lead to attributes of disruptive behavior, being: incivility, psychological violence and physical/sexual violence; with their main antecedents (intrapersonal, interpersonal and organizational being: personality characteristics, stress and work overload; and consequences of: workers' moral/mental distress, compromised patient safety, labor loss, and disruption of communication, collaboration and teamwork. CONCLUSION Analysis of the disruptive behavior concept in healthcare work showed a construct in its theoretical stage that encompasses different disrespectful conduct adopted by health workers in the hospital context, which deserve the attention of leadership for better recognition and proper handling of cases and their consequences.

  17. A calderón-preconditioned single source combined field integral equation for analyzing scattering from homogeneous penetrable objects

    KAUST Repository

    Valdé s, Felipe; Andriulli, Francesco P.; Bagci, Hakan; Michielssen, Eric

    2011-01-01

    A new regularized single source equation for analyzing scattering from homogeneous penetrable objects is presented. The proposed equation is a linear combination of a Calderón-preconditioned single source electric field integral equation and a

  18. Transethnic differences in GWAS signals: A simulation study.

    Science.gov (United States)

    Zanetti, Daniela; Weale, Michael E

    2018-05-07

    Genome-wide association studies (GWASs) have allowed researchers to identify thousands of single nucleotide polymorphisms (SNPs) and other variants associated with particular complex traits. Previous studies have reported differences in the strength and even the direction of GWAS signals across different populations. These differences could be due to a combination of (1) lack of power, (2) allele frequency differences, (3) linkage disequilibrium (LD) differences, and (4) true differences in causal variant effect sizes. To determine whether properties (1)-(3) on their own might be sufficient to explain the patterns previously noted in strong GWAS signals, we simulated case-control data of European, Asian and African ancestry, applying realistic allele frequencies and LD from 1000 Genomes data but enforcing equal causal effect sizes across populations. Much of the observed differences in strong GWAS signals could indeed be accounted for by allele frequency and LD differences, enhanced by the Euro-centric SNP bias and lower SNP coverage found in older GWAS panels. While we cannot rule out a role for true transethnic effect size differences, our results suggest that strong causal effects may be largely shared among human populations, motivating the use of transethnic data for fine-mapping. © 2018 John Wiley & Sons Ltd/University College London.

  19. GWAS as a Driver of Gene Discovery in Cardiometabolic Diseases

    NARCIS (Netherlands)

    Atanasovska, Biljana; Kumar, Vinod; Fu, Jingyuan; Wijmenga, Cisca; Hofker, Marten H.

    2015-01-01

    Cardiometabolic diseases represent a common complex disorder with a strong genetic component. Currently, genome-wide association studies (GWAS) have yielded some 755 single-nucleotide polymorphisms (SNPs) encompassing 366 independent loci that may help to decipher the molecular basis of

  20. Genome-wide association studies (GWAS) of adiposity

    DEFF Research Database (Denmark)

    Oskari Kilpeläinen, Tuomas; Ingelsson, Erik

    2016-01-01

    Adiposity is strongly heritable and one of the leading risk factors for type 2 diabetes, cardiovascular disease, cancer, and premature death. In the past 8 years, genome-wide association studies (GWAS) have greatly increased our understanding of the genes and biological pathways that regulate...

  1. Metrics for Analyzing Quantifiable Differentiation of Designs with Varying Integrity for Hardware Assurance

    Science.gov (United States)

    2017-03-01

    Keywords — Trojan; integrity; trust; quantify; hardware; assurance; verification; metrics ; reference, quality ; profile I. INTRODUCTION A. The Rising...as a framework for benchmarking Trusted Part certifications. Previous work conducted in Trust Metric development has focused on measures at the...the lowest integrities. Based on the analysis, the DI metric shows measurable differentiation between all five Test Article Error Location Error

  2. GWAS meta-analysis and replication identifies three new susceptibility loci for ovarian cancer

    DEFF Research Database (Denmark)

    Pharoah, Paul D P; Tsai, Ya-Yu; Ramus, Susan J

    2013-01-01

    Genome-wide association studies (GWAS) have identified four susceptibility loci for epithelial ovarian cancer (EOC), with another two suggestive loci reaching near genome-wide significance. We pooled data from a GWAS conducted in North America with another GWAS from the UK. We selected the top 24...

  3. SECAD-- a Schema-based Environment for Configuring, Analyzing and Documenting Integrated Fusion Simulations. Final report

    International Nuclear Information System (INIS)

    Shasharina, Svetlana

    2012-01-01

    SECAD is a project that developed a GUI for running integrated fusion simulations as implemented in FACETS and SWIM SciDAC projects. Using the GUI users can submit simulations locally and remotely and visualize the simulation results

  4. An integrated simulation tool for analyzing the Operation and Interdependency of Natural Gas and Electric Power Systems

    OpenAIRE

    PAMBOUR Kwabena A.; CAKIR BURCIN; BOLADO LAVIN Ricardo; DIJKEMA Gerard

    2016-01-01

    In this paper, we present an integrated simulation tool for analyzing the interdependency of natural gas and electric power systems in terms of security of energy supply. In the first part, we develop mathematical models for the individual systems. In part two, we identify the interconnections between both systems and propose a method for coupling the combined simulation model. Next, we develop the algorithm for solving the combined system and integrate this algorithm into a simulation softwa...

  5. ELISA-BASE: an integrated bioinformatics tool for analyzing and tracking ELISA microarray data

    OpenAIRE

    White, Amanda M.; Collett, James R.; Seurynck-Servoss, Shannon L.; Daly, Don S.; Zangar, Richard C.

    2009-01-01

    Summary:ELISA-BASE is an open source database for capturing, organizing and analyzing enzyme-linked immunosorbent assay (ELISA) microarray data. ELISA-BASE is an extension of the BioArray Software Environment (BASE) database system.

  6. The Integrated Approach versus the Traditional Approach: Analyzing the Benefits of a Dance and Transportation Integrated Curriculum

    Science.gov (United States)

    LaMotte, Megan

    2018-01-01

    The purpose of the study was to examine the effects of a dance and transportation integrated curriculum on student learning and engagement. The curriculum, entitled Consequences of Our Actions: Dance and Transportation, synthesized transportation content with the art form of dance. The experimental and control groups were comprised of fifth-grade…

  7. Heritability and GWAS Analyses of Acne in Australian Adolescent Twins.

    Science.gov (United States)

    Mina-Vargas, Angela; Colodro-Conde, Lucía; Grasby, Katrina; Zhu, Gu; Gordon, Scott; Medland, Sarah E; Martin, Nicholas G

    2017-12-01

    Acne vulgaris is a skin disease with a multifactorial and complex pathology. While several twin studies have estimated that acne has a heritability of up to 80%, the genomic elements responsible for the origin and pathology of acne are still undiscovered. Here we performed a twin-based structural equation model, using available data on acne severity for an Australian sample of 4,491 twins and their siblings aged from 10 to 24. This study extends by a factor of 3 an earlier analysis of the genetic factors of acne. Acne severity was rated by nurses on a 4-point scale (1 = absent to 4 = severe) on up to three body sites (face, back, chest) and on up to three occasions (age 12, 14, and 16). The phenotype that we analyzed was the most severe rating at any site or age. The polychoric correlation for monozygotic twins was higher (r MZ = 0.86, 95% CI [0.81, 0.90]) than for dizygotic twins (r DZ = 0.42, 95% CI [0.35, 0.47]). A model that includes additive genetic effects and unique environmental effects was the most parsimonious model to explain the genetic variance of acne severity, and the estimated heritability was 0.85 (95% CI [0.82, 0.87]). We then conducted a genome-wide analysis including an additional 271 siblings - for a total of 4,762 individuals. A genome-wide association study (GWAS) scan did not detect loci associated with the severity of acne at the threshold of 5E-08 but suggestive association was found for three SNPs: rs10515088 locus 5q13.1 (p = 3.9E-07), rs12738078 locus 1p35.5 (p = 6.7E-07), and rs117943429 locus 18q21.2 (p = 9.1E-07). The 5q13.1 locus is close to PIK3R1, a gene that has a potential regulatory effect on sebocyte differentiation.

  8. Analyzing and completing middleware designs for enterprise integration using coloured Petri nets

    NARCIS (Netherlands)

    Fahland, D.; Gierds, C.; Salinesi, C.; Norrie, M.C.; Pastor, O.

    2013-01-01

    Enterprise Integration Patterns allow us to design a middleware system conceptually before actually implementing it. So far, the in-depth analysis of such a design was not feasible, as these patterns are only described informally. We introduce a translation of each of these patterns into a Coloured

  9. Integrating and Analyzing Psychosocial and Stage Theories To Challenge the Development of the Injured Collegiate Athlete.

    Science.gov (United States)

    Harris, Laura L.

    2003-01-01

    Integrated a psychosocial developmental theory (the Kubler-Ross Stage Theory) and a psychological stage theory (the Ross Stage Theory) and a psychological stage theory (the Chickering and Reisser psychosocial and developmental theory) for challenging injured collegiate student-athletes' personal development. A search of online databases from…

  10. Analyzing the non-smooth dynamics induced by a split-path nonlinear integral controller

    NARCIS (Netherlands)

    Hunnekens, B.G.B.; van Loon, S.J.L.M.; van de Wouw, N.; Heemels, W.P.M.H.; Nijmeijer, H.; Ecker, Horst; Steindl, Alois; Jakubek, Stefan

    2014-01-01

    In this paper, we introduce a novel non-smooth integral controller, which aims at achieving a better transient response in terms of overshoot of a feedback controlled dynamical system. The resulting closed-loop system can be represented as a non-smooth system with different continuous dynamics being

  11. Unsupervised text mining for assessing and augmenting GWAS results.

    Science.gov (United States)

    Ailem, Melissa; Role, François; Nadif, Mohamed; Demenais, Florence

    2016-04-01

    Text mining can assist in the analysis and interpretation of large-scale biomedical data, helping biologists to quickly and cheaply gain confirmation of hypothesized relationships between biological entities. We set this question in the context of genome-wide association studies (GWAS), an actively emerging field that contributed to identify many genes associated with multifactorial diseases. These studies allow to identify groups of genes associated with the same phenotype, but provide no information about the relationships between these genes. Therefore, our objective is to leverage unsupervised text mining techniques using text-based cosine similarity comparisons and clustering applied to candidate and random gene vectors, in order to augment the GWAS results. We propose a generic framework which we used to characterize the relationships between 10 genes reported associated with asthma by a previous GWAS. The results of this experiment showed that the similarities between these 10 genes were significantly stronger than would be expected by chance (one-sided p-value<0.01). The clustering of observed and randomly selected gene also allowed to generate hypotheses about potential functional relationships between these genes and thus contributed to the discovery of new candidate genes for asthma. Copyright © 2016 Elsevier Inc. All rights reserved.

  12. Analyzing Unsaturated Flow Patterns in Fractured Rock Using an Integrated Modeling Approach

    International Nuclear Information System (INIS)

    Y.S. Wu; G. Lu; K. Zhang; L. Pan; G.S. Bodvarsson

    2006-01-01

    Characterizing percolation patterns in unsaturated fractured rock has posed a greater challenge to modeling investigations than comparable saturated zone studies, because of the heterogeneous nature of unsaturated media and the great number of variables impacting unsaturated flow. This paper presents an integrated modeling methodology for quantitatively characterizing percolation patterns in the unsaturated zone of Yucca Mountain, Nevada, a proposed underground repository site for storing high-level radioactive waste. The modeling approach integrates a wide variety of moisture, pneumatic, thermal, and isotopic geochemical field data into a comprehensive three-dimensional numerical model for modeling analyses. It takes into account the coupled processes of fluid and heat flow and chemical isotopic transport in Yucca Mountain's highly heterogeneous, unsaturated fractured tuffs. Modeling results are examined against different types of field-measured data and then used to evaluate different hydrogeological conceptualizations and their results of flow patterns in the unsaturated zone. In particular, this model provides a much clearer understanding of percolation patterns and flow behavior through the unsaturated zone, both crucial issues in assessing repository performance. The integrated approach for quantifying Yucca Mountain's flow system is demonstrated to provide a practical modeling tool for characterizing flow and transport processes in complex subsurface systems

  13. An integrated graphic–taxonomic–associative approach to analyze human factors in aviation accidents

    Directory of Open Access Journals (Sweden)

    Gong Lei

    2014-04-01

    Full Text Available Human factors are critical causes of modern aviation accidents. However, existing accident analysis methods encounter limitations in addressing aviation human factors, especially in complex accident scenarios. The existing graphic approaches are effective for describing accident mechanisms within various categories of human factors, but cannot simultaneously describe inadequate human–aircraft–environment interactions and organizational deficiencies effectively, and highly depend on analysts’ skills and experiences. Moreover, the existing methods do not emphasize latent unsafe factors outside accidents. This paper focuses on the above three limitations and proposes an integrated graphic–taxonomic–associative approach. A new graphic model named accident tree (AcciTree, with a two-mode structure and a reaction-based concept, is developed for accident modeling and safety defense identification. The AcciTree model is then integrated with the well-established human factors analysis and classification system (HFACS to enhance both reliability of the graphic part and logicality of the taxonomic part for improving completeness of analysis. An associative hazard analysis technique is further put forward to extend analysis to factors outside accidents, to form extended safety requirements for proactive accident prevention. Two crash examples, a research flight demonstrator by our team and an industrial unmanned aircraft, illustrate that the integrated approach is effective for identifying more unsafe factors and safety requirements.

  14. TypingSuite: Integrated Software for Presenting Stimuli, and Collecting and Analyzing Typing Data

    Science.gov (United States)

    Mazerolle, Erin L.; Marchand, Yannick

    2015-01-01

    Research into typing patterns has broad applications in both psycholinguistics and biometrics (i.e., improving security of computer access via each user's unique typing patterns). We present a new software package, TypingSuite, which can be used for presenting visual and auditory stimuli, collecting typing data, and summarizing and analyzing the…

  15. Interaction debugging : an integral approach to analyze human-robot interaction

    NARCIS (Netherlands)

    Kooijmans, T.; Kanda, T.; Bartneck, C.; Ishiguro, H.; Hagita, N.

    2006-01-01

    Along with the development of interactive robots, controlled experiments and field trials are regularly conducted to stage human-robot interaction. Experience in this field has shown that analyzing human-robot interaction for evaluation purposes fosters the development of improved systems and the

  16. A new approach to analyze strategy map using an integrated BSC and FUZZY DEMATEL

    Directory of Open Access Journals (Sweden)

    Seyed Abdollah Heydariyeh

    2012-01-01

    Full Text Available Today, with ever-increasing competition in global economic conditions, the necessity of effective implementation of strategy map has become an inevitable and necessary. The strategy map represents a general and structured framework for strategic objectives and plays an important role in forming competitive advantages for organizations. It is important to find important factors influencing strategy map and prioritize them based on suitable factors. In this paper, we propose an integration of BSC and Fuzzy DEMATEL technique to rank different items influencing strategy of a production plan. The proposed technique is implemented for real-world case study of glass production.

  17. Integrating and analyzing medical and environmental data using ETL and Business Intelligence tools

    Science.gov (United States)

    Villar, Alejandro; Zarrabeitia, María T.; Fdez-Arroyabe, Pablo; Santurtún, Ana

    2018-06-01

    Processing data that originates from different sources (such as environmental and medical data) can prove to be a difficult task, due to the heterogeneity of variables, storage systems, and file formats that can be used. Moreover, once the amount of data reaches a certain threshold, conventional mining methods (based on spreadsheets or statistical software) become cumbersome or even impossible to apply. Data Extract, Transform, and Load (ETL) solutions provide a framework to normalize and integrate heterogeneous data into a local data store. Additionally, the application of Online Analytical Processing (OLAP), a set of Business Intelligence (BI) methodologies and practices for multidimensional data analysis, can be an invaluable tool for its examination and mining. In this article, we describe a solution based on an ETL + OLAP tandem used for the on-the-fly analysis of tens of millions of individual medical, meteorological, and air quality observations from 16 provinces in Spain provided by 20 different national and regional entities in a diverse array for file types and formats, with the intention of evaluating the effect of several environmental variables on human health in future studies. Our work shows how a sizable amount of data, spread across a wide range of file formats and structures, and originating from a number of different sources belonging to various business domains, can be integrated in a single system that researchers can use for global data analysis and mining.

  18. Integrating and analyzing medical and environmental data using ETL and Business Intelligence tools.

    Science.gov (United States)

    Villar, Alejandro; Zarrabeitia, María T; Fdez-Arroyabe, Pablo; Santurtún, Ana

    2018-03-07

    Processing data that originates from different sources (such as environmental and medical data) can prove to be a difficult task, due to the heterogeneity of variables, storage systems, and file formats that can be used. Moreover, once the amount of data reaches a certain threshold, conventional mining methods (based on spreadsheets or statistical software) become cumbersome or even impossible to apply. Data Extract, Transform, and Load (ETL) solutions provide a framework to normalize and integrate heterogeneous data into a local data store. Additionally, the application of Online Analytical Processing (OLAP), a set of Business Intelligence (BI) methodologies and practices for multidimensional data analysis, can be an invaluable tool for its examination and mining. In this article, we describe a solution based on an ETL + OLAP tandem used for the on-the-fly analysis of tens of millions of individual medical, meteorological, and air quality observations from 16 provinces in Spain provided by 20 different national and regional entities in a diverse array for file types and formats, with the intention of evaluating the effect of several environmental variables on human health in future studies. Our work shows how a sizable amount of data, spread across a wide range of file formats and structures, and originating from a number of different sources belonging to various business domains, can be integrated in a single system that researchers can use for global data analysis and mining.

  19. Integrating and analyzing medical and environmental data using ETL and Business Intelligence tools

    Science.gov (United States)

    Villar, Alejandro; Zarrabeitia, María T.; Fdez-Arroyabe, Pablo; Santurtún, Ana

    2018-03-01

    Processing data that originates from different sources (such as environmental and medical data) can prove to be a difficult task, due to the heterogeneity of variables, storage systems, and file formats that can be used. Moreover, once the amount of data reaches a certain threshold, conventional mining methods (based on spreadsheets or statistical software) become cumbersome or even impossible to apply. Data Extract, Transform, and Load (ETL) solutions provide a framework to normalize and integrate heterogeneous data into a local data store. Additionally, the application of Online Analytical Processing (OLAP), a set of Business Intelligence (BI) methodologies and practices for multidimensional data analysis, can be an invaluable tool for its examination and mining. In this article, we describe a solution based on an ETL + OLAP tandem used for the on-the-fly analysis of tens of millions of individual medical, meteorological, and air quality observations from 16 provinces in Spain provided by 20 different national and regional entities in a diverse array for file types and formats, with the intention of evaluating the effect of several environmental variables on human health in future studies. Our work shows how a sizable amount of data, spread across a wide range of file formats and structures, and originating from a number of different sources belonging to various business domains, can be integrated in a single system that researchers can use for global data analysis and mining.

  20. Comment on 'Large-Scale Cognitive GWAS Meta-Analysis Reveals Tissue-Specific Neural Expression and Potential Nootropic Drug Targets' by Lam et al.

    Science.gov (United States)

    Hill, W David

    2018-04-01

    Intelligence and educational attainment are strongly genetically correlated. This relationship can be exploited by Multi-Trait Analysis of GWAS (MTAG) to add power to Genome-wide Association Studies (GWAS) of intelligence. MTAG allows the user to meta-analyze GWASs of different phenotypes, based on their genetic correlations, to identify association's specific to the trait of choice. An MTAG analysis using GWAS data sets on intelligence and education was conducted by Lam et al. (2017). Lam et al. (2017) reported 70 loci that they described as 'trait specific' to intelligence. This article examines whether the analysis conducted by Lam et al. (2017) has resulted in genetic information about a phenotype that is more similar to education than intelligence.

  1. A discontinuous galerkin time domain-boundary integral method for analyzing transient electromagnetic scattering

    KAUST Repository

    Li, Ping

    2014-07-01

    This paper presents an algorithm hybridizing discontinuous Galerkin time domain (DGTD) method and time domain boundary integral (BI) algorithm for 3-D open region electromagnetic scattering analysis. The computational domain of DGTD is rigorously truncated by analytically evaluating the incoming numerical flux from the outside of the truncation boundary through BI method based on the Huygens\\' principle. The advantages of the proposed method are that it allows the truncation boundary to be conformal to arbitrary (convex/ concave) scattering objects, well-separated scatters can be truncated by their local meshes without losing the physics (such as coupling/multiple scattering) of the problem, thus reducing the total mesh elements. Furthermore, low frequency waves can be efficiently absorbed, and the field outside the truncation domain can be conveniently calculated using the same BI formulation. Numerical examples are benchmarked to demonstrate the accuracy and versatility of the proposed method.

  2. Waste Management: An integrated modeling approach for analyzing change in NWC production processes

    International Nuclear Information System (INIS)

    Christensen, D.C.; Sohn, C.L.; Helm, T.M.; Farish, T.J.; Reid, R.A.

    1991-01-01

    A problem-driven, integrated modeling, decision-support framework has been conceptualized to aid a team of experts determine the set of evolving technologies that should receive additional developmental support. This conceptual framework utilizes a variety of decision aiding models including Flowsheeting, Analytical Hierarchy Process, Linear and Goal Programming, and Object-Oriented Discrete Event Simulation. A number of the technologies under consideration are strong candidates to overcome current plutonium processing problems so that effective technology will be available for implementation in Complex 21. Complex 21 is a participatory, inter-installation planning effort sponsored by US DOE to consolidate and revitalize the nuclear weapons complex facilities by the 21st century. A computer-based dynamic simulation model has been constructed that will allow testing of alternative combinations of developing technologies. The modeling of new configurations of technologies under a number of different operating conditions and material flow assumptions provides information needed for effective decision making for Complex 21. 4 figs

  3. IMPACT_S: integrated multiprogram platform to analyze and combine tests of selection.

    Directory of Open Access Journals (Sweden)

    Emanuel Maldonado

    Full Text Available Among the major goals of research in evolutionary biology are the identification of genes targeted by natural selection and understanding how various regimes of evolution affect the fitness of an organism. In particular, adaptive evolution enables organisms to adapt to changing ecological factors such as diet, temperature, habitat, predatory pressures and prey abundance. An integrative approach is crucial for the identification of non-synonymous mutations that introduce radical changes in protein biochemistry and thus in turn influence the structure and function of proteins. Performing such analyses manually is often a time-consuming process, due to the large number of statistical files generated from multiple approaches, especially when assessing numerous taxa and/or large datasets. We present IMPACT_S, an easy-to-use Graphical User Interface (GUI software, which rapidly and effectively integrates, filters and combines results from three widely used programs for assessing the influence of selection: Codeml (PAML package, Datamonkey and TreeSAAP. It enables the identification and tabulation of sites detected by these programs as evolving under the influence of positive, neutral and/or negative selection in protein-coding genes. IMPACT_S further facilitates the automatic mapping of these sites onto the three-dimensional structures of proteins. Other useful tools incorporated in IMPACT_S include Jmol, Archaeopteryx, Gnuplot, PhyML, a built-in Swiss-Model interface and a PDB downloader. The relevance and functionality of IMPACT_S is shown through a case study on the toxicoferan-reptilian Cysteine-rich Secretory Proteins (CRiSPs. IMPACT_S is a platform-independent software released under GPLv3 license, freely available online from http://impact-s.sourceforge.net.

  4. An integrated strategy for analyzing the unique developmental programs of different myoblast subtypes.

    Directory of Open Access Journals (Sweden)

    2006-02-01

    Full Text Available An important but largely unmet challenge in understanding the mechanisms that govern the formation of specific organs is to decipher the complex and dynamic genetic programs exhibited by the diversity of cell types within the tissue of interest. Here, we use an integrated genetic, genomic, and computational strategy to comprehensively determine the molecular identities of distinct myoblast subpopulations within the Drosophila embryonic mesoderm at the time that cell fates are initially specified. A compendium of gene expression profiles was generated for primary mesodermal cells purified by flow cytometry from appropriately staged wild-type embryos and from 12 genotypes in which myogenesis was selectively and predictably perturbed. A statistical meta-analysis of these pooled datasets--based on expected trends in gene expression and on the relative contribution of each genotype to the detection of known muscle genes--provisionally assigned hundreds of differentially expressed genes to particular myoblast subtypes. Whole embryo in situ hybridizations were then used to validate the majority of these predictions, thereby enabling true-positive detection rates to be estimated for the microarray data. This combined analysis reveals that myoblasts exhibit much greater gene expression heterogeneity and overall complexity than was previously appreciated. Moreover, it implicates the involvement of large numbers of uncharacterized, differentially expressed genes in myogenic specification and subsequent morphogenesis. These findings also underscore a requirement for considerable regulatory specificity for generating diverse myoblast identities. Finally, to illustrate how the developmental functions of newly identified myoblast genes can be efficiently surveyed, a rapid RNA interference assay that can be scored in living embryos was developed and applied to selected genes. This integrated strategy for examining embryonic gene expression and function provides

  5. IMPACT_S: integrated multiprogram platform to analyze and combine tests of selection.

    Science.gov (United States)

    Maldonado, Emanuel; Sunagar, Kartik; Almeida, Daniela; Vasconcelos, Vitor; Antunes, Agostinho

    2014-01-01

    Among the major goals of research in evolutionary biology are the identification of genes targeted by natural selection and understanding how various regimes of evolution affect the fitness of an organism. In particular, adaptive evolution enables organisms to adapt to changing ecological factors such as diet, temperature, habitat, predatory pressures and prey abundance. An integrative approach is crucial for the identification of non-synonymous mutations that introduce radical changes in protein biochemistry and thus in turn influence the structure and function of proteins. Performing such analyses manually is often a time-consuming process, due to the large number of statistical files generated from multiple approaches, especially when assessing numerous taxa and/or large datasets. We present IMPACT_S, an easy-to-use Graphical User Interface (GUI) software, which rapidly and effectively integrates, filters and combines results from three widely used programs for assessing the influence of selection: Codeml (PAML package), Datamonkey and TreeSAAP. It enables the identification and tabulation of sites detected by these programs as evolving under the influence of positive, neutral and/or negative selection in protein-coding genes. IMPACT_S further facilitates the automatic mapping of these sites onto the three-dimensional structures of proteins. Other useful tools incorporated in IMPACT_S include Jmol, Archaeopteryx, Gnuplot, PhyML, a built-in Swiss-Model interface and a PDB downloader. The relevance and functionality of IMPACT_S is shown through a case study on the toxicoferan-reptilian Cysteine-rich Secretory Proteins (CRiSPs). IMPACT_S is a platform-independent software released under GPLv3 license, freely available online from http://impact-s.sourceforge.net.

  6. Nuclear Plant Analyzer desktop workstation: An integrated interactive simulation, visualization and analysis tool

    International Nuclear Information System (INIS)

    Beelman, R.J.

    1991-01-01

    The advanced, best-estimate, reactor thermal-hydraulic codes were originally developed as mainframe computer applications because of speed, precision, memory and mass storage requirements. However, the productivity of numerical reactor safety analysts has historically been hampered by mainframe dependence due to limited mainframe CPU allocation, accessibility and availability, poor mainframe job throughput, and delays in obtaining and difficulty comprehending printed numerical results. The Nuclear Plant Analyzer (NPA) was originally developed as a mainframe computer-graphics aid for reactor safety analysts in addressing the latter consideration. Rapid advances in microcomputer technology have since enabled the installation and execution of these reactor safety codes on desktop computers thereby eliminating mainframe dependence. The need for a complementary desktop graphics display generation and presentation capability, coupled with the need for software standardization and portability, has motivated the redesign of the NPA as a UNIX/X-Windows application suitable for both mainframe and microcomputer

  7. Single Molecule Analysis Research Tool (SMART: an integrated approach for analyzing single molecule data.

    Directory of Open Access Journals (Sweden)

    Max Greenfeld

    Full Text Available Single molecule studies have expanded rapidly over the past decade and have the ability to provide an unprecedented level of understanding of biological systems. A common challenge upon introduction of novel, data-rich approaches is the management, processing, and analysis of the complex data sets that are generated. We provide a standardized approach for analyzing these data in the freely available software package SMART: Single Molecule Analysis Research Tool. SMART provides a format for organizing and easily accessing single molecule data, a general hidden Markov modeling algorithm for fitting an array of possible models specified by the user, a standardized data structure and graphical user interfaces to streamline the analysis and visualization of data. This approach guides experimental design, facilitating acquisition of the maximal information from single molecule experiments. SMART also provides a standardized format to allow dissemination of single molecule data and transparency in the analysis of reported data.

  8. Irradiated-Microsphere Gamma Analyzer (IMGA): an integrated system for HTGR coated particle fuel performance assessment

    International Nuclear Information System (INIS)

    Kania, M.J.; Valentine, K.H.

    1980-02-01

    The Irradiated-Microsphere Gamma Analyzer (IMGA) System, designed and built at ORNL, provides the capability of making statistically accurate failure fraction measurements on irradiated HTGR coated particle fuel. The IMGA records the gamma-ray energy spectra from fuel particles and performs quantitative analyses on these spectra; then, using chemical and physical properties of the gamma emitters it makes a failed-nonfailed decision concerning the ability of the coatings to retain fission products. Actual retention characteristics for the coatings are determined by measuring activity ratios for certain gamma emitters such as 137 Cs/ 95 Zr and 144 Ce/ 95 Zr for metallic fission product retention and 134 Cs/ 137 Cs for an indirect measure of gaseous fission product retention. Data from IMGA (which can be put in the form of n failures observed in N examinations) can be accurately described by the binomial probability distribution model. Using this model, a mathematical relationship between IMGA data (n,N), failure fraction, and confidence level was developed. To determine failure fractions of less than or equal to 1% at confidence levels near 95%, this model dictates that from several hundred to several thousand particles must be examined. The automated particle handler of the IMGA system provides this capability. As a demonstration of failure fraction determination, fuel rod C-3-1 from the OF-2 irradiation capsule was analyzed and failure fraction statistics were applied. Results showed that at the 1% failure fraction level, with a 95% confidence level, the fissile particle batch could not meet requirements; however, the fertile particle exceeded these requirements for the given irradiation temperature and burnup

  9. A framework for analyzing the impact of data integrity/quality on electricity market operations

    Science.gov (United States)

    Choi, Dae Hyun

    This dissertation examines the impact of data integrity/quality in the supervisory control and data acquisition (SCADA) system on real-time locational marginal price (LMP) in electricity market operations. Measurement noise and/or manipulated sensor errors in a SCADA system may mislead system operators about real-time conditions in a power system, which, in turn, may impact the price signals in real-time power markets. This dissertation serves as a first attempt to analytically investigate the impact of bad/malicious data on electric power market operations. In future power system operations, which will probably involve many more sensors, the impact of sensor data integrity/quality on grid operations will become increasingly important. The first part of this dissertation studies from a market participant's perspective a new class of malicious data attacks on state estimation, which subsequently influences the result of the newly emerging look-ahead dispatch models in the real-time power market. In comparison with prior work of cyber-attack on static dispatch where no inter-temporal ramping constraint is considered, we propose a novel attack strategy, named ramp-induced data (RID) attack, with which the attacker can manipulate the limits of ramp constraints of generators in look-ahead dispatch. It is demonstrated that the proposed attack can lead to financial profits via malicious capacity withholding of selected generators, while being undetected by the existing bad data detection algorithm embedded in today's state estimation software. In the second part, we investigate from a system operator's perspective the sensitivity of locational marginal price (LMP) with respect to data corruption-induced state estimation error in real-time power market. Two data corruption scenarios are considered, in which corrupted continuous data (e.g., the power injection/flow and voltage magnitude) falsify power flow estimate whereas corrupted discrete data (e.g., the on/off status of

  10. A GWAS follow-up study reveals the association of the IL12RB2 gene with systemic sclerosis in Caucasian populations

    Science.gov (United States)

    Bossini-Castillo, Lara; Martin, Jose-Ezequiel; Broen, Jasper; Gorlova, Olga; Simeón, Carmen P.; Beretta, Lorenzo; Vonk, Madelon C.; Luis Callejas, Jose; Castellví, Ivan; Carreira, Patricia; José García-Hernández, Francisco; Fernández Castro, Mónica; Coenen, Marieke J.H.; Riemekasten, Gabriela; Witte, Torsten; Hunzelmann, Nicolas; Kreuter, Alexander; Distler, Jörg H.W.; Koeleman, Bobby P.; Voskuyl, Alexandre E.; Schuerwegh, Annemie J.; Palm, Øyvind; Hesselstrand, Roger; Nordin, Annika; Airó, Paolo; Lunardi, Claudio; Scorza, Raffaella; Shiels, Paul; van Laar, Jacob M.; Herrick, Ariane; Worthington, Jane; Denton, Christopher; Tan, Filemon K.; Arnett, Frank C.; Agarwal, Sandeep K.; Assassi, Shervin; Fonseca, Carmen; Mayes, Maureen D.; Radstake, Timothy R.D.J.; Martin, Javier

    2012-01-01

    A single-nucleotide polymorphism (SNP) at the IL12RB2 locus showed a suggestive association signal in a previously published genome-wide association study (GWAS) in systemic sclerosis (SSc). Aiming to reveal the possible implication of the IL12RB2 gene in SSc, we conducted a follow-up study of this locus in different Caucasian cohorts. We analyzed 10 GWAS-genotyped SNPs in the IL12RB2 region (2309 SSc patients and 5161 controls). We then selected three SNPs (rs3790567, rs3790566 and rs924080) based on their significance level in the GWAS, for follow-up in an independent European cohort comprising 3344 SSc and 3848 controls. The most-associated SNP (rs3790567) was further tested in an independent cohort comprising 597 SSc patients and 1139 controls from the USA. After conditional logistic regression analysis of the GWAS data, we selected rs3790567 [PMH= 1.92 × 10−5 odds ratio (OR) = 1.19] as the genetic variant with the firmest independent association observed in the analyzed GWAS peak of association. After the first follow-up phase, only the association of rs3790567 was consistent (PMH= 4.84 × 10−3 OR = 1.12). The second follow-up phase confirmed this finding (Pχ2 = 2.82 × 10−4 OR = 1.34). After performing overall pooled-analysis of all the cohorts included in the present study, the association found for the rs3790567 SNP in the IL12RB2 gene region reached GWAS-level significant association (PMH= 2.82 × 10−9 OR = 1.17). Our data clearly support the IL12RB2 genetic association with SSc, and suggest a relevant role of the interleukin 12 signaling pathway in SSc pathogenesis. PMID:22076442

  11. Analyzing climate change impacts on water resources under uncertainty using an integrated simulation-optimization approach

    Science.gov (United States)

    Zhuang, X. W.; Li, Y. P.; Nie, S.; Fan, Y. R.; Huang, G. H.

    2018-01-01

    An integrated simulation-optimization (ISO) approach is developed for assessing climate change impacts on water resources. In the ISO, uncertainties presented as both interval numbers and probability distributions can be reflected. Moreover, ISO permits in-depth analyses of various policy scenarios that are associated with different levels of economic consequences when the promised water-allocation targets are violated. A snowmelt-precipitation-driven watershed (Kaidu watershed) in northwest China is selected as the study case for demonstrating the applicability of the proposed method. Results of meteorological projections disclose that the incremental trend of temperature (e.g., minimum and maximum values) and precipitation exist. Results also reveal that (i) the system uncertainties would significantly affect water resources allocation pattern (including target and shortage); (ii) water shortage would be enhanced from 2016 to 2070; and (iii) the more the inflow amount decreases, the higher estimated water shortage rates are. The ISO method is useful for evaluating climate change impacts within a watershed system with complicated uncertainties and helping identify appropriate water resources management strategies hedging against drought.

  12. Integrative approach to analyze biodiversity and anti-inflammatory bioactivity of Wedelia medicinal plants.

    Directory of Open Access Journals (Sweden)

    Wen-Ching Lin

    Full Text Available For the development of "medical foods" and/or botanical drugs as defined USA FDA, clear and systemic characterizations of the taxonomy, index phytochemical components, and the functional or medicinal bioactivities of the reputed or candidate medicinal plant are needed. In this study, we used an integrative approach, including macroscopic and microscopic examination, marker gene analysis, and chemical fingerprinting, to authenticate and validate various species/varieties of Wedelia, a reputed medicinal plant that grows naturally and commonly used in Asian countries. The anti-inflammatory bioactivities of Wedelia extracts were then evaluated in a DSS-induced murine colitis model. Different species/varieties of Wedelia exhibited distinguishable morphology and histological structures. Analysis of the ribosomal DNA internal transcribed spacer (ITS region revealed significant differences among these plants. Chemical profiling of test Wedelia species demonstrated candidate index compounds and distinguishable secondary metabolites, such as caffeic acid derivatives, which may serve as phytochemical markers or index for quality control and identification of specific Wedelia species. In assessing their effect on treating DSS induced-murine colitis, we observed that only the phytoextract from W. chinensis species exhibited significant anti-inflammatory bioactivity on DSS-induced murine colitis among the various Wedelia species commonly found in Taiwan. Our results provide a translational research approach that may serve as a useful reference platform for biotechnological applications of traditional phytomedicines. Our findings indicate that specific Wedelia species warrant further investigation for potential treatment of human inflammatory bowel disease.

  13. Integrative gene network construction to analyze cancer recurrence using semi-supervised learning.

    Science.gov (United States)

    Park, Chihyun; Ahn, Jaegyoon; Kim, Hyunjin; Park, Sanghyun

    2014-01-01

    The prognosis of cancer recurrence is an important research area in bioinformatics and is challenging due to the small sample sizes compared to the vast number of genes. There have been several attempts to predict cancer recurrence. Most studies employed a supervised approach, which uses only a few labeled samples. Semi-supervised learning can be a great alternative to solve this problem. There have been few attempts based on manifold assumptions to reveal the detailed roles of identified cancer genes in recurrence. In order to predict cancer recurrence, we proposed a novel semi-supervised learning algorithm based on a graph regularization approach. We transformed the gene expression data into a graph structure for semi-supervised learning and integrated protein interaction data with the gene expression data to select functionally-related gene pairs. Then, we predicted the recurrence of cancer by applying a regularization approach to the constructed graph containing both labeled and unlabeled nodes. The average improvement rate of accuracy for three different cancer datasets was 24.9% compared to existing supervised and semi-supervised methods. We performed functional enrichment on the gene networks used for learning. We identified that those gene networks are significantly associated with cancer-recurrence-related biological functions. Our algorithm was developed with standard C++ and is available in Linux and MS Windows formats in the STL library. The executable program is freely available at: http://embio.yonsei.ac.kr/~Park/ssl.php.

  14. Integrative gene network construction to analyze cancer recurrence using semi-supervised learning.

    Directory of Open Access Journals (Sweden)

    Chihyun Park

    Full Text Available BACKGROUND: The prognosis of cancer recurrence is an important research area in bioinformatics and is challenging due to the small sample sizes compared to the vast number of genes. There have been several attempts to predict cancer recurrence. Most studies employed a supervised approach, which uses only a few labeled samples. Semi-supervised learning can be a great alternative to solve this problem. There have been few attempts based on manifold assumptions to reveal the detailed roles of identified cancer genes in recurrence. RESULTS: In order to predict cancer recurrence, we proposed a novel semi-supervised learning algorithm based on a graph regularization approach. We transformed the gene expression data into a graph structure for semi-supervised learning and integrated protein interaction data with the gene expression data to select functionally-related gene pairs. Then, we predicted the recurrence of cancer by applying a regularization approach to the constructed graph containing both labeled and unlabeled nodes. CONCLUSIONS: The average improvement rate of accuracy for three different cancer datasets was 24.9% compared to existing supervised and semi-supervised methods. We performed functional enrichment on the gene networks used for learning. We identified that those gene networks are significantly associated with cancer-recurrence-related biological functions. Our algorithm was developed with standard C++ and is available in Linux and MS Windows formats in the STL library. The executable program is freely available at: http://embio.yonsei.ac.kr/~Park/ssl.php.

  15. Integrated system for testing, investigation and analyzing of nuclear materials, TIAMAT-N

    International Nuclear Information System (INIS)

    Roth, Maria; Pitigoi, Vasile; Ionescu, Viorel; Constantin, Mihai; Babusi, Octavian

    2010-01-01

    Full text: The paper presents the results obtained in the framework of the project carried out as part of the National Program PNII, Modulus Capacities I, Competition 2008, concerning the performances of the Testing, Investigation and Analyzing System, used in the nuclear materials field. The system will ensure the evaluation of the nuclear structures, including the thermo-mechanical behaviour in connection with the physical-chemical analysis, microstructure and nondestructive investigations. Using last generation equipment and its interconnection to an IT system of monitoring, acquisition and data storage, it aims to implement the investigation methodologies applied in the nuclear area, to harmonize working practices according to the standards and procedures at European and international level. In addition, the system helps to develop a database, which will be continuously updated, with the materials investigated in the different types of tests and specific analyses. The project achievements will be capitalized at national level, sustaining the R and D studies of the National Nuclear Plan but also in the European and International Programs, including EURATOM Projects and Networks of Excellence, collaboration with AECL and COG Canada and participation in the AIEA Program. (authors)

  16. Hemoglobin genetics: recent contributions of GWAS and gene editing

    Science.gov (United States)

    Smith, Elenoe C.; Orkin, Stuart H.

    2016-01-01

    The β-hemoglobinopathies are inherited disorders resulting from altered coding potential or expression of the adult β-globin gene. Impaired expression of β-globin reduces adult hemoglobin (α2β2) production, the hallmark of β-thalassemia. A single-base mutation at codon 6 leads to formation of HbS (α2βS2) and sickle cell disease. While the basis of these diseases is known, therapy remains largely supportive. Bone marrow transplantation is the only curative therapy. Patients with elevated levels of fetal hemoglobin (HbF, α2γ2) as adults exhibit reduced symptoms and enhanced survival. The β-globin gene locus is a paradigm of cell- and developmental stage-specific regulation. Although the principal erythroid cell transcription factors are known, mechanisms responsible for silencing of the γ-globin gene were obscure until application of genome-wide association studies (GWAS). Here, we review findings in the field. GWAS identified BCL11A as a candidate negative regulator of γ-globin expression. Subsequent studies have established BCL11A as a quantitative repressor. GWAS-related single-nucleotide polymorphisms lie within an essential erythroid enhancer of the BCL11A gene. Disruption of a discrete region within the enhancer reduces BCL11A expression and induces HbF expression, providing the basis for gene therapy using gene editing tools. A recently identified, second silencing factor, leukemia/lymphoma-related factor/Pokemon, shares features with BCL11A, including interaction with the nucleosome remodeling deacetylase repressive complex. These findings suggest involvement of a common pathway for HbF silencing. In addition, we discuss other factors that may be involved in γ-globin gene silencing and their potential manipulation for therapeutic benefit in treating the β-hemoglobinopathies. PMID:27340226

  17. An integrated study to analyze soil microbial community structure and metabolic potential in two forest types.

    Science.gov (United States)

    Zhang, Yuguang; Cong, Jing; Lu, Hui; Yang, Caiyun; Yang, Yunfeng; Zhou, Jizhong; Li, Diqiang

    2014-01-01

    Soil microbial metabolic potential and ecosystem function have received little attention owing to difficulties in methodology. In this study, we selected natural mature forest and natural secondary forest and analyzed the soil microbial community and metabolic potential combing the high-throughput sequencing and GeoChip technologies. Phylogenetic analysis based on 16S rRNA sequencing showed that one known archaeal phylum and 15 known bacterial phyla as well as unclassified phylotypes were presented in these forest soils, and Acidobacteria, Protecobacteria, and Actinobacteria were three of most abundant phyla. The detected microbial functional gene groups were related to different biogeochemical processes, including carbon degradation, carbon fixation, methane metabolism, nitrogen cycling, phosphorus utilization, sulfur cycling, etc. The Shannon index for detected functional gene probes was significantly higher (PThe regression analysis showed that a strong positive (Pthe soil microbial functional gene diversity and phylogenetic diversity. Mantel test showed that soil oxidizable organic carbon, soil total nitrogen and cellulose, glucanase, and amylase activities were significantly linked (Pthe relative abundance of corresponded functional gene groups. Variance partitioning analysis showed that a total of 81.58% of the variation in community structure was explained by soil chemical factors, soil temperature, and plant diversity. Therefore, the positive link of soil microbial structure and composition to functional activity related to ecosystem functioning was existed, and the natural secondary forest soil may occur the high microbial metabolic potential. Although the results can't directly reflect the actual microbial populations and functional activities, this study provides insight into the potential activity of the microbial community and associated feedback responses of the terrestrial ecosystem to environmental changes.

  18. Genome-wide prediction models that incorporate de novo GWAS are a powerful new tool for tropical rice improvement

    Science.gov (United States)

    Spindel, J E; Begum, H; Akdemir, D; Collard, B; Redoña, E; Jannink, J-L; McCouch, S

    2016-01-01

    To address the multiple challenges to food security posed by global climate change, population growth and rising incomes, plant breeders are developing new crop varieties that can enhance both agricultural productivity and environmental sustainability. Current breeding practices, however, are unable to keep pace with demand. Genomic selection (GS) is a new technique that helps accelerate the rate of genetic gain in breeding by using whole-genome data to predict the breeding value of offspring. Here, we describe a new GS model that combines RR-BLUP with markers fit as fixed effects selected from the results of a genome-wide-association study (GWAS) on the RR-BLUP training data. We term this model GS + de novo GWAS. In a breeding population of tropical rice, GS + de novo GWAS outperformed six other models for a variety of traits and in multiple environments. On the basis of these results, we propose an extended, two-part breeding design that can be used to efficiently integrate novel variation into elite breeding populations, thus expanding genetic diversity and enhancing the potential for sustainable productivity gains. PMID:26860200

  19. Methods for meta-analysis of multiple traits using GWAS summary statistics.

    Science.gov (United States)

    Ray, Debashree; Boehnke, Michael

    2018-03-01

    Genome-wide association studies (GWAS) for complex diseases have focused primarily on single-trait analyses for disease status and disease-related quantitative traits. For example, GWAS on risk factors for coronary artery disease analyze genetic associations of plasma lipids such as total cholesterol, LDL-cholesterol, HDL-cholesterol, and triglycerides (TGs) separately. However, traits are often correlated and a joint analysis may yield increased statistical power for association over multiple univariate analyses. Recently several multivariate methods have been proposed that require individual-level data. Here, we develop metaUSAT (where USAT is unified score-based association test), a novel unified association test of a single genetic variant with multiple traits that uses only summary statistics from existing GWAS. Although the existing methods either perform well when most correlated traits are affected by the genetic variant in the same direction or are powerful when only a few of the correlated traits are associated, metaUSAT is designed to be robust to the association structure of correlated traits. metaUSAT does not require individual-level data and can test genetic associations of categorical and/or continuous traits. One can also use metaUSAT to analyze a single trait over multiple studies, appropriately accounting for overlapping samples, if any. metaUSAT provides an approximate asymptotic P-value for association and is computationally efficient for implementation at a genome-wide level. Simulation experiments show that metaUSAT maintains proper type-I error at low error levels. It has similar and sometimes greater power to detect association across a wide array of scenarios compared to existing methods, which are usually powerful for some specific association scenarios only. When applied to plasma lipids summary data from the METSIM and the T2D-GENES studies, metaUSAT detected genome-wide significant loci beyond the ones identified by univariate analyses

  20. A calderón-preconditioned single source combined field integral equation for analyzing scattering from homogeneous penetrable objects

    KAUST Repository

    Valdés, Felipe

    2011-06-01

    A new regularized single source equation for analyzing scattering from homogeneous penetrable objects is presented. The proposed equation is a linear combination of a Calderón-preconditioned single source electric field integral equation and a single source magnetic field integral equation. The equation is immune to low-frequency and dense-mesh breakdown, and free from spurious resonances. Unlike dual source formulations, this equation involves operator products that cannot be discretized using standard procedures for discretizing standalone electric, magnetic, and combined field operators. Instead, the single source equation proposed here is discretized using a recently developed technique that achieves a well-conditioned mapping from div- to curl-conforming function spaces, thereby fully respecting the space mapping properties of the operators involved, and guaranteeing accuracy and stability. Numerical results show that the proposed equation and discretization technique give rise to rapidly convergent solutions. They also validate the equation\\'s resonant free character. © 2006 IEEE.

  1. Testing Genetic Pleiotropy with GWAS Summary Statistics for Marginal and Conditional Analyses.

    Science.gov (United States)

    Deng, Yangqing; Pan, Wei

    2017-12-01

    There is growing interest in testing genetic pleiotropy, which is when a single genetic variant influences multiple traits. Several methods have been proposed; however, these methods have some limitations. First, all the proposed methods are based on the use of individual-level genotype and phenotype data; in contrast, for logistical, and other, reasons, summary statistics of univariate SNP-trait associations are typically only available based on meta- or mega-analyzed large genome-wide association study (GWAS) data. Second, existing tests are based on marginal pleiotropy, which cannot distinguish between direct and indirect associations of a single genetic variant with multiple traits due to correlations among the traits. Hence, it is useful to consider conditional analysis, in which a subset of traits is adjusted for another subset of traits. For example, in spite of substantial lowering of low-density lipoprotein cholesterol (LDL) with statin therapy, some patients still maintain high residual cardiovascular risk, and, for these patients, it might be helpful to reduce their triglyceride (TG) level. For this purpose, in order to identify new therapeutic targets, it would be useful to identify genetic variants with pleiotropic effects on LDL and TG after adjusting the latter for LDL; otherwise, a pleiotropic effect of a genetic variant detected by a marginal model could simply be due to its association with LDL only, given the well-known correlation between the two types of lipids. Here, we develop a new pleiotropy testing procedure based only on GWAS summary statistics that can be applied for both marginal analysis and conditional analysis. Although the main technical development is based on published union-intersection testing methods, care is needed in specifying conditional models to avoid invalid statistical estimation and inference. In addition to the previously used likelihood ratio test, we also propose using generalized estimating equations under the

  2. Advances in Integrating Traditional and Omic Biomarkers When Analyzing the Effects of the Mediterranean Diet Intervention in Cardiovascular Prevention

    Science.gov (United States)

    Fitó, Montserrat; Melander, Olle; Martínez, José Alfredo; Toledo, Estefanía; Carpéné, Christian; Corella, Dolores

    2016-01-01

    Intervention with Mediterranean diet (MedDiet) has provided a high level of evidence in primary prevention of cardiovascular events. Besides enhancing protection from classical risk factors, an improvement has also been described in a number of non-classical ones. Benefits have been reported on biomarkers of oxidation, inflammation, cellular adhesion, adipokine production, and pro-thrombotic state. Although the benefits of the MedDiet have been attributed to its richness in antioxidants, the mechanisms by which it exercises its beneficial effects are not well known. It is thought that the integration of omics including genomics, transcriptomics, epigenomics, and metabolomics, into studies analyzing nutrition and cardiovascular diseases will provide new clues regarding these mechanisms. However, omics integration is still in its infancy. Currently, some single-omics analyses have provided valuable data, mostly in the field of genomics. Thus, several gene-diet interactions in determining both intermediate (plasma lipids, etc.) and final cardiovascular phenotypes (stroke, myocardial infarction, etc.) have been reported. However, few studies have analyzed changes in gene expression and, moreover very few have focused on epigenomic or metabolomic biomarkers related to the MedDiet. Nevertheless, these preliminary results can help to better understand the inter-individual differences in cardiovascular risk and dietary response for further applications in personalized nutrition. PMID:27598147

  3. GWAS of clinically defined gout and subtypes identifies multiple susceptibility loci that include urate transporter genes

    NARCIS (Netherlands)

    Nakayama, A.; Nakaoka, H.; Yamamoto, K.; Sakiyama, M.; Shaukat, A.; Toyoda, Y.; Okada, Y.; Kamatani, Y.; Nakamura, T.; Takada, T.; Inoue, K.; Yasujima, T.; Yuasa, H.; Shirahama, Y.; Nakashima, H.; Shimizu, S.; Higashino, T.; Kawamura, Y.; Ogata, H.; Kawaguchi, M.; Ohkawa, Y.; Danjoh, I.; Tokumasu, A.; Ooyama, K.; Ito, T.; Kondo, T.; Wakai, K.; Stiburkova, B.; Pavelka, K.; Stamp, L.K.; Dalbeth, N.; Sakurai, Y.; Suzuki, H; Hosoyamada, M.; Fujimori, S.; Yokoo, T.; Hosoya, T.; Inoue, I.; Takahashi, A.; Kubo, M.; Ooyama, H.; Shimizu, T.; Ichida, K.; Shinomiya, N.; Merriman, T.R.; Matsuo, H.; Andres, M; Joosten, L.A.; Janssen, M.C.H.; Jansen, T.L.; Liote, F.; Radstake, T.R.; Riches, P.L.; So, A.; Tauches, A.K.

    2017-01-01

    OBJECTIVE: A genome-wide association study (GWAS) of gout and its subtypes was performed to identify novel gout loci, including those that are subtype-specific. METHODS: Putative causal association signals from a GWAS of 945 clinically defined gout cases and 1213 controls from Japanese males were

  4. Extending the use of GWAS data by combining data from different genetic platforms

    NARCIS (Netherlands)

    van Iperen, E. P. A.; Hovingh, G. K.; Asselbergs, F. W.; Zwinderman, A. H.

    2017-01-01

    In the past decade many Genome-wide Association Studies (GWAS) were performed that discovered new associations between single-nucleotide polymorphisms (SNPs) and various phenotypes. Imputation methods are widely used in GWAS. They facilitate the phenotype association with variants that are not

  5. MZ twin pairs or MZ singletons in population family-based GWAS? More power in pairs

    NARCIS (Netherlands)

    Minica, C.C.; Boomsma, D.I.; Vink, J.M.; Dolan, C.V.

    2014-01-01

    Family-based genome-wide association studies (GWAS) involve testing the genetic association of (many) genetic variants with the phenotype of interest, while taking into account the relatedness among family members. Occasionally in family-based GWAS, including monozygotic (MZ) twins, the data from

  6. Transient analyzer

    International Nuclear Information System (INIS)

    Muir, M.D.

    1975-01-01

    The design and design philosophy of a high performance, extremely versatile transient analyzer is described. This sub-system was designed to be controlled through the data acquisition computer system which allows hands off operation. Thus it may be placed on the experiment side of the high voltage safety break between the experimental device and the control room. This analyzer provides control features which are extremely useful for data acquisition from PPPL diagnostics. These include dynamic sample rate changing, which may be intermixed with multiple post trigger operations with variable length blocks using normal, peak to peak or integrate modes. Included in the discussion are general remarks on the advantages of adding intelligence to transient analyzers, a detailed description of the characteristics of the PPPL transient analyzer, a description of the hardware, firmware, control language and operation of the PPPL transient analyzer, and general remarks on future trends in this type of instrumentation both at PPPL and in general

  7. Using CForest to Analyze Diffusion Tensor Imaging Data: A Study of White Matter Integrity in Healthy Aging.

    Science.gov (United States)

    McWhinney, Sean R; Tremblay, Antoine; Chevalier, Thérèse M; Lim, Vanessa K; Newman, Aaron J

    2016-12-01

    Healthy aging has been associated with a global reduction in white matter integrity, which is thought to reflect cognitive decline. The present study aimed to investigate this reduction over a broad range of the life span, using diffusion tensor imaging analyzed with conditional inference random forest modeling (CForest). This approach is sensitive to subtle and potentially nonlinear effects over the age continuum and was used to characterize the progression of decline in greater detail than has been possible in the past. Data were collected from 45 healthy individuals ranging in age from 19 to 67 years. Fractional anisotropy (FA) was estimated using probabilistic tractography for a number of major tracts across the brain. Age coincided with a nonlinear decrease in FA, with onset beginning at ∼30 years of age and the steepest declines occurring later in life. However, several tracts showed a transient increase before this decline. The progression of decline varied by tract, with steeper but later decline occurring in more anterior tracts. Finally, strongly right-handed individuals demonstrated relatively preserved FA until more than a decade following the onset of decline of others. These results demonstrate that using a novel, nonparametric analysis approach, previously reported reductions in FA with healthy aging were confirmed, while at the same time, new insight was provided into the onset and progression of decline, with evidence suggesting increases in integrity continuing into adulthood.

  8. Statistical methods to detect novel genetic variants using publicly available GWAS summary data.

    Science.gov (United States)

    Guo, Bin; Wu, Baolin

    2018-03-01

    We propose statistical methods to detect novel genetic variants using only genome-wide association studies (GWAS) summary data without access to raw genotype and phenotype data. With more and more summary data being posted for public access in the post GWAS era, the proposed methods are practically very useful to identify additional interesting genetic variants and shed lights on the underlying disease mechanism. We illustrate the utility of our proposed methods with application to GWAS meta-analysis results of fasting glucose from the international MAGIC consortium. We found several novel genome-wide significant loci that are worth further study. Copyright © 2018 Elsevier Ltd. All rights reserved.

  9. Comparison of fabric analysis of snow samples by Computer-Integrated Polarization Microscopy and Automatic Ice Texture Analyzer

    Science.gov (United States)

    Leisinger, Sabine; Montagnat, Maurine; Heilbronner, Renée; Schneebeli, Martin

    2014-05-01

    Accurate knowledge of fabric anisotropy is crucial to understand the mechanical behavior of snow and firn, but is also important for understanding metamorphism. Computer-Integrated Polarization Microscopy (CIP) method used for the fabric analysis was developed by Heilbronner and Pauli in the early 1990ies and uses a slightly modified traditional polarization microscope for the fabric analysis. First developed for quartz, it can be applied to other uniaxial minerals. Up to now this method was mainly used in structural geology. However, it is also well suited for the fabric analysis of snow, firn and ice. The method is based on the analysis of first- order interference colors images by a slightly modified optical polarization microscope, a grayscale camera and a computer. The optical polarization microscope is featured with high quality objectives, a rotating table and two polarizers that can be introduced above and below the thin section, as well as a full wave plate. Additionally, two quarter-wave plates for circular polarization are needed. Otherwise it is also possible to create circular polarization from a set of crossed polarized images through image processing. A narrow band interference filter transmitting a wavelength between 660 and 700 nm is also required. Finally a monochrome digital camera is used to capture the input images. The idea is to record the change of interference colors while the thin section is being rotated once through 180°. The azimuth and inclination of the c-axis are defined by the color change. Recording the color change through a red filter produces a signal with a well-defined amplitude and phase angle. An advantage of this method lies in the simple conversion of an ordinary optical microscope to a fabric analyzer. The Automatic Ice Texture Analyzer (AITA) as the first fully functional instrument to measure c-axis orientation was developed by Wilson and other (2003). Most recent fabric analysis of snow and firn samples was carried

  10. GWAS of clinically defined gout and subtypes identifies multiple susceptibility loci that include urate transporter genes

    OpenAIRE

    Nakayama, Akiyoshi; Nakaoka, Hirofumi; Yamamoto, Ken; Sakiyama, Masayuki; Shaukat, Amara; Toyoda, Yu; Okada, Yukinori; Kamatani, Yoichiro; Nakamura, Takahiro; Takada, Tappei; Inoue, Katsuhisa; Yasujima, Tomoya; Yuasa, Hiroaki; Shirahama, Yuko; Nakashima, Hiroshi

    2016-01-01

    Objective A genome-wide association study (GWAS) of gout and its subtypes was performed to identify novel gout loci, including those that are subtype-specific. Methods Putative causal association signals from a GWAS of 945 clinically defined gout cases and 1213 controls from Japanese males were replicated with 1396 cases and 1268 controls using a custom chip of 1961 single nucleotide polymorphisms (SNPs). We also first conducted GWASs of gout subtypes. Replication with Caucasian and New Zeala...

  11. qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots

    OpenAIRE

    Turner, Stephen

    2014-01-01

    Summary: Genome-wide association studies (GWAS) have identified thousands of human trait-associated single nucleotide polymorphisms. Here, I describe a freely available R package for visualizing GWAS results using Q-Q and manhattan plots. The qqman package enables the flexible creation of manhattan plots, both genome-wide and for single chromosomes, with optional highlighting of SNPs of interest. Availability: qqman is released under the GNU General Public License, and is freely available on ...

  12. ANALYZING THE INTEGRITY OF PUBLIC ACCOUNTANT AT “CEMERLANG” PUBLIC ACCOUNTANT FIRM IN SURABAYA (PHENOMENOLOGY STUDY

    Directory of Open Access Journals (Sweden)

    Ratna Anggraini Aripratiwi

    2017-12-01

    Full Text Available This study aims to explore the deep meaning of the integrity attitudes that is experienced, felt, and performed by a public accountant in one of the famous KAP in Surabaya, KAP "Cemerlang". Revealing the attitude of the integrity of public accountant is important since there are large number of public accountants who are still dragged into fraud and violations, resulting in unethical decisions. Every public accountant has a different perspective in determining and practicing an attitude of integrity, whether to defend or even release it for a particular purpose that ultimately raises a variety of meanings of pure integrity and pragmatic integrity.

  13. Evaluation of European Schizophrenia GWAS Loci in Asian Populations via Comprehensive Meta-Analyses.

    Science.gov (United States)

    Xiao, Xiao; Luo, Xiong-Jian; Chang, Hong; Liu, Zichao; Li, Ming

    2017-08-01

    Schizophrenia is a severe and highly heritable neuropsychiatric disorder. Recent genetic analyses including genome-wide association studies (GWAS) have implicated multiple genome-wide significant variants for schizophrenia among European populations. However, many of these risk variants were not largely validated in other populations of different ancestry such as Asians. To validate whether these European GWAS significant loci are associated with schizophrenia in Asian populations, we conducted a systematic literature search and meta-analyses on 19 single nucleotide polymorphisms (SNPs) in Asian populations by combining all available case-control and family-based samples, including up to 30,000 individuals. We employed classical fixed (or random) effects inverse variance weighted methods to calculate summary odds ratios (ORs) and 95 % confidence intervals (CIs). Among the 19 GWAS loci, we replicated the risk associations of nine markers (e.g., SNPs at VRK2, ITIH3/4, NDST3, NOTCH4) surpassing significance level (two-tailed P Asian replication samples and initial European GWAS findings, and the successful replications of these GWAS loci in a different ethnic group provide stronger evidence for their clinical associations with schizophrenia. Further studies, focusing on the molecular mechanisms of these GWAS significant loci, will become increasingly important for understanding of the pathogenesis to schizophrenia.

  14. GWAS in a box: statistical and visual analytics of structured associations via GenAMap.

    Directory of Open Access Journals (Sweden)

    Eric P Xing

    Full Text Available With the continuous improvement in genotyping and molecular phenotyping technology and the decreasing typing cost, it is expected that in a few years, more and more clinical studies of complex diseases will recruit thousands of individuals for pan-omic genetic association analyses. Hence, there is a great need for algorithms and software tools that could scale up to the whole omic level, integrate different omic data, leverage rich structure information, and be easily accessible to non-technical users. We present GenAMap, an interactive analytics software platform that 1 automates the execution of principled machine learning methods that detect genome- and phenome-wide associations among genotypes, gene expression data, and clinical or other macroscopic traits, and 2 provides new visualization tools specifically designed to aid in the exploration of association mapping results. Algorithmically, GenAMap is based on a new paradigm for GWAS and PheWAS analysis, termed structured association mapping, which leverages various structures in the omic data. We demonstrate the function of GenAMap via a case study of the Brem and Kruglyak yeast dataset, and then apply it on a comprehensive eQTL analysis of the NIH heterogeneous stock mice dataset and report some interesting findings. GenAMap is available from http://sailing.cs.cmu.edu/genamap.

  15. IVAG: An Integrative Visualization Application for Various Types of Genomic Data Based on R-Shiny and the Docker Platform.

    Science.gov (United States)

    Lee, Tae-Rim; Ahn, Jin Mo; Kim, Gyuhee; Kim, Sangsoo

    2017-12-01

    Next-generation sequencing (NGS) technology has become a trend in the genomics research area. There are many software programs and automated pipelines to analyze NGS data, which can ease the pain for traditional scientists who are not familiar with computer programming. However, downstream analyses, such as finding differentially expressed genes or visualizing linkage disequilibrium maps and genome-wide association study (GWAS) data, still remain a challenge. Here, we introduce a dockerized web application written in R using the Shiny platform to visualize pre-analyzed RNA sequencing and GWAS data. In addition, we have integrated a genome browser based on the JBrowse platform and an automated intermediate parsing process required for custom track construction, so that users can easily build and navigate their personal genome tracks with in-house datasets. This application will help scientists perform series of downstream analyses and obtain a more integrative understanding about various types of genomic data by interactively visualizing them with customizable options.

  16. Note: A portable Raman analyzer for microfluidic chips based on a dichroic beam splitter for integration of imaging and signal collection light paths

    Energy Technology Data Exchange (ETDEWEB)

    Geng, Yijia; Xu, Shuping; Xu, Weiqing, E-mail: xuwq@jlu.edu.cn [State Key Laboratory of Supramolecular Structure and Materials, Institute of Theoretical Chemistry, Jilin University, Changchun 130012 (China); Chen, Lei [State Key Laboratory of Supramolecular Structure and Materials, Institute of Theoretical Chemistry, Jilin University, Changchun 130012 (China); College of Physics, Jilin University, Changchun 130012 (China); Chen, Gang [State Key Laboratory of Supramolecular Structure and Materials, Institute of Theoretical Chemistry, Jilin University, Changchun 130012 (China); College of Chemistry, Jilin University, Changchun 130012 (China); Bi, Wenbin [State Key Laboratory of Supramolecular Structure and Materials, Institute of Theoretical Chemistry, Jilin University, Changchun 130012 (China); School of Chemistry and Environmental Engineering, Changchun University of Science and Technology, Changchun 130022 (China); Cui, Haining [College of Physics, Jilin University, Changchun 130012 (China)

    2015-05-15

    An integrated and portable Raman analyzer featuring an inverted probe fixed on a motor-driving adjustable optical module was designed for the combination of a microfluidic system. It possesses a micro-imaging function. The inverted configuration is advantageous to locate and focus microfluidic channels. Different from commercial micro-imaging Raman spectrometers using manual switchable light path, this analyzer adopts a dichroic beam splitter for both imaging and signal collection light paths, which avoids movable parts and improves the integration and stability of optics. Combined with surface-enhanced Raman scattering technique, this portable Raman micro-analyzer is promising as a powerful tool for microfluidic analytics.

  17. GenToS: Use of Orthologous Gene Information to Prioritize Signals from Human GWAS.

    Directory of Open Access Journals (Sweden)

    Anselm S Hoppmann

    Full Text Available Genome-wide association studies (GWAS evaluate associations between genetic variants and a trait or disease of interest free of prior biological hypotheses. GWAS require stringent correction for multiple testing, with genome-wide significance typically defined as association p-value <5*10-8. This study presents a new tool that uses external information about genes to prioritize SNP associations (GenToS. For a given list of candidate genes, GenToS calculates an appropriate statistical significance threshold and then searches for trait-associated variants in summary statistics from human GWAS. It thereby allows for identifying trait-associated genetic variants that do not meet genome-wide significance. The program additionally tests for enrichment of significant candidate gene associations in the human GWAS data compared to the number expected by chance. As proof of principle, this report used external information from a comprehensive resource of genetically manipulated and systematically phenotyped mice. Based on selected murine phenotypes for which human GWAS data for corresponding traits were publicly available, several candidate gene input lists were derived. Using GenToS for the investigation of candidate genes underlying murine skeletal phenotypes in data from a large human discovery GWAS meta-analysis of bone mineral density resulted in the identification of significantly associated variants in 29 genes. Index variants in 28 of these loci were subsequently replicated in an independent GWAS replication step, highlighting that they are true positive associations. One signal, COL11A1, has not been discovered through GWAS so far and represents a novel human candidate gene for altered bone mineral density. The number of observed genes that contained significant SNP associations in human GWAS based on murine candidate gene input lists was much greater than the number expected by chance across several complex human traits (enrichment p-value as

  18. Identification of loci governing eight agronomic traits using a GBS-GWAS approach and validation by QTL mapping in soya bean.

    Science.gov (United States)

    Sonah, Humira; O'Donoughue, Louise; Cober, Elroy; Rajcan, Istvan; Belzile, François

    2015-02-01

    Soya bean is a major source of edible oil and protein for human consumption as well as animal feed. Understanding the genetic basis of different traits in soya bean will provide important insights for improving breeding strategies for this crop. A genome-wide association study (GWAS) was conducted to accelerate molecular breeding for the improvement of agronomic traits in soya bean. A genotyping-by-sequencing (GBS) approach was used to provide dense genome-wide marker coverage (>47,000 SNPs) for a panel of 304 short-season soya bean lines. A subset of 139 lines, representative of the diversity among these, was characterized phenotypically for eight traits under six environments (3 sites × 2 years). Marker coverage proved sufficient to ensure highly significant associations between the genes known to control simple traits (flower, hilum and pubescence colour) and flanking SNPs. Between one and eight genomic loci associated with more complex traits (maturity, plant height, seed weight, seed oil and protein) were also identified. Importantly, most of these GWAS loci were located within genomic regions identified by previously reported quantitative trait locus (QTL) for these traits. In some cases, the reported QTLs were also successfully validated by additional QTL mapping in a biparental population. This study demonstrates that integrating GBS and GWAS can be used as a powerful complementary approach to classical biparental mapping for dissecting complex traits in soya bean. © 2014 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

  19. A novel integrative method for analyzing eye and hand behaviour during reaching and grasping in an MRI environment.

    Science.gov (United States)

    Lawrence, Jane M; Abhari, Kamyar; Prime, Steven L; Meek, Benjamin P; Desanghere, Loni; Baugh, Lee A; Marotta, Jonathan J

    2011-06-01

    The development of noninvasive neuroimaging techniques, such as fMRI, has rapidly advanced our understanding of the neural systems underlying the integration of visual and motor information. However, the fMRI experimental design is restricted by several environmental elements, such as the presence of the magnetic field and the restricted view of the participant, making it difficult to monitor and measure behaviour. The present article describes a novel, specialized software package developed in our laboratory called Biometric Integration Recording and Analysis (BIRA). BIRA integrates video with kinematic data derived from the hand and eye, acquired using MRI-compatible equipment. The present article demonstrates the acquisition and analysis of eye and hand data using BIRA in a mock (0 Tesla) scanner. A method for collecting and integrating gaze and kinematic data in fMRI studies on visuomotor behaviour has several advantages: Specifically, it will allow for more sophisticated, behaviourally driven analyses and eliminate potential confounds of gaze or kinematic data.

  20. SNPranker 2.0: a gene-centric data mining tool for diseases associated SNP prioritization in GWAS.

    Science.gov (United States)

    Merelli, Ivan; Calabria, Andrea; Cozzi, Paolo; Viti, Federica; Mosca, Ettore; Milanesi, Luciano

    2013-01-01

    The capability of correlating specific genotypes with human diseases is a complex issue in spite of all advantages arisen from high-throughput technologies, such as Genome Wide Association Studies (GWAS). New tools for genetic variants interpretation and for Single Nucleotide Polymorphisms (SNPs) prioritization are actually needed. Given a list of the most relevant SNPs statistically associated to a specific pathology as result of a genotype study, a critical issue is the identification of genes that are effectively related to the disease by re-scoring the importance of the identified genetic variations. Vice versa, given a list of genes, it can be of great importance to predict which SNPs can be involved in the onset of a particular disease, in order to focus the research on their effects. We propose a new bioinformatics approach to support biological data mining in the analysis and interpretation of SNPs associated to pathologies. This system can be employed to design custom genotyping chips for disease-oriented studies and to re-score GWAS results. The proposed method relies (1) on the data integration of public resources using a gene-centric database design, (2) on the evaluation of a set of static biomolecular annotations, defined as features, and (3) on the SNP scoring function, which computes SNP scores using parameters and weights set by users. We employed a machine learning classifier to set default feature weights and an ontological annotation layer to enable the enrichment of the input gene set. We implemented our method as a web tool called SNPranker 2.0 (http://www.itb.cnr.it/snpranker), improving our first published release of this system. A user-friendly interface allows the input of a list of genes, SNPs or a biological process, and to customize the features set with relative weights. As result, SNPranker 2.0 returns a list of SNPs, localized within input and ontologically enriched genes, combined with their prioritization scores. Different

  1. A computer program integrating a multichannel analyzer with gamma analysis for the estimation of 226 Ra concentration in soil samples

    International Nuclear Information System (INIS)

    Wilson, J. E.

    1992-08-01

    A new hardware/software system has been implemented using the existing three-regions-of-interest method for determining the concentration of 226 Ra in soil samples for the Pollutant Assessment Group of the Oak Ridge National Laboratory. Consisting of a personal computer containing a multichannel analyzer, the system utilizes a new program combining the multichannel analyzer with a program analyzing gamma-radiation spectra for 226 Ra concentrations. This program uses a menu interface to minimize and simplify the tasks of system operation

  2. Development of a Simulation Framework for Analyzing Security of Supply in Integrated Gas and Electric Power Systems

    NARCIS (Netherlands)

    Pambour, Kwabena Addo; Erdener, Burcin Cakir; Bolado-Lavin, Ricardo; Dijkema, Gerhard

    2017-01-01

    Gas and power networks are tightly coupled and interact with each other due to physically interconnected facilities. In an integrated gas and power network, a contingency observed in one system may cause iterative cascading failures, resulting in network wide disruptions. Therefore, understanding

  3. Using Groupware to Gather and Analyze Intelligence in a Public Setting: Development of Integral Safety Plans in an Electronic Meeting

    NARCIS (Netherlands)

    Rouwette, E.A.J.A.; Vennix, J.A.M.; Vriens, D.J.

    2003-01-01

    This chapter focuses on the use of groupware to support local governments in activities in the intelligence cycle. Local governments in The Netherlands have a central role in developing integral safety plans for their district. However, in the implementation of safety plans the contribution of

  4. Speed limiter integrated fatigue analyzer (SLIFA) for speed and fatigue control on diesel engine truck and bus

    Science.gov (United States)

    Wahyudi, Haris; Pranoto, Hadi; Leman, A. M.; Sebayang, Darwin; Baba, I.

    2017-09-01

    Every second, the number of road traffic deaths is increased globally with millions more sustaining severe injuries and living with long-term adverse health consequences. Jakarta alone in year 2015 had recorded 556 people died due to road accidents, approximately reached 6.231 road accident cases. The identified major contributory factors of such unfortunate events are both driver fatigue and over speeding habit especially related to the driving of truck and bus. This paper presents the idea on how to control the electronic system from input fuel system of injection pump and the combustion chamber engine will control the valve solenoid in injection pump which can lock and fuel will stop for moment, and speed limit can be success, by using sensor heart rate we can input reduce speed limit when fatigue detection driver. Integration process this tool can be relevant when Speed Limiter Integrated Fatigue Analyser (SLIFA) trial in the diesel engine for truck and bus, the result of this research Speed Limiter Integrated Fatigue Analyser (SLIFA) able to control speed of diesel engine for truck and bus almost 30km/h, 60km/h, and until 70 km/h. The installation of the sensor heart rate as the input speed limit SLIFA would work when the driver is detected to be in the fatigue condition. We make Speed Limiter Integrated Fatigue Analyser (SLIFA) for control and monitoring system for diesel engine in truck and bus. Speed Limiter Integrated Fatigue Analyser (SLIFA) system can save the historical of the speed record, fatigue, rpm, and body temperature of the driver.

  5. Estimating Effect Sizes and Expected Replication Probabilities from GWAS Summary Statistics

    DEFF Research Database (Denmark)

    Holland, Dominic; Wang, Yunpeng; Thompson, Wesley K

    2016-01-01

    Genome-wide Association Studies (GWAS) result in millions of summary statistics ("z-scores") for single nucleotide polymorphism (SNP) associations with phenotypes. These rich datasets afford deep insights into the nature and extent of genetic contributions to complex phenotypes such as psychiatric......-scores, as such knowledge would enhance causal SNP and gene discovery, help elucidate mechanistic pathways, and inform future study design. Here we present a parsimonious methodology for modeling effect sizes and replication probabilities, relying only on summary statistics from GWAS substudies, and a scheme allowing...... for estimating the degree of polygenicity of the phenotype and predicting the proportion of chip heritability explainable by genome-wide significant SNPs in future studies with larger sample sizes. We apply the model to recent GWAS of schizophrenia (N = 82,315) and putamen volume (N = 12,596), with approximately...

  6. Fuels planning: science synthesis and integration; environmental consequences fact sheet 13: Root Disease Analyzer-Armillaria Response Tool (ART)

    Science.gov (United States)

    Geral I. McDonald; Philip D. Tanimoto; Thomas M. Rice; David E. Hall; Jane E. Stewart; Paul J. Zambino; Jonalea R. Tonn; Ned B. Klopfenstein; Mee-Sook Kim

    2005-01-01

    The Root Disease Analyzer-Armillaria Response Tool (ART) is a Web-based tool that estimates Armillaria root disease risk in dry forests of the Western United States. This fact sheet identifies the intended users and uses, required inputs, what the model does and does not do, and tells the user how to obtain the model.

  7. Methods to improve genomic prediction and GWAS using combined Holstein populations

    DEFF Research Database (Denmark)

    Li, Xiujin

    The thesis focuses on methods to improve GWAS and genomic prediction using combined Holstein populations and investigations G by E interaction. The conclusions are: 1) Prediction reliabilities for Brazilian Holsteins can be increased by adding Nordic and Frensh genotyped bulls and a large G by E...... interaction exists between populations. 2) Combining data from Chinese and Danish Holstein populations increases the power of GWAS and detects new QTL regions for milk fatty acid traits. 3) The novel multi-trait Bayesian model efficiently estimates region-specific genomic variances, covariances...

  8. GWAS-based machine learning approach to predict duloxetine response in major depressive disorder.

    Science.gov (United States)

    Maciukiewicz, Malgorzata; Marshe, Victoria S; Hauschild, Anne-Christin; Foster, Jane A; Rotzinger, Susan; Kennedy, James L; Kennedy, Sidney H; Müller, Daniel J; Geraci, Joseph

    2018-04-01

    Major depressive disorder (MDD) is one of the most prevalent psychiatric disorders and is commonly treated with antidepressant drugs. However, large variability is observed in terms of response to antidepressants. Machine learning (ML) models may be useful to predict treatment outcomes. A sample of 186 MDD patients received treatment with duloxetine for up to 8 weeks were categorized as "responders" based on a MADRS change >50% from baseline; or "remitters" based on a MADRS score ≤10 at end point. The initial dataset (N = 186) was randomly divided into training and test sets in a nested 5-fold cross-validation, where 80% was used as a training set and 20% made up five independent test sets. We performed genome-wide logistic regression to identify potentially significant variants related to duloxetine response/remission and extracted the most promising predictors using LASSO regression. Subsequently, classification-regression trees (CRT) and support vector machines (SVM) were applied to construct models, using ten-fold cross-validation. With regards to response, none of the pairs performed significantly better than chance (accuracy p > .1). For remission, SVM achieved moderate performance with an accuracy = 0.52, a sensitivity = 0.58, and a specificity = 0.46, and 0.51 for all coefficients for CRT. The best performing SVM fold was characterized by an accuracy = 0.66 (p = .071), sensitivity = 0.70 and a sensitivity = 0.61. In this study, the potential of using GWAS data to predict duloxetine outcomes was examined using ML models. The models were characterized by a promising sensitivity, but specificity remained moderate at best. The inclusion of additional non-genetic variables to create integrated models may improve prediction. Copyright © 2017. Published by Elsevier Ltd.

  9. State of art report for critical flow model to analyze a break flow in pressurizer of integral type reactor

    Energy Technology Data Exchange (ETDEWEB)

    Kang, Yeon Moon; Lee, D. J.; Yoon, J. H.; Kim, J. P.; Kim, H. Y

    1999-03-01

    At a critical flow condition, the flow rate can't exceed a maximum value for given upstream conditions and the limited flow rate is called as a critical flow rate. The phenomena of critical flow occur at the discharge of a single phase gas or subcooled water through nozzles and pipes. Among the previous researches on critical flow, many accurate correlations on pressure, temperature and flow rate are represented for the single phase gas. However, for the two phase critical flow, the results of previous work showed that there was a large discrepancy between the analytical and experimental data and the data were in agreement for the limited thermodynamic conditions. Thus, further studies are required to enhance the two phase critical flow model. In the integral reactor, the critical flows of nitrogen gas and subcooled water are expected for the break of gas cylinder pipeline connected to the pressurizer. It requires that the inlet shape of the pipe and the nitrogen gas effect should be considered for the critical flow of integral reactor. The nitrogen gas exist in the pressurizer may affect the flow rate of primary coolant, which has been considered only for a few previous researches. Thus, the evaluation of the effect of the nitrogen on the critical flow gas should be preceded for the proper analysis of the critical flow in the integral reactor. In this report, not only the essences of previous work on critical flow were investigated and summarized but also the effect of nitrogen gas and the inlet shape of the pipe on the critical flow were also investigated. (author)

  10. State of art report for critical flow model to analyze a break flow in pressurizer of integral type reactor

    International Nuclear Information System (INIS)

    Kang, Yeon Moon; Lee, D. J.; Yoon, J. H.; Kim, J. P.; Kim, H. Y.

    1999-03-01

    At a critical flow condition, the flow rate can't exceed a maximum value for given upstream conditions and the limited flow rate is called as a critical flow rate. The phenomena of critical flow occur at the discharge of a single phase gas or subcooled water through nozzles and pipes. Among the previous researches on critical flow, many accurate correlations on pressure, temperature and flow rate are represented for the single phase gas. However, for the two phase critical flow, the results of previous work showed that there was a large discrepancy between the analytical and experimental data and the data were in agreement for the limited thermodynamic conditions. Thus, further studies are required to enhance the two phase critical flow model. In the integral reactor, the critical flows of nitrogen gas and subcooled water are expected for the break of gas cylinder pipeline connected to the pressurizer. It requires that the inlet shape of the pipe and the nitrogen gas effect should be considered for the critical flow of integral reactor. The nitrogen gas exist in the pressurizer may affect the flow rate of primary coolant, which has been considered only for a few previous researches. Thus, the evaluation of the effect of the nitrogen on the critical flow gas should be preceded for the proper analysis of the critical flow in the integral reactor. In this report, not only the essences of previous work on critical flow were investigated and summarized but also the effect of nitrogen gas and the inlet shape of the pipe on the critical flow were also investigated. (author)

  11. Predicting cell types and genetic variations contributing to disease by combining GWAS and epigenetic data.

    Directory of Open Access Journals (Sweden)

    Anna Gerasimova

    Full Text Available Genome-wide association studies (GWASs identify single nucleotide polymorphisms (SNPs that are enriched in individuals suffering from a given disease. Most disease-associated SNPs fall into non-coding regions, so that it is not straightforward to infer phenotype or function; moreover, many SNPs are in tight genetic linkage, so that a SNP identified as associated with a particular disease may not itself be causal, but rather signify the presence of a linked SNP that is functionally relevant to disease pathogenesis. Here, we present an analysis method that takes advantage of the recent rapid accumulation of epigenomics data to address these problems for some SNPs. Using asthma as a prototypic example; we show that non-coding disease-associated SNPs are enriched in genomic regions that function as regulators of transcription, such as enhancers and promoters. Identifying enhancers based on the presence of the histone modification marks such as H3K4me1 in different cell types, we show that the location of enhancers is highly cell-type specific. We use these findings to predict which SNPs are likely to be directly contributing to disease based on their presence in regulatory regions, and in which cell types their effect is expected to be detectable. Moreover, we can also predict which cell types contribute to a disease based on overlap of the disease-associated SNPs with the locations of enhancers present in a given cell type. Finally, we suggest that it will be possible to re-analyze GWAS studies with much higher power by limiting the SNPs considered to those in coding or regulatory regions of cell types relevant to a given disease.

  12. Gene-Based Analysis of Regionally Enriched Cortical Genes in GWAS Data Sets of Cognitive Traits and Psychiatric Disorders

    DEFF Research Database (Denmark)

    Ersland, Kari M; Christoforou, Andrea; Stansberg, Christine

    2012-01-01

    the regionally enriched cortical genes to mine a genome-wide association study (GWAS) of the Norwegian Cognitive NeuroGenetics (NCNG) sample of healthy adults for association to nine psychometric tests measures. In addition, we explored GWAS data sets for the serious psychiatric disorders schizophrenia (SCZ) (n...

  13. Development of a Simulation Framework for Analyzing Security of Supply in Integrated Gas and Electric Power Systems

    Directory of Open Access Journals (Sweden)

    Kwabena Addo Pambour

    2017-01-01

    Full Text Available Gas and power networks are tightly coupled and interact with each other due to physically interconnected facilities. In an integrated gas and power network, a contingency observed in one system may cause iterative cascading failures, resulting in network wide disruptions. Therefore, understanding the impacts of the interactions in both systems is crucial for governments, system operators, regulators and operational planners, particularly, to ensure security of supply for the overall energy system. Although simulation has been widely used in the assessment of gas systems as well as power systems, there is a significant gap in simulation models that are able to address the coupling of both systems. In this paper, a simulation framework that models and simulates the gas and power network in an integrated manner is proposed. The framework consists of a transient model for the gas system and a steady state model for the power system based on AC-Optimal Power Flow. The gas and power system model are coupled through an interface which uses the coupling equations to establish the data exchange and coordination between the individual models. The bidirectional interlink between both systems considered in this studies are the fuel gas offtake of gas fired power plants for power generation and the power supply to liquefied natural gas (LNG terminals and electric drivers installed in gas compressor stations and underground gas storage facilities. The simulation framework is implemented into an innovative simulation tool named SAInt (Scenario Analysis Interface for Energy Systems and the capabilities of the tool are demonstrated by performing a contingency analysis for a real world example. Results indicate how a disruption triggered in one system propagates to the other system and affects the operation of critical facilities. In addition, the studies show the importance of using transient gas models for security of supply studies instead of successions of

  14. Investigating the genetic relationship between Alzheimer’s disease and cancer using GWAS summary statistics

    NARCIS (Netherlands)

    Feng, Yen Chen Anne; Cho, Kelly; Lindstrom, Sara; Kraft, Peter; Cormack, Jean; Blalock, Kendra; Campbell, Peter T.; Casey, Graham; Conti, David V.; Edlund, Christopher K.; Figueiredo, Jane; James Gauderman, W.; Gong, Jian; Green, Roger C.; Gruber, Stephen B.; Harju, John F.; Harrison, Tabitha A.; Jacobs, Eric J; Jenkins, Mark A.; Jiao, Shuo; Li, Li; Lin, Yi; Manion, Frank J.; Moreno, Victor; Mukherjee, Bhramar; Peters, Ulrike; Raskin, Leon; Schumacher, Fredrick R.; Seminara, Daniela; Severi, Gianluca; Stenzel, Stephanie L.; Thomas, Duncan C.; Hopper, John L.; Southey, Melissa C.; Makalic, Enes; Schmidt, Daniel F.; Fletcher, Olivia; Peto, Julian; Gibson, Lorna; Dos-Santos-Silva, Isabel; Hunter, David J.; Lindström, Sara; Kraft, Peter; Ahsan, Habib; Whittemore, Alice S.; Waisfisz, Quinten; Meijers-Heijboer, Hanne; Adank, Muriel A.; van der Luijt, Rob B.; Uitterlinden, Andre G; Hofman, Albert; Meindl, Alfons; Schmutzler, Rita K.; Müller-Myhsok, Bertram; Lichtner, Peter; Nevanlinna, Heli; Muranen, Taru A.; Aittomäki, Kristiina; Blomqvist, Carl; Chang-Claude, Jenny; Hein, Rebecca; Dahmen, Norbert; Beckman, Lars; Crisponi, Laura; Hall, Per; Czene, Kamila; Irwanto, Astrid; Liu, Jianjun; Easton, Douglas F.; Turnbull, Clare A.; Rahman, Nazneen; Kote-Jarai, Zsofia; Muir, Kenneth; Giles, Graham G.; Severi, Gianluca; Neal, David E.; Donovan, Jenny L.; Hamdy, Freddie C.; Wiklund, Fredrik; Gronberg, Henrik; Haiman, Christopher; Schumacher, Fred; Travis, Ruth C.; Riboli, Elio; Kraft, Peter; Hunter, David J.; Gapstur, Susan M.; Berndt, Sonja I.; Chanock, Stephen J.; Han, Younghun; Su, Li; Wei, Yongyue; Hung, Rayjean J.; Brhane, Yonathan; McLaughlin, John; Brennan, Paul; McKay, James D.; Bickeböller, Heike; Rosenberger, Albert; Houlston, Richard S.; Caporaso, Neil E; Landi, Maria Teresa; Heinrich, Joachim; Risch, Angela; Wu, Xifeng; Ye, Yuanqing; Christiani, David C.; Amos, Christopher I; Liang, Liming; Driver, Jane A.; IGAP Consortium, Colorectal Transdisciplinary Study (CORECT); Discovery, Biology, and Risk of Inherited Variants in Breast Cancer (DRIVE)

    2017-01-01

    Growing evidence from both epidemiology and basic science suggest an inverse association between Alzheimer’s disease (AD) and cancer. We examined the genetic relationship between AD and various cancer types using GWAS summary statistics from the IGAP and GAME-ON consortia. Sample size ranged from

  15. Functional validation of GWAS gene candidates for abnormal liver function during zebrafish liver development

    Directory of Open Access Journals (Sweden)

    Leah Y. Liu

    2013-09-01

    Genome-wide association studies (GWAS have revealed numerous associations between many phenotypes and gene candidates. Frequently, however, further elucidation of gene function has not been achieved. A recent GWAS identified 69 candidate genes associated with elevated liver enzyme concentrations, which are clinical markers of liver disease. To investigate the role of these genes in liver homeostasis, we narrowed down this list to 12 genes based on zebrafish orthology, zebrafish liver expression and disease correlation. To assess the function of gene candidates during liver development, we assayed hepatic progenitors at 48 hours post fertilization (hpf and hepatocytes at 72 hpf using in situ hybridization following morpholino knockdown in zebrafish embryos. Knockdown of three genes (pnpla3, pklr and mapk10 decreased expression of hepatic progenitor cells, whereas knockdown of eight genes (pnpla3, cpn1, trib1, fads2, slc2a2, pklr, mapk10 and samm50 decreased cell-specific hepatocyte expression. We then induced liver injury in zebrafish embryos using acetaminophen exposure and observed changes in liver toxicity incidence in morphants. Prioritization of GWAS candidates and morpholino knockdown expedites the study of newly identified genes impacting liver development and represents a feasible method for initial assessment of candidate genes to instruct further mechanistic analyses. Our analysis can be extended to GWAS for additional disease-associated phenotypes.

  16. GWAS for executive function and processing speed suggests involvement of the CADM2 gene

    NARCIS (Netherlands)

    C.A. Ibrahim-Verbaas (Carla); J. Bressler; S. Debette (Stéphanie); M. Schuur (Maaike); A.V. Smith; J.C. Bis (Joshua); G. Davies (Gail); S. Trompet (Stella); J.A. Smith; A. Björnsson (Asgeir); L.B. Chibnik (Lori); Y. Liu; V. Vitart (Veronique); M. Kirin (Mirna); K. Petrovic (Katja); O. Polasek (Ozren); L. Zgaga (Lina); C. Fawns-Ritchie; P. Hoffmann (Per); J. Karjalainen (Juha); J. Lahti; D.J. Llewellyn; C.O. Schmidt (Carsten O.); R. Mather; V. Chouraki (Vincent); Q. Sun; S. Resnick (Susan); L.M. Rose (Lynda M.); C. Oldmeadow (Christopher); M. Stewart; B.H. Smith; V. Gudnason (Vilmundur); Q. Yang (Qiong); S.S. Mirza (Saira); J.W. Jukema; P.L. DeJager (Philip L.); T.B. Harris (Tamara); D.C. Liewald (David C.); N. Amin (Najaf); L.H. Coker (Laura); O. Stegle (Oliver); O.L. Lopez; R. Schmidt; A. Teumer (Alexander); I. Ford; N. Karbalai (Nazanin); J.T. Becker (James); M.K. Jonsdottir (Maria K.); R. Au; R.S.N. Fehrmann (Rudolf); S. Herms (Stefan); M.A. Nalls (Michael); W. Zhao; S.T. Turner; K. Yaffe; K. Lohman (Kurt); J.C. van Swieten (John); S.L.R. Kardia; D.S. Knopman (David); W.M. Meeks (William); G. Heiss (Gerardo); E.G. Holliday (Elizabeth); P.W. Schofield; T. Tanaka (Toshiko); D.J. Stott (David J.); J. Wang (Jing); P.M. Ridker (Paul); A.J. Gow; A. Pattie (Alison); J.M. Starr (John); L.J. Hocking; N.J. Armstrong (Nicola J.); S. McLachlan (Stela); L. Shulman (Lee); L.C. Pilling (Luke); G. Eiriksdottir (Gudny); R.J. Scott; N.A. Kochan (Nicole A.); A. Palotie; Y.-C. Hsieh; J.G. Eriksson (Johan G.); A.D. Penman (Alan); R.F. Gottesman (Rebecca); B.A. Oostra (Ben); L. Yu; A.L. DeStefano (Anita L.); A. Beiser; M. Garcia; J.I. Rotter; M.M. Nöthen; A. Hofman (Albert); P.E. Slagboom (Eline); R.G.J. Westendorp; B.M. Buckley (Brendan M.); P.A. Wolf; A.G. Uitterlinden (André); B.M. Psaty (Bruce); H.J. Grabe (Hans Jörgen); S. Bandinelli (Stefania); D.I. Chasman (Daniel); F. Grodstein (Francine); K. Räikkönen (Katri); J.-C. Lambert; D.J. Porteous (David J.); J.F. Price (Jackie F.); P.S. Sachdev (Perminder); L. Ferrucci (Luigi); J. Attia (John); I. Rudan (Igor); C. Hayward; A.F. Wright; J.F. Wilson (James F); S. Cichon (Sven); L. Franke (Lude); H. Schmidt; J. Ding (Jingzhong); A.J. de Craen (Anton); M. Fornage (Myriam); D.A. Bennett (David); I.J. Deary (Ian); M.A. Ikram (Arfan); L.J. Launer (Lenore); A.L. Fitzpatrick; S. Seshadri (Sudha); C.M. van Duijn (Cornelia); T.H. Mosley (Thomas H.)

    2016-01-01

    textabstractTo identify common variants contributing to normal variation in two specific domains of cognitive functioning, we conducted a genome-wide association study (GWAS) of executive functioning and information processing speed in non-demented older adults from the CHARGE (Cohorts for Heart and

  17. meQTL analysis of asthma GWAS loci and DNA methylation

    NARCIS (Netherlands)

    Kumar, Ashish; Soderhall, Cilla; Merid, Simon Kebede; Xu, Chengjian; Koppelman, Gerard; Melen, Erik; Gruzieva, Olena; Kere, Juha; Pershagen, Goran

    2016-01-01

    Background: Asthma is characterized as a chronic inflammation disease and has increased in prevalence over the decades. Genome-wide association studies (GWAS) have implicated several single nucleotide polymorphisms (SNPs) with varying risk estimates for asthma, but the etiology is still not fully

  18. Expression QTL analysis of top loci from GWAS meta-analysis highlights additional schizophrenia candidate genes

    DEFF Research Database (Denmark)

    de Jong, Simone; van Eijk, Kristel R; Zeegers, Dave W L H

    2012-01-01

    of the Psychiatric GWAS consortium (PGC) yielded five novel loci for schizophrenia. In this study, we aim to highlight additional schizophrenia susceptibility loci from the PGC study by combining the top association findings from the discovery stage (9394 schizophrenia cases and 12 462 controls) with expression QTLs...

  19. Power in GWAS: lifting the curse of the clinical cut-off

    NARCIS (Netherlands)

    van der Sluis, S.; Posthuma, D.; Nivard, M.G.; Verhage, M.; Dolan, C.V.

    2013-01-01

    Although genome-wide association studies (GWAS), in general, facilitated important discovery of new biological knowledge about diseases,1, 2, 3 identified variants for psychiatric disorders explain little variation, and insight into the role of genes in highly heritable psychiatric traits remains

  20. A genome-wide association scan (GWAS) for mean telomere length within the COGS project

    DEFF Research Database (Denmark)

    Pooley, Karen A; Bojesen, Stig E; Weischer, Maren

    2013-01-01

    Mean telomere length (TL) in blood cells is heritable and has been reported to be associated with risks of several diseases, including cancer. We conducted a meta-analysis of three GWAS for TL (total n=2240) and selected 1629 variants for replication via the "iCOGS" custom genotyping array. All...

  1. Targeted exonic sequencing of GWAS loci in the high extremes of the plasma lipids distribution

    NARCIS (Netherlands)

    Patel, Aniruddh P.; Peloso, Gina M.; Pirruccello, James P.; Johansen, Christopher T.; Dubé, Joseph B.; Larach, Daniel B.; Ban, Matthew R.; Dallinge-Thie, Geesje M.; Gupta, Namrata; Boehnke, Michael; Abecasis, Gonçalo R.; Kastelein, John J. P.; Hovingh, G. Kees; Hegele, Robert A.; Rader, Daniel J.; Kathiresan, Sekar

    2016-01-01

    Genome-wide association studies (GWAS) for plasma lipid levels have mapped numerous genomic loci, with each region often containing many protein-coding genes. Targeted re-sequencing of exons is a strategy to pinpoint causal variants and genes. We performed solution-based hybrid selection of 9008

  2. Analyzing Local Spatio-Temporal Patterns of Police Calls-for-Service Using Bayesian Integrated Nested Laplace Approximation

    Directory of Open Access Journals (Sweden)

    Hui Luan

    2016-09-01

    Full Text Available This research investigates spatio-temporal patterns of police calls-for-service in the Region of Waterloo, Canada, at a fine spatial and temporal resolution. Modeling was implemented via Bayesian Integrated Nested Laplace Approximation (INLA. Temporal patterns for two-hour time periods, spatial patterns at the small-area scale, and space-time interaction (i.e., unusual departures from overall spatial and temporal patterns were estimated. Temporally, calls-for-service were found to be lowest in the early morning (02:00–03:59 and highest in the evening (20:00–21:59, while high levels of calls-for-service were spatially located in central business areas and in areas characterized by major roadways, universities, and shopping centres. Space-time interaction was observed to be geographically dispersed during daytime hours but concentrated in central business areas during evening hours. Interpreted through the routine activity theory, results are discussed with respect to law enforcement resource demand and allocation, and the advantages of modeling spatio-temporal datasets with Bayesian INLA methods are highlighted.

  3. Re-Ranking Sequencing Variants in the Post-GWAS Era for Accurate Causal Variant Identification

    Science.gov (United States)

    Faye, Laura L.; Machiela, Mitchell J.; Kraft, Peter; Bull, Shelley B.; Sun, Lei

    2013-01-01

    Next generation sequencing has dramatically increased our ability to localize disease-causing variants by providing base-pair level information at costs increasingly feasible for the large sample sizes required to detect complex-trait associations. Yet, identification of causal variants within an established region of association remains a challenge. Counter-intuitively, certain factors that increase power to detect an associated region can decrease power to localize the causal variant. First, combining GWAS with imputation or low coverage sequencing to achieve the large sample sizes required for high power can have the unintended effect of producing differential genotyping error among SNPs. This tends to bias the relative evidence for association toward better genotyped SNPs. Second, re-use of GWAS data for fine-mapping exploits previous findings to ensure genome-wide significance in GWAS-associated regions. However, using GWAS findings to inform fine-mapping analysis can bias evidence away from the causal SNP toward the tag SNP and SNPs in high LD with the tag. Together these factors can reduce power to localize the causal SNP by more than half. Other strategies commonly employed to increase power to detect association, namely increasing sample size and using higher density genotyping arrays, can, in certain common scenarios, actually exacerbate these effects and further decrease power to localize causal variants. We develop a re-ranking procedure that accounts for these adverse effects and substantially improves the accuracy of causal SNP identification, often doubling the probability that the causal SNP is top-ranked. Application to the NCI BPC3 aggressive prostate cancer GWAS with imputation meta-analysis identified a new top SNP at 2 of 3 associated loci and several additional possible causal SNPs at these loci that may have otherwise been overlooked. This method is simple to implement using R scripts provided on the author's website. PMID:23950724

  4. Partitioning heritability by functional category using GWAS summary statistics

    DEFF Research Database (Denmark)

    Finucane, Hilary K.; Bulik-Sullivan, Brendan; Gusev, Alexander

    2015-01-01

    Recent work has demonstrated that some functional categories of the genome contribute disproportionately to the heritability of complex diseases. Here we analyze a broad set of functional elements, including cell type-specific elements, to estimate their polygenic contributions to heritability in...

  5. Development and operation of an integrated sampling probe and gas analyzer for turbulent mixing studies in complex supersonic flows

    Science.gov (United States)

    Wiswall, John D.

    -temporal characteristic scales of the flow on the resulting time-area-averaged concentration measurements. Two series of experiments were performed to verify the probe's design; the first used Schlieren photography and verified that the probe sampled from the supersonic flowfield isokinetically. The second series involved traversing the probe across a free mixing layer of air and helium, to obtain both mean concentration and high frequency measurements. High-frequency data was statistically analyzed and inspection of the Probability Density Function (PDF) of the hot-film response was instrumental to interpret how well the resulting average mixing measurements represent these types of complex flows. The probe is minimally intrusive, has accuracy comparable to its predecessors, has an improved frequency response for mean concentration measurements, and samples from a very small area in the flowfield.

  6. Integrated circuit manufacture and tuning of subassemblies of a statistical analyzer of voltage oscillations (AKON). Izgotovleniye na integral'nykh skhemakh i nastroyka uzlov statisticheskogo analizatora kolebaniy napryazheniya (AKON)

    Energy Technology Data Exchange (ETDEWEB)

    Yermakov, V.F.; Oleynik, V.I.; Sambarov, Yu.M.

    1982-01-01

    The basic circuits and instructions for tuning subassemblies of a statistical analyzer of voltage oscillation are described. The device is intended for monitoring quality of voltage in electric networks in accordance with GOST13109-67. The component base of the device includes integrated circuits of the series 140, 155, 218 and 228.

  7. Results of a "GWAS plus:" general cognitive ability is substantially heritable and massively polygenic.

    Directory of Open Access Journals (Sweden)

    Robert M Kirkpatrick

    Full Text Available We carried out a genome-wide association study (GWAS for general cognitive ability (GCA plus three other analyses of GWAS data that aggregate the effects of multiple single-nucleotide polymorphisms (SNPs in various ways. Our multigenerational sample comprised 7,100 Caucasian participants, drawn from two longitudinal family studies, who had been assessed with an age-appropriate IQ test and had provided DNA samples passing quality screens. We conducted the GWAS across ∼ 2.5 million SNPs (both typed and imputed, using a generalized least-squares method appropriate for the different family structures present in our sample, and subsequently conducted gene-based association tests. We also conducted polygenic prediction analyses under five-fold cross-validation, using two different schemes of weighting SNPs. Using parametric bootstrapping, we assessed the performance of this prediction procedure under the null. Finally, we estimated the proportion of variance attributable to all genotyped SNPs as random effects with software GCTA. The study is limited chiefly by its power to detect realistic single-SNP or single-gene effects, none of which reached genome-wide significance, though some genomic inflation was evident from the GWAS. Unit SNP weights performed about as well as least-squares regression weights under cross-validation, but the performance of both increased as more SNPs were included in calculating the polygenic score. Estimates from GCTA were 35% of phenotypic variance at the recommended biological-relatedness ceiling. Taken together, our results concur with other recent studies: they support a substantial heritability of GCA, arising from a very large number of causal SNPs, each of very small effect. We place our study in the context of the literature-both contemporary and historical-and provide accessible explication of our statistical methods.

  8. Efficient Software for Multi-marker, Region-Based Analysis of GWAS Data

    Directory of Open Access Journals (Sweden)

    Jaleal S. Sanjak

    2016-04-01

    Full Text Available Genome-wide association studies (GWAS have associated many single variants with complex disease, yet the better part of heritable complex disease risk remains unexplained. Analytical tools designed to work under specific population genetic models are needed. Rare variants are increasingly shown to be important in human complex disease, but most existing GWAS data do not cover rare variants. Explicit population genetic models predict that genes contributing to complex traits and experiencing recurrent, unconditionally deleterious, mutation will harbor multiple rare, causative mutations of subtle effect. It is difficult to identify genes harboring rare variants of large effect that contribute to complex disease risk via the single marker association tests typically used in GWAS. Gene/region-based association tests may have the power detect associations by combining information from multiple markers, but have yielded limited success in practice. This is partially because many methods have not been widely applied. Here, we empirically demonstrate the utility of a procedure based on the rank truncated product (RTP method, filtered to reduce the effects of linkage disequilibrium. We apply the procedure to the Wellcome Trust Case Control Consortium (WTCCC data set, and uncover previously unidentified associations, some of which have been replicated in much larger studies. We show that, in the absence of significant rare variant coverage, RTP based methods still have the power to detect associated genes. We recommend that RTP-based methods be applied to all existing GWAS data to maximize the usefulness of those data. For this, we provide efficient software implementing our procedure.

  9. A simulation study of gene-by-environment interactions in GWAS implies ample hidden effects

    Science.gov (United States)

    Marigorta, Urko M.; Gibson, Greg

    2014-01-01

    The switch to a modern lifestyle in recent decades has coincided with a rapid increase in prevalence of obesity and other diseases. These shifts in prevalence could be explained by the release of genetic susceptibility for disease in the form of gene-by-environment (GxE) interactions. Yet, the detection of interaction effects requires large sample sizes, little replication has been reported, and a few studies have demonstrated environmental effects only after summing the risk of GWAS alleles into genetic risk scores (GRSxE). We performed extensive simulations of a quantitative trait controlled by 2500 causal variants to inspect the feasibility to detect gene-by-environment interactions in the context of GWAS. The simulated individuals were assigned either to an ancestral or a modern setting that alters the phenotype by increasing the effect size by 1.05–2-fold at a varying fraction of perturbed SNPs (from 1 to 20%). We report two main results. First, for a wide range of realistic scenarios, highly significant GRSxE is detected despite the absence of individual genotype GxE evidence at the contributing loci. Second, an increase in phenotypic variance after environmental perturbation reduces the power to discover susceptibility variants by GWAS in mixed cohorts with individuals from both ancestral and modern environments. We conclude that a pervasive presence of gene-by-environment effects can remain hidden even though it contributes to the genetic architecture of complex traits. PMID:25101110

  10. Genetic variation in HTR4 and lung function: GWAS follow-up in mouse.

    Science.gov (United States)

    House, John S; Li, Huiling; DeGraff, Laura M; Flake, Gordon; Zeldin, Darryl C; London, Stephanie J

    2015-01-01

    Human genome-wide association studies (GWASs) have identified numerous associations between single nucleotide polymorphisms (SNPs) and pulmonary function. Proving that there is a causal relationship between GWAS SNPs, many of which are noncoding and without known functional impact, and these traits has been elusive. Furthermore, noncoding GWAS-identified SNPs may exert trans-regulatory effects rather than impact the proximal gene. Noncoding variants in 5-hydroxytryptamine (serotonin) receptor 4 (HTR4) are associated with pulmonary function in human GWASs. To gain insight into whether this association is causal, we tested whether Htr4-null mice have altered pulmonary function. We found that HTR4-deficient mice have 12% higher baseline lung resistance and also increased methacholine-induced airway hyperresponsiveness (AHR) as measured by lung resistance (27%), tissue resistance (48%), and tissue elastance (30%). Furthermore, Htr4-null mice were more sensitive to serotonin-induced AHR. In models of exposure to bacterial lipopolysaccharide, bleomycin, and allergic airway inflammation induced by house dust mites, pulmonary function and cytokine profiles in Htr4-null mice differed little from their wild-type controls. The findings of altered baseline lung function and increased AHR in Htr4-null mice support a causal relationship between genetic variation in HTR4 and pulmonary function identified in human GWAS. © FASEB.

  11. Analyzing an Integrated Planning Approach Among Planning Scale and Sector A Case Study of Malang City’s Vision as The City of Education

    Directory of Open Access Journals (Sweden)

    Akhmad Amirudin

    2014-04-01

    Full Text Available Integrated planning is more needed by government today because of the complexity of problems and limited resources. Integrated planning can undertake the problems by giving comprehensive solution and provide how much resources are needed to reach the goal. Integrated planning approach is implied to provide better tools to guide actions towards the development of cities, improvement of human conditions, and ultimately a better urbanism. So the research focused on integrated planning in Malang City based on Malang City’s vision, strategic planning, operational planning, budgeting planning in Malang City to achieve Malang City’s vision as the city of Education. In this study, researcher used qualitative method with descriptive research, which is a research process aims to describe the exact nature / something happened and took place on the research conducted. The research purpose is to identify and describe and analyze the process of Malang City Planning Agency integrate other planning scale and sector in developing planning; and to identify, describe and analyze the process of Malang City Planning Agency integrated all stakeholders in Integrated Planning process. This research use descriptive research method. The reason to use descriptive research method in this study because the principle objectives of this study aimed to describe, illustrate in a systematic, factual and accurate statement of the facts and the relationship between phenomenon. Then qualitative method was directed at the individual's background and a holistic (whole. So in this case should not isolate the individual or organization into a variable or hypothesis, but should view it as part of wholeness. The result of this research in the case study of Malang City has shown thatThe case study of Malang City showed that various sectors recognized but did not pay much attention to Malang City’s vision as City of Education in their plans; however, Regional Mid-term Development

  12. Analyzing Clickstreams

    DEFF Research Database (Denmark)

    Andersen, Jesper; Giversen, Anders; Jensen, Allan H.

    in modern enterprises. In the data warehousing pproach, selected information is extracted in advance and stored in a repository. This approach is used because of its high performance. However, in many situations a logical (rather than physical) integration of data is preferable. Previous web-based data......On-Line Analytical Processing (OLAP) enables analysts to gain insight into data through fast and interactive access to a variety of possible views on information, organized in a dimensional model. The demand for data integration is rapidly becoming larger as more and more information sources appear....... Extensible Markup Language (XML) is fast becoming the new standard for data representation and exchange on the World Wide Web. The rapid emergence of XML data on the web, e.g., business-to-business (B2B) ecommerce, is making it necessary for OLAP and other data analysis tools to handleXML data as well...

  13. Radiometric analyzer

    International Nuclear Information System (INIS)

    Arima, S.; Oda, M.; Miyashita, K.; Takada, M.

    1977-01-01

    A radiometric analyzer for measuring the characteristic values of a sample by radiation includes a humer of radiation measuring subsystems having different ratios of sensitivities to the elements of the sample and linearizing circuits having inverse function characteristics of calibration functions which correspond to the radiation measuring subsystems. A weighing adder operates a desirable linear combination of the outputs of the linearizing circuits. Operators for operating between two or more different linear combinations are included

  14. Contrasting results from GWAS and QTL mapping on wing length in great reed warblers.

    Science.gov (United States)

    Hansson, Bengt; Sigeman, Hanna; Stervander, Martin; Tarka, Maja; Ponnikas, Suvi; Strandh, Maria; Westerdahl, Helena; Hasselquist, Dennis

    2018-04-15

    A major goal in evolutionary biology is to understand the genetic basis of adaptive traits. In migratory birds, wing morphology is such a trait. Our previous work on the great reed warbler (Acrocephalus arundinaceus) shows that wing length is highly heritable and under sexually antagonistic selection. Moreover, a quantitative trait locus (QTL) mapping analysis detected a pronounced QTL for wing length on chromosome 2, suggesting that wing morphology is partly controlled by genes with large effects. Here, we re-evaluate the genetic basis of wing length in great reed warblers using a genomewide association study (GWAS) approach based on restriction site-associated DNA sequencing (RADseq) data. We use GWAS models that account for relatedness between individuals and include covariates (sex, age and tarsus length). The resulting association landscape was flat with no peaks on chromosome 2 or elsewhere, which is in line with expectations for polygenic traits. Analysis of the distribution of p-values did not reveal biases, and the inflation factor was low. Effect sizes were however not uniformly distributed on some chromosomes, and the Z chromosome had weaker associations than autosomes. The level of linkage disequilibrium (LD) in the population decayed to background levels within c. 1 kbp. There could be several reasons to why our QTL study and GWAS gave contrasting results including differences in how associations are modelled (cosegregation in pedigree vs. LD associations), how covariates are accounted for in the models, type of marker used (multi- vs. biallelic), difference in power or a combination of these. Our study highlights that the genetic architecture even of highly heritable traits is difficult to characterize in wild populations. © 2018 John Wiley & Sons Ltd.

  15. Further support for association between GWAS variant for positive emotion and reward systems.

    Science.gov (United States)

    Lancaster, T M; Ihssen, N; Brindley, L M; Linden, D E J

    2017-01-31

    A recent genome-wide association study (GWAS) identified a significant single-nucleotide polymorphism (SNP) for trait-positive emotion at rs322931 on chromosome 1, which was also associated with brain activation in the reward system of healthy individuals when observing positive stimuli in a functional magnetic resonance imaging (fMRI) study. In the current study, we aimed to further validate the role of variation at rs322931 in reward processing. Using a similar fMRI approach, we use two paradigms that elicit a strong ventral striatum (VS) blood oxygen-level dependency (BOLD) response in a sample of young, healthy individuals (N=82). In the first study we use a similar picture-viewing task to the discovery sample (positive>neutral stimuli) to replicate an effect of the variant on emotion processing. In the second study we use a probabilistic reversal learning procedure to identify reward processing during decision-making under uncertainly (reward>punishment). In a region of interest (ROI) analysis of the bilateral VS, we show that the rs322931 genotype was associated with BOLD in the left VS during the positive>neutral contrast (P ROI-CORRECTED =0.045) and during the reward>punishment contrast (P ROI-CORRECTED =0.018), although the effect of passive picture viewing was in the opposite direction from that reported in the discovery sample. These findings suggest that the recently identified GWAS hit may influence positive emotion via individual differences in activity in the key hubs of the brain's reward system. Furthermore, these effects may not be limited to the passive viewing of positive emotional scenes, but may also be observed during dynamic decision-making. This study suggests that future studies of this GWAS locus may yield further insight into the biological mechanisms of psychopathologies characterised by deficits in reward processing and positive emotion.

  16. Molecular genetic studies in Saudi population; identified variants from GWAS and meta-analysis in stroke.

    Science.gov (United States)

    Alharbi, Khalid Khalaf; Ali Khan, Imran; Alotaibi, Mohammad Abdullah; Saud Aloyaid, Abdullah; Al-Basheer, Haifa Abdulaziz; Alghamdi, Naelah Abdullah; Al-Baradie, Raid Saleem; Al-Sulaiman, A M

    2018-01-01

    Stroke is a multifactorial and heterogeneous disorder, correlates with heritability and considered as one of the major diseases. The prior reports performed the variable models such as genome-wide association studies (GWAS), replication, case-control, cross-sectional and meta-analysis studies and still, we lack diagnostic marker in the global world. There are limited studies were carried out in Saudi population, and we aim to investigate the molecular association of single nucleotide polymorphisms (SNPs) identified through GWAS and meta-analysis studies in stroke patients in the Saudi population. In this case-control study, we have opted gender equality of 207 cases and 207 controls from the capital city of Saudi Arabia in King Saud University Hospital. The peripheral blood (5 ml) sample will be collected in two different vacutainers, and three mL of the coagulated blood will be used for lipid analysis (biochemical tests) and two mL will be used for DNA analysis (molecular tests). Genomic DNA will be extracted with the collected blood samples, and specific primers will be designed for the opted SNPs ( SORT1 -rs646218 and OLR1 -rs11053646 polymorphisms) and PCR-RFLP will be performed and randomly DNA sequencing will be carried out to cross check the results. The rs646218 and rs11053646 polymorphisms were significantly associated with allele, genotype and dominant models with and without crude odds ratios (OR's) and Multiple logistic regression analysis (p Saudi population. The current results were in the association with the prior study results documented through GWAS and meta-analysis association. However, other ethnic population studies should be performed to rule out in the human hereditary diseases.

  17. Replication of LDL GWAs hits in PROSPER/PHASE as validation for future (pharmacogenetic analyses

    Directory of Open Access Journals (Sweden)

    Stott David J

    2011-10-01

    Full Text Available Abstract Background The PHArmacogenetic study of Statins in the Elderly at risk (PHASE is a genome wide association study in the PROspective Study of Pravastatin in the Elderly at risk for vascular disease (PROSPER that investigates the genetic variation responsible for the individual variation in drug response to pravastatin. Statins lower LDL-cholesterol in general by 30%, however not in all subjects. Moreover, clinical response is highly variable and adverse effects occur in a minority of patients. In this report we first describe the rationale of the PROSPER/PHASE project and second show that the PROSPER/PHASE study can be used to study pharmacogenetics in the elderly. Methods The genome wide association study (GWAS was conducted using the Illumina 660K-Quad beadchips following manufacturer's instructions. After a stringent quality control 557,192 SNPs in 5,244 subjects were available for analysis. To maximize the availability of genetic data and coverage of the genome, imputation up to 2.5 million autosomal CEPH HapMap SNPs was performed with MACH imputation software. The GWAS for LDL-cholesterol is assessed with an additive linear regression model in PROBABEL software, adjusted for age, sex, and country of origin to account for population stratification. Results Forty-two SNPs reached the GWAS significant threshold of p = 5.0e-08 in 5 genomic loci (APOE/APOC1; LDLR; FADS2/FEN1; HMGCR; PSRC1/CELSR5. The top SNP (rs445925, chromosome 19 with a p-value of p = 2.8e-30 is located within the APOC1 gene and near the APOE gene. The second top SNP (rs6511720, chromosome 19 with a p-value of p = 5.22e-15 is located within the LDLR gene. All 5 genomic loci were previously associated with LDL-cholesterol levels, no novel loci were identified. Replication in WOSCOPS and CARE confirmed our results. Conclusion With the GWAS in the PROSPER/PHASE study we confirm the previously found genetic associations with LDL-cholesterol levels. With this proof

  18. Contamination Analyzer

    Science.gov (United States)

    1994-01-01

    Measurement of the total organic carbon content in water is important in assessing contamination levels in high purity water for power generation, pharmaceutical production and electronics manufacture. Even trace levels of organic compounds can cause defects in manufactured products. The Sievers Model 800 Total Organic Carbon (TOC) Analyzer, based on technology developed for the Space Station, uses a strong chemical oxidizing agent and ultraviolet light to convert organic compounds in water to carbon dioxide. After ionizing the carbon dioxide, the amount of ions is determined by measuring the conductivity of the deionized water. The new technique is highly sensitive, does not require compressed gas, and maintenance is minimal.

  19. Application of a New Integrated Decision Support Tool (i-DST) for Urban Water Infrastructure: Analyzing Water Quality Compliance Pathways for Three Los Angeles Watersheds

    Science.gov (United States)

    Gallo, E. M.; Hogue, T. S.; Bell, C. D.; Spahr, K.; McCray, J. E.

    2017-12-01

    The water quality of receiving streams and waterbodies in urban watersheds are increasingly polluted from stormwater runoff. The implementation of Green Infrastructure (GI), which includes Low Impact Developments (LIDs) and Best Management Practices (BMPs), within a watershed aim to mitigate the effects of urbanization by reducing pollutant loads, runoff volume, and storm peak flow. Stormwater modeling is generally used to assess the impact of GIs implemented within a watershed. These modeling tools are useful for determining the optimal suite of GIs to maximize pollutant load reduction and minimize cost. However, stormwater management for most resource managers and communities also includes the implementation of grey and hybrid stormwater infrastructure. An integrated decision support tool, called i-DST, that allows for the optimization and comprehensive life-cycle cost assessment of grey, green, and hybrid stormwater infrastructure, is currently being developed. The i-DST tool will evaluate optimal stormwater runoff management by taking into account the diverse economic, environmental, and societal needs associated with watersheds across the United States. Three watersheds from southern California will act as a test site and assist in the development and initial application of the i-DST tool. The Ballona Creek, Dominguez Channel, and Los Angeles River Watersheds are located in highly urbanized Los Angeles County. The water quality of the river channels flowing through each are impaired by heavy metals, including copper, lead, and zinc. However, despite being adjacent to one another within the same county, modeling results, using EPA System for Urban Stormwater Treatment and Analysis INtegration (SUSTAIN), found that the optimal path to compliance in each watershed differs significantly. The differences include varied costs, suites of BMPs, and ancillary benefits. This research analyzes how the economic, physical, and hydrological differences between the three

  20. A Highly Stable Marching-on-in-Time Volume Integral Equation Solver for Analyzing Transient Wave Interactions on High-Contrast Scatterers

    KAUST Repository

    Bagci, Hakan

    2014-01-06

    Time domain integral equation (TDIE) solvers represent an attractive alternative to finite difference (FDTD) and finite element (FEM) schemes for analyzing transient electromagnetic interactions on composite scatterers. Current induced on a scatterer, in response to a transient incident field, generates a scattered field. First, the scattered field is expressed as a spatio-temporal convolution of the current and the Green function of the background medium. Then, a TDIE is obtained by enforcing boundary conditions and/or fundamental field relations. TDIEs are often solved for the unknown current using marching on-in-time (MOT) schemes. MOT-TDIE solvers expand the current using local spatio-temporal basis functions. Inserting this expansion into the TDIE and testing the resulting equation in space and time yields a lower triangular system of equations (termed MOT system), which can be solved by marching in time for the coefficients of the current expansion. Stability of the MOT scheme often depends on how accurately the spatio-temporal convolution of the current and the Green function is discretized. In this work, band-limited prolate-based interpolation functions are used as temporal bases in expanding the current and discretizing the spatio-temporal convolution. Unfortunately, these functions are two sided, i.e., they require ”future” current samples for interpolation, resulting in a non-causal MOT system. To alleviate the effect of non-causality and restore the ability to march in time, an extrapolation scheme can be used to estimate the future values of the currents from their past values. Here, an accurate, stable and band-limited extrapolation scheme is developed for this purpose. This extrapolation scheme uses complex exponents, rather than commonly used harmonics, so that propagating and decaying mode fields inside the dielectric scatterers are accurately modeled. The resulting MOT scheme is applied to solving the time domain volume integral equation (VIE

  1. Genetic Susceptibility to Vitiligo: GWAS Approaches for Identifying Vitiligo Susceptibility Genes and Loci

    Science.gov (United States)

    Shen, Changbing; Gao, Jing; Sheng, Yujun; Dou, Jinfa; Zhou, Fusheng; Zheng, Xiaodong; Ko, Randy; Tang, Xianfa; Zhu, Caihong; Yin, Xianyong; Sun, Liangdan; Cui, Yong; Zhang, Xuejun

    2016-01-01

    Vitiligo is an autoimmune disease with a strong genetic component, characterized by areas of depigmented skin resulting from loss of epidermal melanocytes. Genetic factors are known to play key roles in vitiligo through discoveries in association studies and family studies. Previously, vitiligo susceptibility genes were mainly revealed through linkage analysis and candidate gene studies. Recently, our understanding of the genetic basis of vitiligo has been rapidly advancing through genome-wide association study (GWAS). More than 40 robust susceptible loci have been identified and confirmed to be associated with vitiligo by using GWAS. Most of these associated genes participate in important pathways involved in the pathogenesis of vitiligo. Many susceptible loci with unknown functions in the pathogenesis of vitiligo have also been identified, indicating that additional molecular mechanisms may contribute to the risk of developing vitiligo. In this review, we summarize the key loci that are of genome-wide significance, which have been shown to influence vitiligo risk. These genetic loci may help build the foundation for genetic diagnosis and personalize treatment for patients with vitiligo in the future. However, substantial additional studies, including gene-targeted and functional studies, are required to confirm the causality of the genetic variants and their biological relevance in the development of vitiligo. PMID:26870082

  2. A Powerful Approach to Estimating Annotation-Stratified Genetic Covariance via GWAS Summary Statistics.

    Science.gov (United States)

    Lu, Qiongshi; Li, Boyang; Ou, Derek; Erlendsdottir, Margret; Powles, Ryan L; Jiang, Tony; Hu, Yiming; Chang, David; Jin, Chentian; Dai, Wei; He, Qidu; Liu, Zefeng; Mukherjee, Shubhabrata; Crane, Paul K; Zhao, Hongyu

    2017-12-07

    Despite the success of large-scale genome-wide association studies (GWASs) on complex traits, our understanding of their genetic architecture is far from complete. Jointly modeling multiple traits' genetic profiles has provided insights into the shared genetic basis of many complex traits. However, large-scale inference sets a high bar for both statistical power and biological interpretability. Here we introduce a principled framework to estimate annotation-stratified genetic covariance between traits using GWAS summary statistics. Through theoretical and numerical analyses, we demonstrate that our method provides accurate covariance estimates, thereby enabling researchers to dissect both the shared and distinct genetic architecture across traits to better understand their etiologies. Among 50 complex traits with publicly accessible GWAS summary statistics (N total ≈ 4.5 million), we identified more than 170 pairs with statistically significant genetic covariance. In particular, we found strong genetic covariance between late-onset Alzheimer disease (LOAD) and amyotrophic lateral sclerosis (ALS), two major neurodegenerative diseases, in single-nucleotide polymorphisms (SNPs) with high minor allele frequencies and in SNPs located in the predicted functional genome. Joint analysis of LOAD, ALS, and other traits highlights LOAD's correlation with cognitive traits and hints at an autoimmune component for ALS. Copyright © 2017 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

  3. Comparison of Macular Integrity Assessment (MAIA ™, MP-3, and the Humphrey Field Analyzer in the Evaluation of the Relationship between the Structure and Function of the Macula.

    Directory of Open Access Journals (Sweden)

    Kazuyuki Hirooka

    Full Text Available This study was conducted in order to compare relationships between the macular visual field (VF mean sensitivity measured by MAIATM (Macular Integrity Assessment, MP-3, or Humphry field analyzer (HFA and the ganglion cell and inner plexiform layer (GCA thicknesses.This cross-sectional study examined 73 glaucoma patients and 19 normal subjects. All subjects underwent measurements for GCA thickness by Cirrus HD-OCT and static threshold perimetry using MAIATM, MP-3, or HFA. VF and OCT in the retinal view were used to examine both the global relationship between the VF sensitivity and GCA thickness, and the superior hemiretina and inferior hemiretina. The relationship between the GCA thickness and macular sensitivity was examined by Spearman correlation analysis.For each instrument, statistically significant macular VF sensitivity (dB and GCA thickness relationships were observed using the decibel scale (R = 0.547-0.687, all P < 0.001. The highest correlation for the global (R = 0.682 and the superior hemiretina (R = 0.594 GCA thickness-VF mean sensitivity was observed by the HFA. The highest correlation for the inferior hemiretina (R = 0.687 GCA thickness-VF mean sensitivity was observed by the MP-3. Among the three VF measurement instruments, however, no significant differences were found for the structure-function relationships.All three VF measurement instruments found similar structure-function relationships in the central VF.

  4. Effects of GWAS-associated genetic variants on lncRNAs within IBD and T1D candidate loci

    DEFF Research Database (Denmark)

    Mirza, Aashiq H; Kaur, Simranjeet; Brorsson, Caroline A

    2014-01-01

    -nucleotide polymorphisms (SNPs) identified by genome-wide association studies (GWAS) lie outside of the protein coding regions, and map to the non-coding intervals. However, the relationship between phenotype-associated loci and the non-coding regions including the long non-coding RNAs (lncRNAs) is poorly understood. Here......, we systemically identified all annotated IBD and T1D loci-associated lncRNAs, and mapped nominally significant GWAS/ImmunoChip SNPs for IBD and T1D within these lncRNAs. Additionally, we identified tissue-specific cis-eQTLs, and strong linkage disequilibrium (LD) signals associated with these SNPs...... within and in close proximity (+/-5 kb flanking regions) of IBD and T1D loci-associated candidate genes, suggesting that these RNA conformation-altering polymorphisms might be associated with diseased-phenotype. Disruption of lncRNA secondary structure due to presence of GWAS SNPs provides valuable...

  5. Evaluation of common genetic variants identified by GWAS for early onset and morbid obesity in population-based samples

    DEFF Research Database (Denmark)

    den Hoed, M; Luan, J; Langenberg, C

    2013-01-01

    BACKGROUND: Meta-analysis of case-control genome-wide association studies (GWAS) for early onset and morbid obesity identified four variants in/near the PRL, PTER, MAF and NPC1 genes. OBJECTIVE: We aimed to validate association of these variants with obesity-related traits in population-based sam......BACKGROUND: Meta-analysis of case-control genome-wide association studies (GWAS) for early onset and morbid obesity identified four variants in/near the PRL, PTER, MAF and NPC1 genes. OBJECTIVE: We aimed to validate association of these variants with obesity-related traits in population......, these variants, which were identified in a GWAS for early onset and morbid obesity, do not seem to influence obesity-related traits in the general population....

  6. Analyzing an Integrated Planning Approach Among Planning Scale and Sector a Case Study of Malang City's Vision as the City of Education

    OpenAIRE

    Amirudin, Akhmad; Fefta Wijaya, Andy; Yossomsakdi, Samrit

    2014-01-01

    Integrated planning is more needed by government today because of the complexity of problems and limited resources. Integrated planning can undertake the problems by giving comprehensive solution and provide how much resources are needed to reach the goal. Integrated planning approach is implied to provide better tools to guide actions towards the development of cities, improvement of human conditions, and ultimately a better urbanism. So the research focused on integrated planning in Malang ...

  7. Influence of DC arc jets on flow fields analyzed by an integrated numerical model for a DC-RF hybrid plasma

    International Nuclear Information System (INIS)

    Seo, Jun Ho; Park, Jin Myung; Hong, Sang Hee

    2008-01-01

    The influence of DC arc jets on the flow fields in a hybrid plasma torch is numerically analyzed by an integrated direct current-radio frequency (DC-RF) plasma model based on magneto-hydrodynamic formulations. The calculated results reveal that the increase in DC arc gas flow rate raises the axial flow velocity along the central column of the DC-RF hybrid plasma together with the enhanced backflow streams in the peripheral wall region. The temperature profiles on the torch exit plane are little affected due to the reheating process of the central column by the combined RF plasma. Accordingly, the exit enthalpy emitted from the DC-RF hybrid torch can be concentrated to the central column of the plasma and controlled by adjusting the DC arc gas flow rate. The swirl in the sheath gas flow turns out to have the opposite effect on the DC arc gas flow rate. The swirling motion of the sheath gas can reduce the back flows near the induction tube wall as well as the axial velocities in the central column of the plasma. Accordingly, the swirl in the sheath gas flow can be used for the functional operation of the DC-RF hybrid plasma along with the DC arc gas flow rate to suppress the back flows at the wall region and to reduce the excessive interactions between the DC arc jet and the ambient RF plasmas. The effects of DC input current on the flow fields of hybrid plasma are similar to those of the DC arc gas flow rate, but the axial velocities for the higher current relatively quickly decay along the centerline. This is in contrast to the increase in the axial velocity remaining in proportion to the increase in the DC arc gas flow rate all the way up to the exit of the DC-RF hybrid plasma. Accordingly, the present integrated numerical analysis suggests that the hybrid plasma field profiles and the entrainment of ambient air from the torch exit are controllable by adjusting the DC arc gas flow rate, the DC input current and swirl in the sheath gas flow taking advantage of

  8. A Markov blanket-based method for detecting causal SNPs in GWAS

    Directory of Open Access Journals (Sweden)

    Han Bing

    2010-04-01

    Full Text Available Abstract Background Detecting epistatic interactions associated with complex and common diseases can help to improve prevention, diagnosis and treatment of these diseases. With the development of genome-wide association studies (GWAS, designing powerful and robust computational method for identifying epistatic interactions associated with common diseases becomes a great challenge to bioinformatics society, because the study of epistatic interactions often deals with the large size of the genotyped data and the huge amount of combinations of all the possible genetic factors. Most existing computational detection methods are based on the classification capacity of SNP sets, which may fail to identify SNP sets that are strongly associated with the diseases and introduce a lot of false positives. In addition, most methods are not suitable for genome-wide scale studies due to their computational complexity. Results We propose a new Markov Blanket-based method, DASSO-MB (Detection of ASSOciations using Markov Blanket to detect epistatic interactions in case-control GWAS. Markov blanket of a target variable T can completely shield T from all other variables. Thus, we can guarantee that the SNP set detected by DASSO-MB has a strong association with diseases and contains fewest false positives. Furthermore, DASSO-MB uses a heuristic search strategy by calculating the association between variables to avoid the time-consuming training process as in other machine-learning methods. We apply our algorithm to simulated datasets and a real case-control dataset. We compare DASSO-MB to other commonly-used methods and show that our method significantly outperforms other methods and is capable of finding SNPs strongly associated with diseases. Conclusions Our study shows that DASSO-MB can identify a minimal set of causal SNPs associated with diseases, which contains less false positives compared to other existing methods. Given the huge size of genomic dataset

  9. Using prior information from the medical literature in GWAS of oral cancer identifies novel susceptibility variant on chromosome 4--the AdAPT method.

    LENUS (Irish Health Repository)

    Johansson, Mattias

    2012-01-01

    Genome-wide association studies (GWAS) require large sample sizes to obtain adequate statistical power, but it may be possible to increase the power by incorporating complementary data. In this study we investigated the feasibility of automatically retrieving information from the medical literature and leveraging this information in GWAS.

  10. A population genetic interpretation of GWAS findings for human quantitative traits

    Science.gov (United States)

    Bullaughey, Kevin; Hudson, Richard R.; Sella, Guy

    2018-01-01

    Human genome-wide association studies (GWASs) are revealing the genetic architecture of anthropomorphic and biomedical traits, i.e., the frequencies and effect sizes of variants that contribute to heritable variation in a trait. To interpret these findings, we need to understand how genetic architecture is shaped by basic population genetics processes—notably, by mutation, natural selection, and genetic drift. Because many quantitative traits are subject to stabilizing selection and because genetic variation that affects one trait often affects many others, we model the genetic architecture of a focal trait that arises under stabilizing selection in a multidimensional trait space. We solve the model for the phenotypic distribution and allelic dynamics at steady state and derive robust, closed-form solutions for summary statistics of the genetic architecture. Our results provide a simple interpretation for missing heritability and why it varies among traits. They predict that the distribution of variances contributed by loci identified in GWASs is well approximated by a simple functional form that depends on a single parameter: the expected contribution to genetic variance of a strongly selected site affecting the trait. We test this prediction against the results of GWASs for height and body mass index (BMI) and find that it fits the data well, allowing us to make inferences about the degree of pleiotropy and mutational target size for these traits. Our findings help to explain why the GWAS for height explains more of the heritable variance than the similarly sized GWAS for BMI and to predict the increase in explained heritability with study sample size. Considering the demographic history of European populations, in which these GWASs were performed, we further find that most of the associations they identified likely involve mutations that arose shortly before or during the Out-of-Africa bottleneck at sites with selection coefficients around s = 10−3. PMID

  11. GWAS of clinically defined gout and subtypes identifies multiple susceptibility loci that include urate transporter genes.

    Science.gov (United States)

    Nakayama, Akiyoshi; Nakaoka, Hirofumi; Yamamoto, Ken; Sakiyama, Masayuki; Shaukat, Amara; Toyoda, Yu; Okada, Yukinori; Kamatani, Yoichiro; Nakamura, Takahiro; Takada, Tappei; Inoue, Katsuhisa; Yasujima, Tomoya; Yuasa, Hiroaki; Shirahama, Yuko; Nakashima, Hiroshi; Shimizu, Seiko; Higashino, Toshihide; Kawamura, Yusuke; Ogata, Hiraku; Kawaguchi, Makoto; Ohkawa, Yasuyuki; Danjoh, Inaho; Tokumasu, Atsumi; Ooyama, Keiko; Ito, Toshimitsu; Kondo, Takaaki; Wakai, Kenji; Stiburkova, Blanka; Pavelka, Karel; Stamp, Lisa K; Dalbeth, Nicola; Sakurai, Yutaka; Suzuki, Hiroshi; Hosoyamada, Makoto; Fujimori, Shin; Yokoo, Takashi; Hosoya, Tatsuo; Inoue, Ituro; Takahashi, Atsushi; Kubo, Michiaki; Ooyama, Hiroshi; Shimizu, Toru; Ichida, Kimiyoshi; Shinomiya, Nariyoshi; Merriman, Tony R; Matsuo, Hirotaka

    2017-05-01

    A genome-wide association study (GWAS) of gout and its subtypes was performed to identify novel gout loci, including those that are subtype-specific. Putative causal association signals from a GWAS of 945 clinically defined gout cases and 1213 controls from Japanese males were replicated with 1396 cases and 1268 controls using a custom chip of 1961 single nucleotide polymorphisms (SNPs). We also first conducted GWASs of gout subtypes. Replication with Caucasian and New Zealand Polynesian samples was done to further validate the loci identified in this study. In addition to the five loci we reported previously, further susceptibility loci were identified at a genome-wide significance level (pgout cases, and NIPAL1 and FAM35A for the renal underexcretion gout subtype. While NIPAL1 encodes a magnesium transporter, functional analysis did not detect urate transport via NIPAL1, suggesting an indirect association with urate handling. Localisation analysis in the human kidney revealed expression of NIPAL1 and FAM35A mainly in the distal tubules, which suggests the involvement of the distal nephron in urate handling in humans. Clinically ascertained male patients with gout and controls of Caucasian and Polynesian ancestries were also genotyped, and FAM35A was associated with gout in all cases. A meta-analysis of the three populations revealed FAM35A to be associated with gout at a genome-wide level of significance (p meta =3.58×10 -8 ). Our findings including novel gout risk loci provide further understanding of the molecular pathogenesis of gout and lead to a novel concept for the therapeutic target of gout/hyperuricaemia. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

  12. Geographic Differences in Genetic Susceptibility to IgA Nephropathy: GWAS Replication Study and Geospatial Risk Analysis

    NARCIS (Netherlands)

    Kiryluk, Krzysztof; Li, Yifu; Sanna-Cherchi, Simone; Rohanizadegan, Mersedeh; Suzuki, Hitoshi; Eitner, Frank; Snyder, Holly J.; Choi, Murim; Hou, Ping; Scolari, Francesco; Izzi, Claudia; Gigante, Maddalena; Gesualdo, Loreto; Savoldi, Silvana; Amoroso, Antonio; Cusi, Daniele; Zamboli, Pasquale; Julian, Bruce A.; Novak, Jan; Wyatt, Robert J.; Mucha, Krzysztof; Perola, Markus; Kristiansson, Kati; Viktorin, Alexander; Magnusson, Patrik K.; Thorleifsson, Gudmar; Thorsteinsdottir, Unnur; Stefansson, Kari; Boland, Anne; Metzger, Marie; Thibaudin, Lise; Wanner, Christoph; Jager, Kitty J.; Goto, Shin; Maixnerova, Dita; Karnib, Hussein H.; Nagy, Judit; Panzer, Ulf; Xie, Jingyuan; Chen, Nan; Tesar, Vladimir; Narita, Ichiei; Berthoux, Francois; Floege, Jürgen; Stengel, Benedicte; Zhang, Hong; Lifton, Richard P.; Gharavi, Ali G.

    2012-01-01

    IgA nephropathy (IgAN), major cause of kidney failure worldwide, is common in Asians, moderately prevalent in Europeans, and rare in Africans. It is not known if these differences represent variation in genes, environment, or ascertainment. In a recent GWAS, we localized five IgAN susceptibility

  13. Emerging applications of genome-editing technology to examine functionality of GWAS-associated variants for complex traits.

    Science.gov (United States)

    Smith, Andrew J P; Deloukas, Panos; Munroe, Patricia B

    2018-04-13

    Over the last decade, genome-wide association studies (GWAS) have propelled the discovery of thousands of loci associated with complex diseases. The focus is now turning towards the function of these association signals, determining the causal variant(s) amongst those in strong linkage disequilibrium, and identifying their underlying mechanisms, such as long-range gene regulation. Genome-editing techniques utilising zinc-finger nucleases (ZFN), transcription activator-like effector nucleases (TALENs) and clustered regularly-interspaced short palindromic repeats with Cas9 nuclease (CRISPR-Cas9), are becoming the tools of choice to establish functionality for these variants, due to the ability to assess effects of single variants in vivo. This review will discuss examples of how these technologies have begun to aid functional analysis of GWAS loci for complex traits such as cardiovascular disease, type 2 diabetes, cancer, obesity and autoimmune disease. We focus on analysis of variants occurring within non-coding genomic regions, as these comprise the majority of GWAS variants, providing the greatest challenges to determining functionality, and compare editing strategies that provide different levels of evidence for variant functionality. The review describes molecular insights into some of these potentially causal variants, and how these may relate to the pathology of the trait, and look towards future directions for these technologies in post-GWAS analysis, such as base-editing.

  14. Accounting for eXentricities: analysis of the X chromosome in GWAS reveals X-linked genes implicated in autoimmune diseases.

    Directory of Open Access Journals (Sweden)

    Diana Chang

    Full Text Available Many complex human diseases are highly sexually dimorphic, suggesting a potential contribution of the X chromosome to disease risk. However, the X chromosome has been neglected or incorrectly analyzed in most genome-wide association studies (GWAS. We present tailored analytical methods and software that facilitate X-wide association studies (XWAS, which we further applied to reanalyze data from 16 GWAS of different autoimmune and related diseases (AID. We associated several X-linked genes with disease risk, among which (1 ARHGEF6 is associated with Crohn's disease and replicated in a study of ulcerative colitis, another inflammatory bowel disease (IBD. Indeed, ARHGEF6 interacts with a gastric bacterium that has been implicated in IBD. (2 CENPI is associated with three different AID, which is compelling in light of known associations with AID of autosomal genes encoding centromere proteins, as well as established autosomal evidence of pleiotropy between autoimmune diseases. (3 We replicated a previous association of FOXP3, a transcription factor that regulates T-cell development and function, with vitiligo; and (4 we discovered that C1GALT1C1 exhibits sex-specific effect on disease risk in both IBDs. These and other X-linked genes that we associated with AID tend to be highly expressed in tissues related to immune response, participate in major immune pathways, and display differential gene expression between males and females. Combined, the results demonstrate the importance of the X chromosome in autoimmunity, reveal the potential of extensive XWAS, even based on existing data, and provide the tools and incentive to properly include the X chromosome in future studies.

  15. Interactions between household air pollution and GWAS-identified lung cancer susceptibility markers in the Female Lung Cancer Consortium in Asia (FLCCA).

    Science.gov (United States)

    Hosgood, H Dean; Song, Minsun; Hsiung, Chao Agnes; Yin, Zhihua; Shu, Xiao-Ou; Wang, Zhaoming; Chatterjee, Nilanjan; Zheng, Wei; Caporaso, Neil; Burdette, Laurie; Yeager, Meredith; Berndt, Sonja I; Landi, Maria Teresa; Chen, Chien-Jen; Chang, Gee-Chen; Hsiao, Chin-Fu; Tsai, Ying-Huang; Chien, Li-Hsin; Chen, Kuan-Yu; Huang, Ming-Shyan; Su, Wu-Chou; Chen, Yuh-Min; Chen, Chung-Hsing; Yang, Tsung-Ying; Wang, Chih-Liang; Hung, Jen-Yu; Lin, Chien-Chung; Perng, Reury-Perng; Chen, Chih-Yi; Chen, Kun-Chieh; Li, Yao-Jen; Yu, Chong-Jen; Chen, Yi-Song; Chen, Ying-Hsiang; Tsai, Fang-Yu; Kim, Christopher; Seow, Wei Jie; Bassig, Bryan A; Wu, Wei; Guan, Peng; He, Qincheng; Gao, Yu-Tang; Cai, Qiuyin; Chow, Wong-Ho; Xiang, Yong-Bing; Lin, Dongxin; Wu, Chen; Wu, Yi-Long; Shin, Min-Ho; Hong, Yun-Chul; Matsuo, Keitaro; Chen, Kexin; Wong, Maria Pik; Lu, Dara; Jin, Li; Wang, Jiu-Cun; Seow, Adeline; Wu, Tangchun; Shen, Hongbing; Fraumeni, Joseph F; Yang, Pan-Chyr; Chang, I-Shou; Zhou, Baosen; Chanock, Stephen J; Rothman, Nathaniel; Lan, Qing

    2015-03-01

    We previously carried out a multi-stage genome-wide association study (GWAS) on lung cancer among never smokers in the Female Lung Cancer Consortium in Asia (FLCCA) (6,609 cases, 7,457 controls) that identified novel susceptibility loci at 10q25.2, 6q22.2, and 6p21.32, and confirmed two previously identified loci at 5p15.33 and 3q28. Household air pollution (HAP) attributed to solid fuel burning for heating and cooking, is the leading cause of the overall disease burden in Southeast Asia, and is known to contain lung carcinogens. To evaluate the gene-HAP interactions associated with lung cancer in loci independent of smoking, we analyzed data from studies participating in FLCCA with fuel use information available (n = 3; 1,731 cases; 1,349 controls). Coal use was associated with a 30% increased risk of lung cancer (OR 1.3, 95% CI 1.0-1.6). Among the five a priori SNPs identified by our GWAS, two showed a significant interaction with coal use (HLA Class II rs2395185, p = 0.02; TP63 rs4488809 (rs4600802), p = 0.04). The risk of lung cancer associated with coal exposure varied with the respective alleles for these two SNPs. Our observations provide evidence that genetic variation in HLA Class II and TP63 may modify the association between HAP and lung cancer risk. The roles played in the cell cycle and inflammation pathways by the proteins encoded by these two genes provide biological plausibility for these interactions; however, additional replication studies are needed in other non-smoking populations.

  16. AprioriGWAS, a new pattern mining strategy for detecting genetic variants associated with disease through interaction effects.

    Science.gov (United States)

    Zhang, Qingrun; Long, Quan; Ott, Jurg

    2014-06-01

    Identifying gene-gene interaction is a hot topic in genome wide association studies. Two fundamental challenges are: (1) how to smartly identify combinations of variants that may be associated with the trait from astronomical number of all possible combinations; and (2) how to test epistatic interaction when all potential combinations are available. We developed AprioriGWAS, which brings two innovations. (1) Based on Apriori, a successful method in field of Frequent Itemset Mining (FIM) in which a pattern growth strategy is leveraged to effectively and accurately reduce search space, AprioriGWAS can efficiently identify genetically associated genotype patterns. (2) To test the hypotheses of epistasis, we adopt a new conditional permutation procedure to obtain reliable statistical inference of Pearson's chi-square test for the [Formula: see text] contingency table generated by associated variants. By applying AprioriGWAS to age-related macular degeneration (AMD) data, we found that: (1) angiopoietin 1 (ANGPT1) and four retinal genes interact with Complement Factor H (CFH). (2) GO term "glycosaminoglycan biosynthetic process" was enriched in AMD interacting genes. The epistatic interactions newly found by AprioriGWAS on AMD data are likely true interactions, since genes interacting with CFH are retinal genes, and GO term enrichment also verified that interaction between glycosaminoglycans (GAGs) and CFH plays an important role in disease pathology of AMD. By applying AprioriGWAS on Bipolar disorder in WTCCC data, we found variants without marginal effect show significant interactions. For example, multiple-SNP genotype patterns inside gene GABRB2 and GRIA1 (AMPA subunit 1 receptor gene). AMPARs are found in many parts of the brain and are the most commonly found receptor in the nervous system. The GABRB2 mediates the fastest inhibitory synaptic transmission in the central nervous system. GRIA1 and GABRB2 are relevant to mental disorders supported by multiple

  17. GWAS of agronomic traits in soybean collection included in breeding pool in Kazakhstan.

    Science.gov (United States)

    Zatybekov, Alibek; Abugalieva, Saule; Didorenko, Svetlana; Gerasimova, Yelena; Sidorik, Ivan; Anuarbek, Shynar; Turuspekov, Yerlan

    2017-11-14

    In recent years soybean is becoming one of the most important oilseed crops in Kazakhstan. Only within the last ten years (2006-2016), the area under soybean is expanded from 45 thousand hectares (ha) in 2006 to 120 thousand ha in 2016. The general trend of soybean expansion is from south-eastern to eastern and northern regions of the country, where average temperatures are lower and growing seasons are shorter. These new soybean growing territories were poorly examined in terms of general effects on productivity level among the diverse sample of soybean accessions. In this study, phenotypic data were collected in three separate regions of Kazakhstan and entire soybean sample was genotyped for identification of marker-trait associations (MTA). In this study, the collection of 113 accessions representing five different regions of the World was planted in 2015-2016 in northern, eastern, and south-eastern regions of Kazakhstan. It was observed that North American accessions showed the highest yield in four out of six trials especially in Northern Kazakhstan in both years. The entire sample was genotyped with 6 K SNP Illumina array. 4442 SNPs found to be polymorphic and were used for whole genome genotyping purposes. Obtained SNP markers data and field data were used for GWAS (genome-wide association study). 30 SNPs appear to be very significant in 42 MTAs in six studied environments. The study confirms the efficiency of GWAS for the identification of molecular markers which tag important agronomic traits. Overall thirty SNP markers associated with time to flowering and maturation, plant height, number of fertile nodes, seeds per plant and yield were identified. Physical locations of 32 identified out of 42 total MTAs coincide well with positions of known analogous QTLs. This result indicates importance of revealed MTAs for soybean growing regions in Kazakhstan. Obtained results would serve as required prerequisite for forming and realization of specific breeding

  18. Identification and Verification of QTL Associated with Frost Tolerance Using Linkage Mapping and GWAS in Winter Faba Bean.

    Science.gov (United States)

    Sallam, Ahmed; Arbaoui, Mustapha; El-Esawi, Mohamed; Abshire, Nathan; Martsch, Regina

    2016-01-01

    Frost stress is one of the abiotic stresses that causes a significant reduction in winter faba bean yield in Europe. The main objective of this work is to genetically improve frost tolerance in winter faba bean by identifying and validating QTL associated with frost tolerance to be used in marker-assisted selection (MAS). Two different genetic backgrounds were used: a biparental population (BPP) consisting of 101 inbred lines, and 189 genotypes from single seed descent (SSD) from the Gottingen Winter bean Population (GWBP). All experiments were conducted in a frost growth chamber under controlled conditions. Both populations were genotyped using the same set of 189 SNP markers. Visual scoring for frost stress symptoms was used to define frost tolerance in both populations. In addition, leaf fatty acid composition (FAC) and proline content were analyzed in BPP as physiological traits. QTL mapping (for BPP) and genome wide association studies (for GWBP) were performed to detect QTL associated with frost tolerance. High genetic variation between genotypes, and repeatability estimates, were found for all traits. QTL mapping and GWAS identified new putative QTL associated with promising frost tolerance and related traits. A set of 54 SNP markers common in both genetic backgrounds showed a high genetic diversity with polymorphic information content (PIC) ranging from 0.31 to 0.37 and gene diversity ranging from 0.39 to 0.50. This indicates that these markers may be polymorphic for many faba bean populations. Five SNP markers showed a significant marker-trait association with frost tolerance and related traits in both populations. Moreover, synteny analysis between Medicago truncatula (a model legume) and faba bean genomes was performed to identify candidate genes for these markers. Collinearity was evaluated between the faba bean genetic map constructed in this study and the faba bean consensus map, resulting in identifying possible genomic regions in faba bean which may

  19. Identification and Verification of QTL Associated with Frost Tolerance Using Linkage Mapping and GWAS in Winter Faba Bean

    Science.gov (United States)

    Sallam, Ahmed; Arbaoui, Mustapha; El-Esawi, Mohamed; Abshire, Nathan; Martsch, Regina

    2016-01-01

    Frost stress is one of the abiotic stresses that causes a significant reduction in winter faba bean yield in Europe. The main objective of this work is to genetically improve frost tolerance in winter faba bean by identifying and validating QTL associated with frost tolerance to be used in marker-assisted selection (MAS). Two different genetic backgrounds were used: a biparental population (BPP) consisting of 101 inbred lines, and 189 genotypes from single seed descent (SSD) from the Gottingen Winter bean Population (GWBP). All experiments were conducted in a frost growth chamber under controlled conditions. Both populations were genotyped using the same set of 189 SNP markers. Visual scoring for frost stress symptoms was used to define frost tolerance in both populations. In addition, leaf fatty acid composition (FAC) and proline content were analyzed in BPP as physiological traits. QTL mapping (for BPP) and genome wide association studies (for GWBP) were performed to detect QTL associated with frost tolerance. High genetic variation between genotypes, and repeatability estimates, were found for all traits. QTL mapping and GWAS identified new putative QTL associated with promising frost tolerance and related traits. A set of 54 SNP markers common in both genetic backgrounds showed a high genetic diversity with polymorphic information content (PIC) ranging from 0.31 to 0.37 and gene diversity ranging from 0.39 to 0.50. This indicates that these markers may be polymorphic for many faba bean populations. Five SNP markers showed a significant marker-trait association with frost tolerance and related traits in both populations. Moreover, synteny analysis between Medicago truncatula (a model legume) and faba bean genomes was performed to identify candidate genes for these markers. Collinearity was evaluated between the faba bean genetic map constructed in this study and the faba bean consensus map, resulting in identifying possible genomic regions in faba bean which may

  20. Fasting Glucose GWAS Candidate Region Analysis across Ethnic Groups in the Multi-Ethnic Study of Atherosclerosis (MESA)

    OpenAIRE

    Rasmussen-Torvik, L. J.; Guo, X.; Bowden, D. W.; Bertoni, A. G.; Sale, M. M.; Yao, J.; Bluemke, D. A.; Goodarzi, M. O.; Chen, Y. I.; Vaidya, D.; Raffel, L. J.; Papanicolaou, G.J.; Meigs, J. B.; Pankow, J. S.

    2012-01-01

    Genetic variants associated with fasting glucose in European ancestry populations are increasingly well understood. However, the nature of the associations between these SNPs and fasting glucose in other racial and ethnic groups is unclear. We sought to examine regions previously identified to be associated with fasting glucose in Caucasian GWAS across multiple ethnicities in the Multi-Ethnic Study of Atherosclerosis (MESA). Non-diabetic MESA participants with fasting glucose measured at the ...

  1. Comprehensive evaluation of disease- and trait-specific enrichment for eight functional elements among GWAS-identified variants.

    Science.gov (United States)

    Markunas, Christina A; Johnson, Eric O; Hancock, Dana B

    2017-07-01

    Genome-wide association study (GWAS)-identified variants are enriched for functional elements. However, we have limited knowledge of how functional enrichment may differ by disease/trait and tissue type. We tested a broad set of eight functional elements for enrichment among GWAS-identified SNPs (p Enrichment analyses were conducted using logistic regression, with Bonferroni correction. Overall, a significant enrichment was observed for all functional elements, except sequence motifs. Missense SNPs showed the strongest magnitude of enrichment. eQTLs were the only functional element significantly enriched across all diseases/traits. Magnitudes of enrichment were generally similar across diseases/traits, where enrichment was statistically significant. Blood vs. brain tissue effects on enrichment were dependent on disease/trait and functional element (e.g., cardiovascular disease: eQTLs P TissueDifference  = 1.28 × 10 -6 vs. enhancers P TissueDifference  = 0.94). Identifying disease/trait-relevant functional elements and tissue types could provide new insight into the underlying biology, by guiding a priori GWAS analyses (e.g., brain enhancer elements for psychiatric disease) or facilitating post hoc interpretation.

  2. A real-time integrator of storage-area contents for SA 40B or DIDAC 800 analyzers. Use in the digital single-channel mode

    International Nuclear Information System (INIS)

    Rigaudiere, Roger; Daburon, M.-L.

    1976-09-01

    An apparatus was developed in order to sum up, during counting, the channel contents from several storage areas of SA 40 B or DIDAC 800 multichannel analyzers. The pulse number stored in the energy bands interesting the operator are known and if necessary subsequent operation can be modified accordingly. Coupled with an autonomous amplitude encoder, this apparatus can be operated in the digital single-channel mode [fr

  3. Pathway analysis of GWAS provides new insights into genetic susceptibility to 3 inflammatory diseases.

    Directory of Open Access Journals (Sweden)

    Hariklia Eleftherohorinou

    2009-11-01

    Full Text Available Although the introduction of genome-wide association studies (GWAS have greatly increased the number of genes associated with common diseases, only a small proportion of the predicted genetic contribution has so far been elucidated. Studying the cumulative variation of polymorphisms in multiple genes acting in functional pathways may provide a complementary approach to the more common single SNP association approach in understanding genetic determinants of common disease. We developed a novel pathway-based method to assess the combined contribution of multiple genetic variants acting within canonical biological pathways and applied it to data from 14,000 UK individuals with 7 common diseases. We tested inflammatory pathways for association with Crohn's disease (CD, rheumatoid arthritis (RA and type 1 diabetes (T1D with 4 non-inflammatory diseases as controls. Using a variable selection algorithm, we identified variants responsible for the pathway association and evaluated their use for disease prediction using a 10 fold cross-validation framework in order to calculate out-of-sample area under the Receiver Operating Curve (AUC. The generalisability of these predictive models was tested on an independent birth cohort from Northern Finland. Multiple canonical inflammatory pathways showed highly significant associations (p 10(-3-10(-20 with CD, T1D and RA. Variable selection identified on average a set of 205 SNPs (149 genes for T1D, 350 SNPs (189 genes for RA and 493 SNPs (277 genes for CD. The pattern of polymorphisms at these SNPS were found to be highly predictive of T1D (91% AUC and RA (85% AUC, and weakly predictive of CD (60% AUC. The predictive ability of the T1D model (without any parameter refitting had good predictive ability (79% AUC in the Finnish cohort. Our analysis suggests that genetic contribution to common inflammatory diseases operates through multiple genes interacting in functional pathways.

  4. GWAS-based pathway analysis differentiates between fluid and crystallized intelligence.

    Science.gov (United States)

    Christoforou, A; Espeseth, T; Davies, G; Fernandes, C P D; Giddaluru, S; Mattheisen, M; Tenesa, A; Harris, S E; Liewald, D C; Payton, A; Ollier, W; Horan, M; Pendleton, N; Haggarty, P; Djurovic, S; Herms, S; Hoffman, P; Cichon, S; Starr, J M; Lundervold, A; Reinvang, I; Steen, V M; Deary, I J; Le Hellard, S

    2014-09-01

    Cognitive abilities vary among people. About 40-50% of this variability is due to general intelligence (g), which reflects the positive correlation among individuals' scores on diverse cognitive ability tests. g is positively correlated with many life outcomes, such as education, occupational status and health, motivating the investigation of its underlying biology. In psychometric research, a distinction is made between general fluid intelligence (gF) - the ability to reason in novel situations - and general crystallized intelligence (gC) - the ability to apply acquired knowledge. This distinction is supported by developmental and cognitive neuroscience studies. Classical epidemiological studies and recent genome-wide association studies (GWASs) have established that these cognitive traits have a large genetic component. However, no robust genetic associations have been published thus far due largely to the known polygenic nature of these traits and insufficient sample sizes. Here, using two GWAS datasets, in which the polygenicity of gF and gC traits was previously confirmed, a gene- and pathway-based approach was undertaken with the aim of characterizing and differentiating their genetic architecture. Pathway analysis, using genes selected on the basis of relaxed criteria, revealed notable differences between these two traits. gF appeared to be characterized by genes affecting the quantity and quality of neurons and therefore neuronal efficiency, whereas long-term depression (LTD) seemed to underlie gC. Thus, this study supports the gF-gC distinction at the genetic level and identifies functional annotations and pathways worthy of further investigation. © 2014 The Authors. Genes, Brain and Behavior published by International Behavioural and Neural Genetics Society and John Wiley & Sons Ltd.

  5. Development of an integrated optimization method for analyzing effect of energy conversion efficiency under uncertainty – A case study of Bayingolin Mongol Autonomous Prefecture, China

    International Nuclear Information System (INIS)

    Jin, S.W.; Li, Y.P.; Huang, G.H.; Hao, Q.; Nie, S.

    2015-01-01

    Highlights: • Superiority–inferiority full-infinite mixed-integer method is developed. • The method can tackle uncertainties of fuzzy sets, crisp and functional intervals. • The method is applied to a real case of planning energy system. • Effects of energy-conversion efficiency on energy systems are analyzed. • Results can support policy enactment of conversion efficiency improvement. - Abstract: In this study, a superiority–inferiority full-infinite mixed-integer programming (SFMP) method is developed for analyzing the effect of energy conversion efficiency under uncertainty. SFMP can effectively tackle uncertainties expressed as fuzzy sets, crisp intervals and functional intervals, it also can directly reflect relationships among multiple fuzzy sets through varying superiority and inferiority degrees with a high computational efficiency. Then the developed SFMP is applied to a real case of planning energy system for Bayingolin Mongol Autonomous Prefecture, where multiple scenarios related to different energy-conversion efficiency are concerned. Results for energy processing, energy conversion, capacity expansion, pollutant emission and system cost have been generated. It is proved that SFMP is an effective approach to deal with the uncertainties in energy systems with interactive and uncertain characteristics. A variety of uncertainties existed in energy conversion processes and impact factors could affect the modeling result. Results show that improvement of energy-conversion efficiency can effectively facilitate reducing energy resources consumption, optimizing energy generation pattern, decreasing capacity expansion, as well as mitigating pollutant emissions. Results also reveal that, for the study area, electric power has a highest energy saving potential among heating, oil processing, coal washing and refining. Results can help decision makers to generate desired alternatives that can facilitate policy enactment of conversion efficiency

  6. Integration

    DEFF Research Database (Denmark)

    Emerek, Ruth

    2004-01-01

    Bidraget diskuterer de forskellige intergrationsopfattelse i Danmark - og hvad der kan forstås ved vellykket integration......Bidraget diskuterer de forskellige intergrationsopfattelse i Danmark - og hvad der kan forstås ved vellykket integration...

  7. Integrated Chemical and Microorganism Monitoring of Air Using Gas Chromatography/Ion Mobility Spectometry: Toward an Expanded-Use Volatile Organic Analyzer (VOA)

    Science.gov (United States)

    Eiceman, G. A.

    1999-01-01

    The work described in this research program originated with the choice by NASA of an ion mobility spectrometer for air quality monitoring on-board the international spacestation. Though the gas chromatograph-ion mobility spectrometer analyzer known as VOA met or exceeded expectations, limitations in the basic understanding of response and the utilization of foundational principles into usable technology was considered unacceptable. In this research program, a comprehensive model for the origins of mobility spectra was proposed, tested and verified. The principles considered responsible for the appearance of mobility spectra have now been elucidated through this project. This understanding has been applied in automated identification of mobility spectra using neural networks and routine procedures for this now exist. Finally, the limitation on linear range has been shown to be a technical limitation and not a fundamental limitation so that a hardware component was crafted to extend the linear range of a mobility spectrometer by 10X. This project has led to one Ph.D. dissertation and one MS thesis. In addition, over ten public presentations at professional meetings and six journal publications have resulted from this program of research. The findings are so plentiful that total analysis of the findings may require four to six years or more. The findings confirm that the decision to use VOA was sound and that the chemical and physical principles of mobility spectrometry are both understandable and predictable.

  8. [Integrity].

    Science.gov (United States)

    Gómez Rodríguez, Rafael Ángel

    2014-01-01

    To say that someone possesses integrity is to claim that that person is almost predictable about responses to specific situations, that he or she can prudentially judge and to act correctly. There is a closed interrelationship between integrity and autonomy, and the autonomy rests on the deeper moral claim of all humans to integrity of the person. Integrity has two senses of significance for medical ethic: one sense refers to the integrity of the person in the bodily, psychosocial and intellectual elements; and in the second sense, the integrity is the virtue. Another facet of integrity of the person is la integrity of values we cherish and espouse. The physician must be a person of integrity if the integrity of the patient is to be safeguarded. The autonomy has reduced the violations in the past, but the character and virtues of the physician are the ultimate safeguard of autonomy of patient. A field very important in medicine is the scientific research. It is the character of the investigator that determines the moral quality of research. The problem arises when legitimate self-interests are replaced by selfish, particularly when human subjects are involved. The final safeguard of moral quality of research is the character and conscience of the investigator. Teaching must be relevant in the scientific field, but the most effective way to teach virtue ethics is through the example of the a respected scientist.

  9. Mechanistic phenotypes: an aggregative phenotyping strategy to identify disease mechanisms using GWAS data.

    Directory of Open Access Journals (Sweden)

    Jonathan D Mosley

    Full Text Available A single mutation can alter cellular and global homeostatic mechanisms and give rise to multiple clinical diseases. We hypothesized that these disease mechanisms could be identified using low minor allele frequency (MAF<0.1 non-synonymous SNPs (nsSNPs associated with "mechanistic phenotypes", comprised of collections of related diagnoses. We studied two mechanistic phenotypes: (1 thrombosis, evaluated in a population of 1,655 African Americans; and (2 four groupings of cancer diagnoses, evaluated in 3,009 white European Americans. We tested associations between nsSNPs represented on GWAS platforms and mechanistic phenotypes ascertained from electronic medical records (EMRs, and sought enrichment in functional ontologies across the top-ranked associations. We used a two-step analytic approach whereby nsSNPs were first sorted by the strength of their association with a phenotype. We tested associations using two reverse genetic models and standard additive and recessive models. In the second step, we employed a hypothesis-free ontological enrichment analysis using the sorted nsSNPs to identify functional mechanisms underlying the diagnoses comprising the mechanistic phenotypes. The thrombosis phenotype was solely associated with ontologies related to blood coagulation (Fisher's p = 0.0001, FDR p = 0.03, driven by the F5, P2RY12 and F2RL2 genes. For the cancer phenotypes, the reverse genetics models were enriched in DNA repair functions (p = 2×10-5, FDR p = 0.03 (POLG/FANCI, SLX4/FANCP, XRCC1, BRCA1, FANCA, CHD1L while the additive model showed enrichment related to chromatid segregation (p = 4×10-6, FDR p = 0.005 (KIF25, PINX1. We were able to replicate nsSNP associations for POLG/FANCI, BRCA1, FANCA and CHD1L in independent data sets. Mechanism-oriented phenotyping using collections of EMR-derived diagnoses can elucidate fundamental disease mechanisms.

  10. Evaluation of novel candidate variations and their interactions related to bipolar disorders: Analysis of GWAS data

    Directory of Open Access Journals (Sweden)

    Acikel C

    2016-11-01

    , have prioritized similar SNP profiles as predictors of bipolar disorders, in contrast to MDR, which has found different SNPs through analysis of two-way and three-way interactions. The reduced number of associated SNPs discovered by MDR, without loss in the classification performance, would facilitate validation studies and decision support models, and would reduce the cost to develop predictive and diagnostic tests. Nevertheless, we need to emphasize that translation of genomic models to the clinical setting requires models with higher classification performance. Keywords: Bipolar disorders, GWAS, MDR, Data Mining, SNP, Decision Support

  11. Assessment of Five Chilling Tolerance Traits and GWAS Mapping in Rice Using the USDA Mini-Core Collection

    Directory of Open Access Journals (Sweden)

    Michael R. Schläppi

    2017-06-01

    Full Text Available Rice (Oryza sativa L. is often exposed to cool temperatures during spring planting in temperate climates. A better understanding of genetic pathways regulating chilling tolerance will enable breeders to develop varieties with improved tolerance during germination and young seedling stages. To dissect chilling tolerance, five assays were developed; one assay for the germination stage, one assay for the germination and seedling stage, and three for the seedling stage. Based on these assays, five chilling tolerance indices were calculated and assessed using 202 O. sativa accessions from the Rice Mini-Core (RMC collection. Significant differences between RMC accessions made the five indices suitable for genome-wide association study (GWAS based quantitative trait loci (QTL mapping. For young seedling stage indices, japonica and indica subspecies clustered into chilling tolerant and chilling sensitive accessions, respectively, while both subspecies had similar low temperature germinability distributions. Indica subspecies were shown to have chilling acclimation potential. GWAS mapping uncovered 48 QTL at 39 chromosome regions distributed across all 12 rice chromosomes. Interestingly, there was no overlap between the germination and seedling stage QTL. Also, 18 QTL and 32 QTL were in regions discovered in previously reported bi-parental and GWAS based QTL mapping studies, respectively. Two novel low temperature seedling survivability (LTSS–QTL, qLTSS3-4 and qLTSS4-1, were not in a previously reported QTL region. QTL with strong effect alleles identified in this study will be useful for marker assisted breeding efforts to improve chilling tolerance in rice cultivars and enhance gene discovery for chilling tolerance.

  12. Genetic dissection of photoperiod response based on GWAS of pre-anthesis phase duration in spring barley.

    Directory of Open Access Journals (Sweden)

    Ahmad M Alqudah

    Full Text Available Heading time is a complex trait, and natural variation in photoperiod responses is a major factor controlling time to heading, adaptation and grain yield. In barley, previous heading time studies have been mainly conducted under field conditions to measure total days to heading. We followed a novel approach and studied the natural variation of time to heading in a world-wide spring barley collection (218 accessions, comprising of 95 photoperiod-sensitive (Ppd-H1 and 123 accessions with reduced photoperiod sensitivity (ppd-H1 to long-day (LD through dissecting pre-anthesis development into four major stages and sub-phases. The study was conducted under greenhouse (GH conditions (LD; 16/8 h; ∼20/∼16°C day/night. Genotyping was performed using a genome-wide high density 9K single nucleotide polymorphisms (SNPs chip which assayed 7842 SNPs. We used the barley physical map to identify candidate genes underlying genome-wide association scans (GWAS. GWAS for pre-anthesis stages/sub-phases in each photoperiod group provided great power for partitioning genetic effects on floral initiation and heading time. In addition to major genes known to regulate heading time under field conditions, several novel QTL with medium to high effects, including new QTL having major effects on developmental stages/sub-phases were found to be associated in this study. For example, highly associated SNPs tagged the physical regions around HvCO1 (barley CONSTANS1 and BFL (BARLEY FLORICAULA/LEAFY genes. Based upon our GWAS analysis, we propose a new genetic network model for each photoperiod group, which includes several newly identified genes, such as several HvCO-like genes, belonging to different heading time pathways in barley.

  13. GWAS for plant growth stages and yield components in spring wheat (Triticum aestivum L.) harvested in three regions of Kazakhstan.

    Science.gov (United States)

    Turuspekov, Yerlan; Baibulatova, Aida; Yermekbayev, Kanat; Tokhetova, Laura; Chudinov, Vladimir; Sereda, Grigoriy; Ganal, Martin; Griffiths, Simon; Abugalieva, Saule

    2017-11-14

    Spring wheat is the largest agricultural crop grown in Kazakhstan with an annual sowing area of 12 million hectares in 2016. Annually, the country harvests around 15 million tons of high quality grain. Despite environmental stress factors it is predicted that the use of new technologies may lead to increases in productivity from current levels of 1.5 to up to 3 tons per hectare. One way of improving wheat productivity is by the application of new genomic oriented approaches in plant breeding projects. Genome wide association studies (GWAS) are emerging as powerful tools for the understanding of the inheritance of complex traits via utilization of high throughput genotyping technologies and phenotypic assessments of plant collections. In this study, phenotyping and genotyping data on 194 spring wheat accessions from Kazakhstan, Russia, Europe, and CIMMYT were assessed for the identification of marker-trait associations (MTA) of agronomic traits by using GWAS. Field trials in Northern, Central and Southern regions of Kazakhstan using 194 spring wheat accessions revealed strong correlations of yield with booting date, plant height, biomass, number of spikes per plant, and number of kernels per spike. The accessions from Europe and CIMMYT showed high breeding potential for Southern and Central regions of the country in comparison with the performance of the local varieties. The GGE biplot method, using average yield per plant, suggested a clear separation of accessions into their three breeding origins in relationship to the three environments in which they were evaluated. The genetic variation in the three groups of accessions was further studied using 3245 polymorphic SNP (single nucleotide polymorphism) markers. The application of Principal Coordinate analysis clearly grouped the 194 accessions into three clades according to their breeding origins. GWAS on data from nine field trials allowed the identification of 114 MTAs for 12 different agronomic traits. Field

  14. GWAS signals across the HLA regions: revealing a clue for common etiology underlying infectious tumors and other immunity diseases

    Institute of Scientific and Technical Information of China (English)

    Yin Yao Shugart; Ying Wang; Wei-Hua Jia; Yi-Xin Zeng

    2011-01-01

    Increasing evidence suggests that multiple genes in the human leukocyte antigen (HLA) regions play an important role in development of cancers and immunity disorders. However, the biological mechanisms of the HLA associations are not well understood. We recently conducted a survey of all genome-wide association studies (GWAS) with significant findings in the HLA regions and concluded that diseases such as cancer and immune disorders are more likely to be associated with genetic variants located in the HLA regions than other diseases. This finding is suggestive for testing a hypothesis of a common etiology of infectious tumors and other immunity diseases.

  15. Replication of LDL GWAs hits in PROSPER/PHASE as validation for future (pharmaco)genetic analyses

    LENUS (Irish Health Repository)

    Trompet, Stella

    2011-10-06

    Abstract Background The PHArmacogenetic study of Statins in the Elderly at risk (PHASE) is a genome wide association study in the PROspective Study of Pravastatin in the Elderly at risk for vascular disease (PROSPER) that investigates the genetic variation responsible for the individual variation in drug response to pravastatin. Statins lower LDL-cholesterol in general by 30%, however not in all subjects. Moreover, clinical response is highly variable and adverse effects occur in a minority of patients. In this report we first describe the rationale of the PROSPER\\/PHASE project and second show that the PROSPER\\/PHASE study can be used to study pharmacogenetics in the elderly. Methods The genome wide association study (GWAS) was conducted using the Illumina 660K-Quad beadchips following manufacturer\\'s instructions. After a stringent quality control 557,192 SNPs in 5,244 subjects were available for analysis. To maximize the availability of genetic data and coverage of the genome, imputation up to 2.5 million autosomal CEPH HapMap SNPs was performed with MACH imputation software. The GWAS for LDL-cholesterol is assessed with an additive linear regression model in PROBABEL software, adjusted for age, sex, and country of origin to account for population stratification. Results Forty-two SNPs reached the GWAS significant threshold of p = 5.0e-08 in 5 genomic loci (APOE\\/APOC1; LDLR; FADS2\\/FEN1; HMGCR; PSRC1\\/CELSR5). The top SNP (rs445925, chromosome 19) with a p-value of p = 2.8e-30 is located within the APOC1 gene and near the APOE gene. The second top SNP (rs6511720, chromosome 19) with a p-value of p = 5.22e-15 is located within the LDLR gene. All 5 genomic loci were previously associated with LDL-cholesterol levels, no novel loci were identified. Replication in WOSCOPS and CARE confirmed our results. Conclusion With the GWAS in the PROSPER\\/PHASE study we confirm the previously found genetic associations with LDL-cholesterol levels. With this proof

  16. Characterizing associations and SNP-environment interactions for GWAS-identified prostate cancer risk markers--results from BPC3.

    Directory of Open Access Journals (Sweden)

    Sara Lindstrom

    2011-02-01

    Full Text Available Genome-wide association studies (GWAS have identified multiple single nucleotide polymorphisms (SNPs associated with prostate cancer risk. However, whether these associations can be consistently replicated, vary with disease aggressiveness (tumor stage and grade and/or interact with non-genetic potential risk factors or other SNPs is unknown. We therefore genotyped 39 SNPs from regions identified by several prostate cancer GWAS in 10,501 prostate cancer cases and 10,831 controls from the NCI Breast and Prostate Cancer Cohort Consortium (BPC3. We replicated 36 out of 39 SNPs (P-values ranging from 0.01 to 10⁻²⁸. Two SNPs located near KLK3 associated with PSA levels showed differential association with Gleason grade (rs2735839, P = 0.0001 and rs266849, P = 0.0004; case-only test, where the alleles associated with decreasing PSA levels were inversely associated with low-grade (as defined by Gleason grade < 8 tumors but positively associated with high-grade tumors. No other SNP showed differential associations according to disease stage or grade. We observed no effect modification by SNP for association with age at diagnosis, family history of prostate cancer, diabetes, BMI, height, smoking or alcohol intake. Moreover, we found no evidence of pair-wise SNP-SNP interactions. While these SNPs represent new independent risk factors for prostate cancer, we saw little evidence for effect modification by other SNPs or by the environmental factors examined.

  17. Large-Scale Cognitive GWAS Meta-Analysis Reveals Tissue-Specific Neural Expression and Potential Nootropic Drug Targets

    Directory of Open Access Journals (Sweden)

    Max Lam

    2017-11-01

    Full Text Available Here, we present a large (n = 107,207 genome-wide association study (GWAS of general cognitive ability (“g”, further enhanced by combining results with a large-scale GWAS of educational attainment. We identified 70 independent genomic loci associated with general cognitive ability. Results showed significant enrichment for genes causing Mendelian disorders with an intellectual disability phenotype. Competitive pathway analysis implicated the biological processes of neurogenesis and synaptic regulation, as well as the gene targets of two pharmacologic agents: cinnarizine, a T-type calcium channel blocker, and LY97241, a potassium channel inhibitor. Transcriptome-wide and epigenome-wide analysis revealed that the implicated loci were enriched for genes expressed across all brain regions (most strongly in the cerebellum. Enrichment was exclusive to genes expressed in neurons but not oligodendrocytes or astrocytes. Finally, we report genetic correlations between cognitive ability and disparate phenotypes including psychiatric disorders, several autoimmune disorders, longevity, and maternal age at first birth.

  18. A 40 GHz fully integrated circuit with a vector network analyzer and a coplanar-line-based detection area for circulating tumor cell analysis using 65 nm CMOS technology

    Science.gov (United States)

    Nakanishi, Taiki; Matsunaga, Maya; Kobayashi, Atsuki; Nakazato, Kazuo; Niitsu, Kiichi

    2018-03-01

    A 40-GHz fully integrated CMOS-based circuit for circulating tumor cells (CTC) analysis, consisting of an on-chip vector network analyzer (VNA) and a highly sensitive coplanar-line-based detection area is presented in this paper. In this work, we introduce a fully integrated architecture that eliminates unwanted parasitic effects. The proposed analyzer was designed using 65 nm CMOS technology, and SPICE and MWS simulations were used to validate its operation. The simulation confirmed that the proposed circuit can measure S-parameter shifts resulting from the addition of various types of tumor cells to the detection area, the data of which are provided in a previous study: the |S 21| values for HepG2, A549, and HEC-1-A cells are -0.683, -0.580, and -0.623 dB, respectively. Additionally, the measurement demonstrated an S-parameters reduction of -25.7% when a silicone resin was put on the circuit. Hence, the proposed system is expected to contribute to cancer diagnosis.

  19. Digital Microfluidics Sample Analyzer

    Science.gov (United States)

    Pollack, Michael G.; Srinivasan, Vijay; Eckhardt, Allen; Paik, Philip Y.; Sudarsan, Arjun; Shenderov, Alex; Hua, Zhishan; Pamula, Vamsee K.

    2010-01-01

    Three innovations address the needs of the medical world with regard to microfluidic manipulation and testing of physiological samples in ways that can benefit point-of-care needs for patients such as premature infants, for which drawing of blood for continuous tests can be life-threatening in their own right, and for expedited results. A chip with sample injection elements, reservoirs (and waste), droplet formation structures, fluidic pathways, mixing areas, and optical detection sites, was fabricated to test the various components of the microfluidic platform, both individually and in integrated fashion. The droplet control system permits a user to control droplet microactuator system functions, such as droplet operations and detector operations. Also, the programming system allows a user to develop software routines for controlling droplet microactuator system functions, such as droplet operations and detector operations. A chip is incorporated into the system with a controller, a detector, input and output devices, and software. A novel filler fluid formulation is used for the transport of droplets with high protein concentrations. Novel assemblies for detection of photons from an on-chip droplet are present, as well as novel systems for conducting various assays, such as immunoassays and PCR (polymerase chain reaction). The lab-on-a-chip (a.k.a., lab-on-a-printed-circuit board) processes physiological samples and comprises a system for automated, multi-analyte measurements using sub-microliter samples of human serum. The invention also relates to a diagnostic chip and system including the chip that performs many of the routine operations of a central labbased chemistry analyzer, integrating, for example, colorimetric assays (e.g., for proteins), chemiluminescence/fluorescence assays (e.g., for enzymes, electrolytes, and gases), and/or conductometric assays (e.g., for hematocrit on plasma and whole blood) on a single chip platform.

  20. Bacterial Genetic Architecture of Ecological Interactions in Co-culture by GWAS-Taking Escherichia coli and Staphylococcus aureus as an Example.

    Science.gov (United States)

    He, Xiaoqing; Jin, Yi; Ye, Meixia; Chen, Nan; Zhu, Jing; Wang, Jingqi; Jiang, Libo; Wu, Rongling

    2017-01-01

    How a species responds to such a biotic environment in the community, ultimately leading to its evolution, has been a topic of intense interest to ecological evolutionary biologists. Until recently, limited knowledge was available regarding the genotypic changes that underlie phenotypic changes. Our study implemented GWAS (Genome-Wide Association Studies) to illustrate the genetic architecture of ecological interactions that take place in microbial populations. By choosing 45 such interspecific pairs of Escherichia coli and Staphylococcus aureus strains that were all genotyped throughout the entire genome, we employed Q-ROADTRIPS to analyze the association between single SNPs and microbial abundance measured at each time point for bacterial populations reared in monoculture and co-culture, respectively. We identified a large number of SNPs and indels across the genomes (35.69 G clean data of E. coli and 50.41 G of S. aureus ). We reported 66 and 111 SNPs that were associated with interaction in E. coli and S. aureus , respectively. 23 out of 66 polymorphic changes resulted in amino acid alterations.12 significant genes, such as murE, treA, argS , and relA , which were also identified in previous evolutionary studies. In S. aureus , 111 SNPs detected in coding sequences could be divided into 35 non-synonymous and 76 synonymous SNPs. Our study illustrated the potential of genome-wide association methods for studying rapidly evolving traits in bacteria. Genetic association study methods will facilitate the identification of genetic elements likely to cause phenotypes of interest and provide targets for further laboratory investigation.

  1. 'Integration'

    DEFF Research Database (Denmark)

    Olwig, Karen Fog

    2011-01-01

    , while the countries have adopted disparate policies and ideologies, differences in the actual treatment and attitudes towards immigrants and refugees in everyday life are less clear, due to parallel integration programmes based on strong similarities in the welfare systems and in cultural notions...... of equality in the three societies. Finally, it shows that family relations play a central role in immigrants’ and refugees’ establishment of a new life in the receiving societies, even though the welfare society takes on many of the social and economic functions of the family....

  2. Association between GWAS-identified lung adenocarcinoma susceptibility loci and EGFR mutations in never-smoking Asian women, and comparison with findings from Western populations

    NARCIS (Netherlands)

    Seow, Wei Jie; Matsuo, Keitaro; Hsiung, Chao Agnes; Shiraishi, Kouya; Song, Minsun; Kim, Hee Nam; Wong, Maria Pik; Hong, Yun-Chul; Hosgood, H. Dean; Wang, Zhaoming; Chang, I-Shou; Wang, Jiu-Cun; Chatterjee, Nilanjan; Tucker, Margaret; Wei, Hu; Mitsudomi, Tetsuya; Zheng, Wei; Kim, Jin Hee; Zhou, Baosen; Caporaso, Neil E; Albanes, Demetrius; Shin, Min-Ho; Chung, Lap Ping; An, She-Juan; Wang, Ping; Zheng, Hong; Yatabe, Yasushi; Zhang, Xu-Chao; Kim, Young Tae; Shu, Xiao Ou; Kim, Young-Chul; Bassig, Bryan A.; Chang, Jiang; Ho, James Chung Man; Ji, Bu Tian; Kubo, Michiaki; Daigo, Yataro; Ito, Hidemi; Momozawa, Yukihide; Ashikawa, Kyota; Kamatani, Yoichiro; Honda, Takayuki; Sakamoto, Hiromi; Kunitoh, Hideo; Tsuta, Koji; Watanabe, Shun-Ichi; Nokihara, Hiroshi; Miyagi, Yohei; Nakayama, Haruhiko; Matsumoto, Shingo; Tsuboi, Masahiro; Goto, Koichi; Yin, Zhihua; Shi, Jianxin; Takahashi, Atsushi; Goto, Akiteru; Minamiya, Yoshihiro; Shimizu, Kimihiro; Tanaka, Kazumi; Wu, Tangchun; Wei, Fusheng; Wong, Jason Y Y; Matsuda, Fumihiko; Su, Jian; Kim, Yeul Hong; Oh, In-Jae; Song, Fengju; Lee, Victor Ho Fun; Su, Wu-Chou; Chen, Yuh-Min; Chang, Gee-Chen; Chen, Kuan-Yu; Huang, Ming-Shyan; Yang, Pan-Chyr; Lin, Hsien-Chih; Xiang, Yong-Bing; Seow, Adeline; Park, Jae Yong; Kweon, Sun-Seog; Chen, Chien-Jen; Li, Haixin; Gao, Yu Tang; Wu, Chen; Qian, Biyun; Lu, Daru; Liu, Jianjun; Jeon, Hyo-Sung; Hsiao, Chin-Fu; Sung, Jae Sook; Tsai, Ying-Huang; Jung, Yoo Jin; Guo, Huan; Hu, Zhibin; Wang, Wen-Chang; Chung, Charles C.; Lawrence, Charles; Burdett, Laurie; Yeager, Meredith; Jacobs, Kevin B.; Hutchinson, Amy; Berndt, Sonja I.; He, Xingzhou; Wu, Wei; Wang, Junwen; Li, Yuqing; Choi, Jin Eun; Park, Kyong Hwa; Sung, Sook Whan; Liu, Li; Kang, Chang Hyun; Hu, Lingmin; Chen, Chung-Hsing; Yang, Tsung-Ying; Xu, Jun; Guan, Peng; Tan, Wen; Wang, Chih-Liang; Sihoe, Alan Dart Loon; Chen, Ying; Choi, Yi Young; Hung, Jen-Yu; Kim, Jun Suk; Yoon, Ho-Il; Cai, Qiuyin; Lin, Chien-Chung; Park, In Kyu; Xu, Ping; Dong, Jing; Kim, Christopher; He, Qincheng; Perng, Reury-Perng; Chen, Chih-Yi; Vermeulen, Roel; Wu, Junjie; Lim, Wei-Yen; Chen, Kun-Chieh; Chan, John K C; Chu, Minjie; Li, Yao-Jen; Li, Jihua; Chen, Hongyan; Yu, Chong-Jen; Jin, Li; Lo, Yen-Li; Chen, Ying-Hsiang; Fraumeni, Joseph F.; Liu, Jie; Yamaji, Taiki; Yang, Yang; Hicks, Belynda; Wyatt, Kathleen; Li, Shengchao A; Dai, Juncheng; Ma, Hongxia; Jin, Guangfu; Song, Bao; Wang, Zhehai; Cheng, Sensen; Li, Xuelian; Ren, Yangwu; Cui, Ping; Iwasaki, Motoki; Shimazu, Taichi; Tsugane, Shoichiro; Zhu, Junjie; Jiang, Gening; Fei, Ke; Wu, Guoping; Chien, Li-Hsin; Chen, Hui-Ling; Su, Yu-Chun; Tsai, Fang-Yu; Chen, Yi-Song; Yu, Jinming; Stevens, Victoria L; Laird-Offringa, Ite A; Marconett, Crystal N; Lin, Dongxin; Chen, Kexin; Wu, Yi-Long; Landi, Maria Teresa; Shen, Hongbing; Rothman, Nathaniel; Kohno, Takashi; Chanock, Stephen J.; Lan, Qing

    2017-01-01

    To evaluate associations by EGFR mutation status for lung adenocarcinoma risk among never-smoking Asian women, we conducted a meta-analysis of 11 loci previously identified in genome-wide association studies (GWAS). Genotyping in an additional 10,780 never-smoking cases and 10,938 never-smoking

  3. Replication and meta-analysis of GWAS identified susceptibility loci in Kawasaki disease confirm the importance of B lymphoid tyrosine kinase (BLK) in disease susceptibility

    NARCIS (Netherlands)

    Chang, Chia-Jung; Kuo, Ho-Chang; Chang, Jeng-Sheng; Lee, Jong-Keuk; Tsai, Fuu-Jen; Khor, Chiea Chuen; Chang, Li-Ching; Chen, Shih-Ping; Ko, Tai-Ming; Liu, Yi-Min; Chen, Ying-Ju; Hong, Young Mi; Jang, Gi Young; Hibberd, Martin L.; Kuijpers, Taco; Burgner, David; Levin, Michael; Burns, Jane C.; Davila, Sonia; Chen, Yuan-Tsong; Chen, Chien-Hsiun; Wu, Jer-Yuarn; Lee, Yi-Ching; Liang, Chi-Di; Hwang, Kao-Pin; Chang, Luan-Yin; Huang, Li-Min; Chen, Ming-Ren; Chi, Hsin; Huang, Fu-Yuan; Chiu, Nan-Chang; Lee, Meng-Luen; Huang, Yhu-Chering; Hwang, Betau; Lee, Pi-Chang; Yoo, Jeong-Jin; Park, In-Sook; Hong, Soo-Jong; Kim, Kwi-Joo; Kim, Jae-Jung; Sohn, Saejung; Young Jang, Gi; Ha, Kee-Soo; Nam, Hyo-Kyoung; Byeon, Jung-Hye; Yun, Sin Weon; Han, Myung Ki; Kuipers, Irene M.; Ottenkamp, Jaap J.; Biezeveld, Maarten

    2013-01-01

    The BLK and CD40 loci have been associated with Kawasaki disease (KD) in two genome-wide association studies (GWAS) conducted in a Taiwanese population of Han Chinese ancestry (Taiwanese) and in Japanese cohorts. Here we build on these findings with replication studies of the BLK and CD40 loci in

  4. Meta-GWAS Accuracy and Power (MetaGAP Calculator Shows that Hiding Heritability Is Partially Due to Imperfect Genetic Correlations across Studies.

    Directory of Open Access Journals (Sweden)

    Ronald de Vlaming

    2017-01-01

    Full Text Available Large-scale genome-wide association results are typically obtained from a fixed-effects meta-analysis of GWAS summary statistics from multiple studies spanning different regions and/or time periods. This approach averages the estimated effects of genetic variants across studies. In case genetic effects are heterogeneous across studies, the statistical power of a GWAS and the predictive accuracy of polygenic scores are attenuated, contributing to the so-called 'missing heritability'. Here, we describe the online Meta-GWAS Accuracy and Power (MetaGAP calculator (available at www.devlaming.eu which quantifies this attenuation based on a novel multi-study framework. By means of simulation studies, we show that under a wide range of genetic architectures, the statistical power and predictive accuracy provided by this calculator are accurate. We compare the predictions from the MetaGAP calculator with actual results obtained in the GWAS literature. Specifically, we use genomic-relatedness-matrix restricted maximum likelihood to estimate the SNP heritability and cross-study genetic correlation of height, BMI, years of education, and self-rated health in three large samples. These estimates are used as input parameters for the MetaGAP calculator. Results from the calculator suggest that cross-study heterogeneity has led to attenuation of statistical power and predictive accuracy in recent large-scale GWAS efforts on these traits (e.g., for years of education, we estimate a relative loss of 51-62% in the number of genome-wide significant loci and a relative loss in polygenic score R2 of 36-38%. Hence, cross-study heterogeneity contributes to the missing heritability.

  5. pKWmEB: integration of Kruskal-Wallis test with empirical Bayes under polygenic background control for multi-locus genome-wide association study.

    Science.gov (United States)

    Ren, Wen-Long; Wen, Yang-Jun; Dunwell, Jim M; Zhang, Yuan-Ming

    2018-03-01

    Although nonparametric methods in genome-wide association studies (GWAS) are robust in quantitative trait nucleotide (QTN) detection, the absence of polygenic background control in single-marker association in genome-wide scans results in a high false positive rate. To overcome this issue, we proposed an integrated nonparametric method for multi-locus GWAS. First, a new model transformation was used to whiten the covariance matrix of polygenic matrix K and environmental noise. Using the transferred model, Kruskal-Wallis test along with least angle regression was then used to select all the markers that were potentially associated with the trait. Finally, all the selected markers were placed into multi-locus model, these effects were estimated by empirical Bayes, and all the nonzero effects were further identified by a likelihood ratio test for true QTN detection. This method, named pKWmEB, was validated by a series of Monte Carlo simulation studies. As a result, pKWmEB effectively controlled false positive rate, although a less stringent significance criterion was adopted. More importantly, pKWmEB retained the high power of Kruskal-Wallis test, and provided QTN effect estimates. To further validate pKWmEB, we re-analyzed four flowering time related traits in Arabidopsis thaliana, and detected some previously reported genes that were not identified by the other methods.

  6. Genome-wide association mapping including phenotypes from relatives without genotypes in a single-step (ssGWAS for 6-week body weight in broiler chickens

    Directory of Open Access Journals (Sweden)

    Huiyu eWang

    2014-05-01

    Full Text Available The purpose of this study was to compare results obtained from various methodologies for genome-wide association studies, when applied to real data, in terms of number and commonality of regions identified and their genetic variance explained, computational speed, and possible pitfalls in interpretations of results. Methodologies include: two iteratively reweighted single-step genomic BLUP procedures (ssGWAS1 and ssGWAS2, a single-marker model (CGWAS, and BayesB. The ssGWAS methods utilize genomic breeding values (GEBVs based on combined pedigree, genomic and phenotypic information, while CGWAS and BayesB only utilize phenotypes from genotyped animals or pseudo-phenotypes. In this study, ssGWAS was performed by converting GEBVs to SNP marker effects. Unequal variances for markers were incorporated for calculating weights into a new genomic relationship matrix. SNP weights were refined iteratively. The data was body weight at 6 weeks on 274,776 broiler chickens, of which 4553 were genotyped using a 60k SNP chip. Comparison of genomic regions was based on genetic variances explained by local SNP regions (20 SNPs. After 3 iterations, the noise was greatly reduced of ssGWAS1 and results are similar to that of CGWAS, with 4 out of the top 10 regions in common. In contrast, for BayesB, the plot was dominated by a single region explaining 23.1% of the genetic variance. This same region was found by ssGWAS1 with the same rank, but the amount of genetic variation attributed to the region was only 3%. These finding emphasize the need for caution when comparing and interpreting results from various methods, and highlight that detected associations, and strength of association, strongly depends on methodologies and details of implementations. BayesB appears to overly shrink regions to zero, while overestimating the amount of genetic variation attributed to the remaining SNP effects. The real world is most likely a compromise between methods and remains to

  7. Web server attack analyzer

    OpenAIRE

    Mižišin, Michal

    2013-01-01

    Web server attack analyzer - Abstract The goal of this work was to create prototype of analyzer of injection flaws attacks on web server. Proposed solution combines capabilities of web application firewall and web server log analyzer. Analysis is based on configurable signatures defined by regular expressions. This paper begins with summary of web attacks, followed by detection techniques analysis on web servers, description and justification of selected implementation. In the end are charact...

  8. Electron attachment analyzer

    International Nuclear Information System (INIS)

    Popp, P.; Grosse, H.J.; Leonhardt, J.; Mothes, S.; Oppermann, G.

    1984-01-01

    The invention concerns an electron attachment analyzer for detecting traces of electroaffine substances in electronegative gases, especially in air. The analyzer can be used for monitoring working places, e. g., in operating theatres. The analyzer consists of two electrodes inserted in a base frame of insulating material (quartz or ceramics) and a high-temperature resistant radiation source ( 85 Kr, 3 H, or 63 Ni)

  9. Nuclear power plant analyzer

    International Nuclear Information System (INIS)

    Stritar, A.

    1986-01-01

    The development of Nuclear Power Plant Analyzers in USA is described. There are two different types of Analyzers under development in USA, the forst in Idaho and Los Alamos national Lab, the second in brookhaven National lab. That one is described in detail. The computer hardware and the mathematical models of the reactor vessel thermalhydraulics are described. (author)

  10. Analyzing Peace Pedagogies

    Science.gov (United States)

    Haavelsrud, Magnus; Stenberg, Oddbjorn

    2012-01-01

    Eleven articles on peace education published in the first volume of the Journal of Peace Education are analyzed. This selection comprises peace education programs that have been planned or carried out in different contexts. In analyzing peace pedagogies as proposed in the 11 contributions, we have chosen network analysis as our method--enabling…

  11. Analyzing in the present

    DEFF Research Database (Denmark)

    Revsbæk, Line; Tanggaard, Lene

    2015-01-01

    The article presents a notion of “analyzing in the present” as a source of inspiration in analyzing qualitative research materials. The term emerged from extensive listening to interview recordings during everyday commuting to university campus. Paying attention to the way different parts of vari...

  12. Gearbox vibration diagnostic analyzer

    Science.gov (United States)

    1992-01-01

    This report describes the Gearbox Vibration Diagnostic Analyzer installed in the NASA Lewis Research Center's 500 HP Helicopter Transmission Test Stand to monitor gearbox testing. The vibration of the gearbox is analyzed using diagnostic algorithms to calculate a parameter indicating damaged components.

  13. Fiscal 1998 achievement report on regional consortium research and development project. Venture business fostering regional consortium--Creation of key industries (Development of a ultrahigh-sensitivity micro-integrated analyzing system); 1998 nendo chokokando micro shusekika bunseki system no kaihatsu seika hokokusho

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2000-03-01

    Biotechnology and micro-machining technology are merged into the above-named system capable of high-speed high-precision clinical examination of trace specimens. In the development of element technologies indispensable for system construction, research and development is conducted of laser processing technology for integration, extremely weak signal detecting technology, micro-electrode manufacturing technology for micro-sensors, micro-contact printing technology, micro-sensors, integrated coatings and micro-columns, elucidation of blood flow characteristics in micro-scale elements, micro-integrated analyzing system control technology, etc. These element technologies are integrated for a success in the development of a micro-scale polymerase chain reaction (PCR) device which is necessary for the development of micro-integrated blood analyzing system for various blood components and for the demagnification of a gene analyzing system. Surveys etc. are conducted for the commercialization of the devices mentioned above. (NEDO)

  14. Two‐phase designs for joint quantitative‐trait‐dependent and genotype‐dependent sampling in post‐GWAS regional sequencing

    Science.gov (United States)

    Espin‐Garcia, Osvaldo; Craiu, Radu V.

    2017-01-01

    ABSTRACT We evaluate two‐phase designs to follow‐up findings from genome‐wide association study (GWAS) when the cost of regional sequencing in the entire cohort is prohibitive. We develop novel expectation‐maximization‐based inference under a semiparametric maximum likelihood formulation tailored for post‐GWAS inference. A GWAS‐SNP (where SNP is single nucleotide polymorphism) serves as a surrogate covariate in inferring association between a sequence variant and a normally distributed quantitative trait (QT). We assess test validity and quantify efficiency and power of joint QT‐SNP‐dependent sampling and analysis under alternative sample allocations by simulations. Joint allocation balanced on SNP genotype and extreme‐QT strata yields significant power improvements compared to marginal QT‐ or SNP‐based allocations. We illustrate the proposed method and evaluate the sensitivity of sample allocation to sampling variation using data from a sequencing study of systolic blood pressure. PMID:29239496

  15. Comparing Analytic Methods for Longitudinal GWAS and a Case-Study Evaluating Chemotherapy Course Length in Pediatric AML. A Report from the Children’s Oncology Group.

    Directory of Open Access Journals (Sweden)

    Marijana Vujkovic

    2016-08-01

    Full Text Available Regression analysis is commonly used in genome-wide association studies (GWAS to test genotype-phenotype associations but restricts the phenotype to a single observation for each individual. There is an increasing need for analytic methods for longitudinally collected phenotype data. Several methods have been proposed to perform longitudinal GWAS for family-based studies but few methods are described for unrelated populations. We compared the performance of three statistical approaches for longitudinal GWAS in unrelated subjectes: (1 principal component-based generalized estimating equations (PC-GEE; (2 principal component-based linear mixed effects model (PC-LMEM; (3 kinship coefficient matrix-based linear mixed effects model (KIN-LMEM, in a study of single-nucleotide polymorphisms (SNPs on the duration of 4 courses of chemotherapy in 624 unrelated children with de novo acute myeloid leukemia (AML genotyped on the Illumina 2.5M OmniQuad from the COG studies AAML0531 and AAML1031.In this study we observed an exaggerated type I error with PC-GEE in SNPs with minor allele frequencies < 0.05, wheras KIN-LMEM produces more than expected type II errors. PC-MEM showed balanced type I and type II errors for the observed versus expected P-values in comparison to competing approaches. In general, a strong concordance was observed between the P-values with the different approaches, in particular among P-values < 0.01 where the between-method AUCs exceed 99%. PC-LMEM accounts for genetic relatedness and correlations among repeated phenotype measures, shows minimal genome-wide inflation of type I errors, and yields high power. We therefore recommend PC-LMEM as a robust analytic approach for GWAS of longitudinal data in unrelated populations.

  16. DISC1 conditioned GWAS for psychosis proneness in a large Finnish birth cohort.

    Directory of Open Access Journals (Sweden)

    Liisa Tomppo

    Full Text Available BACKGROUND: Genetic evidence implicates the DISC1 gene in the etiology of a number of mental illnesses. Previously, we have reported association between DISC1 and measures of psychosis proneness, the Revised Social Anhedonia Scale (RSAS and Revised Physical Anhedonia Scale (RPAS, in the Northern Finland Birth Cohort 1966 (NFBC66. As part of the studies of this Finnish birth cohort genome-wide association analysis has recently been performed. METHODOLOGY: In the present study, we re-analyzed the genome-wide association data with regard to these two measures of psychosis proneness, conditioning on our previous DISC1 observation. From the original NFBC66 sample (N = 12 058, 4 561 individuals provided phenotype and genotype data. No markers were significant at the genome-wide level. However, several genes with biological relevance to mental illnesses were highlighted through loci displaying suggestive evidence for association (≥3 SNP with P<10E-4. These included the protein coding genes, CXCL3, KIAA1128, LCT, MED13L, TMCO7, TTN, and the micro RNA MIR620. CONCLUSIONS: By conditioning a previous genome-wide association study on DISC1, we have been able to identify eight genes as associating to psychosis proneness. Further, these molecules predominantly link to the DISC1 pathway, strengthening the evidence for the role of this gene network in the etiology of mental illness. The use of quantitative measures of psychosis proneness in a large population cohort will make these findings, once verified; more generalized to a broad selection of disorders related to psychoses and psychosis proneness.

  17. Miniature mass analyzer

    CERN Document Server

    Cuna, C; Lupsa, N; Cuna, S; Tuzson, B

    2003-01-01

    The paper presents the concept of different mass analyzers that were specifically designed as small dimension instruments able to detect with great sensitivity and accuracy the main environmental pollutants. The mass spectrometers are very suited instrument for chemical and isotopic analysis, needed in environmental surveillance. Usually, this is done by sampling the soil, air or water followed by laboratory analysis. To avoid drawbacks caused by sample alteration during the sampling process and transport, the 'in situ' analysis is preferred. Theoretically, any type of mass analyzer can be miniaturized, but some are more appropriate than others. Quadrupole mass filter and trap, magnetic sector, time-of-flight and ion cyclotron mass analyzers can be successfully shrunk, for each of them some performances being sacrificed but we must know which parameters are necessary to be kept unchanged. To satisfy the miniaturization criteria of the analyzer, it is necessary to use asymmetrical geometries, with ion beam obl...

  18. Analysis of 60 reported glioma risk SNPs replicates published GWAS findings but fails to replicate associations from published candidate-gene studies.

    Science.gov (United States)

    Walsh, Kyle M; Anderson, Erik; Hansen, Helen M; Decker, Paul A; Kosel, Matt L; Kollmeyer, Thomas; Rice, Terri; Zheng, Shichun; Xiao, Yuanyuan; Chang, Jeffrey S; McCoy, Lucie S; Bracci, Paige M; Wiemels, Joe L; Pico, Alexander R; Smirnov, Ivan; Lachance, Daniel H; Sicotte, Hugues; Eckel-Passow, Jeanette E; Wiencke, John K; Jenkins, Robert B; Wrensch, Margaret R

    2013-02-01

    Genomewide association studies (GWAS) and candidate-gene studies have implicated single-nucleotide polymorphisms (SNPs) in at least 45 different genes as putative glioma risk factors. Attempts to validate these associations have yielded variable results and few genetic risk factors have been consistently replicated. We conducted a case-control study of Caucasian glioma cases and controls from the University of California San Francisco (810 cases, 512 controls) and the Mayo Clinic (852 cases, 789 controls) in an attempt to replicate previously reported genetic risk factors for glioma. Sixty SNPs selected from the literature (eight from GWAS and 52 from candidate-gene studies) were successfully genotyped on an Illumina custom genotyping panel. Eight SNPs in/near seven different genes (TERT, EGFR, CCDC26, CDKN2A, PHLDB1, RTEL1, TP53) were significantly associated with glioma risk in the combined dataset (P 0.05). Although several confirmed associations are located near genes long known to be involved in gliomagenesis (e.g., EGFR, CDKN2A, TP53), these associations were first discovered by the GWAS approach and are in noncoding regions. These results highlight that the deficiencies of the candidate-gene approach lay in selecting both appropriate genes and relevant SNPs within these genes. © 2012 WILEY PERIODICALS, INC.

  19. On-Demand Urine Analyzer, Phase II

    Data.gov (United States)

    National Aeronautics and Space Administration — The overall goal of this program (through Phase III) is to develop an analyzer that can be integrated into International Space Station (ISS) toilets to measure key...

  20. The more from East-Asian, the better: risk prediction of colorectal cancer risk by GWAS-identified SNPs among Japanese.

    Science.gov (United States)

    Abe, Makiko; Ito, Hidemi; Oze, Isao; Nomura, Masatoshi; Ogawa, Yoshihiro; Matsuo, Keitaro

    2017-12-01

    Little is known about the difference of genetic predisposition for CRC between ethnicities; however, many genetic traits common to colorectal cancer have been identified. This study investigated whether more SNPs identified in GWAS in East Asian population could improve the risk prediction of Japanese and explored possible application of genetic risk groups as an instrument of the risk communication. 558 Patients histologically verified colorectal cancer and 1116 first-visit outpatients were included for derivation study, and 547 cases and 547 controls were for replication study. Among each population, we evaluated prediction models for the risk of CRC that combined the genetic risk group based on SNPs from GWASs in European-population and a similarly developed model adding SNPs from GWASs in East Asian-population. We examined whether adding East Asian-specific SNPs would improve the discrimination. Six SNPs (rs6983267, rs4779584, rs4444235, rs9929218, rs10936599, rs16969681) from 23 SNPs by European-based GWAS and five SNPs (rs704017, rs11196172, rs10774214, rs647161, rs2423279) among ten SNPs by Asian-based GWAS were selected in CRC risk prediction model. Compared with a 6-SNP-based model, an 11-SNP model including Asian GWAS-SNPs showed improved discrimination capacity in Receiver operator characteristic analysis. A model with 11 SNPs resulted in statistically significant improvement in both derivation (P = 0.0039) and replication studies (P = 0.0018) compared with six SNP model. We estimated cumulative risk of CRC by using genetic risk group based on 11 SNPs and found that the cumulative risk at age 80 is approximately 13% in the high-risk group while 6% in the low-risk group. We constructed a more efficient CRC risk prediction model with 11 SNPs including newly identified East Asian-based GWAS SNPs (rs704017, rs11196172, rs10774214, rs647161, rs2423279). Risk grouping based on 11 SNPs depicted lifetime difference of CRC risk. This might be useful for

  1. Extraction spectrophotometric analyzer

    International Nuclear Information System (INIS)

    Batik, J.; Vitha, F.

    1985-01-01

    Automation is discussed of extraction spectrophotometric determination of uranium in a solution. Uranium is extracted from accompanying elements in an HCl medium with a solution of tributyl phosphate in benzene. The determination is performed by measuring absorbance at 655 nm in a single-phase ethanol-water-benzene-tributyl phosphate medium. The design is described of an analyzer consisting of an analytical unit and a control unit. The analyzer performance promises increased productivity of labour, improved operating and hygiene conditions, and mainly more accurate results of analyses. (J.C.)

  2. Analyzing an Aging ISS

    Science.gov (United States)

    Scharf, R.

    2014-01-01

    The ISS External Survey integrates the requirements for photographic and video imagery of the International Space Station (ISS) for the engineering, operations, and science communities. An extensive photographic survey was performed on all Space Shuttle flights to the ISS and continues to be performed daily, though on a level much reduced by the limited available imagery. The acquired video and photo imagery is used for both qualitative and quantitative assessments of external deposition and contamination, surface degradation, dynamic events, and MMOD strikes. Many of these assessments provide important information about ISS surfaces and structural integrity as the ISS ages. The imagery is also used to assess and verify the physical configuration of ISS structure, appendages, and components.

  3. Americal options analyzed differently

    NARCIS (Netherlands)

    Nieuwenhuis, J.W.

    2003-01-01

    In this note we analyze in a discrete-time context and with a finite outcome space American options starting with the idea that every tradable should be a martingale under a certain measure. We believe that in this way American options become more understandable to people with a good working

  4. Analyzing Political Television Advertisements.

    Science.gov (United States)

    Burson, George

    1992-01-01

    Presents a lesson plan to help students understand that political advertisements often mislead, lie, or appeal to emotion. Suggests that the lesson will enable students to examine political advertisements analytically. Includes a worksheet to be used by students to analyze individual political advertisements. (DK)

  5. Centrifugal analyzer development

    International Nuclear Information System (INIS)

    Burtis, C.A.; Bauer, M.L.; Bostick, W.D.

    1976-01-01

    The development of the centrifuge fast analyzer (CFA) is reviewed. The development of a miniature CFA with computer data analysis is reported and applications for automated diagnostic chemical and hematological assays are discussed. A portable CFA system with microprocessor was adapted for field assays of air and water samples for environmental pollutants, including ammonia, nitrates, nitrites, phosphates, sulfates, and silica. 83 references

  6. Soft Decision Analyzer

    Science.gov (United States)

    Lansdowne, Chatwin; Steele, Glen; Zucha, Joan; Schlesinger, Adam

    2013-01-01

    We describe the benefit of using closed-loop measurements for a radio receiver paired with a counterpart transmitter. We show that real-time analysis of the soft decision output of a receiver can provide rich and relevant insight far beyond the traditional hard-decision bit error rate (BER) test statistic. We describe a Soft Decision Analyzer (SDA) implementation for closed-loop measurements on single- or dual- (orthogonal) channel serial data communication links. The analyzer has been used to identify, quantify, and prioritize contributors to implementation loss in live-time during the development of software defined radios. This test technique gains importance as modern receivers are providing soft decision symbol synchronization as radio links are challenged to push more data and more protocol overhead through noisier channels, and software-defined radios (SDRs) use error-correction codes that approach Shannon's theoretical limit of performance.

  7. KWU Nuclear Plant Analyzer

    International Nuclear Information System (INIS)

    Bennewitz, F.; Hummel, R.; Oelmann, K.

    1986-01-01

    The KWU Nuclear Plant Analyzer is a real time engineering simulator based on the KWU computer programs used in plant transient analysis and licensing. The primary goal is to promote the understanding of the technical and physical processes of a nuclear power plant at an on-site training facility. Thus the KWU Nuclear Plant Analyzer is available with comparable low costs right at the time when technical questions or training needs arise. This has been achieved by (1) application of the transient code NLOOP; (2) unrestricted operator interaction including all simulator functions; (3) using the mainframe computer Control Data Cyber 176 in the KWU computing center; (4) four color graphic displays controlled by a dedicated graphic computer, no control room equipment; and (5) coupling of computers by telecommunication via telephone

  8. Analyzed Using Statistical Moments

    International Nuclear Information System (INIS)

    Oltulu, O.

    2004-01-01

    Diffraction enhanced imaging (DEl) technique is a new x-ray imaging method derived from radiography. The method uses a monorheumetten x-ray beam and introduces an analyzer crystal between an object and a detector Narrow angular acceptance of the analyzer crystal generates an improved contrast over the evaluation radiography. While standart radiography can produce an 'absorption image', DEl produces 'apparent absorption' and 'apparent refraction' images with superior quality. Objects with similar absorption properties may not be distinguished with conventional techniques due to close absorption coefficients. This problem becomes more dominant when an object has scattering properties. A simple approach is introduced to utilize scattered radiation to obtain 'pure absorption' and 'pure refraction' images

  9. Emission spectrometric isotope analyzer

    International Nuclear Information System (INIS)

    Mauersberger, K.; Meier, G.; Nitschke, W.; Rose, W.; Schmidt, G.; Rahm, N.; Andrae, G.; Krieg, D.; Kuefner, W.; Tamme, G.; Wichlacz, D.

    1982-01-01

    An emission spectrometric isotope analyzer has been designed for determining relative abundances of stable isotopes in gaseous samples in discharge tubes, in liquid samples, and in flowing gaseous samples. It consists of a high-frequency generator, a device for defined positioning of discharge tubes, a grating monochromator with oscillating slit and signal converter, signal generator, window discriminator, AND connection, read-out display, oscillograph, gas dosing device and chemical conversion system with carrier gas source and vacuum pump

  10. PhosphoSiteAnalyzer

    DEFF Research Database (Denmark)

    Bennetzen, Martin V; Cox, Jürgen; Mann, Matthias

    2012-01-01

    an algorithm to retrieve kinase predictions from the public NetworKIN webpage in a semiautomated way and applies hereafter advanced statistics to facilitate a user-tailored in-depth analysis of the phosphoproteomic data sets. The interface of the software provides a high degree of analytical flexibility......Phosphoproteomic experiments are routinely conducted in laboratories worldwide, and because of the fast development of mass spectrometric techniques and efficient phosphopeptide enrichment methods, researchers frequently end up having lists with tens of thousands of phosphorylation sites...... and is designed to be intuitive for most users. PhosphoSiteAnalyzer is a freeware program available at http://phosphosite.sourceforge.net ....

  11. Electrodynamic thermogravimetric analyzer

    International Nuclear Information System (INIS)

    Spjut, R.E.; Bar-Ziv, E.; Sarofim, A.F.; Longwell, J.P.

    1986-01-01

    The design and operation of a new device for studying single-aerosol-particle kinetics at elevated temperatures, the electrodynamic thermogravimetric analyzer (EDTGA), was examined theoretically and experimentally. The completed device consists of an electrodynamic balance modified to permit particle heating by a CO 2 laser, temperature measurement by a three-color infrared-pyrometry system, and continuous weighing by a position-control system. In this paper, the position-control, particle-weight-measurement, heating, and temperature-measurement systems are described and their limitations examined

  12. Analyzing Chinese Financial Reporting

    Institute of Scientific and Technical Information of China (English)

    SABRINA; ZHANG

    2008-01-01

    If the world’s capital markets could use a harmonized accounting framework it would not be necessary for a comparison between two or more sets of accounting standards. However,there is much to do before this becomes reality.This article aims to pres- ent a general overview of China’s General Accepted Accounting Principles(GAAP), U.S.General Accepted Accounting Principles and International Financial Reporting Standards(IFRS),and to analyze the differ- ences among IFRS,U.S.GAAP and China GAAP using fixed assets as an example.

  13. Inductive dielectric analyzer

    International Nuclear Information System (INIS)

    Agranovich, Daniel; Popov, Ivan; Ben Ishai, Paul; Feldman, Yuri; Polygalov, Eugene

    2017-01-01

    One of the approaches to bypass the problem of electrode polarization in dielectric measurements is the free electrode method. The advantage of this technique is that, the probing electric field in the material is not supplied by contact electrodes, but rather by electromagnetic induction. We have designed an inductive dielectric analyzer based on a sensor comprising two concentric toroidal coils. In this work, we present an analytic derivation of the relationship between the impedance measured by the sensor and the complex dielectric permittivity of the sample. The obtained relationship was successfully employed to measure the dielectric permittivity and conductivity of various alcohols and aqueous salt solutions. (paper)

  14. Plutonium solution analyzer

    International Nuclear Information System (INIS)

    Burns, D.A.

    1994-09-01

    A fully automated analyzer has been developed for plutonium solutions. It was assembled from several commercially available modules, is based upon segmented flow analysis, and exhibits precision about an order of magnitude better than commercial units (0.5%-O.05% RSD). The system was designed to accept unmeasured, untreated liquid samples in the concentration range 40-240 g/L and produce a report with sample identification, sample concentrations, and an abundance of statistics. Optional hydraulics can accommodate samples in the concentration range 0.4-4.0 g/L. Operating at a typical rate of 30 to 40 samples per hour, it consumes only 0.074 mL of each sample and standard, and generates waste at the rate of about 1.5 mL per minute. No radioactive material passes through its multichannel peristaltic pump (which remains outside the glovebox, uncontaminated) but rather is handled by a 6-port, 2-position chromatography-type loop valve. An accompanying computer is programmed in QuickBASIC 4.5 to provide both instrument control and data reduction. The program is truly user-friendly and communication between operator and instrument is via computer screen displays and keyboard. Two important issues which have been addressed are waste minimization and operator safety (the analyzer can run in the absence of an operator, once its autosampler has been loaded)

  15. Multiple capillary biochemical analyzer

    Science.gov (United States)

    Dovichi, N.J.; Zhang, J.Z.

    1995-08-08

    A multiple capillary analyzer allows detection of light from multiple capillaries with a reduced number of interfaces through which light must pass in detecting light emitted from a sample being analyzed, using a modified sheath flow cuvette. A linear or rectangular array of capillaries is introduced into a rectangular flow chamber. Sheath fluid draws individual sample streams through the cuvette. The capillaries are closely and evenly spaced and held by a transparent retainer in a fixed position in relation to an optical detection system. Collimated sample excitation radiation is applied simultaneously across the ends of the capillaries in the retainer. Light emitted from the excited sample is detected by the optical detection system. The retainer is provided by a transparent chamber having inward slanting end walls. The capillaries are wedged into the chamber. One sideways dimension of the chamber is equal to the diameter of the capillaries and one end to end dimension varies from, at the top of the chamber, slightly greater than the sum of the diameters of the capillaries to, at the bottom of the chamber, slightly smaller than the sum of the diameters of the capillaries. The optical system utilizes optic fibers to deliver light to individual photodetectors, one for each capillary tube. A filter or wavelength division demultiplexer may be used for isolating fluorescence at particular bands. 21 figs.

  16. Plutonium solution analyzer

    Energy Technology Data Exchange (ETDEWEB)

    Burns, D.A.

    1994-09-01

    A fully automated analyzer has been developed for plutonium solutions. It was assembled from several commercially available modules, is based upon segmented flow analysis, and exhibits precision about an order of magnitude better than commercial units (0.5%-O.05% RSD). The system was designed to accept unmeasured, untreated liquid samples in the concentration range 40-240 g/L and produce a report with sample identification, sample concentrations, and an abundance of statistics. Optional hydraulics can accommodate samples in the concentration range 0.4-4.0 g/L. Operating at a typical rate of 30 to 40 samples per hour, it consumes only 0.074 mL of each sample and standard, and generates waste at the rate of about 1.5 mL per minute. No radioactive material passes through its multichannel peristaltic pump (which remains outside the glovebox, uncontaminated) but rather is handled by a 6-port, 2-position chromatography-type loop valve. An accompanying computer is programmed in QuickBASIC 4.5 to provide both instrument control and data reduction. The program is truly user-friendly and communication between operator and instrument is via computer screen displays and keyboard. Two important issues which have been addressed are waste minimization and operator safety (the analyzer can run in the absence of an operator, once its autosampler has been loaded).

  17. Mapping of HKT1;5 Gene in Barley Using GWAS Approach and Its Implication in Salt Tolerance Mechanism

    Science.gov (United States)

    Hazzouri, Khaled M.; Khraiwesh, Basel; Amiri, Khaled M. A.; Pauli, Duke; Blake, Tom; Shahid, Mohammad; Mullath, Sangeeta K.; Nelson, David; Mansour, Alain L.; Salehi-Ashtiani, Kourosh; Purugganan, Michael; Masmoudi, Khaled

    2018-01-01

    Sodium (Na+) accumulation in the cytosol will result in ion homeostasis imbalance and toxicity of transpiring leaves. Studies of salinity tolerance in the diploid wheat ancestor Triticum monococcum showed that HKT1;5-like gene was a major gene in the QTL for salt tolerance, named Nax2. In the present study, we were interested in investigating the molecular mechanisms underpinning the role of the HKT1;5 gene in salt tolerance in barley (Hordeum vulgare). A USDA mini-core collection of 2,671 barley lines, part of a field trial was screened for salinity tolerance, and a Genome Wide Association Study (GWAS) was performed. Our results showed important SNPs that are correlated with salt tolerance that mapped to a region where HKT1;5 ion transporter located on chromosome four. Furthermore, sodium (Na+) and potassium (K+) content analysis revealed that tolerant lines accumulate more sodium in roots and leaf sheaths, than in the sensitive ones. In contrast, sodium concentration was reduced in leaf blades of the tolerant lines under salt stress. In the absence of NaCl, the concentration of Na+ and K+ were the same in the roots, leaf sheaths and leaf blades between the tolerant and the sensitive lines. In order to study the molecular mechanism behind that, alleles of the HKT1;5 gene from five tolerant and five sensitive barley lines were cloned and sequenced. Sequence analysis did not show the presence of any polymorphism that distinguishes between the tolerant and sensitive alleles. Our real-time RT-PCR experiments, showed that the expression of HKT1;5 gene in roots of the tolerant line was significantly induced after challenging the plants with salt stress. In contrast, in leaf sheaths the expression was decreased after salt treatment. In sensitive lines, there was no difference in the expression of HKT1;5 gene in leaf sheath under control and saline conditions, while a slight increase in the expression was observed in roots after salt treatment. These results provide

  18. Mapping of HKT1;5 Gene in Barley Using GWAS Approach and Its Implication in Salt Tolerance Mechanism

    Directory of Open Access Journals (Sweden)

    Khaled M. Hazzouri

    2018-02-01

    Full Text Available Sodium (Na+ accumulation in the cytosol will result in ion homeostasis imbalance and toxicity of transpiring leaves. Studies of salinity tolerance in the diploid wheat ancestor Triticum monococcum showed that HKT1;5-like gene was a major gene in the QTL for salt tolerance, named Nax2. In the present study, we were interested in investigating the molecular mechanisms underpinning the role of the HKT1;5 gene in salt tolerance in barley (Hordeum vulgare. A USDA mini-core collection of 2,671 barley lines, part of a field trial was screened for salinity tolerance, and a Genome Wide Association Study (GWAS was performed. Our results showed important SNPs that are correlated with salt tolerance that mapped to a region where HKT1;5 ion transporter located on chromosome four. Furthermore, sodium (Na+ and potassium (K+ content analysis revealed that tolerant lines accumulate more sodium in roots and leaf sheaths, than in the sensitive ones. In contrast, sodium concentration was reduced in leaf blades of the tolerant lines under salt stress. In the absence of NaCl, the concentration of Na+ and K+ were the same in the roots, leaf sheaths and leaf blades between the tolerant and the sensitive lines. In order to study the molecular mechanism behind that, alleles of the HKT1;5 gene from five tolerant and five sensitive barley lines were cloned and sequenced. Sequence analysis did not show the presence of any polymorphism that distinguishes between the tolerant and sensitive alleles. Our real-time RT-PCR experiments, showed that the expression of HKT1;5 gene in roots of the tolerant line was significantly induced after challenging the plants with salt stress. In contrast, in leaf sheaths the expression was decreased after salt treatment. In sensitive lines, there was no difference in the expression of HKT1;5 gene in leaf sheath under control and saline conditions, while a slight increase in the expression was observed in roots after salt treatment. These

  19. Properties and modeling of GWAS when complex disease risk is due to non-complementing, deleterious mutations in genes of large effect.

    Directory of Open Access Journals (Sweden)

    Kevin R Thornton

    Full Text Available Current genome-wide association studies (GWAS have high power to detect intermediate frequency SNPs making modest contributions to complex disease, but they are underpowered to detect rare alleles of large effect (RALE. This has led to speculation that the bulk of variation for most complex diseases is due to RALE. One concern with existing models of RALE is that they do not make explicit assumptions about the evolution of a phenotype and its molecular basis. Rather, much of the existing literature relies on arbitrary mapping of phenotypes onto genotypes obtained either from standard population-genetic simulation tools or from non-genetic models. We introduce a novel simulation of a 100-kilobase gene region, based on the standard definition of a gene, in which mutations are unconditionally deleterious, are continuously arising, have partially recessive and non-complementing effects on phenotype (analogous to what is widely observed for most Mendelian disorders, and are interspersed with neutral markers that can be genotyped. Genes evolving according to this model exhibit a characteristic GWAS signature consisting of an excess of marginally significant markers. Existing tests for an excess burden of rare alleles in cases have low power while a simple new statistic has high power to identify disease genes evolving under our model. The structure of linkage disequilibrium between causative mutations and significantly associated markers under our model differs fundamentally from that seen when rare causative markers are assumed to be neutral. Rather than tagging single haplotypes bearing a large number of rare causative alleles, we find that significant SNPs in a GWAS tend to tag single causative mutations of small effect relative to other mutations in the same gene. Our results emphasize the importance of evaluating the power to detect associations under models that are genetically and evolutionarily motivated.

  20. Trace impurity analyzer

    International Nuclear Information System (INIS)

    Schneider, W.J.; Edwards, D. Jr.

    1979-01-01

    The desirability for long-term reliability of large scale helium refrigerator systems used on superconducting accelerator magnets has necessitated detection of impurities to levels of a few ppM. An analyzer that measures trace impurity levels of condensable contaminants in concentrations of less than a ppM in 15 atm of He is described. The instrument makes use of the desorption temperature at an indicated pressure of the various impurities to determine the type of contaminant. The pressure rise at that temperature yields a measure of the contaminant level of the impurity. A LN 2 cryogenic charcoal trap is also employed to measure air impurities (nitrogen and oxygen) to obtain the full range of contaminant possibilities. The results of this detector which will be in use on the research and development helium refrigerator of the ISABELLE First-Cell is described

  1. Analyzing Water's Optical Absorption

    Science.gov (United States)

    2002-01-01

    A cooperative agreement between World Precision Instruments (WPI), Inc., and Stennis Space Center has led the UltraPath(TM) device, which provides a more efficient method for analyzing the optical absorption of water samples at sea. UltraPath is a unique, high-performance absorbance spectrophotometer with user-selectable light path lengths. It is an ideal tool for any study requiring precise and highly sensitive spectroscopic determination of analytes, either in the laboratory or the field. As a low-cost, rugged, and portable system capable of high- sensitivity measurements in widely divergent waters, UltraPath will help scientists examine the role that coastal ocean environments play in the global carbon cycle. UltraPath(TM) is a trademark of World Precision Instruments, Inc. LWCC(TM) is a trademark of World Precision Instruments, Inc.

  2. PDA: Pooled DNA analyzer

    Directory of Open Access Journals (Sweden)

    Lin Chin-Yu

    2006-04-01

    Full Text Available Abstract Background Association mapping using abundant single nucleotide polymorphisms is a powerful tool for identifying disease susceptibility genes for complex traits and exploring possible genetic diversity. Genotyping large numbers of SNPs individually is performed routinely but is cost prohibitive for large-scale genetic studies. DNA pooling is a reliable and cost-saving alternative genotyping method. However, no software has been developed for complete pooled-DNA analyses, including data standardization, allele frequency estimation, and single/multipoint DNA pooling association tests. This motivated the development of the software, 'PDA' (Pooled DNA Analyzer, to analyze pooled DNA data. Results We develop the software, PDA, for the analysis of pooled-DNA data. PDA is originally implemented with the MATLAB® language, but it can also be executed on a Windows system without installing the MATLAB®. PDA provides estimates of the coefficient of preferential amplification and allele frequency. PDA considers an extended single-point association test, which can compare allele frequencies between two DNA pools constructed under different experimental conditions. Moreover, PDA also provides novel chromosome-wide multipoint association tests based on p-value combinations and a sliding-window concept. This new multipoint testing procedure overcomes a computational bottleneck of conventional haplotype-oriented multipoint methods in DNA pooling analyses and can handle data sets having a large pool size and/or large numbers of polymorphic markers. All of the PDA functions are illustrated in the four bona fide examples. Conclusion PDA is simple to operate and does not require that users have a strong statistical background. The software is available at http://www.ibms.sinica.edu.tw/%7Ecsjfann/first%20flow/pda.htm.

  3. A genome-wide association scan (GWAS) for mean telomere length within the COGS project: identified loci show little association with hormone-related cancer risk

    OpenAIRE

    Pooley, K. A.; Bojesen, S. E.; Weischer, M.; Nielsen, S. F.; Thompson, D.; Amin Al Olama, A.; Michailidou, K.; Tyrer, J. P.; Benlloch, S.; Brown, J.; Audley, T.; Luben, R.; Khaw, K.-T.; Neal, D. E.; Hamdy, F. C.

    2013-01-01

    Mean telomere length (TL) in blood cells is heritable and has been reported to be associated with risks of several diseases, including cancer. We conducted a meta-analysis of three GWAS for TL (total n=2240) and selected 1629 variants for replication via the ?iCOGS? custom genotyping array. All ?200 000 iCOGS variants were analysed with TL, and those displaying associations in healthy controls (n = 15 065) were further tested in breast cancer cases (n = 11 024). We found a novel TL associatio...

  4. A framework to analyze emissions implications of manufacturing shifts in the industrial sector through integrating bottom-up energy models and economic input-output environmental life cycle assessment models

    Science.gov (United States)

    Future year emissions depend highly on the evolution of the economy, technology and current and future regulatory drivers. A scenario framework was adopted to analyze various technology development pathways and societal change while considering existing regulations and future unc...

  5. A framework to analyze emissions implications of manufacturing shifts in the industrial sector through integrating bottom-up energy models and economic input/output environmental life cycle assessment models

    Science.gov (United States)

    Future year emissions depend highly on economic, technological, societal and regulatory drivers. A scenario framework was adopted to analyze technology development pathways and changes in consumer preferences, and evaluate resulting emissions growth patterns while considering fut...

  6. Analyzing Pseudophosphatase Function.

    Science.gov (United States)

    Hinton, Shantá D

    2016-01-01

    Pseudophosphatases regulate signal transduction cascades, but their mechanisms of action remain enigmatic. Reflecting this mystery, the prototypical pseudophosphatase STYX (phospho-serine-threonine/tyrosine-binding protein) was named with allusion to the river of the dead in Greek mythology to emphasize that these molecules are "dead" phosphatases. Although proteins with STYX domains do not catalyze dephosphorylation, this in no way precludes their having other functions as integral elements of signaling networks. Thus, understanding their roles in signaling pathways may mark them as potential novel drug targets. This chapter outlines common strategies used to characterize the functions of pseudophosphatases, using as an example MK-STYX [mitogen-activated protein kinase (MAPK) phospho-serine-threonine/tyrosine binding], which has been linked to tumorigenesis, apoptosis, and neuronal differentiation. We start with the importance of "restoring" (when possible) phosphatase activity in a pseudophosphatase so that the active mutant may be used as a comparison control throughout immunoprecipitation and mass spectrometry analyses. To this end, we provide protocols for site-directed mutagenesis, mammalian cell transfection, co-immunoprecipitation, phosphatase activity assays, and immunoblotting that we have used to investigate MK-STYX and the active mutant MK-STYXactive. We also highlight the importance of utilizing RNA interference (RNAi) "knockdown" technology to determine a cellular phenotype in various cell lines. Therefore, we outline our protocols for introducing short hairpin RNA (shRNA) expression plasmids into mammalians cells and quantifying knockdown of gene expression with real-time quantitative PCR (qPCR). A combination of cellular, molecular, biochemical, and proteomic techniques has served as powerful tools in identifying novel functions of the pseudophosphatase MK-STYX. Likewise, the information provided here should be a helpful guide to elucidating the

  7. A neutron activation analyzer

    International Nuclear Information System (INIS)

    Westphal, G.P.; Lemmel, H.; Grass, F.; De Regge, P.P.; Burns, K.; Markowicz, A.

    2005-01-01

    Dubbed 'Analyzer' because of its simplicity, a neutron activation analysis facility for short-lived isomeric transitions is based on a low-cost rabbit system and an adaptive digital filter which are controlled by a software performing irradiation control, loss-free gamma-spectrometry, spectra evaluation, nuclide identification and calculation of concentrations in a fully automatic flow of operations. Designed for TRIGA reactors and constructed from inexpensive plastic tubing and an aluminum in-core part, the rabbit system features samples of 5 ml and 10 ml with sample separation at 150 ms and 200 ms transport time or 25 ml samples without separation at a transport time of 300 ms. By automatically adapting shaping times to pulse intervals the preloaded digital filter gives best throughput at best resolution up to input counting rates of 10 6 cps. Loss-free counting enables quantitative correction of counting losses of up to 99%. As a test of system reproducibility in sample separation geometry, K, Cl, Mn, Mg, Ca, Sc, and V have been determined in various reference materials at excellent agreement with consensus values. (author)

  8. Downhole Fluid Analyzer Development

    Energy Technology Data Exchange (ETDEWEB)

    Bill Turner

    2006-11-28

    A novel fiber optic downhole fluid analyzer has been developed for operation in production wells. This device will allow real-time determination of the oil, gas and water fractions of fluids from different zones in a multizone or multilateral completion environment. The device uses near infrared spectroscopy and induced fluorescence measurement to unambiguously determine the oil, water and gas concentrations at all but the highest water cuts. The only downhole components of the system are the fiber optic cable and windows. All of the active components--light sources, sensors, detection electronics and software--will be located at the surface, and will be able to operate multiple downhole probes. Laboratory testing has demonstrated that the sensor can accurately determine oil, water and gas fractions with a less than 5 percent standard error. Once installed in an intelligent completion, this sensor will give the operating company timely information about the fluids arising from various zones or multilaterals in a complex completion pattern, allowing informed decisions to be made on controlling production. The research and development tasks are discussed along with a market analysis.

  9. Climate Model Diagnostic Analyzer

    Science.gov (United States)

    Lee, Seungwon; Pan, Lei; Zhai, Chengxing; Tang, Benyang; Kubar, Terry; Zhang, Zia; Wang, Wei

    2015-01-01

    The comprehensive and innovative evaluation of climate models with newly available global observations is critically needed for the improvement of climate model current-state representation and future-state predictability. A climate model diagnostic evaluation process requires physics-based multi-variable analyses that typically involve large-volume and heterogeneous datasets, making them both computation- and data-intensive. With an exploratory nature of climate data analyses and an explosive growth of datasets and service tools, scientists are struggling to keep track of their datasets, tools, and execution/study history, let alone sharing them with others. In response, we have developed a cloud-enabled, provenance-supported, web-service system called Climate Model Diagnostic Analyzer (CMDA). CMDA enables the physics-based, multivariable model performance evaluations and diagnoses through the comprehensive and synergistic use of multiple observational data, reanalysis data, and model outputs. At the same time, CMDA provides a crowd-sourcing space where scientists can organize their work efficiently and share their work with others. CMDA is empowered by many current state-of-the-art software packages in web service, provenance, and semantic search.

  10. Analyzing Visibility Configurations.

    Science.gov (United States)

    Dachsbacher, C

    2011-04-01

    Many algorithms, such as level of detail rendering and occlusion culling methods, make decisions based on the degree of visibility of an object, but do not analyze the distribution, or structure, of the visible and occluded regions across surfaces. We present an efficient method to classify different visibility configurations and show how this can be used on top of existing methods based on visibility determination. We adapt co-occurrence matrices for visibility analysis and generalize them to operate on clusters of triangular surfaces instead of pixels. We employ machine learning techniques to reliably classify the thus extracted feature vectors. Our method allows perceptually motivated level of detail methods for real-time rendering applications by detecting configurations with expected visual masking. We exemplify the versatility of our method with an analysis of area light visibility configurations in ray tracing and an area-to-area visibility analysis suitable for hierarchical radiosity refinement. Initial results demonstrate the robustness, simplicity, and performance of our method in synthetic scenes, as well as real applications.

  11. PR Interval Associated Genes, Atrial Remodeling and Rhythm Outcome of Catheter Ablation of Atrial Fibrillation—A Gene-Based Analysis of GWAS Data

    Directory of Open Access Journals (Sweden)

    Daniela Husser

    2017-12-01

    Full Text Available Background: PR interval prolongation has recently been shown to associate with advanced left atrial remodeling and atrial fibrillation (AF recurrence after catheter ablation. While different genome-wide association studies (GWAS have implicated 13 loci to associate with the PR interval as an AF endophenotype their subsequent associations with AF remodeling and response to catheter ablation are unknown. Here, we perform a gene-based analysis of GWAS data to test the hypothesis that PR interval candidate genes also associate with left atrial remodeling and arrhythmia recurrence following AF catheter ablation.Methods and Results: Samples from 660 patients with paroxysmal (n = 370 or persistent AF (n = 290 undergoing AF catheter ablation were genotyped for ~1,000,000 SNPs. Gene-based association was investigated using VEGAS (versatile gene-based association study. Among the 13 candidate genes, SLC8A1, MEIS1, ITGA9, SCN5A, and SOX5 associated with the PR interval. Of those, ITGA9 and SOX5 were significantly associated with left atrial low voltage areas and left atrial diameter and subsequently with AF recurrence after radiofrequency catheter ablation.Conclusion: This study suggests contributions of ITGA9 and SOX5 to AF remodeling expressed as PR interval prolongation, low voltage areas and left atrial dilatation and subsequently to response to catheter ablation. Future and larger studies are necessary to replicate and apply these findings with the aim of designing AF pathophysiology-based multi-locus risk scores.

  12. Identification of novel type 1 diabetes candidate genes by integrating genome-wide association data, protein-protein interactions, and human pancreatic islet gene expression

    DEFF Research Database (Denmark)

    Bergholdt, Regine; Brorsson, Caroline; Palleja, Albert

    2012-01-01

    Genome-wide association studies (GWAS) have heralded a new era in susceptibility locus discovery in complex diseases. For type 1 diabetes, >40 susceptibility loci have been discovered. However, GWAS do not inevitably lead to identification of the gene or genes in a given locus associated with dis......-cells. Our results provide novel insight to the mechanisms behind type 1 diabetes pathogenesis and, thus, may provide the basis for the design of novel treatment strategies.......Genome-wide association studies (GWAS) have heralded a new era in susceptibility locus discovery in complex diseases. For type 1 diabetes, >40 susceptibility loci have been discovered. However, GWAS do not inevitably lead to identification of the gene or genes in a given locus associated...... with disease, and they do not typically inform the broader context in which the disease genes operate. Here, we integrated type 1 diabetes GWAS data with protein-protein interactions to construct biological networks of relevance for disease. A total of 17 networks were identified. To prioritize...

  13. Analyzing the Biology on the System Level

    OpenAIRE

    Tong, Wei

    2016-01-01

    Although various genome projects have provided us enormous static sequence information, understanding of the sophisticated biology continues to require integrating the computational modeling, system analysis, technology development for experiments, and quantitative experiments all together to analyze the biology architecture on various levels, which is just the origin of systems biology subject. This review discusses the object, its characteristics, and research attentions in systems biology,...

  14. Nuclear plant analyzer desktop workstation

    International Nuclear Information System (INIS)

    Beelman, R.J.

    1990-01-01

    In 1983 the U.S. Nuclear Regulatory Commission (USNRC) commissioned the Idaho National Engineering Laboratory (INEL) to develop a Nuclear Plant Analyzer (NPA). The NPA was envisioned as a graphical aid to assist reactor safety analysts in comprehending the results of thermal-hydraulic code calculations. The development was to proceed in three distinct phases culminating in a desktop reactor safety workstation. The desktop NPA is now complete. The desktop NPA is a microcomputer based reactor transient simulation, visualization and analysis tool developed at INEL to assist an analyst in evaluating the transient behavior of nuclear power plants by means of graphic displays. The NPA desktop workstation integrates advanced reactor simulation codes with online computer graphics allowing reactor plant transient simulation and graphical presentation of results. The graphics software, written exclusively in ANSI standard C and FORTRAN 77 and implemented over the UNIX/X-windows operating environment, is modular and is designed to interface to the NRC's suite of advanced thermal-hydraulic codes to the extent allowed by that code. Currently, full, interactive, desktop NPA capabilities are realized only with RELAP5

  15. An integrated in silico approach to analyze the involvement of single amino acid polymorphisms in FANCD1/BRCA2-PALB2 and FANCD1/BRCA2-RAD51 complex.

    Science.gov (United States)

    Doss, C George Priya; Nagasundaram, N

    2014-11-01

    Fanconi anemia (FA) is an autosomal recessive human disease characterized by genomic instability and a marked increase in cancer risk. The importance of FANCD1 gene is manifested by the fact that deleterious amino acid substitutions were found to confer susceptibility to hereditary breast and ovarian cancers. Attaining experimental knowledge about the possible disease-associated substitutions is laborious and time consuming. The recent introduction of genome variation analyzing in silico tools have the capability to identify the deleterious variants in an efficient manner. In this study, we conducted in silico variation analysis of deleterious non-synonymous SNPs at both functional and structural level in the breast cancer and FA susceptibility gene BRCA2/FANCD1. To identify and characterize deleterious mutations in this study, five in silico tools based on two different prediction methods namely pathogenicity prediction (SIFT, PolyPhen, and PANTHER), and protein stability prediction (I-Mutant 2.0 and MuStab) were analyzed. Based on the deleterious scores that overlap in these in silico approaches, and the availability of three-dimensional structures, structure analysis was carried out with the major mutations that occurred in the native protein coded by FANCD1/BRCA2 gene. In this work, we report the results of the first molecular dynamics (MD) simulation study performed to analyze the structural level changes in time scale level with respect to the native and mutated protein complexes (G25R, W31C, W31R in FANCD1/BRCA2-PALB2, and F1524V, V1532F in FANCD1/BRCA2-RAD51). Analysis of the MD trajectories indicated that predicted deleterious variants alter the structural behavior of BRCA2-PALB2 and BRCA2-RAD51 protein complexes. In addition, statistical analysis was employed to test the significance of these in silico tool predictions. Based on these predictions, we conclude that the identification of disease-related SNPs by in silico methods, in combination with MD

  16. Modelo hipercubo integrado a um algoritmo genético para análise de sistemas médicos emergenciais em rodovias The hypercube queuing model integrated to a genetic algorithm to analyze emergency medical systems on highways

    Directory of Open Access Journals (Sweden)

    Ana Paula Iannoni

    2006-04-01

    Full Text Available O modelo hipercubo, conhecido na literatura de problemas de localização de sistemas servidor para cliente, é um modelo baseado em teoria de filas espacialmente distribuídas e aproximações Markovianas. O modelo pode ser modificado para analisar os sistemas de atendimentos emergenciais (SAEs em rodovias, considerando as particularidades da política de despacho destes sistemas. Neste estudo, combinou-se o modelo hipercubo com um algoritmo genético para otimizar a configuração e operação de SAEs em rodovias. A abordagem é efetiva para apoiar decisões relacionadas ao planejamento e operação destes sistemas, por exemplo, em determinar o tamanho ideal para as áreas de cobertura de cada ambulância, de forma a minimizar o tempo médio de resposta aos usuários e o desbalanceamento das cargas de trabalho das ambulâncias. Os resultados computacionais desta abordagem foram analisados utilizando dados reais do sistema Anjos do Asfalto (rodovia Presidente Dutra.The hypercube model, well-known in the literature on problems of server-to-customer localization systems, is based on the spatially distributed queuing theory and Markovian analysis approximations. The model can be modified to analyze Emergency Medical Systems (EMSs on highways, considering the particularities of these systems' dispatching policies. In this study, we combine the hypercube model with a genetic algorithm to optimize the configuration and operation of EMSs on highways. This approach is effective to support planning and operation decisions, such as determining the ideal size of the area each ambulance should cover to minimize not only the average time of response to the user but also ambulance workload imbalances, as well as generating a Pareto efficient boundary between these measures. The computational results of this approach were analyzed using real data Anjos do Asfalto EMS (which covers the Presidente Dutra highway.

  17. Association between GWAS-identified lung adenocarcinoma susceptibility loci and EGFR mutations in never-smoking Asian women, and comparison with findings from Western populations.

    Science.gov (United States)

    Seow, Wei Jie; Matsuo, Keitaro; Hsiung, Chao Agnes; Shiraishi, Kouya; Song, Minsun; Kim, Hee Nam; Wong, Maria Pik; Hong, Yun-Chul; Hosgood, H Dean; Wang, Zhaoming; Chang, I-Shou; Wang, Jiu-Cun; Chatterjee, Nilanjan; Tucker, Margaret; Wei, Hu; Mitsudomi, Tetsuya; Zheng, Wei; Kim, Jin Hee; Zhou, Baosen; Caporaso, Neil E; Albanes, Demetrius; Shin, Min-Ho; Chung, Lap Ping; An, She-Juan; Wang, Ping; Zheng, Hong; Yatabe, Yasushi; Zhang, Xu-Chao; Kim, Young Tae; Shu, Xiao-Ou; Kim, Young-Chul; Bassig, Bryan A; Chang, Jiang; Ho, James Chung Man; Ji, Bu-Tian; Kubo, Michiaki; Daigo, Yataro; Ito, Hidemi; Momozawa, Yukihide; Ashikawa, Kyota; Kamatani, Yoichiro; Honda, Takayuki; Sakamoto, Hiromi; Kunitoh, Hideo; Tsuta, Koji; Watanabe, Shun-Ichi; Nokihara, Hiroshi; Miyagi, Yohei; Nakayama, Haruhiko; Matsumoto, Shingo; Tsuboi, Masahiro; Goto, Koichi; Yin, Zhihua; Shi, Jianxin; Takahashi, Atsushi; Goto, Akiteru; Minamiya, Yoshihiro; Shimizu, Kimihiro; Tanaka, Kazumi; Wu, Tangchun; Wei, Fusheng; Wong, Jason Y Y; Matsuda, Fumihiko; Su, Jian; Kim, Yeul Hong; Oh, In-Jae; Song, Fengju; Lee, Victor Ho Fun; Su, Wu-Chou; Chen, Yuh-Min; Chang, Gee-Chen; Chen, Kuan-Yu; Huang, Ming-Shyan; Yang, Pan-Chyr; Lin, Hsien-Chih; Xiang, Yong-Bing; Seow, Adeline; Park, Jae Yong; Kweon, Sun-Seog; Chen, Chien-Jen; Li, Haixin; Gao, Yu-Tang; Wu, Chen; Qian, Biyun; Lu, Daru; Liu, Jianjun; Jeon, Hyo-Sung; Hsiao, Chin-Fu; Sung, Jae Sook; Tsai, Ying-Huang; Jung, Yoo Jin; Guo, Huan; Hu, Zhibin; Wang, Wen-Chang; Chung, Charles C; Lawrence, Charles; Burdett, Laurie; Yeager, Meredith; Jacobs, Kevin B; Hutchinson, Amy; Berndt, Sonja I; He, Xingzhou; Wu, Wei; Wang, Junwen; Li, Yuqing; Choi, Jin Eun; Park, Kyong Hwa; Sung, Sook Whan; Liu, Li; Kang, Chang Hyun; Hu, Lingmin; Chen, Chung-Hsing; Yang, Tsung-Ying; Xu, Jun; Guan, Peng; Tan, Wen; Wang, Chih-Liang; Sihoe, Alan Dart Loon; Chen, Ying; Choi, Yi Young; Hung, Jen-Yu; Kim, Jun Suk; Yoon, Ho-Il; Cai, Qiuyin; Lin, Chien-Chung; Park, In Kyu; Xu, Ping; Dong, Jing; Kim, Christopher; He, Qincheng; Perng, Reury-Perng; Chen, Chih-Yi; Vermeulen, Roel; Wu, Junjie; Lim, Wei-Yen; Chen, Kun-Chieh; Chan, John K C; Chu, Minjie; Li, Yao-Jen; Li, Jihua; Chen, Hongyan; Yu, Chong-Jen; Jin, Li; Lo, Yen-Li; Chen, Ying-Hsiang; Fraumeni, Joseph F; Liu, Jie; Yamaji, Taiki; Yang, Yang; Hicks, Belynda; Wyatt, Kathleen; Li, Shengchao A; Dai, Juncheng; Ma, Hongxia; Jin, Guangfu; Song, Bao; Wang, Zhehai; Cheng, Sensen; Li, Xuelian; Ren, Yangwu; Cui, Ping; Iwasaki, Motoki; Shimazu, Taichi; Tsugane, Shoichiro; Zhu, Junjie; Jiang, Gening; Fei, Ke; Wu, Guoping; Chien, Li-Hsin; Chen, Hui-Ling; Su, Yu-Chun; Tsai, Fang-Yu; Chen, Yi-Song; Yu, Jinming; Stevens, Victoria L; Laird-Offringa, Ite A; Marconett, Crystal N; Lin, Dongxin; Chen, Kexin; Wu, Yi-Long; Landi, Maria Teresa; Shen, Hongbing; Rothman, Nathaniel; Kohno, Takashi; Chanock, Stephen J; Lan, Qing

    2017-01-15

    To evaluate associations by EGFR mutation status for lung adenocarcinoma risk among never-smoking Asian women, we conducted a meta-analysis of 11 loci previously identified in genome-wide association studies (GWAS). Genotyping in an additional 10,780 never-smoking cases and 10,938 never-smoking controls from Asia confirmed associations with eight known single nucleotide polymorphisms (SNPs). Two new signals were observed at genome-wide significance (P Asian women and highlight the importance of how the germline could inform risk for specific tumour mutation patterns, which could have important translational implications. Published by Oxford University Press 2016. This work is written by US Government employees and is in the public domain in the US.

  18. Multichannel analyzer development in CAMAC

    International Nuclear Information System (INIS)

    Nagy, J.Z.; Zarandy, A.

    1988-01-01

    The data acquisition in TOKAMAK experiments some CAMAC modules have been developed. The modules are the following: 64 K analyzer memory, 32 K analyzer memory, 6-channel pulse peak analyzer memory which contains the 32 K analyzer memory and eight AD-converters

  19. A low frequency variant within the GWAS locus of MTNR1B affects fasting glucose concentrations: genetic risk is modulated by obesity.

    Science.gov (United States)

    Been, L F; Hatfield, J L; Shankar, A; Aston, C E; Ralhan, S; Wander, G S; Mehra, N K; Singh, J R; Mulvihill, J J; Sanghera, D K

    2012-11-01

    Two common variants (rs1387153, rs10830963) in MTNR1B have been reported to have independent effects on fasting blood glucose (FBG) levels with increased risk to type 2 diabetes (T2D) in recent genome-wide association studies (GWAS). In this investigation, we report the association of these two variants, and an additional variant (rs1374645) within the GWAS locus of MTNR1B with FBG, 2h glucose, insulin resistance (HOMA IR), β-cell function (HOMA B), and T2D in our sample of Asian Sikhs from India. Our cohort comprised 2222 subjects [1201 T2D, 1021 controls]. None of these SNPs was associated with T2D in this cohort. Our data also could not confirm association of rs1387153 and rs10830963 with FBG phenotype. However, upon stratifying data according to body mass index (BMI) (low ≤ 25 kg/m(2) and high > 25 kg/m(2)) in normoglycemic subjects (n = 1021), the rs1374645 revealed a strong association with low FBG levels in low BMI group (β = -0.073, p = 0.002, Bonferroni p = 0.01) compared to the high BMI group (β = 0.015, p = 0.50). We also detected a strong evidence of interaction between rs1374645 and BMI with respect to FBG levels (p = 0.002). Our data provide new information about the significant impact of another MTNR1B variant on FBG levels that appears to be modulated by BMI. Future confirmation on independent datasets and functional studies will be required to define the role of this variant in fasting glucose variation. Published by Elsevier B.V.

  20. Genome-Wide Association Study (GWAS) and Genome-Wide Environment Interaction Study (GWEIS) of Depressive Symptoms in African American and Hispanic/Latina Women

    Science.gov (United States)

    Dunn, Erin C.; Wiste, Anna; Radmanesh, Farid; Almli, Lynn M.; Gogarten, Stephanie M.; Sofer, Tamar; Faul, Jessica D.; Kardia, Sharon L.R.; Smith, Jennifer A.; Weir, David R.; Zhao, Wei; Soare, Thomas W.; Mirza, Saira S.; Hek, Karin; Tiemeier, Henning W.; Goveas, Joseph S.; Sarto, Gloria E.; Snively, Beverly M.; Cornelis, Marilyn; Koenen, Karestan C.; Kraft, Peter; Purcell, Shaun; Ressler, Kerry J.; Rosand, Jonathan; Wassertheil-Smoller, Sylvia; Smoller, Jordan W.

    2016-01-01

    Background Genome-wide association studies (GWAS) have been unable to identify variants linked to depression. We hypothesized that examining depressive symptoms and considering gene-environment interaction (G×E) might improve efficiency for gene discovery. We therefore conducted a GWAS and genome-wide environment interaction study (GWEIS) of depressive symptoms. Methods Using data from the SHARe cohort of the Women’s Health Initiative, comprising African Americans (n=7179) and Hispanics/Latinas (n=3138), we examined genetic main effects and G×E with stressful life events and social support. We also conducted a heritability analysis using genome-wide complex trait analysis (GCTA). Replication was attempted in four independent cohorts. Results No SNPs achieved genome-wide significance for main effects in either discovery sample. The top signals in African Americans were rs73531535 (located 20kb from GPR139, p=5.75×10−8) and rs75407252 (intronic to CACNA2D3, p=6.99×10−7). In Hispanics/Latinas, the top signals were rs2532087 (located 27kb from CD38, p=2.44×10−7) and rs4542757 (intronic to DCC, p=7.31×10−7). In the GWEIS with stressful life events, one interaction signal was genome-wide significant in African Americans (rs4652467; p=4.10×10−10; located 14kb from CEP350). This interaction was not observed in a smaller replication cohort. Although heritability estimates for depressive symptoms and stressful life events were each less than 10%, they were strongly genetically correlated (rG=0.95), suggesting that common variation underlying depressive symptoms and stressful life event exposure, though modest on their own, were highly overlapping in this sample. Conclusions Our results underscore the need for larger samples, more GWEIS, and greater investigation into genetic and environmental determinants of depressive symptoms in minorities. PMID:27038408

  1. A tandem parallel plate analyzer

    International Nuclear Information System (INIS)

    Hamada, Y.; Fujisawa, A.; Iguchi, H.; Nishizawa, A.; Kawasumi, Y.

    1996-11-01

    By a new modification of a parallel plate analyzer the second-order focus is obtained in an arbitrary injection angle. This kind of an analyzer with a small injection angle will have an advantage of small operational voltage, compared to the Proca and Green analyzer where the injection angle is 30 degrees. Thus, the newly proposed analyzer will be very useful for the precise energy measurement of high energy particles in MeV range. (author)

  2. Digital Multi Channel Analyzer Enhancement

    International Nuclear Information System (INIS)

    Gonen, E.; Marcus, E.; Wengrowicz, U.; Beck, A.; Nir, J.; Sheinfeld, M.; Broide, A.; Tirosh, D.

    2002-01-01

    A cement analyzing system based on radiation spectroscopy had been developed [1], using novel digital approach for real-time, high-throughput and low-cost Multi Channel Analyzer. The performance of the developed system had a severe problem: the resulted spectrum suffered from lack of smoothness, it was very noisy and full of spikes and surges, therefore it was impossible to use this spectrum for analyzing the cement substance. This paper describes the work carried out to improve the system performance

  3. PM 3655 PHILIPS Logic analyzer

    CERN Multimedia

    A logic analyzer is an electronic instrument that captures and displays multiple signals from a digital system or digital circuit. A logic analyzer may convert the captured data into timing diagrams, protocol decodes, state machine traces, assembly language, or may correlate assembly with source-level software. Logic Analyzers have advanced triggering capabilities, and are useful when a user needs to see the timing relationships between many signals in a digital system.

  4. Replication study for the association of 9 East Asian GWAS-derived loci with susceptibility to type 2 diabetes in a Japanese population.

    Directory of Open Access Journals (Sweden)

    Kensuke Sakai

    Full Text Available AIMS: East Asian genome-wide association studies (GWAS for type 2 diabetes identified 8 loci with genome-wide significance, and 2 loci with a borderline association. However, the associations of these loci except MAEA locus with type 2 diabetes have not been evaluated in independent East Asian cohorts. We performed a replication study to investigate the association of these susceptibility loci with type 2 diabetes in an independent Japanese population. METHODS: We genotyped 7,379 Japanese participants (5,315 type 2 diabetes and 2,064 controls for each of the 9 single nucleotide polymorphisms (SNPs, rs7041847 in GLIS3, rs6017317 in FITM2-R3HDML-HNF4A, rs6467136 near GCCI-PAX4, rs831571 near PSMD6, rs9470794 in ZFAND3, rs3786897 in PEPD, rs1535500 in KCNK16, rs16955379 in CMIP, and rs17797882 near WWOX. Because the sample size in this study was not sufficient to replicate single SNP associations, we constructed a genetic risk score (GRS by summing a number of risk alleles of the 9 SNPs, and examined the association of the GRS with type 2 diabetes using logistic regression analysis. RESULTS: With the exception of rs1535500 in KCNK16, all SNPs had the same direction of effect (odds ratio [OR]>1.0 as in the original reports. The GRS constructed from the 9 SNPs was significantly associated with type 2 diabetes in the Japanese population (p = 4.0 × 10(-4, OR = 1.05, 95% confidence interval: 1.02-1.09. In quantitative trait analyses, rs16955379 in CMIP was nominally associated with a decreased homeostasis model assessment of β-cell function and with increased fasting plasma glucose, but neither the individual SNPs nor the GRS showed a significant association with the glycemic traits. CONCLUSIONS: These results indicate that 9 loci that were identified in the East Asian GWAS meta-analysis have a significant effect on the susceptibility to type 2 diabetes in the Japanese population.

  5. Multichannel analyzer type CMA-3

    International Nuclear Information System (INIS)

    Czermak, A.; Jablonski, J.; Ostrowicz, A.

    1978-01-01

    Multichannel analyzer CMA-3 is designed for two-parametric analysis with operator controlled logical windows. It is implemented in CAMAC standard. A single crate contains all required modules and is controlled by the PDP-11/10 minicomputer. Configuration of CMA-3 is shown. CMA-3 is the next version of the multichannel analyzer described in report No 958/E-8. (author)

  6. Analyzing data files in SWAN

    CERN Document Server

    Gajam, Niharika

    2016-01-01

    Traditionally analyzing data happens via batch-processing and interactive work on the terminal. The project aims to provide another way of analyzing data files: A cloud-based approach. It aims to make it a productive and interactive environment through the combination of FCC and SWAN software.

  7. Revisiting QTL Affecting Clinical Mastitis by High-Density GWAS and Resequencing in the Finnish Ayrshire Dairy Cattle

    DEFF Research Database (Denmark)

    Vilkki, Johanna; Iso-Touru, Terhi; Schulman, Nina F

    Mastitis is the most common disease of dairy cattle, causing high economic losses each year. Studies to locate QTL affecting clinical mastitis and milk somatic cell counts have been carried out to increase our understanding of the disease. As part of the EU FP7 Quantomics project, we have used most...... recent genomic tools to characterize QTL affecting mastitis incidence in the Finnish Ayrshire cattle. Clinical mastitis diagnoses from -15 to 50 days and 51 to 300 days of first lactation and SCC (geometric mean of SCS observations between 5 to 170 days of first lactation) were included. In total, 1920...... progeny tested bulls were genotyped with the Illumina BovineSNP50 chip. After quality control, 38473 SNPs were analyzed using a mixed linear model (software package DMU). Associations (5% Bonferroni threshold) were detected in 9 peaks on 5 chromosomes. A set of 238 of the bulls were re...

  8. A genome-wide association scan (GWAS) for mean telomere length within the COGS project: identified loci show little association with hormone-related cancer risk

    Science.gov (United States)

    Pooley, Karen A.; Bojesen, Stig E.; Weischer, Maren; Nielsen, Sune F.; Thompson, Deborah; Amin Al Olama, Ali; Michailidou, Kyriaki; Tyrer, Jonathan P.; Benlloch, Sara; Brown, Judith; Audley, Tina; Luben, Robert; Khaw, K-T; Neal, David E.; Hamdy, Freddie C.; Donovan, Jenny L.; Kote-Jarai, Zsofia; Baynes, Caroline; Shah, Mitul; Bolla, Manjeet K.; Wang, Qin; Dennis, Joe; Dicks, Ed; Yang, Rongxi; Rudolph, Anja; Schildkraut, Joellen; Chang-Claude, Jenny; Burwinkel, Barbara; Chenevix-Trench, Georgia; Pharoah, Paul D. P.; Berchuck, Andrew; Eeles, Rosalind A.; Easton, Douglas F.; Dunning, Alison M.; Nordestgaard, Børge G.

    2013-01-01

    Mean telomere length (TL) in blood cells is heritable and has been reported to be associated with risks of several diseases, including cancer. We conducted a meta-analysis of three GWAS for TL (total n=2240) and selected 1629 variants for replication via the “iCOGS” custom genotyping array. All ∼200 000 iCOGS variants were analysed with TL, and those displaying associations in healthy controls (n = 15 065) were further tested in breast cancer cases (n = 11 024). We found a novel TL association (Ptrend < 4 × 10−10) at 3p14.4 close to PXK and evidence (Ptrend < 7 × 10−7) for TL loci at 6p22.1 (ZNF311) and 20q11.2 (BCL2L1). We additionally confirmed (Ptrend < 5 × 10−14) the previously reported loci at 3q26.2 (TERC), 5p15.3 (TERT) and 10q24.3 (OBFC1) and found supportive evidence (Ptrend < 5 × 10−4) for the published loci at 2p16.2 (ACYP2), 4q32.2 (NAF1) and 20q13.3 (RTEL1). SNPs tagging these loci explain TL differences of up to 731 bp (corresponding to 18% of total TL in healthy individuals), however, they display little direct evidence for association with breast, ovarian or prostate cancer risks. PMID:23900074

  9. A genome-wide association scan (GWAS) for mean telomere length within the COGS project: identified loci show little association with hormone-related cancer risk.

    Science.gov (United States)

    Pooley, Karen A; Bojesen, Stig E; Weischer, Maren; Nielsen, Sune F; Thompson, Deborah; Amin Al Olama, Ali; Michailidou, Kyriaki; Tyrer, Jonathan P; Benlloch, Sara; Brown, Judith; Audley, Tina; Luben, Robert; Khaw, K-T; Neal, David E; Hamdy, Freddie C; Donovan, Jenny L; Kote-Jarai, Zsofia; Baynes, Caroline; Shah, Mitul; Bolla, Manjeet K; Wang, Qin; Dennis, Joe; Dicks, Ed; Yang, Rongxi; Rudolph, Anja; Schildkraut, Joellen; Chang-Claude, Jenny; Burwinkel, Barbara; Chenevix-Trench, Georgia; Pharoah, Paul D P; Berchuck, Andrew; Eeles, Rosalind A; Easton, Douglas F; Dunning, Alison M; Nordestgaard, Børge G

    2013-12-15

    Mean telomere length (TL) in blood cells is heritable and has been reported to be associated with risks of several diseases, including cancer. We conducted a meta-analysis of three GWAS for TL (total n=2240) and selected 1629 variants for replication via the "iCOGS" custom genotyping array. All ∼200 000 iCOGS variants were analysed with TL, and those displaying associations in healthy controls (n = 15 065) were further tested in breast cancer cases (n = 11 024). We found a novel TL association (Ptrend < 4 × 10(-10)) at 3p14.4 close to PXK and evidence (Ptrend < 7 × 10(-7)) for TL loci at 6p22.1 (ZNF311) and 20q11.2 (BCL2L1). We additionally confirmed (Ptrend < 5 × 10(-14)) the previously reported loci at 3q26.2 (TERC), 5p15.3 (TERT) and 10q24.3 (OBFC1) and found supportive evidence (Ptrend < 5 × 10(-4)) for the published loci at 2p16.2 (ACYP2), 4q32.2 (NAF1) and 20q13.3 (RTEL1). SNPs tagging these loci explain TL differences of up to 731 bp (corresponding to 18% of total TL in healthy individuals), however, they display little direct evidence for association with breast, ovarian or prostate cancer risks.

  10. [Automated analyzer of enzyme immunoassay].

    Science.gov (United States)

    Osawa, S

    1995-09-01

    Automated analyzers for enzyme immunoassay can be classified by several points of view: the kind of labeled antibodies or enzymes, detection methods, the number of tests per unit time, analytical time and speed per run. In practice, it is important for us consider the several points such as detection limits, the number of tests per unit time, analytical range, and precision. Most of the automated analyzers on the market can randomly access and measure samples. I will describe the recent advance of automated analyzers reviewing their labeling antibodies and enzymes, the detection methods, the number of test per unit time and analytical time and speed per test.

  11. DEMorphy, German Language Morphological Analyzer

    OpenAIRE

    Altinok, Duygu

    2018-01-01

    DEMorphy is a morphological analyzer for German. It is built onto large, compactified lexicons from German Morphological Dictionary. A guesser based on German declension suffixed is also provided. For German, we provided a state-of-art morphological analyzer. DEMorphy is implemented in Python with ease of usability and accompanying documentation. The package is suitable for both academic and commercial purposes wit a permissive licence.

  12. A Categorization of Dynamic Analyzers

    Science.gov (United States)

    Lujan, Michelle R.

    1997-01-01

    Program analysis techniques and tools are essential to the development process because of the support they provide in detecting errors and deficiencies at different phases of development. The types of information rendered through analysis includes the following: statistical measurements of code, type checks, dataflow analysis, consistency checks, test data,verification of code, and debugging information. Analyzers can be broken into two major categories: dynamic and static. Static analyzers examine programs with respect to syntax errors and structural properties., This includes gathering statistical information on program content, such as the number of lines of executable code, source lines. and cyclomatic complexity. In addition, static analyzers provide the ability to check for the consistency of programs with respect to variables. Dynamic analyzers in contrast are dependent on input and the execution of a program providing the ability to find errors that cannot be detected through the use of static analysis alone. Dynamic analysis provides information on the behavior of a program rather than on the syntax. Both types of analysis detect errors in a program, but dynamic analyzers accomplish this through run-time behavior. This paper focuses on the following broad classification of dynamic analyzers: 1) Metrics; 2) Models; and 3) Monitors. Metrics are those analyzers that provide measurement. The next category, models, captures those analyzers that present the state of the program to the user at specified points in time. The last category, monitors, checks specified code based on some criteria. The paper discusses each classification and the techniques that are included under them. In addition, the role of each technique in the software life cycle is discussed. Familiarization with the tools that measure, model and monitor programs provides a framework for understanding the program's dynamic behavior from different, perspectives through analysis of the input

  13. CSTT Update: Fuel Quality Analyzer

    Energy Technology Data Exchange (ETDEWEB)

    Brosha, Eric L. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Lujan, Roger W. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Mukundan, Rangachary [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Rockward, Tommy [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Romero, Christopher J. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Williams, Stefan [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Wilson, Mahlon S. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2018-02-06

    These are slides from a presentation. The following topics are covered: project background (scope and approach), developing the prototype (timeline), update on intellectual property, analyzer comparisons (improving humidification, stabilizing the baseline, applying clean-up strategy, impact of ionomer content and improving clean-up), proposed operating mode, considerations for testing in real-world conditions (Gen 1 analyzer electronics development, testing partner identified, field trial planning), summary, and future work.

  14. Integration of mouse and human genome-wide association data identifies KCNIP4 as an asthma gene.

    Directory of Open Access Journals (Sweden)

    Blanca E Himes

    Full Text Available Asthma is a common chronic respiratory disease characterized by airway hyperresponsiveness (AHR. The genetics of asthma have been widely studied in mouse and human, and homologous genomic regions have been associated with mouse AHR and human asthma-related phenotypes. Our goal was to identify asthma-related genes by integrating AHR associations in mouse with human genome-wide association study (GWAS data. We used Efficient Mixed Model Association (EMMA analysis to conduct a GWAS of baseline AHR measures from males and females of 31 mouse strains. Genes near or containing SNPs with EMMA p-values <0.001 were selected for further study in human GWAS. The results of the previously reported EVE consortium asthma GWAS meta-analysis consisting of 12,958 diverse North American subjects from 9 study centers were used to select a subset of homologous genes with evidence of association with asthma in humans. Following validation attempts in three human asthma GWAS (i.e., Sepracor/LOCCS/LODO/Illumina, GABRIEL, DAG and two human AHR GWAS (i.e., SHARP, DAG, the Kv channel interacting protein 4 (KCNIP4 gene was identified as nominally associated with both asthma and AHR at a gene- and SNP-level. In EVE, the smallest KCNIP4 association was at rs6833065 (P-value 2.9e-04, while the strongest associations for Sepracor/LOCCS/LODO/Illumina, GABRIEL, DAG were 1.5e-03, 1.0e-03, 3.1e-03 at rs7664617, rs4697177, rs4696975, respectively. At a SNP level, the strongest association across all asthma GWAS was at rs4697177 (P-value 1.1e-04. The smallest P-values for association with AHR were 2.3e-03 at rs11947661 in SHARP and 2.1e-03 at rs402802 in DAG. Functional studies are required to validate the potential involvement of KCNIP4 in modulating asthma susceptibility and/or AHR. Our results suggest that a useful approach to identify genes associated with human asthma is to leverage mouse AHR association data.

  15. ASDA - Advanced Suit Design Analyzer computer program

    Science.gov (United States)

    Bue, Grant C.; Conger, Bruce C.; Iovine, John V.; Chang, Chi-Min

    1992-01-01

    An ASDA model developed to evaluate the heat and mass transfer characteristics of advanced pressurized suit design concepts for low pressure or vacuum planetary applications is presented. The model is based on a generalized 3-layer suit that uses the Systems Integrated Numerical Differencing Analyzer '85 in conjunction with a 41-node FORTRAN routine. The latter simulates the transient heat transfer and respiratory processes of a human body in a suited environment. The user options for the suit encompass a liquid cooled garment, a removable jacket, a CO2/H2O permeable layer, and a phase change layer.

  16. An Updated and Comprehensive Meta-Analysis of Association Between Seven Hot Loci Polymorphisms from Eight GWAS and Glioma Risk.

    Science.gov (United States)

    Wu, Qiang; Peng, Yanyan; Zhao, Xiaotao

    2016-09-01

    Eight genome-wide association studies (GWASs) found that seven loci (rs2736100, rs4295627, rs4977756, rs498872, rs11979158, rs2252586, rs6010620) polymorphisms could elevate the risk of glioma, one of the most common types of primary brain cancer in adults. However, the replication studies about these seven loci obtained inconsistent results. In order to derive a more accurate estimation about the relationship between the selected single-nucleotide polymorphism (SNP) and susceptibility to glioma, we conducted a meta-analysis containing all eligible published case control studies to evaluate the association. An overall literature search was conducted using the database of PubMed, Science Direct, China national knowledge infrastructure (CNKI), and Embase. Seventeen articles with 25 studies were included in the meta-analysis. Glioma risk (odds ratio, OR; 95 % confidential interval, 95 %CI) was estimated with the random-effect model or the fixed-effects model. STATA 12.0 was applied to analyze all statistical data. Results showed that seven hot loci were all associated with increased risk of glioma (rs2736100, OR = 1.28, 95 %CI = 1.23-1.32; rs4295627, OR = 1.34, 95 %CI = 1.21-1.47; rs4977756, OR = 1.24, 95 %CI = 1.20-1.28; rs498872, OR = 1.24, 95 %CI = 1.15-1.33; rs6010620, OR = 1.29, 95 %CI = 1.24-1.35; rs11979158: OR = 1.18, 95 %CI = 1.10-1.25; rs2252586: OR = 1.18, 95 %CI = 1.10-1.25). Additionally, subgroup analysis by stages of glioma found that variation of rs11979158 had stronger relationship with high-grade (OR = 1.32, 95 %CI = 1.19-1.45) than low-grade glioma (OR = 1.12, 95 % CI = 1.03-1.21). Similarly, stratified analysis of rs2252586 by stages revealed the similar trend, with OR of 1.26 (95 %CI = 1.17-1.35) in high-grade glioma and OR of 1.15 (95 %CI = 1.08-1.22) in low-grade glioma. In summary, the present study showed that mutations of the seven loci could elevate

  17. On-Demand Urine Analyzer

    Science.gov (United States)

    Farquharson, Stuart; Inscore, Frank; Shende, Chetan

    2010-01-01

    A lab-on-a-chip was developed that is capable of extracting biochemical indicators from urine samples and generating their surface-enhanced Raman spectra (SERS) so that the indicators can be quantified and identified. The development was motivated by the need to monitor and assess the effects of extended weightlessness, which include space motion sickness and loss of bone and muscle mass. The results may lead to developments of effective exercise programs and drug regimes that would maintain astronaut health. The analyzer containing the lab-on-a- chip includes materials to extract 3- methylhistidine (a muscle-loss indicator) and Risedronate (a bone-loss indicator) from the urine sample and detect them at the required concentrations using a Raman analyzer. The lab-on- a-chip has both an extractive material and a SERS-active material. The analyzer could be used to monitor the onset of diseases, such as osteoporosis.

  18. Device for analyzing a solution

    International Nuclear Information System (INIS)

    Marchand, Joseph.

    1978-01-01

    The device enables a solution containing an antigen to be analyzed by the radio-immunology technique without coming up against the problems of antigen-antibody complex and free antigen separation. This device, for analyzing a solution containing a biological compound capable of reacting with an antagonistic compound specific of the biological compound, features a tube closed at its bottom end and a component set and immobilized in the bottom of the tube so as to leave a capacity between the bottom of the tube and its lower end. The component has a large developed surface and is so shaped that it allows the solution to be analyzed to have access to the bottom of the tube; it is made of a material having some elastic deformation and able to take up a given quantity of the biological compound or of the antagonistic compound specific of the biological compound [fr

  19. Multichannel analyzer embedded in FPGA

    International Nuclear Information System (INIS)

    Garcia D, A.; Hernandez D, V. M.; Vega C, H. R.; Ordaz G, O. O.; Bravo M, I.

    2017-10-01

    Ionizing radiation has different applications, so it is a very significant and useful tool, which in turn can be dangerous for living beings if they are exposed to uncontrolled doses. However, due to its characteristics, it cannot be perceived by any of the senses of the human being, so that in order to know the presence of it, radiation detectors and additional devices are required to quantify and classify it. A multichannel analyzer is responsible for separating the different pulse heights that are generated in the detectors, in a certain number of channels; according to the number of bits of the analog to digital converter. The objective of the work was to design and implement a multichannel analyzer and its associated virtual instrument, for nuclear spectrometry. The components of the multichannel analyzer were created in VHDL hardware description language and packaged in the Xilinx Vivado design suite, making use of resources such as the ARM processing core that the System on Chip Zynq contains and the virtual instrument was developed on the LabView programming graphics platform. The first phase was to design the hardware architecture to be embedded in the FPGA and for the internal control of the multichannel analyzer the application was generated for the ARM processor in C language. For the second phase, the virtual instrument was developed for the management, control and visualization of the results. The data obtained as a result of the development of the system were observed graphically in a histogram showing the spectrum measured. The design of the multichannel analyzer embedded in FPGA was tested with two different radiation detection systems (hyper-pure germanium and scintillation) which allowed determining that the spectra obtained are similar in comparison with the commercial multichannel analyzers. (Author)

  20. Loviisa nuclear power plant analyzer

    International Nuclear Information System (INIS)

    Porkholm, K.; Nurmilaukas, P.; Tiihonen, O.; Haenninen, M.; Puska, E.

    1992-12-01

    The APROS Simulation Environment has been developed since 1986 by Imatran Voima Oy (IVO) and the Technical Research Centre of Finland (VTT). It provides tools, solution algorithms and process components for use in different simulation systems for design, analysis and training purposes. One of its main nuclear applications is the Loviisa Nuclear Power Plant Analyzer (LPA). The Loviisa Plant Analyzer includes all the important plant components both in the primary and in the secondary circuits. In addition, all the main control systems, the protection system and the high voltage electrical systems are included. (orig.)

  1. IPAD: the Integrated Pathway Analysis Database for Systematic Enrichment Analysis.

    Science.gov (United States)

    Zhang, Fan; Drabier, Renee

    2012-01-01

    Next-Generation Sequencing (NGS) technologies and Genome-Wide Association Studies (GWAS) generate millions of reads and hundreds of datasets, and there is an urgent need for a better way to accurately interpret and distill such large amounts of data. Extensive pathway and network analysis allow for the discovery of highly significant pathways from a set of disease vs. healthy samples in the NGS and GWAS. Knowledge of activation of these processes will lead to elucidation of the complex biological pathways affected by drug treatment, to patient stratification studies of new and existing drug treatments, and to understanding the underlying anti-cancer drug effects. There are approximately 141 biological human pathway resources as of Jan 2012 according to the Pathguide database. However, most currently available resources do not contain disease, drug or organ specificity information such as disease-pathway, drug-pathway, and organ-pathway associations. Systematically integrating pathway, disease, drug and organ specificity together becomes increasingly crucial for understanding the interrelationships between signaling, metabolic and regulatory pathway, drug action, disease susceptibility, and organ specificity from high-throughput omics data (genomics, transcriptomics, proteomics and metabolomics). We designed the Integrated Pathway Analysis Database for Systematic Enrichment Analysis (IPAD, http://bioinfo.hsc.unt.edu/ipad), defining inter-association between pathway, disease, drug and organ specificity, based on six criteria: 1) comprehensive pathway coverage; 2) gene/protein to pathway/disease/drug/organ association; 3) inter-association between pathway, disease, drug, and organ; 4) multiple and quantitative measurement of enrichment and inter-association; 5) assessment of enrichment and inter-association analysis with the context of the existing biological knowledge and a "gold standard" constructed from reputable and reliable sources; and 6) cross-linking of

  2. The security analyzer: A security analyzer program written in Prolog

    International Nuclear Information System (INIS)

    Zimmerman, B.D.; Densley, P.J.

    1986-09-01

    The Security Analyzer is a software tool capable of analyzing the effectiveness of a facility's security system. It is written in the Prolog logic programming computer language, using entity-relationship data modeling techniques. The program performs the following functions: (1) provides descriptive, locational and operational status information about intrusion detectors and assessment devices (i.e., ''sensors'' and ''cameras'') upon request; (2) provides for storage and retrieval of maintenance history information for various components of the security system (including intrusion detectors), and allows for changing that information as desired; (3) provides a ''search'' mode, wherein all paths are found from any specified physical location to another specified location which satisfy user chosen ''intruder detection'' probability and elapsed time criteria (i.e., the program finds the ''weakest paths'' from a security point of view). The first two of these functions can be provided fairly easily with a conventional database program; the third function could be provided using Fortran or some similar language, though with substantial difficulty. In the Security Analyzer program, all these functions are provided in a simple and straight-forward manner. This simplicity is possible because the program is written in the symbolic (as opposed to numeric) processing language Prolog, and because the knowledge base is structured according to entity-relationship modeling principles. Also, the use of Prolog and the entity-relationship modeling technique allows the capabilities of the Security analyzer program, both for knowledge base interrogation and for searching-type operations, to be easily expanded in ways that would be very difficult for a numeric and more algorithmically deterministic language such as Fortran to duplicate. 4 refs

  3. Methods of analyzing crude oil

    Science.gov (United States)

    Cooks, Robert Graham; Jjunju, Fred Paul Mark; Li, Anyin; Rogan, Iman S.

    2017-08-15

    The invention generally relates to methods of analyzing crude oil. In certain embodiments, methods of the invention involve obtaining a crude oil sample, and subjecting the crude oil sample to mass spectrometry analysis. In certain embodiments, the method is performed without any sample pre-purification steps.

  4. Therapy Talk: Analyzing Therapeutic Discourse

    Science.gov (United States)

    Leahy, Margaret M.

    2004-01-01

    Therapeutic discourse is the talk-in-interaction that represents the social practice between clinician and client. This article invites speech-language pathologists to apply their knowledge of language to analyzing therapy talk and to learn how talking practices shape clinical roles and identities. A range of qualitative research approaches,…

  5. The Convertible Arbitrage Strategy Analyzed

    NARCIS (Netherlands)

    Loncarski, I.; Ter Horst, J.R.; Veld, C.H.

    2006-01-01

    This paper analyzes convertible bond arbitrage on the Canadian market for the period 1998 to 2004.Convertible bond arbitrage is the combination of a long position in convertible bonds and a short position in the underlying stocks. Convertible arbitrage has been one of the most successful strategies

  6. Analyzing the complexity of nanotechnology

    NARCIS (Netherlands)

    Vries, de M.J.; Schummer, J.; Baird, D.

    2006-01-01

    Nanotechnology is a highly complex technological development due to many uncertainties in our knowledge about it. The Dutch philosopher Herman Dooyeweerd has developed a conceptual framework that can be used (1) to analyze the complexity of technological developments and (2) to see how priorities

  7. Proton-beam energy analyzer

    International Nuclear Information System (INIS)

    Belan, V.N.; Bolotin, L.I.; Kiselev, V.A.; Linnik, A.F.; Uskov, V.V.

    1989-01-01

    The authors describe a magnetic analyzer for measurement of proton-beam energy in the range from 100 keV to 25 MeV. The beam is deflected in a uniform transverse magnetic field and is registered by photographing a scintillation screen. The energy spectrum of the beam is constructed by microphotometry of the photographic film

  8. Identification of a regulatory variant that binds FOXA1 and FOXA2 at the CDC123/CAMK1D type 2 diabetes GWAS locus.

    Directory of Open Access Journals (Sweden)

    Marie P Fogarty

    2014-09-01

    Full Text Available Many of the type 2 diabetes loci identified through genome-wide association studies localize to non-protein-coding intronic and intergenic regions and likely contain variants that regulate gene transcription. The CDC123/CAMK1D type 2 diabetes association signal on chromosome 10 spans an intergenic region between CDC123 and CAMK1D and also overlaps the CDC123 3'UTR. To gain insight into the molecular mechanisms underlying the association signal, we used open chromatin, histone modifications and transcription factor ChIP-seq data sets from type 2 diabetes-relevant cell types to identify SNPs overlapping predicted regulatory regions. Two regions containing type 2 diabetes-associated variants were tested for enhancer activity using luciferase reporter assays. One SNP, rs11257655, displayed allelic differences in transcriptional enhancer activity in 832/13 and MIN6 insulinoma cells as well as in human HepG2 hepatocellular carcinoma cells. The rs11257655 risk allele T showed greater transcriptional activity than the non-risk allele C in all cell types tested. Using electromobility shift and supershift assays we demonstrated that the rs11257655 risk allele showed allele-specific binding to FOXA1 and FOXA2. We validated FOXA1 and FOXA2 enrichment at the rs11257655 risk allele using allele-specific ChIP in human islets. These results suggest that rs11257655 affects transcriptional activity through altered binding of a protein complex that includes FOXA1 and FOXA2, providing a potential molecular mechanism at this GWAS locus.

  9. Genome Wide Association Studies (GWAS Identify QTL on SSC2 and SSC17 Affecting Loin Peak Shear Force in Crossbred Commercial Pigs.

    Directory of Open Access Journals (Sweden)

    Chunyan Zhang

    Full Text Available Of all the meat quality traits, tenderness is considered the most important with regard to eating quality and market value. In this study we have utilised genome wide association studies (GWAS for peak shear force (PSF of loin muscle as a measure of tenderness for 1,976 crossbred commercial pigs, genotyped for 42,721 informative SNPs using the Illumina PorcineSNP60 Beadchip. Four 1 Mb genomic regions, three on SSC2 (at 4 Mb, 5 Mb and 109 Mb and one on SSC17 (at 20 Mb, were detected which collectively explained about 15.30% and 3.07% of the total genetic and phenotypic variance for PSF respectively. Markers ASGA0008566, ASGA0008695, DRGA0003285 and ASGA0075615 in the four regions were strongly associated with the effects. Analysis of the reference genome sequence in the region with the most important SNPs for SSC2_5 identified FRMD8, SLC25A45 and LTBP3 as potential candidate genes for meat tenderness on the basis of functional annotation of these genes. The region SSC2_109 was close to a previously reported candidate gene CAST; however, the very weak LD between DRGA0003285 (the best marker representing region SSC2_109 and CAST indicated the potential for additional genes which are distinct from, or interact with, CAST to affect meat tenderness. Limited information of known genes in regions SSC2_109 and SSC17_20 restricts further analysis. Re-sequencing of these regions for informative animals may help to resolve the molecular architecture and identify new candidate genes and causative mutations affecting this trait. These findings contribute significantly to our knowledge of the genomic regions affecting pork shear force and will potentially lead to new insights into the molecular mechanisms regulating meat tenderness.

  10. Replication and meta-analysis of GWAS identified susceptibility loci in Kawasaki disease confirm the importance of B lymphoid tyrosine kinase (BLK in disease susceptibility.

    Directory of Open Access Journals (Sweden)

    Chia-Jung Chang

    Full Text Available The BLK and CD40 loci have been associated with Kawasaki disease (KD in two genome-wide association studies (GWAS conducted in a Taiwanese population of Han Chinese ancestry (Taiwanese and in Japanese cohorts. Here we build on these findings with replication studies of the BLK and CD40 loci in populations of Korean and European descent. The BLK region was significantly associated with KD susceptibility in both populations. Within the BLK gene the rs2736340-located linkage disequilibrium (LD comprising the promoter and first intron was strongly associated with KD, with the combined results of Asian studies including Taiwanese, Japanese, and Korean populations (2,539 KD patients and 7,021 controls providing very compelling evidence of association (rs2736340, OR = 1.498, 1.354-1.657; P = 4.74×10(-31. We determined the percentage of B cells present in the peripheral blood mononuclear cell (PBMC population and the expression of BLK in the peripheral blood leukocytes (leukocytes of KD patients during the acute and convalescent stages. The percentage of B cells in the PBMC population and the expression of BLK in leukocytes were induced in patients in the acute stage of KD. In B cell lines derived from KD patients, and in purified B cells from KD patients obtained during the acute stage, those with the risk allele of rs2736340 expressed significantly lower levels of BLK. These results suggest that peripheral B cells play a pathogenic role during the acute stage of KD. Decreased BLK expression in peripheral blood B cells may alter B cell function and predispose individuals to KD. These associative data suggest a role for B cells during acute KD. Understanding the functional implications may facilitate the development of B cell-mediated therapy for KD.

  11. Analyzer for gamma cameras diagnostic

    International Nuclear Information System (INIS)

    Oramas Polo, I.; Osorio Deliz, J. F.; Diaz Garcia, A.

    2013-01-01

    This research work was carried out to develop an analyzer for gamma cameras diagnostic. It is composed of an electronic system that includes hardware and software capabilities, and operates from the acquisition of the 4 head position signals of a gamma camera detector. The result is the spectrum of the energy delivered by nuclear radiation coming from the camera detector head. This system includes analog processing of position signals from the camera, digitization and the subsequent processing of the energy signal in a multichannel analyzer, sending data to a computer via a standard USB port and processing of data in a personal computer to obtain the final histogram. The circuits are composed of an analog processing board and a universal kit with micro controller and programmable gate array. (Author)

  12. Methods for Analyzing Social Media

    DEFF Research Database (Denmark)

    Jensen, Jakob Linaa

    2013-01-01

    Social media is becoming increasingly attractive for users. It is a fast way to communicate ideas and a key source of information. It is therefore one of the most influential mediums of communication of our time and an important area for audience research. The growth of social media invites many...... new questions such as: How can we analyze social media? Can we use traditional audience research methods and apply them to online content? Which new research strategies have been developed? Which ethical research issues and controversies do we have to pay attention to? This book focuses on research...... strategies and methods for analyzing social media and will be of interest to researchers and practitioners using social media, as well as those wanting to keep up to date with the subject....

  13. New approach to analyzing vulnerability

    International Nuclear Information System (INIS)

    O'Callaghan, P.B.; Carlson, R.L.; Riedeman, G.W.

    1986-01-01

    The Westinghouse Hanford Company (WHC) has recently completed construction of the Fuel Cycle Plant (FCP) at Richland, Washington. At start-up the facility will fabricate driver fuel for the Fast Flux Test Facility in the Secure Automated Fabrication line. After construction completion, but before facility certification, the Department of Energy (DOE) Richland Operation Office requested that a vulnerability analysis be performed which assumed multiple insiders as a threat to the security system. A unique method of analyzing facility vulnerabilities was developed at the Security Applications Center (SAC), which is managed by WHC for DOE. The method that was developed verifies a previous vulnerability assessment, as well as introducing a modeling technique which analyzes security alarms in relation to delaying factors and possible insider activities. With this information it is possible to assess the relative strength or weakness of various possible routes to and from a target within a facility

  14. Analyzing the Facebook Friendship Graph

    OpenAIRE

    Catanese, Salvatore; De Meo, Pasquale; Ferrara, Emilio; Fiumara, Giacomo

    2010-01-01

    Online Social Networks (OSN) during last years acquired a huge and increasing popularity as one of the most important emerging Web phenomena, deeply modifying the behavior of users and contributing to build a solid substrate of connections and relationships among people using the Web. In this preliminary work paper, our purpose is to analyze Facebook, considering a significant sample of data reflecting relationships among subscribed users. Our goal is to extract, from this platform, relevant ...

  15. Sulfur Dioxide Analyzer Instrument Handbook

    Energy Technology Data Exchange (ETDEWEB)

    Springston, Stephen R. [Brookhaven National Lab. (BNL), Upton, NY (United States)

    2016-05-01

    The Sulfur Dioxide Analyzer measures sulfur dioxide based on absorbance of UV light at one wavelength by SO2 molecules which then decay to a lower energy state by emitting UV light at a longer wavelength. Specifically, SO2 + hυ1 →SO2 *→SO2 + hυ2 The emitted light is proportional to the concentration of SO2 in the optical cell. External communication with the analyzer is available through an Ethernet port configured through the instrument network of the AOS systems. The Model 43i-TLE is part of the i-series of Thermo Scientific instruments. The i-series instruments are designed to interface with external computers through the proprietary Thermo Scientific iPort Software. However, this software is somewhat cumbersome and inflexible. Brookhaven National Laboratory (BNL) has written an interface program in National Instruments LabView that both controls the Model 43i-TLE Analyzer AND queries the unit for all measurement and housekeeping data. The LabView vi (the software program written by BNL) ingests all raw data from the instrument and outputs raw data files in a uniform data format similar to other instruments in the AOS and described more fully in Section 6.0 below.

  16. Remote Laser Diffraction PSD Analyzer

    International Nuclear Information System (INIS)

    Batcheller, T.A.; Huestis, G.M.; Bolton, S.M.

    2000-01-01

    Particle size distribution (PSD) analysis of radioactive slurry samples were obtained using a modified off-the-shelf classical laser light scattering particle size analyzer. A Horiba Instruments Inc. Model La-300 PSD analyzer, which has a 0.1 to 600 micron measurement range, was modified for remote application in a hot cell (gamma radiation) environment. The general details of the modifications to this analyzer are presented in this paper. This technology provides rapid and simple PSD analysis, especially down in the fine and microscopic particle size regime. Particle size analysis of these radioactive slurries down in this smaller range was not achievable - making this technology far superior than the traditional methods used previously. Remote deployment and utilization of this technology is in an exploratory stage. The risk of malfunction in this radiation environment is countered by gaining of this tremendously useful fundamental engineering data. Successful acquisition of this data, in conjunction with other characterization analyses, provides important information that can be used in the myriad of potential radioactive waste management alternatives

  17. A new uranium automatic analyzer

    International Nuclear Information System (INIS)

    Xia Buyun; Zhu Yaokun; Wang Bin; Cong Peiyuan; Zhang Lan

    1993-01-01

    A new uranium automatic analyzer based on the flow injection analysis (FIA) principle has been developed. It consists of a multichannel peristaltic pump, an injection valve, a photometric detector, a single-chip microprocessor system and electronic circuit. The new designed multifunctional auto-injection valve can automatically change the injection volume of the sample and the channels so that the determination ranges and items can easily be changed. It also can make the instrument vary the FIA operation modes that it has functions of a universal instrument. A chromatographic column with extractant-containing resin was installed in the manifold of the analyzer for the concentration and separation of trace uranium. The 2-(5-bromo-2-pyridylazo)-5-diethyl-aminophenol (Br-PADAP) was used as colour reagent. Uranium was determined in the aqueous solution by adding cetyl-pyridium bromide (CPB). The uranium in the solution in the range 0.02-500 mg · L -1 can be directly determined without any pretreatment. A sample throughput rate of 30-90 h -1 and reproducibility of 1-2% were obtained. The analyzer has been satisfactorily applied to the laboratory and the plant

  18. Remote Laser Diffraction PSD Analyzer

    International Nuclear Information System (INIS)

    Batcheller, Thomas Aquinas; Huestis, Gary Michael; Bolton, Steven Michael

    2000-01-01

    Particle size distribution (PSD) analysis of radioactive slurry samples were obtained using a modified ''off-the-shelf'' classical laser light scattering particle size analyzer. A Horiba Instruments Inc. Model La-300 PSD analyzer, which has a 0.1 to 600 micron measurement range, was modified for remote application in a ''hot cell'' (gamma radiation) environment. The general details of the modifications to this analyzer are presented in this paper. This technology provides rapid and simple PSD analysis, especially down in the fine and microscopic particle size regime. Particle size analysis of these radioactive slurries down in this smaller range was not achievable--making this technology far superior than the traditional methods used previously. Remote deployment and utilization of this technology is in an exploratory stage. The risk of malfunction in this radiation environment is countered by gaining of this tremendously useful fundamental engineering data. Successful acquisition of this data, in conjunction with other characterization analyses, provides important information that can be used in the myriad of potential radioactive waste management alternatives

  19. Analyzing Big Data in Psychology: A Split/Analyze/Meta-Analyze Approach

    Directory of Open Access Journals (Sweden)

    Mike W.-L. Cheung

    2016-05-01

    Full Text Available Big data is a field that has traditionally been dominated by disciplines such as computer science and business, where mainly data-driven analyses have been performed. Psychology, a discipline in which a strong emphasis is placed on behavioral theories and empirical research, has the potential to contribute greatly to the big data movement. However, one challenge to psychologists – and probably the most crucial one – is that most researchers may not have the necessary programming and computational skills to analyze big data. In this study we argue that psychologists can also conduct big data research and that, rather than trying to acquire new programming and computational skills, they should focus on their strengths, such as performing psychometric analyses and testing theories using multivariate analyses to explain phenomena. We propose a split/analyze/meta-analyze approach that allows psychologists to easily analyze big data. Two real datasets are used to demonstrate the proposed procedures in R. A new research agenda related to the analysis of big data in psychology is outlined at the end of the study.

  20. Analyzing Big Data in Psychology: A Split/Analyze/Meta-Analyze Approach.

    Science.gov (United States)

    Cheung, Mike W-L; Jak, Suzanne

    2016-01-01

    Big data is a field that has traditionally been dominated by disciplines such as computer science and business, where mainly data-driven analyses have been performed. Psychology, a discipline in which a strong emphasis is placed on behavioral theories and empirical research, has the potential to contribute greatly to the big data movement. However, one challenge to psychologists-and probably the most crucial one-is that most researchers may not have the necessary programming and computational skills to analyze big data. In this study we argue that psychologists can also conduct big data research and that, rather than trying to acquire new programming and computational skills, they should focus on their strengths, such as performing psychometric analyses and testing theories using multivariate analyses to explain phenomena. We propose a split/analyze/meta-analyze approach that allows psychologists to easily analyze big data. Two real datasets are used to demonstrate the proposed procedures in R. A new research agenda related to the analysis of big data in psychology is outlined at the end of the study.

  1. The security analyzer, a security analyzer program written in Prolog

    International Nuclear Information System (INIS)

    Zimmerman, B.D.; Densley, P.J.; Carlson, R.L.

    1987-01-01

    A technique has been developed to characterize a nuclear facility and measure the strengths and weaknesses of the physical protection system. It utilizes the artificial intelligence capabilities available in the prolog programming language to probe a facility's defenses and find potential attack paths that meet designated search criteria. As sensors or barriers become inactive due to maintenance, failure, or inclement weather conditions, the protection system can rapidly be reanalyzed to discover weaknesses that would need to be strengthened by alternative means. Conversely, proposed upgrades and enhancements can be easily entered into the database and their effect measured against a variety of potential adversary attacks. Thus the security analyzer is a tool that aids the protection planner as well as the protection operations staff

  2. The Aqueduct Global Flood Analyzer

    Science.gov (United States)

    Iceland, Charles

    2015-04-01

    As population growth and economic growth take place, and as climate change accelerates, many regions across the globe are finding themselves increasingly vulnerable to flooding. A recent OECD study of the exposure of the world's large port cities to coastal flooding found that 40 million people were exposed to a 1 in 100 year coastal flood event in 2005, and the total value of exposed assets was about US 3,000 billion, or 5% of global GDP. By the 2070s, those numbers were estimated to increase to 150 million people and US 35,000 billion, or roughly 9% of projected global GDP. Impoverished people in developing countries are particularly at risk because they often live in flood-prone areas and lack the resources to respond. WRI and its Dutch partners - Deltares, IVM-VU University Amsterdam, Utrecht University, and PBL Netherlands Environmental Assessment Agency - are in the initial stages of developing a robust set of river flood and coastal storm surge risk measures that show the extent of flooding under a variety of scenarios (both current and future), together with the projected human and economic impacts of these flood scenarios. These flood risk data and information will be accessible via an online, easy-to-use Aqueduct Global Flood Analyzer. We will also investigate the viability, benefits, and costs of a wide array of flood risk reduction measures that could be implemented in a variety of geographic and socio-economic settings. Together, the activities we propose have the potential for saving hundreds of thousands of lives and strengthening the resiliency and security of many millions more, especially those who are most vulnerable. Mr. Iceland will present Version 1.0 of the Aqueduct Global Flood Analyzer and provide a preview of additional elements of the Analyzer to be released in the coming years.

  3. Fuel analyzer; Analisador de combustiveis

    Energy Technology Data Exchange (ETDEWEB)

    Cozzolino, Roberval [RS Motors, Indaiatuba, SP (Brazil)

    2008-07-01

    The current technology 'COMBUSTIMETRO' aims to examine the fuel through performance of the engine, as the role of the fuel is to produce energy for the combustion engine in the form of which is directly proportional to the quality and type of fuel. The 'COMBUSTIMETRO' has an engine that always keeps the same entry of air, fuel and fixed point of ignition. His operation is monitored by sensors (Sonda Lambda, RPM and Gases Analyzer) connected to a processor that performs calculations and records the information, generate reports and graphs. (author)

  4. Handheld Fluorescence Microscopy based Flow Analyzer.

    Science.gov (United States)

    Saxena, Manish; Jayakumar, Nitin; Gorthi, Sai Siva

    2016-03-01

    Fluorescence microscopy has the intrinsic advantages of favourable contrast characteristics and high degree of specificity. Consequently, it has been a mainstay in modern biological inquiry and clinical diagnostics. Despite its reliable nature, fluorescence based clinical microscopy and diagnostics is a manual, labour intensive and time consuming procedure. The article outlines a cost-effective, high throughput alternative to conventional fluorescence imaging techniques. With system level integration of custom-designed microfluidics and optics, we demonstrate fluorescence microscopy based imaging flow analyzer. Using this system we have imaged more than 2900 FITC labeled fluorescent beads per minute. This demonstrates high-throughput characteristics of our flow analyzer in comparison to conventional fluorescence microscopy. The issue of motion blur at high flow rates limits the achievable throughput in image based flow analyzers. Here we address the issue by computationally deblurring the images and show that this restores the morphological features otherwise affected by motion blur. By further optimizing concentration of the sample solution and flow speeds, along with imaging multiple channels simultaneously, the system is capable of providing throughput of about 480 beads per second.

  5. GWAS, Cytomegalovirus Infection, and Schizophrenia

    DEFF Research Database (Denmark)

    Grove, Jakob; Børglum, Anders; Pearce, Brad D

    2014-01-01

    In recent years, good progress has been made in uncovering the genetic underpinnings of schizophrenia. Even so, as a polygenic disorder, schizophrenia has a complex etiology that is far from understood. Meanwhile, data are being collected enabling the study of interactions between genes...... and the environment. A confluence of data from genetic and environmental exposure studies point to the role of infections and immunity in the pathophysiology of schizophrenia. In a recent study by Børglum et al., a single nucleotide polymorphism (SNP) in the gene CTNNA3 was identified that may provide clues to gene......-environment interactions. The carriers of the minor allele for the SNP had a fivefold risk of later developing schizophrenia if their mothers were CMV positive, while the children not carrying the allele had no excess risk from maternal CMV. In the current paper, we summarize recent advances to clarify a possible...

  6. Gene set analysis for GWAS

    DEFF Research Database (Denmark)

    Debrabant, Birgit; Soerensen, Mette

    2014-01-01

    Abstract We discuss the use of modified Kolmogorov-Smirnov (KS) statistics in the context of gene set analysis and review corresponding null and alternative hypotheses. Especially, we show that, when enhancing the impact of highly significant genes in the calculation of the test statistic, the co...

  7. Compact Microwave Fourier Spectrum Analyzer

    Science.gov (United States)

    Savchenkov, Anatoliy; Matsko, Andrey; Strekalov, Dmitry

    2009-01-01

    A compact photonic microwave Fourier spectrum analyzer [a Fourier-transform microwave spectrometer, (FTMWS)] with no moving parts has been proposed for use in remote sensing of weak, natural microwave emissions from the surfaces and atmospheres of planets to enable remote analysis and determination of chemical composition and abundances of critical molecular constituents in space. The instrument is based on a Bessel beam (light modes with non-zero angular momenta) fiber-optic elements. It features low power consumption, low mass, and high resolution, without a need for any cryogenics, beyond what is achievable by the current state-of-the-art in space instruments. The instrument can also be used in a wide-band scatterometer mode in active radar systems.

  8. Nuclear plant analyzer development at INEL

    International Nuclear Information System (INIS)

    Laats, E.T.; Russell, K.D.; Stewart, H.D.

    1983-01-01

    The Office of Nuclear Regulatory Research of the US Nuclear Regulatory Commission (NRC) has sponsored development of a software-hardware system called the Nuclear Plant Analyzer (NPA). This paper describes the status of the NPA project at the INEL after one year of development. When completed, the NPA will be an integrated network of analytical tools for performing reactor plant analyses. Development of the NPA in FY-1983 progressed along two parallel pathways; namely, conceptual planning and software development. Regarding NPA planning, and extensive effort was conducted to define the function requirements of the NPA, conceptual design, and hardware needs. Regarding software development conducted in FY-1983, all development was aimed toward demonstrating the basic concept and feasibility of the NPA. Nearly all software was developed and resides on the INEL twin Control Data Corporation 176 mainframe computers

  9. Charge Analyzer Responsive Local Oscillations

    Science.gov (United States)

    Krause, Linda Habash; Thornton, Gary

    2015-01-01

    The first transatlantic radio transmission, demonstrated by Marconi in December of 1901, revealed the essential role of the ionosphere for radio communications. This ionized layer of the upper atmosphere controls the amount of radio power transmitted through, reflected off of, and absorbed by the atmospheric medium. Low-frequency radio signals can propagate long distances around the globe via repeated reflections off of the ionosphere and the Earth's surface. Higher frequency radio signals can punch through the ionosphere to be received at orbiting satellites. However, any turbulence in the ionosphere can distort these signals, compromising the performance or even availability of space-based communication and navigations systems. The physics associated with this distortion effect is analogous to the situation when underwater images are distorted by convecting air bubbles. In fact, these ionospheric features are often called 'plasma bubbles' since they exhibit some of the similar behavior as underwater air bubbles. These events, instigated by solar and geomagnetic storms, can cause communication and navigation outages that last for hours. To help understand and predict these outages, a world-wide community of space scientists and technologists are devoted to researching this topic. One aspect of this research is to develop instruments capable of measuring the ionospheric plasma bubbles. Figure 1 shows a photo of the Charge Analyzer Responsive to Local Oscillations (CARLO), a new instrument under development at NASA Marshall Space Flight Center (MSFC). It is a frequency-domain ion spectrum analyzer designed to measure the distributions of ionospheric turbulence from 1 Hz to 10 kHz (i.e., spatial scales from a few kilometers down to a few centimeters). This frequency range is important since it focuses on turbulence scales that affect VHF/UHF satellite communications, GPS systems, and over-the-horizon radar systems. CARLO is based on the flight-proven Plasma Local

  10. Diffractive interference optical analyzer (DiOPTER)

    Science.gov (United States)

    Sasikumar, Harish; Prasad, Vishnu; Pal, Parama; Varma, Manoj M.

    2016-03-01

    This report demonstrates a method for high-resolution refractometric measurements using, what we have termed as, a Diffractive Interference Optical Analyzer (DiOpter). The setup consists of a laser, polarizer, a transparent diffraction grating and Si-photodetectors. The sensor is based on the differential response of diffracted orders to bulk refractive index changes. In these setups, the differential read-out of the diffracted orders suppresses signal drifts and enables time-resolved determination of refractive index changes in the sample cell. A remarkable feature of this device is that under appropriate conditions, the measurement sensitivity of the sensor can be enhanced by more than two orders of magnitude due to interference between multiply reflected diffracted orders. A noise-equivalent limit of detection (LoD) of 6x10-7 RIU was achieved in glass. This work focuses on devices with integrated sample well, made on low-cost PDMS. As the detection methodology is experimentally straightforward, it can be used across a wide array of applications, ranging from detecting changes in surface adsorbates via binding reactions to estimating refractive index (and hence concentration) variations in bulk samples. An exciting prospect of this technique is the potential integration of this device to smartphones using a simple interface based on transmission mode configuration. In a transmission configuration, we were able to achieve an LoD of 4x10-4 RIU which is sufficient to explore several applications in food quality testing and related fields. We are envisioning the future of this platform as a personal handheld optical analyzer for applications ranging from environmental sensing to healthcare and quality testing of food products.

  11. Radiation energy detector and analyzer

    International Nuclear Information System (INIS)

    Roberts, T.G.

    1981-01-01

    A radiation detector array and a method for measuring the spectral content of radiation. The radiation sensor or detector is an array or stack of thin solid-electrolyte batteries. The batteries, arranged in a stack, may be composed of independent battery cells or may be arranged so that adjacent cells share a common terminal surface. This common surface is possible since the polarity of the batteries with respect to an adjacent battery is unrestricted, allowing a reduction in component parts of the assembly and reducing the overall stack length. Additionally, a test jig or chamber for allowing rapid measurement of the voltage across each battery is disclosed. A multichannel recorder and display may be used to indicate the voltage gradient change across the cells, or a small computer may be used for rapidly converting these voltage readings to a graph of radiation intensity versus wavelength or energy. The behavior of the batteries when used as a radiation detector and analyzer are such that the voltage measurements can be made at leisure after the detector array has been exposed to the radiation, and it is not necessary to make rapid measurements as is now done

  12. Solar Probe ANalyzer for Ions - Laboratory Performance

    Science.gov (United States)

    Livi, R.; Larson, D. E.; Kasper, J. C.; Korreck, K. E.; Whittlesey, P. L.

    2017-12-01

    The Parker Solar Probe (PSP) mission is a heliospheric satellite that will orbit the Sun closer than any prior mission to date with a perihelion of 35 solar radii (RS) and an aphelion of 10 RS. PSP includes the Solar Wind Electrons Alphas and Protons (SWEAP) instrument suite, which in turn consists of four instruments: the Solar Probe Cup (SPC) and three Solar Probe ANalyzers (SPAN) for ions and electrons. Together, this suite will take local measurements of particles and electromagnetic fields within the Sun's corona. SPAN-Ai has completed flight calibration and spacecraft integration and is set to be launched in July of 2018. The main mode of operation consists of an electrostatic analyzer (ESA) at its aperture followed by a Time-of-Flight section to measure the energy and mass per charge (m/q) of the ambient ions. SPAN-Ai's main objective is to measure solar wind ions within an energy range of 5 eV - 20 keV, a mass/q between 1-60 [amu/q] and a field of view of 2400x1200. Here we will show flight calibration results and performance.

  13. Analyzing rare diseases terms in biomedical terminologies

    Directory of Open Access Journals (Sweden)

    Erika Pasceri

    2012-03-01

    Full Text Available Rare disease patients too often face common problems, including the lack of access to correct diagnosis, lack of quality information on the disease, lack of scientific knowledge of the disease, inequities and difficulties in access to treatment and care. These things could be changed by implementing a comprehensive approach to rare diseases, increasing international cooperation in scientific research, by gaining and sharing scientific knowledge about and by developing tools for extracting and sharing knowledge. A significant aspect to analyze is the organization of knowledge in the biomedical field for the proper management and recovery of health information. For these purposes, the sources needed have been acquired from the Office of Rare Diseases Research, the National Organization of Rare Disorders and Orphanet, organizations that provide information to patients and physicians and facilitate the exchange of information among different actors involved in this field. The present paper shows the representation of rare diseases terms in biomedical terminologies such as MeSH, ICD-10, SNOMED CT and OMIM, leveraging the fact that these terminologies are integrated in the UMLS. At the first level, it was analyzed the overlap among sources and at a second level, the presence of rare diseases terms in target sources included in UMLS, working at the term and concept level. We found that MeSH has the best representation of rare diseases terms.

  14. Analyzing composability of applications on MPSoC platforms

    NARCIS (Netherlands)

    Kumar, A.; Mesman, B.; Theelen, B.D.; Corporaal, H.; Yajun, H.

    2008-01-01

    Modern day applications require use of multi-processor systems for reasons of erformance, scalability and power efficiency. As more and more applications are integrated in a single system, mapping and analyzing them on a multi-processor platform becomes a multidimensional problem. Each possible set

  15. A framework to analyze emissions implications of ...

    Science.gov (United States)

    Future year emissions depend highly on the evolution of the economy, technology and current and future regulatory drivers. A scenario framework was adopted to analyze various technology development pathways and societal change while considering existing regulations and future uncertainty in regulations and evaluate resulting emissions growth patterns. The framework integrates EPA’s energy systems model with an economic Input-Output (I/O) Life Cycle Assessment model. The EPAUS9r MARKAL database is assembled from a set of technologies to represent the U.S. energy system within MARKAL bottom-up technology rich energy modeling framework. The general state of the economy and consequent demands for goods and services from these sectors are taken exogenously in MARKAL. It is important to characterize exogenous inputs about the economy to appropriately represent the industrial sector outlook for each of the scenarios and case studies evaluated. An economic input-output (I/O) model of the US economy is constructed to link up with MARKAL. The I/O model enables user to change input requirements (e.g. energy intensity) for different sectors or the share of consumer income expended on a given good. This gives end-users a mechanism for modeling change in the two dimensions of technological progress and consumer preferences that define the future scenarios. The framework will then be extended to include environmental I/O framework to track life cycle emissions associated

  16. Update on the USNRC's nuclear plant analyzer

    International Nuclear Information System (INIS)

    Laats, E.T.

    1987-01-01

    The Nuclear Plant Analyzer (NPA) is the U.S. Nuclear Regulatory Commission's (NRC's) state-of-the-art nuclear reactor simulation capability. This computer software package integrates high fidelity nuclear reactor simulation codes such as the TRAC and RELAPS series of codes with color graphics display techniques and advanced workstation hardware. An overview of this program was given at the 1984 Summer Computer Simulation Conference (SCSC), with selected topics discussed at the 1985 and 1986 SCSCs. This paper addresses these activities and related experiences. First, The Class VI computer implementation is discussed. The trade-offs between gaining significantly greater computational speed and central memory, with the loss of performance due to many more simultaneous users is shown. Second, the goal of the super-minicomputer implementation is to produce a very cost-effective system that utilizes advanced (multi-dimensional, two-phase coolant) simulation capabilities at real wall-clock simulation times. Benchmarking of the initial super-minicomputer implementation is discussed. Finally, the technical and economic feasibility is addressed for implementing the super-minicomputer version of the NPA with the RELAPS simulation code onto the Black Fox full scope nuclear power plant simulator

  17. PSAIA – Protein Structure and Interaction Analyzer

    Directory of Open Access Journals (Sweden)

    Vlahoviček Kristian

    2008-04-01

    Full Text Available Abstract Background PSAIA (Protein Structure and Interaction Analyzer was developed to compute geometric parameters for large sets of protein structures in order to predict and investigate protein-protein interaction sites. Results In addition to most relevant established algorithms, PSAIA offers a new method PIADA (Protein Interaction Atom Distance Algorithm for the determination of residue interaction pairs. We found that PIADA produced more satisfactory results than comparable algorithms implemented in PSAIA. Particular advantages of PSAIA include its capacity to combine different methods to detect the locations and types of interactions between residues and its ability, without any further automation steps, to handle large numbers of protein structures and complexes. Generally, the integration of a variety of methods enables PSAIA to offer easier automation of analysis and greater reliability of results. PSAIA can be used either via a graphical user interface or from the command-line. Results are generated in either tabular or XML format. Conclusion In a straightforward fashion and for large sets of protein structures, PSAIA enables the calculation of protein geometric parameters and the determination of location and type for protein-protein interaction sites. XML formatted output enables easy conversion of results to various formats suitable for statistic analysis. Results from smaller data sets demonstrated the influence of geometry on protein interaction sites. Comprehensive analysis of properties of large data sets lead to new information useful in the prediction of protein-protein interaction sites.

  18. Nuclear plant analyzer development and analysis applications

    International Nuclear Information System (INIS)

    Laats, E.T.

    1984-01-01

    The Nuclear Plant Analyzer (NPA) is being developed as the U.S. Nuclear Regulatory Commission's (NRC's) state of the art safety analysis and engineering tool to address key nuclear plant safety issues. The NPA integrates the NRC's computerized reactor behavior simulation codes such as RELAP5 and TRAC-BWR, both of which are well-developed computer graphics programs, and large repositories of reactor design and experimental data. Utilizing the complex reactor behavior codes as well as the experiment data repositories enables simulation applications of the NPA that are generally not possible with more simplistic, less mechanistic reactor behavior codes. These latter codes are used in training simulators or with other NPA-type software packages and are limited to displaying calculated data only. This paper describes four applications of the NPA in assisting reactor safety analyses. Two analyses evaluated reactor operating procedures, during off-normal operation, for a pressurized water reactor (PWR) and a boiling water reactor (BWR), respectively. The third analysis was performed in support of a reactor safety experiment conducted in the Semiscale facility. The final application demonstrated the usefulness of atmospheric dispersion computer codes for site emergency planning purposes. An overview of the NPA and how it supported these analyses are the topics of this paper

  19. Association between the European GWAS-identified susceptibility locus at chromosome 4p16 and the risk of atrial septal defect: a case-control study in Southwest China and a meta-analysis.

    Directory of Open Access Journals (Sweden)

    Li Zhao

    Full Text Available Atrial septal defect (ASD is the third most frequent type of congenital heart anomaly, featuring shunting of blood between the two atria. Gene-environment interaction remains to be an acknowledged cause for ASD occurrence. A recent European genome-wide association study (GWAS of congenital heart disease (CHD identified 3 susceptibility SNPs at chromosome 4p16 associated with ASD: rs870142, rs16835979 and rs6824295. A Chinese-GWAS of CHD conducted in the corresponding period did not reveal the 3 susceptibility SNPs, but reported 2 different risk SNPs: rs2474937 and rs1531070. Therefore, we aimed to investigate the associations between the 3 European GWAS-identified susceptibility SNPs and ASD risk in the Han population in southwest China. Additionally, to increase the robustness of our current analysis, we conducted a meta-analysis combining published studies and our current case-control study. We performed association, linkage disequilibrium, and haplotype analysis among the 3 SNPs in 190 ASD cases and 225 age-, sex-, and ethnicity-matched healthy controls. Genotype and allele frequencies among the 3 SNPs showed statistically significant differences between the cases and controls. Our study found that individuals carrying the allele T of rs870142, the allele A of rs16835979, and the allele T of rs6824295 had a respective 50.1% (odds ratio (OR = 1.501, 95% confidence interval (CI = 1.122-2.009, PFDR-BH = 0.018, 48.5% (OR = 1.485, 95%CI = 1.109-1.987, PFDR-BH = 0.012, and 38.6% (OR = 1.386, 95%CI = 1.042-1.844, PFDR-BH = 0.025 increased risk to develop ASD than wild-type allele carriers in our study cohort. In the haplotype analysis, we identified a disease-risk haplotype (TAT (OR = 1.540, 95%CI = 1.030-2.380, PFDR-BH = 0.016. Our meta-analysis also showed that the investigated SNP was associated with ASD risk (combined OR (95%CI = 1.35 (1.24-1.46, P < 0.00001. Our study provides compelling evidence to motivate better understanding of the etiology

  20. Integrating genome-wide association study and expression quantitative trait loci data identifies multiple genes and gene set associated with neuroticism.

    Science.gov (United States)

    Fan, Qianrui; Wang, Wenyu; Hao, Jingcan; He, Awen; Wen, Yan; Guo, Xiong; Wu, Cuiyan; Ning, Yujie; Wang, Xi; Wang, Sen; Zhang, Feng

    2017-08-01

    Neuroticism is a fundamental personality trait with significant genetic determinant. To identify novel susceptibility genes for neuroticism, we conducted an integrative analysis of genomic and transcriptomic data of genome wide association study (GWAS) and expression quantitative trait locus (eQTL) study. GWAS summary data was driven from published studies of neuroticism, totally involving 170,906 subjects. eQTL dataset containing 927,753 eQTLs were obtained from an eQTL meta-analysis of 5311 samples. Integrative analysis of GWAS and eQTL data was conducted by summary data-based Mendelian randomization (SMR) analysis software. To identify neuroticism associated gene sets, the SMR analysis results were further subjected to gene set enrichment analysis (GSEA). The gene set annotation dataset (containing 13,311 annotated gene sets) of GSEA Molecular Signatures Database was used. SMR single gene analysis identified 6 significant genes for neuroticism, including MSRA (p value=2.27×10 -10 ), MGC57346 (p value=6.92×10 -7 ), BLK (p value=1.01×10 -6 ), XKR6 (p value=1.11×10 -6 ), C17ORF69 (p value=1.12×10 -6 ) and KIAA1267 (p value=4.00×10 -6 ). Gene set enrichment analysis observed significant association for Chr8p23 gene set (false discovery rate=0.033). Our results provide novel clues for the genetic mechanism studies of neuroticism. Copyright © 2017. Published by Elsevier Inc.

  1. Integral or integrated marketing

    Directory of Open Access Journals (Sweden)

    Davčik Nebojša

    2006-01-01

    Full Text Available Marketing theorists and experts try to develop business efficient organization and to get marketing performance at higher, business integrated level since its earliest beginnings. The core issue in this paperwork is the dialectic and practical approach dilemma should we develop integrated or integral marketing approach in the organization. The presented company cases as well as dialectic and functional explanations of this dilemma clearly shows that integrated marketing is narrower approach than integral marketing if we take as focal point new, unique and completed entity. In the integration the essence is in getting different parts together, which do not have to make necessary the new entity. The key elements in the definition of the integral marketing are necessity and holistic, e.g. necessity to develop new, holistic entity.

  2. Update on the USNRC's Nuclear Plant Analyzer

    International Nuclear Information System (INIS)

    Laats, E.T.

    1987-01-01

    The Nuclear Plant Analyzer (NPA) is the US Nuclear Regulatory Commission's (NRC's) state-of-the-art nuclear reactor simulation capability. This computer software package integrates high fidelity nuclear reactor simulation codes such as the TRAC and RELAP5 series of codes with color graphics display techniques and advanced workstation hardware. An overview of this program was given at the 1984 Summer Computer Simulation Conference (SCSC), with selected topics discussed at the 1985 and 1986 SCSCs. Since the 1984 presentation, major redirections of this NRC program have been taken. The original NPA system was developed for operation on a Control Data Corporation CYBER 176 computer, technology that is some 10 to 15 years old. The NPA system has recently been implemented on Class VI computers to gain increased computational capabilities, and is now being implemented on super-minicomputers for use by the scientific community and possibly by the commercial nuclear power plant simulator community. This paper addresses these activities and related experiences. First, the Class VI computer implementation is discussed. The trade-offs between gaining significantly greater computational speed and central memory, with the loss of performance due to many more simultaneous users is shown. Second, the goal of the super-minicomputer implementation is to produce a very cost-effective system that utilizes advanced (multi-dimensional, two-phase coolant) simulation capabilities at real wall-clock simulation times. Benchmarking of the initial super-minicomputer implementation is discussed. Finally, the technical and economic feasibility is addressed for implementing the super-minicomputer version of the NPA with the RELAP5 simulation code onto the Black Fox full scope nuclear power plant simulator

  3. Methyl-Analyzer--whole genome DNA methylation profiling.

    Science.gov (United States)

    Xin, Yurong; Ge, Yongchao; Haghighi, Fatemeh G

    2011-08-15

    Methyl-Analyzer is a python package that analyzes genome-wide DNA methylation data produced by the Methyl-MAPS (methylation mapping analysis by paired-end sequencing) method. Methyl-MAPS is an enzymatic-based method that uses both methylation-sensitive and -dependent enzymes covering >80% of CpG dinucleotides within mammalian genomes. It combines enzymatic-based approaches with high-throughput next-generation sequencing technology to provide whole genome DNA methylation profiles. Methyl-Analyzer processes and integrates sequencing reads from methylated and unmethylated compartments and estimates CpG methylation probabilities at single base resolution. Methyl-Analyzer is available at http://github.com/epigenomics/methylmaps. Sample dataset is available for download at http://epigenomicspub.columbia.edu/methylanalyzer_data.html. fgh3@columbia.edu Supplementary data are available at Bioinformatics online.

  4. Integral-preserving integrators

    International Nuclear Information System (INIS)

    McLaren, D I; Quispel, G R W

    2004-01-01

    Ordinary differential equations having a first integral may be solved numerically using one of several methods, with the integral preserved to machine accuracy. One such method is the discrete gradient method. It is shown here that the order of the method can be bootstrapped repeatedly to higher orders of accuracy. The method is illustrated using the Henon-Heiles system. (letter to the editor)

  5. Organization of a multichannel analyzer for gamma ray spectrometry

    International Nuclear Information System (INIS)

    Robinet, Genevieve

    1988-06-01

    This report describes the software organization of a medium scale multichannel analyzer for qualitative and quantitative measurements of the gamma rays emitted by radioactive samples. The first part reminds basis of radioactivity, principle of gamma ray detection, and data processing used for interpretation of a nuclear spectrum. The second part describes first the general organization of the software and then gives some details on interactivity, multidetector capabilites, and integration of complex algorithms for peak search and nuclide identification;problems encountered during the design phase are mentioned and solutions are given. Basic ideas are presented for further developments, such as expert system which should improve interpretation of the results. This present software has been integrated in a manufactured multichannel analyzer named 'POLYGAM NU416'. [fr

  6. SEAscan 3.5: A simulator performance analyzer

    International Nuclear Information System (INIS)

    Dennis, T.; Eisenmann, S.

    1990-01-01

    SEAscan 3.5 is a personal computer based tool developed to analyze the dynamic performance of nuclear power plant training simulators. The system has integrated features to provide its own human featured performance. In this paper, the program is described as a tool for the analysis of training simulator performance. The structure and operating characteristics of SEAscan 3.5 are described. The hardcopy documents are shown to aid in verification of conformance to ANSI/ANS-3.5-1985

  7. ADAM: Analyzer for Dialectal Arabic Morphology

    Directory of Open Access Journals (Sweden)

    Wael Salloum

    2014-12-01

    Full Text Available While Modern Standard Arabic (MSA has many resources, Arabic Dialects, the primarily spoken local varieties of Arabic, are quite impoverished in this regard. In this article, we present ADAM (Analyzer for Dialectal Arabic Morphology. ADAM is a poor man’s solution to quickly develop morphological analyzers for dialectal Arabic. ADAM has roughly half the out-of-vocabulary rate of a state-of-the-art MSA analyzer and is comparable in its recall performance to an Egyptian dialectal morphological analyzer that took years and expensive resources to build.

  8. Immigrant Integration: Acculturation and Social Integration

    Directory of Open Access Journals (Sweden)

    Astrid HAMBERGER

    2009-11-01

    Full Text Available This article tackles the concept of “immigrant integration” as it is analyzed by different authors in the international migration field. In this article, I will use the terms “refugee” and “immigrant” as equivalent to each other due to the interchangeable character of these concepts throughout the integration literature. First, the article brings into discussion the definitional and conceptual battle around the concept of immigrant “integration”, and second, it will describe and analyze cultural and social integration with their presupposing processes.

  9. Four integration patterns

    DEFF Research Database (Denmark)

    Bygstad, Bendik; Nielsen, Peter Axel; Munkvold, Bjørn Erik

    2010-01-01

    This paper aims to contribute to a theory of integration within the field of IS project management. Integration is a key IS project management issue when new systems are developed and implemented into an increasingly integrated information infrastructure in corporate and governmental organizations....... Expanding the perspective of traditional project management research, we draw extensively on central insights from IS research. Building on socio-technical IS research and Software Engineering research we suggest four generic patterns of integration: Big Bang, Stakeholder Integration, Technical Integration...... and Socio-Technical Integration. We analyze and describe the advantages and disadvantages of each pattern. The four patterns are ideal types. To explore the forces and challenges in these patterns three longitudinal case studies were conducted. In particular we investigate the management challenges for each...

  10. Integrative modeling of eQTLs and cis-regulatory elements suggests mechanisms underlying cell type specificity of eQTLs.

    Directory of Open Access Journals (Sweden)

    Christopher D Brown

    Full Text Available Genetic variants in cis-regulatory elements or trans-acting regulators frequently influence the quantity and spatiotemporal distribution of gene transcription. Recent interest in expression quantitative trait locus (eQTL mapping has paralleled the adoption of genome-wide association studies (GWAS for the analysis of complex traits and disease in humans. Under the hypothesis that many GWAS associations tag non-coding SNPs with small effects, and that these SNPs exert phenotypic control by modifying gene expression, it has become common to interpret GWAS associations using eQTL data. To fully exploit the mechanistic interpretability of eQTL-GWAS comparisons, an improved understanding of the genetic architecture and causal mechanisms of cell type specificity of eQTLs is required. We address this need by performing an eQTL analysis in three parts: first we identified eQTLs from eleven studies on seven cell types; then we integrated eQTL data with cis-regulatory element (CRE data from the ENCODE project; finally we built a set of classifiers to predict the cell type specificity of eQTLs. The cell type specificity of eQTLs is associated with eQTL SNP overlap with hundreds of cell type specific CRE classes, including enhancer, promoter, and repressive chromatin marks, regions of open chromatin, and many classes of DNA binding proteins. These associations provide insight into the molecular mechanisms generating the cell type specificity of eQTLs and the mode of regulation of corresponding eQTLs. Using a random forest classifier with cell specific CRE-SNP overlap as features, we demonstrate the feasibility of predicting the cell type specificity of eQTLs. We then demonstrate that CREs from a trait-associated cell type can be used to annotate GWAS associations in the absence of eQTL data for that cell type. We anticipate that such integrative, predictive modeling of cell specificity will improve our ability to understand the mechanistic basis of human

  11. Time-delay analyzer with continuous discretization

    International Nuclear Information System (INIS)

    Bayatyan, G.L.; Darbinyan, K.T.; Mkrtchyan, K.K.; Stepanyan, S.S.

    1988-01-01

    A time-delay analyzer is described which when triggered by a start pulse of adjustable duration performs continuous discretization of the analyzed signal within nearly 22 ns time intervals, the recording in a memory unit with following slow read-out of the information to the computer and its processing. The time-delay analyzer consists of four CAMAC-VECTOR systems of unit width. With its help one can separate comparatively short, small-amplitude rare signals against the background of quasistationary noise processes. 4 refs.; 3 figs

  12. Systems Analyze Water Quality in Real Time

    Science.gov (United States)

    2010-01-01

    A water analyzer developed under Small Business Innovation Research (SBIR) contracts with Kennedy Space Center now monitors treatment processes at water and wastewater facilities around the world. Originally designed to provide real-time detection of nutrient levels in hydroponic solutions for growing plants in space, the ChemScan analyzer, produced by ASA Analytics Inc., of Waukesha, Wisconsin, utilizes spectrometry and chemometric algorithms to automatically analyze multiple parameters in the water treatment process with little need for maintenance, calibration, or operator intervention. The company has experienced a compound annual growth rate of 40 percent over its 15-year history as a direct result of the technology's success.

  13. Low Gravity Drug Stability Analyzer, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — The overall goal of this proposed program (through Phase III) is to build a space-worthy Drug Stability Analyzer that can determine the extent of drug degradation....

  14. New high voltage parallel plate analyzer

    International Nuclear Information System (INIS)

    Hamada, Y.; Kawasumi, Y.; Masai, K.; Iguchi, H.; Fujisawa, A.; Abe, Y.

    1992-01-01

    A new modification on the parallel plate analyzer for 500 keV heavy ions to eliminate the effect of the intense UV and visible radiations, is successfully conducted. Its principle and results are discussed. (author)

  15. Analyzing the economic impacts of transportation projects.

    Science.gov (United States)

    2013-09-01

    The main goal of the study is to explore methods, approaches and : analytical software tools for analyzing economic activity that results from largescale : transportation investments in Connecticut. The primary conclusion is that the : transportation...

  16. Digital dynamic amplitude-frequency spectra analyzer

    International Nuclear Information System (INIS)

    Kalinnikov, V.A.; )

    2006-01-01

    The spectra analyzer is intended for the dynamic spectral analysis of signals physical installations and noise filtering. The recurrence Fourier transformation algorithm is used in the digital dynamic analyzer. It is realized on the basis of the fast logic FPGA matrix and the special signal ADSP microprocessor. The discretization frequency is 2 kHz-10 MHz. The number of calculated spectral coefficients is not less 512. The functional fast-action is 20 ns [ru

  17. FST Based Morphological Analyzer for Hindi Language

    OpenAIRE

    Deepak Kumar; Manjeet Singh; Seema Shukla

    2012-01-01

    Hindi being a highly inflectional language, FST (Finite State Transducer) based approach is most efficient for developing a morphological analyzer for this language. The work presented in this paper uses the SFST (Stuttgart Finite State Transducer) tool for generating the FST. A lexicon of root words is created. Rules are then added for generating inflectional and derivational words from these root words. The Morph Analyzer developed was used in a Part Of Speech (POS) Tagger based on Stanford...

  18. Enrichment of colorectal cancer associations in functional regions: Insight for using epigenomics data in the analysis of whole genome sequence-imputed GWAS data.

    Directory of Open Access Journals (Sweden)

    Stephanie A Bien

    Full Text Available The evaluation of less frequent genetic variants and their effect on complex disease pose new challenges for genomic research. To investigate whether epigenetic data can be used to inform aggregate rare-variant association methods (RVAM, we assessed whether variants more significantly associated with colorectal cancer (CRC were preferentially located in non-coding regulatory regions, and whether enrichment was specific to colorectal tissues.Active regulatory elements (ARE were mapped using data from 127 tissues and cell-types from NIH Roadmap Epigenomics and Encyclopedia of DNA Elements (ENCODE projects. We investigated whether CRC association p-values were more significant for common variants inside versus outside AREs, or 2 inside colorectal (CR AREs versus AREs of other tissues and cell-types. We employed an integrative epigenomic RVAM for variants with allele frequency <1%. Gene sets were defined as ARE variants within 200 kilobases of a transcription start site (TSS using either CR ARE or ARE from non-digestive tissues. CRC-set association p-values were used to evaluate enrichment of less frequent variant associations in CR ARE versus non-digestive ARE.ARE from 126/127 tissues and cell-types were significantly enriched for stronger CRC-variant associations. Strongest enrichment was observed for digestive tissues and immune cell types. CR-specific ARE were also enriched for stronger CRC-variant associations compared to ARE combined across non-digestive tissues (p-value = 9.6 × 10-4. Additionally, we found enrichment of stronger CRC association p-values for rare variant sets of CR ARE compared to non-digestive ARE (p-value = 0.029.Integrative epigenomic RVAM may enable discovery of less frequent variants associated with CRC, and ARE of digestive and immune tissues are most informative. Although distance-based aggregation of less frequent variants in CR ARE surrounding TSS showed modest enrichment, future association studies would likely

  19. Analyzing and Specifying Reusable Security Requirements

    Science.gov (United States)

    2003-09-01

    avionics applications and ecommerce applications need to specify levels of identification, authentication, authorization, integrity, privacy , etc. At...sections specifying functional requirements. Thus, the functional requirements for an embedded avionics application and an ecommerce website may have... Privacy (a.k.a., confidentiality), which is the degree to which sensitive data and communications are kept private from unauthorized individuals and

  20. Financial integration and liquidity crises

    NARCIS (Netherlands)

    Castiglionesi, Fabio; Feriozzi, F.; Lorenzoni, G.

    2017-01-01

    This paper analyzes the effects of financial integration on the stability of the banking system. Financial integration allows banks in different regions to smooth local liquidity shocks by borrowing and lending on a common interbank market. We show under which conditions financial integration

  1. A new automatic analyzer for uranium determination

    International Nuclear Information System (INIS)

    Xia Buyun; Zhu Yaokun; Wang Bin; Cong Peiyan; Zhang Lan

    1992-08-01

    An intellectual automatic analyzer for uranium based on the principle of flow injection analysis (FIA) has been developed. It can directly determine the uranium solution in range of 0.02 to 500 mg/L without any pre-process. A chromatographic column with extractant, in which the trace uranium is concentrated and separated, has special ability to enrich uranium, is connected to the manifold of the analyzer. The analyzer is suited for trace uranium determination in varies samples. The 2-(5-bromo-2-pyridylazo)-5-diethyl-aminophenol (Br-PADAP) is used as color reagent. Uranium is determined in aqueous solution by adding cation surfactant, cetyl-pyridinium bromide (PCB). The rate of analysis is 30 to 90 samples per hour. The relative standard deviation of determination is 1% ∼ 2%. The analyzer has been used in factories and laboratory, and the results are satisfied. The determination range can easily be changed by using a multi-function auto-injection valve that changes the injection volume of the sample and channels. So, it could adopt varies FIA operation modes to meet the needs of FIA determination for other substance. The analyzer has universal functions

  2. New ultra small battery operated portable multi-channel analyzer

    International Nuclear Information System (INIS)

    Wolf, M.A.; Umbarger, C.J.

    1979-01-01

    A newly designed portable multi-channel analyzer (MCA) has been developd at Los Alamos that has much improved physical and performance characteristics over previous designs. Namely, the instrument is very compact (25 cm wide x 14 cm deep x 21 cm high) and has a mass of 4.2 Kg (9.2 lb). The device has 1024 channels and is microprocessor controlled. The instrument has most of the standard features of present laboratory-based pulse height analyzers, including CRT display, region of interest integration, etc. Battery life of the MCA is nearly eight hours, with full charging over night. An accessory case carries a small audio cassette recorder for data storage. The case also contains two different NaI(Tl) detectors

  3. Scintiscans data analyzer model AS-10

    International Nuclear Information System (INIS)

    Malesa, J.; Wierzbicki, W.

    1975-01-01

    The principle of work and construction elements of the device made up for scintiscans data analyzation by ''square root scaling'' is presented. The device is equipped with cassette tape recorder type MK-125, made in Poland serving like scintiscans data bank, and with scintiscans data analyzation three programs. The cassette of two types, C-60 and C-90, is applied with working time of 2 x 30 min. and 2 x 45 min. respectivly. Results of scintiscans data analysation are printed by electric typewriter at figures in form of digital scintigram. (author)

  4. Analyzing Engineered Nanoparticles using Photothermal Infrared Spectroscopy

    DEFF Research Database (Denmark)

    Yamada, Shoko

    . To facilitate occupational safety and health there is a need to develop instruments to monitor and analyze nanoparticles in the industry, research and urban environments. The aim of this Ph.D. project was to develop new sensors that can analyze engineered nanoparticles. Two sensors were studied: (i......) a miniaturized toxicity sensor based on electrochemistry and (ii) a photothermal spectrometer based on tensile-stressed mechanical resonators (string resonators). Miniaturization of toxicity sensor targeting engineered nanoparticles was explored. This concept was based on the results of the biodurability test...

  5. Analyzing Web Behavior in Indoor Retail Spaces

    OpenAIRE

    Ren, Yongli; Tomko, Martin; Salim, Flora; Ong, Kevin; Sanderson, Mark

    2015-01-01

    We analyze 18 million rows of Wi-Fi access logs collected over a one year period from over 120,000 anonymized users at an inner-city shopping mall. The anonymized dataset gathered from an opt-in system provides users' approximate physical location, as well as Web browsing and some search history. Such data provides a unique opportunity to analyze the interaction between people's behavior in physical retail spaces and their Web behavior, serving as a proxy to their information needs. We find: ...

  6. Analyzing Log Files using Data-Mining

    Directory of Open Access Journals (Sweden)

    Marius Mihut

    2008-01-01

    Full Text Available Information systems (i.e. servers, applications and communication devices create a large amount of monitoring data that are saved as log files. For analyzing them, a data-mining approach is helpful. This article presents the steps which are necessary for creating an ‘analyzing instrument’, based on an open source software called Waikato Environment for Knowledge Analysis (Weka [1]. For exemplification, a system log file created by a Windows-based operating system, is used as input file.

  7. BWR plant analyzer development at BNL

    International Nuclear Information System (INIS)

    Cheng, H.S.; Wulff, W.; Mallen, A.N.; Lekach, S.V.; Stritar, A.; Cerbone, R.J.

    1985-01-01

    Advanced technology for high-speed interactive nuclear power plant simulations is of great value for timely resolution of safety issues, for plant monitoring, and for computer-aided emergency responses to an accident. Presented is the methodology employed at BNL to develop a BWR plant analyzer capable of simulating severe plant transients at much faster than real-time process speeds. Five modeling principles are established and a criterion is given for selecting numerical procedures and efficient computers to achieve the very high simulation speeds. Typical results are shown to demonstrate the modeling fidelity of the BWR plant analyzer

  8. X-ray fluorescence analyzer arrangement

    International Nuclear Information System (INIS)

    Vatai, Endre; Ando, Laszlo; Gal, Janos.

    1981-01-01

    An x-ray fluorescence analyzer for the quantitative determination of one or more elements of complex samples is reported. The novelties of the invention are the excitation of the samples by x-rays or γ-radiation, the application of a balanced filter pair as energy selector, and the measurement of the current or ion charge of ionization detectors used as sensors. Due to the increased sensitivity and accuracy, the novel design can extend the application fields of x-ray fluorescence analyzers. (A.L.)

  9. A Novel Architecture For Multichannel Analyzer

    International Nuclear Information System (INIS)

    Marcus, E.; Elhanani, I.; Nir, J.; Ellenbogen, M.; Kadmon, Y.; Tirosh, D.

    1999-01-01

    A novel digital approach to real-time, high-throughput, low-cost Multichannel Analyzer (MCA) for radiation spectroscopy is being presented. The MCA input is a shaped nuclear pulse sampled at a high rate, using an Analog-to-Digital Converter (ADC) chip. The digital samples are analyzed by a state-of-the-art Field Programmable Gate Away (FPGA). A customized algorithm is utilized to estimate the peak of the pulse, to reject pile-up and to eliminate processing dead time. The valid pulses estimated peaks are transferred to a micro controller system that creates the histogram and controls the Human Machine Interface (HMI)

  10. Fluidization quality analyzer for fluidized beds

    Science.gov (United States)

    Daw, C.S.; Hawk, J.A.

    1995-07-25

    A control loop and fluidization quality analyzer for a fluidized bed utilizes time varying pressure drop measurements. A fast-response pressure transducer measures the overall bed pressure drop, or over some segment of the bed, and the pressure drop signal is processed to produce an output voltage which changes with the degree of fluidization turbulence. 9 figs.

  11. SINDA, Systems Improved Numerical Differencing Analyzer

    Science.gov (United States)

    Fink, L. C.; Pan, H. M. Y.; Ishimoto, T.

    1972-01-01

    Computer program has been written to analyze group of 100-node areas and then provide for summation of any number of 100-node areas to obtain temperature profile. SINDA program options offer user variety of methods for solution of thermal analog modes presented in network format.

  12. Analyzing the Acoustic Beat with Mobile Devices

    Science.gov (United States)

    Kuhn, Jochen; Vogt, Patrik; Hirth, Michael

    2014-01-01

    In this column, we have previously presented various examples of how physical relationships can be examined by analyzing acoustic signals using smartphones or tablet PCs. In this example, we will be exploring the acoustic phenomenon of small beats, which is produced by the overlapping of two tones with a low difference in frequency ?f. The…

  13. Automatic radioxenon analyzer for CTBT monitoring

    International Nuclear Information System (INIS)

    Bowyer, T.W.; Abel, K.H.; Hensley, W.K.

    1996-12-01

    Over the past 3 years, with support from US DOE's NN-20 Comprehensive Test Ban Treaty (CTBT) R ampersand D program, PNNL has developed and demonstrated a fully automatic analyzer for collecting and measuring the four Xe radionuclides, 131m Xe(11.9 d), 133m Xe(2.19 d), 133 Xe (5.24 d), and 135 Xe(9.10 h), in the atmosphere. These radionuclides are important signatures in monitoring for compliance to a CTBT. Activity ratios permit discriminating radioxenon from nuclear detonation and that from nuclear reactor operations, nuclear fuel reprocessing, or medical isotope production and usage. In the analyzer, Xe is continuously and automatically separated from the atmosphere at flow rates of about 7 m 3 /h on sorption bed. Aliquots collected for 6-12 h are automatically analyzed by electron-photon coincidence spectrometry to produce sensitivities in the range of 20-100 μBq/m 3 of air, about 100-fold better than with reported laboratory-based procedures for short time collection intervals. Spectral data are automatically analyzed and the calculated radioxenon concentrations and raw gamma- ray spectra automatically transmitted to data centers

  14. How to Analyze Company Using Social Network?

    Science.gov (United States)

    Palus, Sebastian; Bródka, Piotr; Kazienko, Przemysław

    Every single company or institution wants to utilize its resources in the most efficient way. In order to do so they have to be have good structure. The new way to analyze company structure by utilizing existing within company natural social network and example of its usage on Enron company are presented in this paper.

  15. Environmental applications of the centrifugal fast analyzer

    International Nuclear Information System (INIS)

    Goldstein, G.; Strain, J.E.; Bowling, J.L.

    1975-12-01

    The centrifugal fast analyzer (GeMSAEC Fast Analyzer) was applied to the analysis of pollutants in air and water. Since data acquisition and processing are computer controlled, considerable effort went into devising appropriate software. A modified version of the standard FOCAL interpreter was developed which includes special machine language functions for data timing, acquisition, and storage, and also permits chaining together of programs stored on a disk. Programs were written and experimental procedures developed to implement spectrophotometric, turbidimetric, kinetic (including initial-rate, fixed-time, and variable-time techniques), and chemiluminescence methods of analysis. Analytical methods were developed for the following elements and compounds: SO 2 , O 3 , Ca, Cr, Cu, Fe, Mg, Se(IV), Zn, Cl - , I - , NO 2 - , PO 4 -3 , S -2 , and SO 4 -2 . In many cases, standard methods could be adapted to the centrifugal analyzer, in others new methods were employed. In general, analyses performed with the centrifugal fast analyzer were faster, more precise, and more accurate than with conventional instrumentation

  16. Analyzing Vessel Behavior Using Process Mining

    NARCIS (Netherlands)

    Maggi, F.M.; Mooij, A.J.; Aalst, W.M.P. van der

    2013-01-01

    In the maritime domain, electronic sensors such as AIS receivers and radars collect large amounts of data about the vessels in a certain geographical area. We investigate the use of process mining techniques for analyzing the behavior of the vessels based on these data. In the context of maritime

  17. Strengthening 4-H by Analyzing Enrollment Data

    Science.gov (United States)

    Hamilton, Stephen F.; Northern, Angela; Neff, Robert

    2014-01-01

    The study reported here used data from the ACCESS 4-H Enrollment System to gain insight into strengthening New York State's 4-H programming. Member enrollment lists from 2009 to 2012 were analyzed using Microsoft Excel to determine trends and dropout rates. The descriptive data indicate declining 4-H enrollment in recent years and peak enrollment…

  18. A case study of analyzing student teachers' concept images of the ...

    African Journals Online (AJOL)

    This paper presents a tool for analyzing student teachers' concept images of the definite integral. The tool shows the basic concepts that underpin the concept of the definite integral and displays them in terms of process and object conceptions within various representations in the context of area under a curve. The use of ...

  19. Statistical Methods in Integrative Genomics

    Science.gov (United States)

    Richardson, Sylvia; Tseng, George C.; Sun, Wei

    2016-01-01

    Statistical methods in integrative genomics aim to answer important biology questions by jointly analyzing multiple types of genomic data (vertical integration) or aggregating the same type of data across multiple studies (horizontal integration). In this article, we introduce different types of genomic data and data resources, and then review statistical methods of integrative genomics, with emphasis on the motivation and rationale of these methods. We conclude with some summary points and future research directions. PMID:27482531

  20. Methodology for analyzing risk at nuclear facilities

    International Nuclear Information System (INIS)

    Yoo, Hosik; Lee, Nayoung; Ham, Taekyu; Seo, Janghoon

    2015-01-01

    Highlights: • A new methodology for evaluating the risk at nuclear facilities was developed. • Five measures reflecting all factors that should be concerned to assess risk were developed. • The attributes on NMAC and nuclear security culture are included as attributes for analyzing. • The newly developed methodology can be used to evaluate risk of both existing facility and future nuclear system. - Abstract: A methodology for evaluating risks at nuclear facilities is developed in this work. A series of measures is drawn from the analysis of factors that determine risks. Five measures are created to evaluate risks at nuclear facilities. These include the legal and institutional framework, material control, physical protection system effectiveness, human resources, and consequences. Evaluation attributes are developed for each measure and specific values are given in order to calculate the risk value quantitatively. Questionnaires are drawn up on whether or not a state has properly established a legal and regulatory framework (based on international standards). These questionnaires can be a useful measure for comparing the status of the physical protection regime between two countries. Analyzing an insider threat is not an easy task and no methodology has been developed for this purpose. In this study, attributes that could quantitatively evaluate an insider threat, in the case of an unauthorized removal of nuclear materials, are developed by adopting the Nuclear Material Accounting & Control (NMAC) system. The effectiveness of a physical protection system, P(E), could be analyzed by calculating the probability of interruption, P(I), and the probability of neutralization, P(N). In this study, the Tool for Evaluating Security System (TESS) code developed by KINAC is used to calculate P(I) and P(N). Consequence is an important measure used to analyze risks at nuclear facilities. This measure comprises radiological, economic, and social damage. Social and

  1. Integrative Pedagogical Bioethics

    Directory of Open Access Journals (Sweden)

    Anna Hubenko

    2014-07-01

    Full Text Available The state of bioethics in Ukraine, as well as in the world has been analyzed in this article. The author offers a model of integrative pedagogical bioethics and substantiates the necessity of the organization of the bioethics education and confirms the topicality of adoption of the new specialty – educator-bioethicist. The author defines the structure and method of the educational process and the new curriculum «Integrative Bioethics» for preparing educator-bioethicist specialist.

  2. Development of pulse neutron coal analyzer

    International Nuclear Information System (INIS)

    Jing Shiwie; Gu Deshan; Qiao Shuang; Liu Yuren; Liu Linmao; Jing Shiwei

    2005-01-01

    This article introduced the development of pulsed neutron coal analyzer by pulse fast-thermal neutron analysis technology in the Radiation Technology Institute of Northeast Normal University. The 14 MeV pulse neutron generator and bismuth germanate detector and 4096 multichannel analyzer were applied in this system. The multiple linear regression method employed to process data solved the interferential problem of multiple elements. The prototype (model MZ-MKFY) had been applied in Changshan and Jilin power plant for about a year. The results of measuring the main parameters of coal such as low caloric power, whole total water, ash content, volatile content, and sulfur content, with precision acceptable to the coal industry, are presented

  3. Real time speech formant analyzer and display

    Science.gov (United States)

    Holland, George E.; Struve, Walter S.; Homer, John F.

    1987-01-01

    A speech analyzer for interpretation of sound includes a sound input which converts the sound into a signal representing the sound. The signal is passed through a plurality of frequency pass filters to derive a plurality of frequency formants. These formants are converted to voltage signals by frequency-to-voltage converters and then are prepared for visual display in continuous real time. Parameters from the inputted sound are also derived and displayed. The display may then be interpreted by the user. The preferred embodiment includes a microprocessor which is interfaced with a television set for displaying of the sound formants. The microprocessor software enables the sound analyzer to present a variety of display modes for interpretive and therapeutic used by the user.

  4. Analyzing public health policy: three approaches.

    Science.gov (United States)

    Coveney, John

    2010-07-01

    Policy is an important feature of public and private organizations. Within the field of health as a policy arena, public health has emerged in which policy is vital to decision making and the deployment of resources. Public health practitioners and students need to be able to analyze public health policy, yet many feel daunted by the subject's complexity. This article discusses three approaches that simplify policy analysis: Bacchi's "What's the problem?" approach examines the way that policy represents problems. Colebatch's governmentality approach provides a way of analyzing the implementation of policy. Bridgman and Davis's policy cycle allows for an appraisal of public policy development. Each approach provides an analytical framework from which to rigorously study policy. Practitioners and students of public health gain much in engaging with the politicized nature of policy, and a simple approach to policy analysis can greatly assist one's understanding and involvement in policy work.

  5. Miniature multichannel analyzer for process monitoring

    International Nuclear Information System (INIS)

    Halbig, J.K.; Klosterbuer, S.F.; Russo, P.A.; Sprinkle, J.K. Jr.; Stephens, M.M.; Wiig, L.G.; Ianakiev, K.D.

    1993-01-01

    A new, 4,000-channel analyzer has been developed for gamma-ray spectroscopy applications. A design philosophy of hardware and software building blocks has been combined with design goals of simplicity, compactness, portability, and reliability. The result is a miniature, modular multichannel analyzer (MMMCA), which offers solution to a variety of nondestructive assay (NDA) needs in many areas of general application, independent of computer platform or operating system. Detector-signal analog electronics, the bias supply, and batteries are included in the virtually pocket-size, low-power MMMCA unit. The MMMCA features digital setup and control, automated data reduction, and automated quality assurance. Areas of current NDA applications include on-line continuous (process) monitoring, process material holdup measurements, and field inspections

  6. Testing the Application for Analyzing Structured Entities

    Directory of Open Access Journals (Sweden)

    Ion IVAN

    2011-01-01

    Full Text Available The paper presents the testing process of the application for the analysis of structured text entities. The structured entities are presented. Quality characteristics of structured entities are identified and analyzed. The design and building processes are presented. Rules for building structured entities are described. The steps of building the application for the analysis of structured text entities are presented. The objective of the testing process is defined. Ways of testing the application on components and as a whole are established. A testing strategy for different objectives is proposed. The behavior of users during the testing period is analyzed. Statistical analysis regarding the behavior of users in processes of infinite resources access are realized.

  7. A new approach to analyzing vulnerability

    International Nuclear Information System (INIS)

    O'Callaghan, P.B.; Carlson, R.L.; Riedeman, G.W.

    1986-01-01

    The Westinghouse Hanford Company (WHC) has recently completed construction of the Fuel Cycle Plant (FCP) at Richland, Washington. At start-up the facility will fabricate driver fuel for the Fast Flux Test Facility in the Secure Automated Fabrication line. After construction completion, but before facility certification, the Department of Energy (DOE) Richland Operation Office requested that a vulnerability analysis be performed which assumed multiple insiders as a threat to the security system. A unique method of analyzing facility vulnerabilities was developed at the Security Applications Center (SAC), which is managed by WHC for DOE. The method that was developed verifies a previous vulnerability assessment, as well as introducing a modeling technique which analyzes security alarms in relation to delaying factors and possible insider activities. With this information it is possible to assess the relative strength or weakness of various possible routes to and from a target within a facility,

  8. Real-time airborne particle analyzer

    Science.gov (United States)

    Reilly, Peter T.A.

    2012-10-16

    An aerosol particle analyzer includes a laser ablation chamber, a gas-filled conduit, and a mass spectrometer. The laser ablation chamber can be operated at a low pressure, which can be from 0.1 mTorr to 30 mTorr. The ablated ions are transferred into a gas-filled conduit. The gas-filled conduit reduces the electrical charge and the speed of ablated ions as they collide and mix with buffer gases in the gas-filled conduit. Preferably, the gas filled-conduit includes an electromagnetic multipole structure that collimates the nascent ions into a beam, which is guided into the mass spectrometer. Because the gas-filled conduit allows storage of vast quantities of the ions from the ablated particles, the ions from a single ablated particle can be analyzed multiple times and by a variety of techniques to supply statistically meaningful analysis of composition and isotope ratios.

  9. Development of a nuclear plant analyzer (NPA)

    International Nuclear Information System (INIS)

    De Vlaminck, M.; Mampaey, L.; Vanhoenacker, L.; Bastenaire, F.

    1990-01-01

    A Nuclear Plant Analyzer has been developed by TRACTABEL. Three distinct functional units make up the Nuclear Plant Analyser, a model builder, a run time unit and an analysis unit. The model builder is intended to build simulation models which describe on the one hand the geometric structure and initial conditions of a given plant and on the other hand command control logics and reactor protection systems. The run time unit carries out dialog between the user and the thermal-hydraulic code. The analysis unit is aimed at deep analyzing of the transient results. The model builder is being tested in the framework of the International Standard Problem ISP-26, which is the simulation of a LOCA on the Japanese ROSA facility

  10. Computer-based radionuclide analyzer system

    International Nuclear Information System (INIS)

    Ohba, Kengo; Ishizuka, Akira; Kobayashi, Akira; Ohhashi, Hideaki; Tsuruoka, Kimitoshi.

    1978-01-01

    The radionuclide analysis in nuclear power plants, practiced for the purpose of monitoring the quality of the primary loop water, the confirmation of the performance of reactor cleanup system and monitoring the radioactive waste effluent, is an important job. Important as it is, it requires considerable labor of experts, because the samples to be analyzed are multifarious and very large in number, and in addition, this job depends much on manual work. With a view of saving the labor, simplifying and standardizing the work, reducing radiation exposure, and automatizing the work of analysis, the computerized analyzer system has been worked out. The results of its performance test at the operating power plant have proved that the development has fairly accomplished the objects and that the system is well useful. The developmental work was carried out by the cooperation between The Tokyo Electric Power Co. and Toshiba in about 4 years from 1974 to this year. (auth.)

  11. Neutral Particle Analyzer Diagnostic on NSTX

    International Nuclear Information System (INIS)

    Medley, S.S.; Roquemore, A.L.

    2004-01-01

    The Neutral Particle Analyzer (NPA) diagnostic on the National Spherical Torus Experiment (NSTX) utilizes a PPPL-designed E||B spectrometer that measures the energy spectra of minority hydrogen and bulk deuterium species simultaneously with 39 energy channels per mass specie and a time resolution of 1 ms. The calibrated energy range is E = 0.5-150 keV and the energy resolution varies from AE/E = 3-7% over the surface of the microchannel plate detector

  12. Analyzing Gender Stereotyping in Bollywood Movies

    OpenAIRE

    Madaan, Nishtha; Mehta, Sameep; Agrawaal, Taneea S; Malhotra, Vrinda; Aggarwal, Aditi; Saxena, Mayank

    2017-01-01

    The presence of gender stereotypes in many aspects of society is a well-known phenomenon. In this paper, we focus on studying such stereotypes and bias in Hindi movie industry (Bollywood). We analyze movie plots and posters for all movies released since 1970. The gender bias is detected by semantic modeling of plots at inter-sentence and intra-sentence level. Different features like occupation, introduction of cast in text, associated actions and descriptions are captured to show the pervasiv...

  13. Neutral Particle Analyzer Diagnostic on NSTX

    Energy Technology Data Exchange (ETDEWEB)

    S.S. Medley; A.L. Roquemore

    2004-03-16

    The Neutral Particle Analyzer (NPA) diagnostic on the National Spherical Torus Experiment (NSTX) utilizes a PPPL-designed E||B spectrometer that measures the energy spectra of minority hydrogen and bulk deuterium species simultaneously with 39 energy channels per mass specie and a time resolution of 1 ms. The calibrated energy range is E = 0.5-150 keV and the energy resolution varies from AE/E = 3-7% over the surface of the microchannel plate detector.

  14. Information decomposition method to analyze symbolical sequences

    International Nuclear Information System (INIS)

    Korotkov, E.V.; Korotkova, M.A.; Kudryashov, N.A.

    2003-01-01

    The information decomposition (ID) method to analyze symbolical sequences is presented. This method allows us to reveal a latent periodicity of any symbolical sequence. The ID method is shown to have advantages in comparison with application of the Fourier transformation, the wavelet transform and the dynamic programming method to look for latent periodicity. Examples of the latent periods for poetic texts, DNA sequences and amino acids are presented. Possible origin of a latent periodicity for different symbolical sequences is discussed

  15. Analyzing the Existing Undergraduate Engineering Leadership Skills

    OpenAIRE

    Hamed M. Almalki; Luis Rabelo; Charles Davis; Hammad Usmani; Debra Hollister; Alfonso Sarmiento

    2016-01-01

    Purpose: Studying and analyzing the undergraduate engineering students' leadership skills to discover their potential leadership strengths and weaknesses. This study will unveil potential ways to enhance the ways we teach engineering leadership. The research has great insights that might assist engineering programs to improve curricula for the purpose of better engineering preparation to meet industry's demands. Methodology and Findings: 441 undergraduate engineering students have been s...

  16. General methods for analyzing bounded proportion data

    OpenAIRE

    Hossain, Abu

    2017-01-01

    This thesis introduces two general classes of models for analyzing proportion response variable when the response variable Y can take values between zero and one, inclusive of zero and/or one. The models are inflated GAMLSS model and generalized Tobit GAMLSS model. The inflated GAMLSS model extends the flexibility of beta inflated models by allowing the distribution on (0,1) of the continuous component of the dependent variable to come from any explicit or transformed (i.e. logit or truncated...

  17. The analyzing of Dove marketing strategy

    Institute of Scientific and Technical Information of China (English)

    Guo; Yaohui

    2015-01-01

    <正>1.Introduction In this report,I try to analyze the related information about DOVE chocolate.Firstly,I would like to introduce this product.Dove chocolate is one of a series of products launched by the world’s largest pet food and snack food manufacturers,U.S.multinational food company Mars(Mars).Entered China in 1989,It becomes China’s leading brand of chocolate in

  18. Analyzing negative ties in social networks

    Directory of Open Access Journals (Sweden)

    Mankirat Kaur

    2016-03-01

    Full Text Available Online social networks are a source of sharing information and maintaining personal contacts with other people through social interactions and thus forming virtual communities online. Social networks are crowded with positive and negative relations. Positive relations are formed by support, endorsement and friendship and thus, create a network of well-connected users whereas negative relations are a result of opposition, distrust and avoidance creating disconnected networks. Due to increase in illegal activities such as masquerading, conspiring and creating fake profiles on online social networks, exploring and analyzing these negative activities becomes the need of hour. Usually negative ties are treated in same way as positive ties in many theories such as balance theory and blockmodeling analysis. But the standard concepts of social network analysis do not yield same results in respect of each tie. This paper presents a survey on analyzing negative ties in social networks through various types of network analysis techniques that are used for examining ties such as status, centrality and power measures. Due to the difference in characteristics of flow in positive and negative tie networks some of these measures are not applicable on negative ties. This paper also discusses new methods that have been developed specifically for analyzing negative ties such as negative degree, and h∗ measure along with the measures based on mixture of positive and negative ties. The different types of social network analysis approaches have been reviewed and compared to determine the best approach that can appropriately identify the negative ties in online networks. It has been analyzed that only few measures such as Degree and PN centrality are applicable for identifying outsiders in network. For applicability in online networks, the performance of PN measure needs to be verified and further, new measures should be developed based upon negative clique concept.

  19. Testing the Application for Analyzing Structured Entities

    OpenAIRE

    Ion IVAN; Bogdan VINTILA

    2011-01-01

    The paper presents the testing process of the application for the analysis of structured text entities. The structured entities are presented. Quality characteristics of structured entities are identified and analyzed. The design and building processes are presented. Rules for building structured entities are described. The steps of building the application for the analysis of structured text entities are presented. The objective of the testing process is defined. Ways of testing the applicat...

  20. Evaluation of the Air Void Analyzer

    Science.gov (United States)

    2013-07-01

    concrete using image analysis: Petrography of cementitious materials. ASTM STP 1215. S.M. DeHayes and D. Stark, eds. Philadelphia, PA: American...Administration (FHWA). 2006. Priority, market -ready technologies and innovations: Air Void Analyzer. Washington D.C. PDF file. Germann Instruments (GI). 2011...tests and properties of concrete and concrete-making materials. STP 169D. West Conshohocken, PA: ASTM International. Magura, D.D. 1996. Air void

  1. Modeling and Analyzing Electric Vehicle Charging

    DEFF Research Database (Denmark)

    Andersen, Ove; Krogh, Benjamin Bjerre; Thomsen, Christian

    2016-01-01

    , such as wind turbines. To both enable a smart grid and the use of renewable energy, it is essential to know when and where an EV is plugged into the power grid and what battery capacity is available. In this paper, we present a generic spatio-temporal data-warehouse model for storing detailed information...... on all aspects of charging EVs, including integration with the electricity prices from a spot market. The proposed data warehouse is fully implemented and currently contains 2.5 years of charging data from 176 EVs. We describe the date warehouse model and the implementation including complex operations...

  2. Semantic analyzability in children's understanding of idioms.

    Science.gov (United States)

    Gibbs, R W

    1991-06-01

    This study investigated the role of semantic analyzability in children's understanding of idioms. Kindergartners and first, third, and fourth graders listened to idiomatic expressions either alone or at the end of short story contexts. Their task was to explain verbally the intended meanings of these phrases and then to choose their correct idiomatic interpretations. The idioms presented to the children differed in their degree of analyzability. Some idioms were highly analyzable or decomposable, with the meanings of their parts contributing independently to their overall figurative meanings. Other idioms were nondecomposable because it was difficult to see any relation between a phrase's individual components and the idiom's figurative meaning. The results showed that younger children (kindergartners and first graders) understood decomposable idioms better than they did nondecomposable phrases. Older children (third and fourth graders) understood both kinds of idioms equally well in supporting contexts, but were better at interpreting decomposable idioms than they were at understanding nondecomposable idioms without contextual information. These findings demonstrate that young children better understand idiomatic phrases whose individual parts independently contribute to their overall figurative meanings.

  3. A Raman-Based Portable Fuel Analyzer

    Science.gov (United States)

    Farquharson, Stuart

    2010-08-01

    Fuel is the single most import supply during war. Consider that the US Military is employing over 25,000 vehicles in Iraq and Afghanistan. Most fuel is obtained locally, and must be characterized to ensure proper operation of these vehicles. Fuel properties are currently determined using a deployed chemical laboratory. Unfortunately, each sample requires in excess of 6 hours to characterize. To overcome this limitation, we have developed a portable fuel analyzer capable of determine 7 fuel properties that allow determining fuel usage. The analyzer uses Raman spectroscopy to measure the fuel samples without preparation in 2 minutes. The challenge, however, is that as distilled fractions of crude oil, all fuels are composed of hundreds of hydrocarbon components that boil at similar temperatures, and performance properties can not be simply correlated to a single component, and certainly not to specific Raman peaks. To meet this challenge, we measured over 800 diesel and jet fuels from around the world and used chemometrics to correlate the Raman spectra to fuel properties. Critical to the success of this approach is laser excitation at 1064 nm to avoid fluorescence interference (many fuels fluoresce) and a rugged interferometer that provides 0.1 cm-1 wavenumber (x-axis) accuracy to guarantee accurate correlations. Here we describe the portable fuel analyzer, the chemometric models, and the successful determination of these 7 fuel properties for over 100 unknown samples provided by the US Marine Corps, US Navy, and US Army.

  4. Method of stabilizing single channel analyzers

    International Nuclear Information System (INIS)

    Fasching, G.E.; Patton, G.H.

    1975-01-01

    A method and the apparatus to reduce the drift of single channel analyzers are described. Essentially, this invention employs a time-sharing or multiplexing technique to insure that the outputs from two single channel analyzers (SCAS) maintain the same count ratio regardless of variations in the threshold voltage source or voltage changes, the multiplexing technique is accomplished when a flip flop, actuated by a clock, changes state to switch the output from the individual SCAS before these outputs are sent to a ratio counting scalar. In the particular system embodiment disclosed that illustrates this invention, the sulfur content of coal is determined by subjecting the coal to radiation from a neutron producing source. A photomultiplier and detector system equates the transmitted gamma radiation to an analog voltage signal and sends the same signal after amplification, to a SCA system that contains the invention. Therein, at least two single channel analyzers scan the analog signal over different parts of a spectral region. The two outputs may then be sent to a digital multiplexer so that the output from the multiplexer contains counts falling within two distinct segments of the region. By dividing the counts from the multiplexer by each other, the percentage of sulfur within the coal sample under observation may be determined. (U.S.)

  5. Integrated economics

    International Nuclear Information System (INIS)

    Bratton, T.J.

    1992-01-01

    This article offers ideas for evaluating integrated solid waste management systems through the use of a conceptual cost overview. The topics of the article include the integrated solid waste management system; making assumptions about community characteristics, waste generation rates, waste collection responsibility, integrated system components, sizing and economic life of system facilities, system implementation schedule, facility ownership, and system administration; integrated system costs; integrated system revenues; system financing; cost projections; and making decisions

  6. Does energy integrate?

    International Nuclear Information System (INIS)

    Hira, Anil; Amaya, Libardo

    2003-01-01

    Amidst the international movement to privatize and deregulate electricity and gas sectors of economies, the question of the integration of those sectors has been somewhat underestimated. In fact, the integration of energy markets across boundaries is occurring. We examine this process in three regions: Europe, Central America, and South America. We analyze the forces driving integration in each area, and estimate the prospects for progress. We take a close look at Nordpool, which is now the most integrated market in the world, to see if it can serve as a model for other regions. We close with a set of conditions that we suggest are necessary for a successful international integration of energy markets

  7. Does energy integrate?

    International Nuclear Information System (INIS)

    Hira, A.; Amaya, L.

    2003-01-01

    Amidst the international movement to privatize and deregulate electricity and gas sectors of economics, the question of the integration of those sectors has been somewhat underestimated. In fact, the integration of energy markets across boundaries is occurring. We examine this process in three regions: Europe, Central America, and South America. We analyze the forces driving integration in each area, and estimate the prospects for progress. We take a close look at Nordpool, which is now the most integrated market in the world, to see if it can serve as a model for other regions. We close with a set of conditions that we suggest are necessary for a successful international integration of energy markets. (author)

  8. Mass spectrometer calibration of Cosmic Dust Analyzer

    Science.gov (United States)

    Ahrens, Thomas J.; Gupta, Satish C.; Jyoti, G.; Beauchamp, J. L.

    2003-02-01

    The time-of-flight (TOF) mass spectrometer (MS) of the Cosmic Dust Analyzer (CDA) instrument aboard the Cassini spacecraft is expected to be placed in orbit about Saturn to sample submicrometer-diameter ring particles and impact ejecta from Saturn's satellites. The CDA measures a mass spectrum of each particle that impacts the chemical analyzer sector of the instrument. Particles impact a Rh target plate at velocities of 1-100 km/s and produce some 10-8 to 10-5 times the particle mass of positive valence, single-charged ions. These are analyzed via a TOF MS. Initial tests employed a pulsed N2 laser acting on samples of kamacite, pyrrhotite, serpentine, olivine, and Murchison meteorite induced bursts of ions which were detected with a microchannel plate and a charge sensitive amplifier (CSA). Pulses from the N2 laser (1011 W/cm2) are assumed to simulate particle impact. Using aluminum alloy as a test sample, each pulse produces a charge of ~4.6 pC (mostly Al+1), whereas irradiation of a stainless steel target produces a ~2.8 pC (Fe+1) charge. Thus the present system yields ~10-5% of the laser energy in resulting ions. A CSA signal indicates that at the position of the microchannel plate, the ion detector geometry is such that some 5% of the laser-induced ions are collected in the CDA geometry. Employing a multichannel plate detector in this MS yields for Al-Mg-Cu alloy and kamacite targets well-defined peaks at 24 (Mg+1), 27(Al+1), and 64 (Cu+1) and 56 (Fe+1), 58 (Ni+1), and 60 (Ni+1) dalton, respectively.

  9. Remote Laser Diffraction Particle Size Distribution Analyzer

    Energy Technology Data Exchange (ETDEWEB)

    Batcheller, Thomas Aquinas; Huestis, Gary Michael; Bolton, Steven Michael

    2001-03-01

    In support of a radioactive slurry sampling and physical characterization task, an “off-the-shelf” laser diffraction (classical light scattering) particle size analyzer was utilized for remote particle size distribution (PSD) analysis. Spent nuclear fuel was previously reprocessed at the Idaho Nuclear Technology and Engineering Center (INTEC—formerly recognized as the Idaho Chemical Processing Plant) which is on DOE’s INEEL site. The acidic, radioactive aqueous raffinate streams from these processes were transferred to 300,000 gallon stainless steel storage vessels located in the INTEC Tank Farm area. Due to the transfer piping configuration in these vessels, complete removal of the liquid can not be achieved. Consequently, a “heel” slurry remains at the bottom of an “emptied” vessel. Particle size distribution characterization of the settled solids in this remaining heel slurry, as well as suspended solids in the tank liquid, is the goal of this remote PSD analyzer task. A Horiba Instruments Inc. Model LA-300 PSD analyzer, which has a 0.1 to 600 micron measurement range, was modified for remote application in a “hot cell” (gamma radiation) environment. This technology provides rapid and simple PSD analysis, especially down in the fine and microscopic particle size regime. Particle size analysis of these radioactive slurries down in this smaller range was not previously achievable—making this technology far superior than the traditional methods used. Successful acquisition of this data, in conjunction with other characterization analyses, provides important information that can be used in the myriad of potential radioactive waste management alternatives.

  10. IRISpy: Analyzing IRIS Data in Python

    Science.gov (United States)

    Ryan, Daniel; Christe, Steven; Mumford, Stuart; Baruah, Ankit; Timothy, Shelbe; Pereira, Tiago; De Pontieu, Bart

    2017-08-01

    IRISpy is a new community-developed open-source software library for analysing IRIS level 2 data. It is written in Python, a free, cross-platform, general-purpose, high-level programming language. A wide array of scientific computing software packages have already been developed in Python, from numerical computation (NumPy, SciPy, etc.), to visualization and plotting (matplotlib), to solar-physics-specific data analysis (SunPy). IRISpy is currently under development as a SunPy-affiliated package which means it depends on the SunPy library, follows similar standards and conventions, and is developed with the support of of the SunPy development team. IRISpy’s has two primary data objects, one for analyzing slit-jaw imager data and another for analyzing spectrograph data. Both objects contain basic slicing, indexing, plotting, and animating functionality to allow users to easily inspect, reduce and analyze the data. As part of this functionality the objects can output SunPy Maps, TimeSeries, Spectra, etc. of relevant data slices for easier inspection and analysis. Work is also ongoing to provide additional data analysis functionality including derivation of systematic measurement errors (e.g. readout noise), exposure time correction, residual wavelength calibration, radiometric calibration, and fine scale pointing corrections. IRISpy’s code base is publicly available through github.com and can be contributed to by anyone. In this poster we demonstrate IRISpy’s functionality and future goals of the project. We also encourage interested users to become involved in further developing IRISpy.

  11. Semantics based approach for analyzing disease-target associations.

    Science.gov (United States)

    Kaalia, Rama; Ghosh, Indira

    2016-08-01

    A complex disease is caused by heterogeneous biological interactions between genes and their products along with the influence of environmental factors. There have been many attempts for understanding the cause of these diseases using experimental, statistical and computational methods. In the present work the objective is to address the challenge of representation and integration of information from heterogeneous biomedical aspects of a complex disease using semantics based approach. Semantic web technology is used to design Disease Association Ontology (DAO-db) for representation and integration of disease associated information with diabetes as the case study. The functional associations of disease genes are integrated using RDF graphs of DAO-db. Three semantic web based scoring algorithms (PageRank, HITS (Hyperlink Induced Topic Search) and HITS with semantic weights) are used to score the gene nodes on the basis of their functional interactions in the graph. Disease Association Ontology for Diabetes (DAO-db) provides a standard ontology-driven platform for describing genes, proteins, pathways involved in diabetes and for integrating functional associations from various interaction levels (gene-disease, gene-pathway, gene-function, gene-cellular component and protein-protein interactions). An automatic instance loader module is also developed in present work that helps in adding instances to DAO-db on a large scale. Our ontology provides a framework for querying and analyzing the disease associated information in the form of RDF graphs. The above developed methodology is used to predict novel potential targets involved in diabetes disease from the long list of loose (statistically associated) gene-disease associations. Copyright © 2016 Elsevier Inc. All rights reserved.

  12. Grid and Data Analyzing and Security

    Directory of Open Access Journals (Sweden)

    Fatemeh SHOKRI

    2012-12-01

    Full Text Available This paper examines the importance of secure structures in the process of analyzing and distributing information with aid of Grid-based technologies. The advent of distributed network has provided many practical opportunities for detecting and recording the time of events, and made efforts to identify the events and solve problems of storing information such as being up-to-date and documented. In this regard, the data distribution systems in a network environment should be accurate. As a consequence, a series of continuous and updated data must be at hand. In this case, Grid is the best answer to use data and resource of organizations by common processing.

  13. The kpx, a program analyzer for parallelization

    International Nuclear Information System (INIS)

    Matsuyama, Yuji; Orii, Shigeo; Ota, Toshiro; Kume, Etsuo; Aikawa, Hiroshi.

    1997-03-01

    The kpx is a program analyzer, developed as a common technological basis for promoting parallel processing. The kpx consists of three tools. The first is ktool, that shows how much execution time is spent in program segments. The second is ptool, that shows parallelization overhead on the Paragon system. The last is xtool, that shows parallelization overhead on the VPP system. The kpx, designed to work for any FORTRAN cord on any UNIX computer, is confirmed to work well after testing on Paragon, SP2, SR2201, VPP500, VPP300, Monte-4, SX-4 and T90. (author)

  14. A low power Multi-Channel Analyzer

    International Nuclear Information System (INIS)

    Anderson, G.A.; Brackenbush, L.W.

    1993-06-01

    The instrumentation used in nuclear spectroscopy is generally large, is not portable, and requires a lot of power. Key components of these counting systems are the computer and the Multi-Channel Analyzer (MCA). To assist in performing measurements requiring portable systems, a small, very low power MCA has been developed at Pacific Northwest Laboratory (PNL). This MCA is interfaced with a Hewlett Packard palm top computer for portable applications. The MCA can also be connected to an IBM/PC for data storage and analysis. In addition, a real-time time display mode allows the user to view the spectra as they are collected

  15. The SPAR thermal analyzer: Present and future

    Science.gov (United States)

    Marlowe, M. B.; Whetstone, W. D.; Robinson, J. C.

    The SPAR thermal analyzer, a system of finite-element processors for performing steady-state and transient thermal analyses, is described. The processors communicate with each other through the SPAR random access data base. As each processor is executed, all pertinent source data is extracted from the data base and results are stored in the data base. Steady state temperature distributions are determined by a direct solution method for linear problems and a modified Newton-Raphson method for nonlinear problems. An explicit and several implicit methods are available for the solution of transient heat transfer problems. Finite element plotting capability is available for model checkout and verification.

  16. Light-weight analyzer for odor recognition

    Energy Technology Data Exchange (ETDEWEB)

    Vass, Arpad A; Wise, Marcus B

    2014-05-20

    The invention provides a light weight analyzer, e.g., detector, capable of locating clandestine graves. The detector utilizes the very specific and unique chemicals identified in the database of human decompositional odor. This detector, based on specific chemical compounds found relevant to human decomposition, is the next step forward in clandestine grave detection and will take the guess-work out of current methods using canines and ground-penetrating radar, which have historically been unreliable. The detector is self contained, portable and built for field use. Both visual and auditory cues are provided to the operator.

  17. Analyzing water/wastewater infrastructure interdependencies

    International Nuclear Information System (INIS)

    Gillette, J. L.; Fisher, R. E.; Peerenboom, J. P.; Whitfield, R. G.

    2002-01-01

    This paper describes four general categories of infrastructure interdependencies (physical, cyber, geographic, and logical) as they apply to the water/wastewater infrastructure, and provides an overview of one of the analytic approaches and tools used by Argonne National Laboratory to evaluate interdependencies. Also discussed are the dimensions of infrastructure interdependency that create spatial, temporal, and system representation complexities that make analyzing the water/wastewater infrastructure particularly challenging. An analytical model developed to incorporate the impacts of interdependencies on infrastructure repair times is briefly addressed

  18. Analyzing Argumentation In Rich, Natural Contexts

    Directory of Open Access Journals (Sweden)

    Anita Reznitskaya

    2008-02-01

    Full Text Available The paper presents the theoretical and methodological aspects of research on the development of argument- ation in elementary school children. It presents a theoretical framework detailing psychological mechanisms responsible for the acquisition and transfer of argumentative discourse and demonstrates several applications of the framework, described in sufficient detail to guide future empirical investigations of oral, written, individual, or group argumentation performance. Software programs capable of facilitating data analysis are identified and their uses illustrated. The analytic schemes can be used to analyze large amounts of verbal data with reasonable precision and efficiency. The conclusion addresses more generally the challenges for and possibilities of empirical study of the development of argumentation.

  19. Nonlinear single-spin spectrum analyzer.

    Science.gov (United States)

    Kotler, Shlomi; Akerman, Nitzan; Glickman, Yinnon; Ozeri, Roee

    2013-03-15

    Qubits have been used as linear spectrum analyzers of their environments. Here we solve the problem of nonlinear spectral analysis, required for discrete noise induced by a strongly coupled environment. Our nonperturbative analytical model shows a nonlinear signal dependence on noise power, resulting in a spectral resolution beyond the Fourier limit as well as frequency mixing. We develop a noise characterization scheme adapted to this nonlinearity. We then apply it using a single trapped ion as a sensitive probe of strong, non-Gaussian, discrete magnetic field noise. Finally, we experimentally compared the performance of equidistant vs Uhrig modulation schemes for spectral analysis.

  20. Thermo Scientific Ozone Analyzer Instrument Handbook

    Energy Technology Data Exchange (ETDEWEB)

    Springston, S. R. [Brookhaven National Lab. (BNL), Upton, NY (United States)

    2016-03-01

    The primary measurement output from the Thermo Scientific Ozone Analyzer is the concentration of the analyte (O3) reported at 1-s resolution in units of ppbv in ambient air. Note that because of internal pneumatic switching limitations the instrument only makes an independent measurement every 4 seconds. Thus, the same concentration number is repeated roughly 4 times at the uniform, monotonic 1-s time base used in the AOS systems. Accompanying instrument outputs include sample temperatures, flows, chamber pressure, lamp intensities and a multiplicity of housekeeping information. There is also a field for operator comments made at any time while data is being collected.

  1. Development of a Portable Water Quality Analyzer

    Directory of Open Access Journals (Sweden)

    Germán COMINA

    2010-08-01

    Full Text Available A portable water analyzer based on a voltammetric electronic tongue has been developed. The system uses an electrochemical cell with two working electrodes as sensors, a computer controlled potentiostat, and software based on multivariate data analysis for pattern recognition. The system is suitable to differentiate laboratory made and real in-situ river water samples contaminated with different amounts of Escherichia coli. This bacteria is not only one of the main indicators for water quality, but also a main concern for public health, affecting especially people living in high-burden, resource-limiting settings.

  2. CRISP90 - SOFTWARE DESIGN ANALYZER SYSTEM

    Science.gov (United States)

    Tausworthe, R. C.

    1994-01-01

    The CRISP90 Software Design Analyzer System, an update of CRISP-80, is a set of programs forming a software design and documentation tool which supports top-down, hierarchic, modular, structured design and programming methodologies. The quality of a computer program can often be significantly influenced by the design medium in which the program is developed. The medium must foster the expression of the programmer's ideas easily and quickly, and it must permit flexible and facile alterations, additions, and deletions to these ideas as the design evolves. The CRISP90 software design analyzer system was developed to provide the PDL (Programmer Design Language) programmer with such a design medium. A program design using CRISP90 consists of short, English-like textual descriptions of data, interfaces, and procedures that are imbedded in a simple, structured, modular syntax. The display is formatted into two-dimensional, flowchart-like segments for a graphic presentation of the design. Together with a good interactive full-screen editor or word processor, the CRISP90 design analyzer becomes a powerful tool for the programmer. In addition to being a text formatter, the CRISP90 system prepares material that would be tedious and error prone to extract manually, such as a table of contents, module directory, structure (tier) chart, cross-references, and a statistics report on the characteristics of the design. Referenced modules are marked by schematic logic symbols to show conditional, iterative, and/or concurrent invocation in the program. A keyword usage profile can be generated automatically and glossary definitions inserted into the output documentation. Another feature is the capability to detect changes that were made between versions. Thus, "change-bars" can be placed in the output document along with a list of changed pages and a version history report. Also, items may be marked as "to be determined" and each will appear on a special table until the item is

  3. Real-Time IPMI Protocol Analyzer

    CERN Document Server

    Kozak, T; Makowski, D

    2011-01-01

    The Advanced Telecommunications Computing Ar- chitecture (ATCA) is a modern platform, which gains popularity, not only in telecommunication, but also in others fields like High Energy Physics (HEP) experiments. Computing systems based on ATCA provide high performance and efficiency and are char- acterized by significant reliability, availability and serviceability. ATCA offers these features because of an integrated manage- ment system realized by the Intelligent Platform Management Interface (IPMI) implemented on dedicated Intelligent Platform Management Controller (IPMC). IPMC is required on each ATCA board to fulfill the ATCA standard and is responsible for many vital procedures performed to support proper operation of ATCA system. It covers, among others, activation and deactivations of modules, monitoring of actual parameters or controlling fans. The commercially available IPMI implementations are expensive and often not suited to demands of specific ATCA applications and available hardware. Thus, many r...

  4. Analyzing endocrine system conservation and evolution.

    Science.gov (United States)

    Bonett, Ronald M

    2016-08-01

    Analyzing variation in rates of evolution can provide important insights into the factors that constrain trait evolution, as well as those that promote diversification. Metazoan endocrine systems exhibit apparent variation in evolutionary rates of their constituent components at multiple levels, yet relatively few studies have quantified these patterns and analyzed them in a phylogenetic context. This may be in part due to historical and current data limitations for many endocrine components and taxonomic groups. However, recent technological advancements such as high-throughput sequencing provide the opportunity to collect large-scale comparative data sets for even non-model species. Such ventures will produce a fertile data landscape for evolutionary analyses of nucleic acid and amino acid based endocrine components. Here I summarize evolutionary rate analyses that can be applied to categorical and continuous endocrine traits, and also those for nucleic acid and protein-based components. I emphasize analyses that could be used to test whether other variables (e.g., ecology, ontogenetic timing of expression, etc.) are related to patterns of rate variation and endocrine component diversification. The application of phylogenetic-based rate analyses to comparative endocrine data will greatly enhance our understanding of the factors that have shaped endocrine system evolution. Copyright © 2016 Elsevier Inc. All rights reserved.

  5. Improving respiration measurements with gas exchange analyzers.

    Science.gov (United States)

    Montero, R; Ribas-Carbó, M; Del Saz, N F; El Aou-Ouad, H; Berry, J A; Flexas, J; Bota, J

    2016-12-01

    Dark respiration measurements with open-flow gas exchange analyzers are often questioned for their low accuracy as their low values often reach the precision limit of the instrument. Respiration was measured in five species, two hypostomatous (Vitis Vinifera L. and Acanthus mollis) and three amphistomatous, one with similar amount of stomata in both sides (Eucalyptus citriodora) and two with different stomata density (Brassica oleracea and Vicia faba). CO 2 differential (ΔCO 2 ) increased two-fold with no change in apparent R d , when the two leaves with higher stomatal density faced outside. These results showed a clear effect of the position of stomata on ΔCO 2 . Therefore, it can be concluded that leaf position is important to guarantee the improvement of respiration measurements increasing ΔCO 2 without affecting the respiration results by leaf or mass units. This method will help to increase the accuracy of leaf respiration measurements using gas exchange analyzers. Copyright © 2016 Elsevier GmbH. All rights reserved.

  6. Analyzing delay causes in Egyptian construction projects

    Directory of Open Access Journals (Sweden)

    Mohamed M. Marzouk

    2014-01-01

    Full Text Available Construction delays are common problems in civil engineering projects in Egypt. These problems occur frequently during project life-time leading to disputes and litigation. Therefore, it is essential to study and analyze causes of construction delays. This research presents a list of construction delay causes retrieved from literature. The feedback of construction experts was obtained through interviews. Subsequently, a questionnaire survey was prepared. The questionnaire survey was distributed to thirty-three construction experts who represent owners, consultants, and contractor’s organizations. Frequency Index, Severity Index, and Importance Index are calculated and according to the highest values of them the top ten delay causes of construction projects in Egypt are determined. A case study is analyzed and compared to the most important delay causes in the research. Statistical analysis is carried out using analysis of variance ANOVA method to test delay causes, obtained from the survey. The test results reveal good correlation between groups while there is significant difference between them for some delay causes and finally roadmap for prioritizing delay causes groups is presented.

  7. Analyzing Virtual Physics Simulations with Tracker

    Science.gov (United States)

    Claessens, Tom

    2017-12-01

    In the physics teaching community, Tracker is well known as a user-friendly open source video analysis software, authored by Douglas Brown. With this tool, the user can trace markers indicated on a video or on stroboscopic photos and perform kinematic analyses. Tracker also includes a data modeling tool that allows one to fit some theoretical equations of motion onto experimentally obtained data. In the field of particle mechanics, Tracker has been effectively used for learning and teaching about projectile motion, "toss up" and free-fall vertical motion, and to explain the principle of mechanical energy conservation. Also, Tracker has been successfully used in rigid body mechanics to interpret the results of experiments with rolling/slipping cylinders and moving rods. In this work, I propose an original method in which Tracker is used to analyze virtual computer simulations created with a physics-based motion solver, instead of analyzing video recording or stroboscopic photos. This could be an interesting approach to study kinematics and dynamics problems in physics education, in particular when there is no or limited access to physical labs. I demonstrate the working method with a typical (but quite challenging) problem in classical mechanics: a slipping/rolling cylinder on a rough surface.

  8. Automatic analyzing device for chlorine ion

    International Nuclear Information System (INIS)

    Sugibayashi, Shinji; Morikawa, Yoshitake; Fukase, Kazuo; Kashima, Hiromasa.

    1997-01-01

    The present invention provides a device of automatically analyzing a trance amount of chlorine ions contained in feedwater, condensate and reactor water of a BWR type power plant. Namely, zero-adjustment or span calibration in this device is conducted as follows. (1) A standard chlorine ion liquid is supplied from a tank to a mixer by a constant volume pump, and the liquid is diluted and mixed with purified water to form a standard liquid. (2) The pH of the standard liquid is adjusted by a pH adjuster. (3) The standard liquid is supplied to an electrode cell to conduct zero adjustment or span calibration. Chlorine ions in a specimen are measured by the device of the present invention as follows. (1) The specimen is supplied to a head tank through a line filter. (2) The pH of the specimen is adjusted by a pH adjuster. (3) The specimen is supplied to an electrode cell to electrically measure the concentration of the chlorine ions in the specimen. The device of the present invention can automatically analyze trance amount of chlorine ions at a high accuracy, thereby capable of improving the sensitivity, reducing an operator's burden and radiation exposure. (I.S.)

  9. Plutonium solution analyzer. Revised February 1995

    International Nuclear Information System (INIS)

    Burns, D.A.

    1995-02-01

    A fully automated analyzer has been developed for plutonium solutions. It was assembled from several commercially available modules, is based upon segmented flow analysis, and exhibits precision about an order of magnitude better than commercial units (0.5%--0.05% RSD). The system was designed to accept unmeasured, untreated liquid samples in the concentration range 40--240 g/l: and produce a report with sample identification, sample concentrations, and an abundance of statistics. Optional hydraulics can accommodate samples in the concentration range 0.4--4.0 g/y. Operating at a typical rate of 30 to 40 samples per hour, it consumes only 0.074 ml of each sample and standard, and generates waste at the rate of about 1.5 ml per minute. No radioactive material passes through its multichannel peristaltic pump (which remains outside the glovebox, uncontaminated) but rather is handled by a 6-port, 2-position chromatography-type loop valve. An accompanying computer is programmed in QuickBASIC 4.5 to provide both instrument control and data reduction. The program is truly user-friendly and communication between operator and instrument is via computer screen displays and keyboard. Two important issues which have been addressed are waste minimization and operator safety (the analyzer can run in the absence of an operator, once its autosampler has been loaded)

  10. Optoacoustic 13C-breath test analyzer

    Science.gov (United States)

    Harde, Hermann; Helmrich, Günther; Wolff, Marcus

    2010-02-01

    The composition and concentration of exhaled volatile gases reflects the physical ability of a patient. Therefore, a breath analysis allows to recognize an infectious disease in an organ or even to identify a tumor. One of the most prominent breath tests is the 13C-urea-breath test, applied to ascertain the presence of the bacterium helicobacter pylori in the stomach wall as an indication of a gastric ulcer. In this contribution we present a new optical analyzer that employs a compact and simple set-up based on photoacoustic spectroscopy. It consists of two identical photoacoustic cells containing two breath samples, one taken before and one after capturing an isotope-marked substrate, where the most common isotope 12C is replaced to a large extent by 13C. The analyzer measures simultaneously the relative CO2 isotopologue concentrations in both samples by exciting the molecules on specially selected absorption lines with a semiconductor laser operating at a wavelength of 2.744 μm. For a reliable diagnosis changes of the 13CO2 concentration of 1% in the exhaled breath have to be detected at a concentration level of this isotope in the breath of about 500 ppm.

  11. Automated Root Tracking with "Root System Analyzer"

    Science.gov (United States)

    Schnepf, Andrea; Jin, Meina; Ockert, Charlotte; Bol, Roland; Leitner, Daniel

    2015-04-01

    Crucial factors for plant development are water and nutrient availability in soils. Thus, root architecture is a main aspect of plant productivity and needs to be accurately considered when describing root processes. Images of root architecture contain a huge amount of information, and image analysis helps to recover parameters describing certain root architectural and morphological traits. The majority of imaging systems for root systems are designed for two-dimensional images, such as RootReader2, GiA Roots, SmartRoot, EZ-Rhizo, and Growscreen, but most of them are semi-automated and involve mouse-clicks in each root by the user. "Root System Analyzer" is a new, fully automated approach for recovering root architectural parameters from two-dimensional images of root systems. Individual roots can still be corrected manually in a user interface if required. The algorithm starts with a sequence of segmented two-dimensional images showing the dynamic development of a root system. For each image, morphological operators are used for skeletonization. Based on this, a graph representation of the root system is created. A dynamic root architecture model helps to determine which edges of the graph belong to an individual root. The algorithm elongates each root at the root tip and simulates growth confined within the already existing graph representation. The increment of root elongation is calculated assuming constant growth. For each root, the algorithm finds all possible paths and elongates the root in the direction of the optimal path. In this way, each edge of the graph is assigned to one or more coherent roots. Image sequences of root systems are handled in such a way that the previous image is used as a starting point for the current image. The algorithm is implemented in a set of Matlab m-files. Output of Root System Analyzer is a data structure that includes for each root an identification number, the branching order, the time of emergence, the parent

  12. Buccal microbiology analyzed by infrared spectroscopy

    Science.gov (United States)

    de Abreu, Geraldo Magno Alves; da Silva, Gislene Rodrigues; Khouri, Sônia; Favero, Priscila Pereira; Raniero, Leandro; Martin, Airton Abrahão

    2012-01-01

    Rapid microbiological identification and characterization are very important in dentistry and medicine. In addition to dental diseases, pathogens are directly linked to cases of endocarditis, premature delivery, low birth weight, and loss of organ transplants. Fourier Transform Infrared Spectroscopy (FTIR) was used to analyze oral pathogens Aggregatibacter actinomycetemcomitans ATCC 29523, Aggregatibacter actinomycetemcomitans-JP2, and Aggregatibacter actinomycetemcomitans which was clinically isolated from the human blood-CI. Significant spectra differences were found among each organism allowing the identification and characterization of each bacterial species. Vibrational modes in the regions of 3500-2800 cm-1, the 1484-1420 cm-1, and 1000-750 cm-1 were used in this differentiation. The identification and classification of each strain were performed by cluster analysis achieving 100% separation of strains. This study demonstrated that FTIR can be used to decrease the identification time, compared to the traditional methods, of fastidious buccal microorganisms associated with the etiology of the manifestation of periodontitis.

  13. Sensors and Automated Analyzers for Radionuclides

    International Nuclear Information System (INIS)

    Grate, Jay W.; Egorov, Oleg B.

    2003-01-01

    The production of nuclear weapons materials has generated large quantities of nuclear waste and significant environmental contamination. We have developed new, rapid, automated methods for determination of radionuclides using sequential injection methodologies to automate extraction chromatographic separations, with on-line flow-through scintillation counting for real time detection. This work has progressed in two main areas: radionuclide sensors for water monitoring and automated radiochemical analyzers for monitoring nuclear waste processing operations. Radionuclide sensors have been developed that collect and concentrate radionuclides in preconcentrating minicolumns with dual functionality: chemical selectivity for radionuclide capture and scintillation for signal output. These sensors can detect pertechnetate to below regulatory levels and have been engineered into a prototype for field testing. A fully automated process monitor has been developed for total technetium in nuclear waste streams. This instrument performs sample acidification, speciation adjustment, separation and detection in fifteen minutes or less

  14. Nuclear Plant Analyzer: Installation manual. Volume 1

    International Nuclear Information System (INIS)

    Snider, D.M.; Wagner, K.L.; Grush, W.H.; Jones, K.R.

    1995-01-01

    This report contains the installation instructions for the Nuclear Plant Analyzer (NPA) System. The NPA System consists of the Computer Visual System (CVS) program, the NPA libraries, the associated utility programs. The NPA was developed at the Idaho National Engineering Laboratory under the sponsorship of the US Nuclear Regulatory Commission to provide a highly flexible graphical user interface for displaying the results of these analysis codes. The NPA also provides the user with a convenient means of interactively controlling the host program through user-defined pop-up menus. The NPA was designed to serve primarily as an analysis tool. After a brief introduction to the Computer Visual System and the NPA, an analyst can quickly create a simple picture or set of pictures to aide in the study of a particular phenomenon. These pictures can range from simple collections of square boxes and straight lines to complex representations of emergency response information displays

  15. Method and apparatus for analyzing ionizable materials

    International Nuclear Information System (INIS)

    Ehrlich, B.J.; Hall, R.C.; Thiede, P.W.

    1979-01-01

    An apparatus and method are described for analyzing a solution of ionizable compounds in a liquid. The solution is irradiated with electromagnetic radiation to ionize the compounds and the electrical conductivity of the solution is measured. The radiation may be X-rays, ultra-violet, infra-red or microwaves. The solution may be split into two streams, only one of which is irradiated, the other being used as a reference by comparing conductivities of the two streams. The liquid must be nonionizable and is preferably a polar solvent. The invention provides an analysis technique useful in liquid chromatography and in gas chromatography after dissolving the eluted gases in a suitable solvent. Electrical conductivity measurements performed on the irradiated eluent provide a quantitative indication of the ionizable materials existing within the eluent stream and a qualitative indication of the purity of the eluent stream. (author)

  16. Analyzing Options for Airborne Emergency Wireless Communications

    Energy Technology Data Exchange (ETDEWEB)

    Michael Schmitt; Juan Deaton; Curt Papke; Shane Cherry

    2008-03-01

    In the event of large-scale natural or manmade catastrophic events, access to reliable and enduring commercial communication systems is critical. Hurricane Katrina provided a recent example of the need to ensure communications during a national emergency. To ensure that communication demands are met during these critical times, Idaho National Laboratory (INL) under the guidance of United States Strategic Command has studied infrastructure issues, concerns, and vulnerabilities associated with an airborne wireless communications capability. Such a capability could provide emergency wireless communications until public/commercial nodes can be systematically restored. This report focuses on the airborne cellular restoration concept; analyzing basic infrastructure requirements; identifying related infrastructure issues, concerns, and vulnerabilities and offers recommended solutions.

  17. Analyzing and forecasting the European social climate

    Directory of Open Access Journals (Sweden)

    Liliana DUGULEANĂ

    2015-06-01

    Full Text Available The paper uses the results of the sample survey Eurobarometer, which has been requested by the European Commission. The social climate index is used to measure the level of perceptions of population by taking into account their personal situation and their perspective at national level. The paper makes an analysis of the evolution of social climate indices for the countries of European Union and offers information about the expectations of population of analyzed countries. The obtained results can be compared with the forecasting of Eurobarometer, on short term of one year and medium term of five years. Modelling the social climate index and its influence factors offers useful information about the efficiency of social protection and inclusion policies.

  18. Analyzing Demand: Hegemonic Masculinity and Feminine Prostitution

    Directory of Open Access Journals (Sweden)

    Beatriz Ranea Triviño

    2016-12-01

    Full Text Available In this article, it is presented an exploratory research in which we analyzed the relationship between the construction of hegemonic masculinity and consumption of female prostitution. We have focused our attention on the experiences, attitudes and perceptions of young heterosexual men who have ever paid for sex. Following with a quantitative method of analysis, we conducted six semi-structured interviews with men between 18 to 35 years old. The analysis of the interviews shows the different demographic characteristics, such as, frequency of payment for sexual services, diversity of motivations, spaces where prostitutes are searched, opinions on prostitution and prostitutes. The main conclusions of this study are that the discourses of the interviewees reproduce gender stereotypes and gender sexual roles. And it is suggested that prostitution can be interpreted as a scenario where these men performance their hegemonic masculinity.

  19. Using wavelet features for analyzing gamma lines

    International Nuclear Information System (INIS)

    Medhat, M.E.; Abdel-hafiez, A.; Hassan, M.F.; Ali, M.A.; Uzhinskii, V.V.

    2004-01-01

    Data processing methods for analyzing gamma ray spectra with symmetric bell-shaped peaks form are considered. In many cases the peak form is symmetrical bell shaped in particular a Gaussian case is the most often used due to many physical reasons. The problem is how to evaluate parameters of such peaks, i.e. their positions, amplitudes and also their half-widths, that is for a single peak and overlapped peaks. Through wavelet features by using Marr wavelet (Mexican Hat) as a correlation method, it could be to estimate the optimal wavelet parameters and to locate peaks in the spectrum. The performance of the proposed method and others shows a better quality of wavelet transform method

  20. Analyzing petabytes of data with Hadoop

    CERN Multimedia

    CERN. Geneva

    2009-01-01

    Abstract The open source Apache Hadoop project provides a powerful suite of tools for storing and analyzing petabytes of data using commodity hardware. After several years of production use inside of web companies like Yahoo! and Facebook and nearly a year of commercial support and development by Cloudera, the technology is spreading rapidly through other disciplines, from financial services and government to life sciences and high energy physics. The talk will motivate the design of Hadoop and discuss some key implementation details in depth. It will also cover the major subprojects in the Hadoop ecosystem, go over some example applications, highlight best practices for deploying Hadoop in your environment, discuss plans for the future of the technology, and provide pointers to the many resources available for learning more. In addition to providing more information about the Hadoop platform, a major goal of this talk is to begin a dialogue with the ATLAS research team on how the tools commonly used in t...

  1. Analyzer of neutron flux in real time

    International Nuclear Information System (INIS)

    Rojas S, A.S.; Carrillo M, R.A.; Balderas, E.G.

    1999-01-01

    With base in the study of the real signals of neutron flux of instability events occurred in the Laguna Verde nuclear power plant where the nucleus oscillation phenomena of the reactor are in the 0 to 2.5 Hz range, it has been seen the possibility about the development a surveillance and diagnostic equipment capable to analyze in real time the behavior of nucleus in this frequencies range. An important method for surveillance the stability of the reactor nucleus is the use of the Power spectral density which allows to determine the frequencies and amplitudes contained in the signals. It is used an instrument carried out by LabVIEW graphic programming with a data acquisition card of 16 channels which works at Windows 95/98 environment. (Author)

  2. Nuclear plant analyzer development and analysis applications

    International Nuclear Information System (INIS)

    Laats, E.T.

    1984-10-01

    The Nuclear Plant Analyzer (NPA) is being developed as the US Nuclear Regulatory Commission's (NRC's) state of the art safety analysis and engineering tool to address key nuclear plant safety issues. This paper describes four applications of the NPA in assisting reactor safety analyses. Two analyses evaluated reactor operating procedures, during off-normal operation, for a pressurized water reactor (PWR) and a boiling water reactor (BWR), respectively. The third analysis was performed in support of a reactor safety experiment conducted in the Semiscale facility. The final application demonstrated the usefulness of atmospheric dispersion computer codes for site emergency planning purposes. An overview of the NPA and how it supported these analyses are the topics of this paper

  3. Analyzing Strategic Business Rules through Simulation Modeling

    Science.gov (United States)

    Orta, Elena; Ruiz, Mercedes; Toro, Miguel

    Service Oriented Architecture (SOA) holds promise for business agility since it allows business process to change to meet new customer demands or market needs without causing a cascade effect of changes in the underlying IT systems. Business rules are the instrument chosen to help business and IT to collaborate. In this paper, we propose the utilization of simulation models to model and simulate strategic business rules that are then disaggregated at different levels of an SOA architecture. Our proposal is aimed to help find a good configuration for strategic business objectives and IT parameters. The paper includes a case study where a simulation model is built to help business decision-making in a context where finding a good configuration for different business parameters and performance is too complex to analyze by trial and error.

  4. Analyzing, Modelling, and Designing Software Ecosystems

    DEFF Research Database (Denmark)

    Manikas, Konstantinos

    as the software development and distribution by a set of actors dependent on each other and the ecosystem. We commence on the hypothesis that the establishment of a software ecosystem on the telemedicine services of Denmark would address these issues and investigate how a software ecosystem can foster...... the development, implementation, and use of telemedicine services. We initially expand the theory of software ecosystems by contributing to the definition and understanding of software ecosystems, providing means of analyzing existing and designing new ecosystems, and defining and measuring the qualities...... of software ecosystems. We use these contributions to design a software ecosystem in the telemedicine services of Denmark with (i) a common platform that supports and promotes development from different actors, (ii) high software interaction, (iii) strong social network of actors, (iv) robust business...

  5. Structural factoring approach for analyzing stochastic networks

    Science.gov (United States)

    Hayhurst, Kelly J.; Shier, Douglas R.

    1991-01-01

    The problem of finding the distribution of the shortest path length through a stochastic network is investigated. A general algorithm for determining the exact distribution of the shortest path length is developed based on the concept of conditional factoring, in which a directed, stochastic network is decomposed into an equivalent set of smaller, generally less complex subnetworks. Several network constructs are identified and exploited to reduce significantly the computational effort required to solve a network problem relative to complete enumeration. This algorithm can be applied to two important classes of stochastic path problems: determining the critical path distribution for acyclic networks and the exact two-terminal reliability for probabilistic networks. Computational experience with the algorithm was encouraging and allowed the exact solution of networks that have been previously analyzed only by approximation techniques.

  6. RELAP5 nuclear plant analyzer capabilities

    International Nuclear Information System (INIS)

    Wagner, R.J.; Ransom, V.H.

    1982-01-01

    An interactive execution capability has been developed for the RELAP5 code which permits it to be used as a Nuclear Plant Analyzer. This capability has been demonstrated using a simplified primary and secondary loop model of a PWR. A variety of loss-of-feed-water accidents have been simulated using this model. The computer execution time on a CDC Cyber 176 is one half of the transient simulation time so that the results can be displayed in real time. The results of the demonstration problems are displayed in digital form on a color schematic of the plant model using a Textronics 4027 CRT terminal. The interactive feature allows the user to enter commands in much the same manner as a reactor operator

  7. Statistical network analysis for analyzing policy networks

    DEFF Research Database (Denmark)

    Robins, Garry; Lewis, Jenny; Wang, Peng

    2012-01-01

    and policy network methodology is the development of statistical modeling approaches that can accommodate such dependent data. In this article, we review three network statistical methods commonly used in the current literature: quadratic assignment procedures, exponential random graph models (ERGMs......To analyze social network data using standard statistical approaches is to risk incorrect inference. The dependencies among observations implied in a network conceptualization undermine standard assumptions of the usual general linear models. One of the most quickly expanding areas of social......), and stochastic actor-oriented models. We focus most attention on ERGMs by providing an illustrative example of a model for a strategic information network within a local government. We draw inferences about the structural role played by individuals recognized as key innovators and conclude that such an approach...

  8. Accuracy of CNV Detection from GWAS Data.

    Directory of Open Access Journals (Sweden)

    Dandan Zhang

    2011-01-01

    Full Text Available Several computer programs are available for detecting copy number variants (CNVs using genome-wide SNP arrays. We evaluated the performance of four CNV detection software suites--Birdsuite, Partek, HelixTree, and PennCNV-Affy--in the identification of both rare and common CNVs. Each program's performance was assessed in two ways. The first was its recovery rate, i.e., its ability to call 893 CNVs previously identified in eight HapMap samples by paired-end sequencing of whole-genome fosmid clones, and 51,440 CNVs identified by array Comparative Genome Hybridization (aCGH followed by validation procedures, in 90 HapMap CEU samples. The second evaluation was program performance calling rare and common CNVs in the Bipolar Genome Study (BiGS data set (1001 bipolar cases and 1033 controls, all of European ancestry as measured by the Affymetrix SNP 6.0 array. Accuracy in calling rare CNVs was assessed by positive predictive value, based on the proportion of rare CNVs validated by quantitative real-time PCR (qPCR, while accuracy in calling common CNVs was assessed by false positive/false negative rates based on qPCR validation results from a subset of common CNVs. Birdsuite recovered the highest percentages of known HapMap CNVs containing >20 markers in two reference CNV datasets. The recovery rate increased with decreased CNV frequency. In the tested rare CNV data, Birdsuite and Partek had higher positive predictive values than the other software suites. In a test of three common CNVs in the BiGS dataset, Birdsuite's call was 98.8% consistent with qPCR quantification in one CNV region, but the other two regions showed an unacceptable degree of accuracy. We found relatively poor consistency between the two "gold standards," the sequence data of Kidd et al., and aCGH data of Conrad et al. Algorithms for calling CNVs especially common ones need substantial improvement, and a "gold standard" for detection of CNVs remains to be established.

  9. GWAS identifies four novel eosinophilic esophagitis loci

    NARCIS (Netherlands)

    Sleiman, Patrick M. A.; Wang, Mei-Lun; Cianferoni, Antonella; Aceves, Seema; Gonsalves, Nirmala; Nadeau, Kari; Bredenoord, Albert J.; Furuta, Glenn T.; Spergel, Jonathan M.; Hakonarson, Hakon

    2014-01-01

    Eosinophilic esophagitis (EoE) is an allergic disorder characterized by infiltration of the oesophagus with eosinophils. We had previously reported association of the TSLP/WDR36 locus with EoE. Here we report genome-wide significant associations at four additional loci; c11orf30 and STAT6, which

  10. Network analysis of metabolite GWAS hits

    DEFF Research Database (Denmark)

    Matone, Alice; Scott-Boyer, Marie-Pier; Carayol, Jerome

    2016-01-01

    BACKGROUND AND SCOPE: Weight loss success is dependent on the ability to refrain from regaining the lost weight in time. This feature was shown to be largely variable among individuals, and these differences, with their underlying molecular processes, are diverse and not completely elucidated. Al...

  11. Integrative Analysis of Genetic, Genomic, and Phenotypic Data for Ethanol Behaviors: A Network-Based Pipeline for Identifying Mechanisms and Potential Drug Targets.

    Science.gov (United States)

    Bogenpohl, James W; Mignogna, Kristin M; Smith, Maren L; Miles, Michael F

    2017-01-01

    Complex behavioral traits, such as alcohol abuse, are caused by an interplay of genetic and environmental factors, producing deleterious functional adaptations in the central nervous system. The long-term behavioral consequences of such changes are of substantial cost to both the individual and society. Substantial progress has been made in the last two decades in understanding elements of brain mechanisms underlying responses to ethanol in animal models and risk factors for alcohol use disorder (AUD) in humans. However, treatments for AUD remain largely ineffective and few medications for this disease state have been licensed. Genome-wide genetic polymorphism analysis (GWAS) in humans, behavioral genetic studies in animal models and brain gene expression studies produced by microarrays or RNA-seq have the potential to produce nonbiased and novel insight into the underlying neurobiology of AUD. However, the complexity of such information, both statistical and informational, has slowed progress toward identifying new targets for intervention in AUD. This chapter describes one approach for integrating behavioral, genetic, and genomic information across animal model and human studies. The goal of this approach is to identify networks of genes functioning in the brain that are most relevant to the underlying mechanisms of a complex disease such as AUD. We illustrate an example of how genomic studies in animal models can be used to produce robust gene networks that have functional implications, and to integrate such animal model genomic data with human genetic studies such as GWAS for AUD. We describe several useful analysis tools for such studies: ComBAT, WGCNA, and EW_dmGWAS. The end result of this analysis is a ranking of gene networks and identification of their cognate hub genes, which might provide eventual targets for future therapeutic development. Furthermore, this combined approach may also improve our understanding of basic mechanisms underlying gene x

  12. Gauge Integral

    Directory of Open Access Journals (Sweden)

    Coghetto Roland

    2017-10-01

    Full Text Available Some authors have formalized the integral in the Mizar Mathematical Library (MML. The first article in a series on the Darboux/Riemann integral was written by Noboru Endou and Artur Korniłowicz: [6]. The Lebesgue integral was formalized a little later [13] and recently the integral of Riemann-Stieltjes was introduced in the MML by Keiko Narita, Kazuhisa Nakasho and Yasunari Shidama [12].

  13. Composing, Analyzing and Validating Software Models

    Science.gov (United States)

    Sheldon, Frederick T.

    1998-10-01

    This research has been conducted at the Computational Sciences Division of the Information Sciences Directorate at Ames Research Center (Automated Software Engineering Grp). The principle work this summer has been to review and refine the agenda that were carried forward from last summer. Formal specifications provide good support for designing a functionally correct system, however they are weak at incorporating non-functional performance requirements (like reliability). Techniques which utilize stochastic Petri nets (SPNs) are good for evaluating the performance and reliability for a system, but they may be too abstract and cumbersome from the stand point of specifying and evaluating functional behavior. Therefore, one major objective of this research is to provide an integrated approach to assist the user in specifying both functionality (qualitative: mutual exclusion and synchronization) and performance requirements (quantitative: reliability and execution deadlines). In this way, the merits of a powerful modeling technique for performability analysis (using SPNs) can be combined with a well-defined formal specification language. In doing so, we can come closer to providing a formal approach to designing a functionally correct system that meets reliability and performance goals.

  14. VECTOR INTEGRATION

    NARCIS (Netherlands)

    Thomas, E. G. F.

    2012-01-01

    This paper deals with the theory of integration of scalar functions with respect to a measure with values in a, not necessarily locally convex, topological vector space. It focuses on the extension of such integrals from bounded measurable functions to the class of integrable functions, proving

  15. Relativistic effects in the calibration of electrostatic electron analyzers. I. Toroidal analyzers

    Energy Technology Data Exchange (ETDEWEB)

    Keski Rahkonen, O [Helsinki University of Technology, Espoo (Finland). Laboratory of Physics; Krause, M O [Oak Ridge National Lab., Tenn. (USA)

    1978-02-01

    Relativistic correction terms up to the second order are derived for the kinetic energy of an electron travelling along the circular central trajectory of a toroidal analyzer. Furthermore, a practical energy calibration equation of the spherical sector plate analyzer is written for the variable-plate-voltage recording mode. Accurate measurements with a spherical analyzer performed using kinetic energies from 600 to 2100 eV are in good agreement with this theory showing our approximation (neglect of fringing fields, and source and detector geometry) is realistic enough for actual calibration purposes.

  16. Nuclear Plant Analyzer development at the Idaho National Engineering Laboratory

    International Nuclear Information System (INIS)

    Laats, E.T.

    1986-10-01

    The Nuclear Plant Analyzer (NPA) is a state-of-the-art safety analysis and engineering tool being used to address key nuclear power plant safety issues. Under the sponsorship of the US Nuclear Regulatory Commission (NRC), the NPA has been developed to integrate the NRC's computerized reactor behavior simulation codes such as RELAP5, TRAC-BWR and TRAC-PWR, with well-developed computer color graphics programs and large repositories of reactor design and experimental data. An important feature of the NPA is the capability to allow an analyst to redirect a RELAP5 or TRAC calculation as it progresses through its simulated scenario. The analyst can have the same power plant control capabilities as the operator of an actual plant. The NPA resides on the dual Control Data Corporation Cyber 176 mainframe computers at the Idaho National Engineering Laboratory and Cray-1S computers at the Los Alamos National Laboratory (LANL) and Kirtland Air Force Weapons Laboratory (KAFWL)

  17. UVB DNA dosimeters analyzed by polymerase chain reactors

    International Nuclear Information System (INIS)

    Yoshida, Hiroko; Regan, J.D.; Florida Inst. of Tech., Melbourne, FL

    1997-01-01

    Purified bacteriophage λ DNA was dried on a UV-transparent polymer film and served as a UVB dosimeter for personal and ecological applications. Bacteriophage λ DNA was chosen because it is commercially available and inexpensive, and its entire sequence is known. Each dosimeter contained two sets of DNA sandwiched between UV-transparent polymer films, one exposed to solar radiation (experimental) and another protected from UV radiation by black paper (control). The DNA dosimeter was then analyzed by a polymerase chain reaction (PCR) that amplifies a 500 base pair specific region of λ DNA. Photoinduced damage in DNA blocks polymerase from synthesizing a new strand; therefore, the amount of amplified product in UV-exposed DNA was reduced from that found in control DNA. The dried λ DNA dosimeter is compact, robust, safe and transportable, stable over long storage times and provides the total UVB dose integrated over the exposure time. (author)

  18. Urban forests and pollution mitigation: Analyzing ecosystem services and disservices

    International Nuclear Information System (INIS)

    Escobedo, Francisco J.; Kroeger, Timm; Wagner, John E.

    2011-01-01

    The purpose of this paper is to integrate the concepts of ecosystem services and disservices when assessing the efficacy of using urban forests for mitigating pollution. A brief review of the literature identifies some pollution mitigation ecosystem services provided by urban forests. Existing ecosystem services definitions and typologies from the economics and ecological literature are adapted and applied to urban forest management and the concepts of ecosystem disservices from natural and semi-natural systems are discussed. Examples of the urban forest ecosystem services of air quality and carbon dioxide sequestration are used to illustrate issues associated with assessing their efficacy in mitigating urban pollution. Development of urban forest management alternatives that mitigate pollution should consider scale, contexts, heterogeneity, management intensities and other social and economic co-benefits, tradeoffs, and costs affecting stakeholders and urban sustainability goals. - Environmental managers should analyze ecosystem services and disservices when developing urban forest management alternatives for mitigating urban pollution.

  19. Analyzing the Bitcoin Network: The First Four Years

    Directory of Open Access Journals (Sweden)

    Matthias Lischke

    2016-03-01

    Full Text Available In this explorative study, we examine the economy and transaction network of the decentralized digital currency Bitcoin during the first four years of its existence. The objective is to develop insights into the evolution of the Bitcoin economy during this period. For this, we establish and analyze a novel integrated dataset that enriches data from the Bitcoin blockchain with off-network data such as business categories and geo-locations. Our analyses reveal the major Bitcoin businesses and markets. Our results also give insights on the business distribution by countries and how businesses evolve over time. We also show that there is a gambling network that features many very small transactions. Furthermore, regional differences in the adoption and business distribution could be found. In the network analysis, the small world phenomenon is investigated and confirmed for several subgraphs of the Bitcoin network.

  20. Nuclear Plant Analyzer development at the Idaho National Engineering Laboratory

    International Nuclear Information System (INIS)

    Laats, E.T.; Beelman, R.J.; Charlton, T.R.; Hampton, N.L.; Burtt, J.D.

    1985-01-01

    The Nuclear Plant Analyzer (NPA) is a state-of-the-art safety analysis and engineering tool being used to address key nuclear power plant safety issues. The NPA has been developed to integrate the NRC's computerized reactor behavior simulation codes such as RELAP5, TRAC-BWR, and TRAC-PWR, with well-developed computer graphics programs and large repositories of reactor design and experimental data. An important feature of the NAP is the capability to allow an analyst to redirect a RELAP5 or TRAC calculation as it progresses through its simulated scenario. The analyst can have the same power plant control capabilities as the operator of an actual plant. The NPA resides on the dual CDS Cyber-176 mainframe computers at the INEL and is being converted to operate on a Cray-1S computer at the LANL. The subject of this paper is the program conducted at the INEL

  1. Plasma diagnostics with a retarding potential analyzer

    International Nuclear Information System (INIS)

    Jack, T.M.

    1996-01-01

    The plasma rocket is located at NASA Johnson Space Center. To produce a thrust in space, an inert gas is ionized into a plasma and heated in the linear section of a tokamak fusion device. The magnetic field used to contain the plasma has a magnitude of 2--10 kGauss. The plasma plume has a variable thrust and specific impulse. A high temperature retarding potential analyzer (RPA) is being developed to characterize the plasma in the plume and at the edge of the magnetically contained plasma. The RPA measures the energy and density of ions or electrons entering into its solid angle of collection. An oscilloscope displays the ion flux versus the collected current. All measurements are made relative to the facility ground. Testing of this device involves the determination of its output parameters, sensitivity, and responses to a wide range of energies and densities. Each grid will be tested individually by changing only its voltage and observing the output from the RPA. To verify that the RPA is providing proper output, it is compared to the output from a Langmuir or Faraday probe

  2. Analyzing the development of Indonesia shrimp industry

    Science.gov (United States)

    Wati, L. A.

    2018-04-01

    This research aimed to analyze the development of shrimp industry in Indonesia. Porter’s Diamond Theory was used for analysis. The Porter’s Diamond theory is one of framework for industry analysis and business strategy development. The Porter’s Diamond theory has five forces that determine the competitive intensity in an industry, namely (1) the threat of substitute products, (2) the threat of competition, (3) the threat of new entrants, (4) bargaining power of suppliers, and (5) bargaining power of consumers. The development of Indonesian shrimp industry pretty good, explained by Porter Diamond Theory analysis. Analysis of Porter Diamond Theory through four main components namely factor conditions; demand condition; related and supporting industries; and firm strategy, structure and rivalry coupled with a two-component supporting (regulatory the government and the factor of chance). Based on the result of this research show that two-component supporting (regulatory the government and the factor of chance) have positive. Related and supporting industries have negative, firm and structure strategy have negative, rivalry has positive, factor condition have positive (except science and technology resources).

  3. Analyzing Spatiotemporal Anomalies through Interactive Visualization

    Directory of Open Access Journals (Sweden)

    Tao Zhang

    2014-06-01

    Full Text Available As we move into the big data era, data grows not just in size, but also in complexity, containing a rich set of attributes, including location and time information, such as data from mobile devices (e.g., smart phones, natural disasters (e.g., earthquake and hurricane, epidemic spread, etc. We are motivated by the rising challenge and build a visualization tool for exploring generic spatiotemporal data, i.e., records containing time location information and numeric attribute values. Since the values often evolve over time and across geographic regions, we are particularly interested in detecting and analyzing the anomalous changes over time/space. Our analytic tool is based on geographic information system and is combined with spatiotemporal data mining algorithms, as well as various data visualization techniques, such as anomaly grids and anomaly bars superimposed on the map. We study how effective the tool may guide users to find potential anomalies through demonstrating and evaluating over publicly available spatiotemporal datasets. The tool for spatiotemporal anomaly analysis and visualization is useful in many domains, such as security investigation and monitoring, situation awareness, etc.

  4. Alternative approach to analyzing occupational mortality data

    International Nuclear Information System (INIS)

    Gilbert, E.S.; Buchanan, J.A.

    1984-01-01

    It is widely recognized that analyzing occupational mortality by calculating standardized mortality ratios based on death rates from the general population is subject to a number of limitations. An alternative approach described in this report takes advantage of the fact that comparisons of mortality by subgroups and assessments of trends in mortality are often of equal or greater interest than overall assessments and that such comparisons do not require an external control. A computer program MOX (Mortality and Occupational Exposure) is available for performing the needed calculations for several diseases. MOX was written to asses the effect of radiation exposure on Hanford nuclear workers. For this application, analyses have been based on cumulative exposure computed (by MOX) from annual records of radiation exposure obtained from personal dosimeter readings. This program provides tests for differences and trends among subcategories defined by variables such as length of employment, job category, or exposure measurements and also provides control for age, calendar year, and several other potentially confounding variables. 29 references, 2 tables

  5. Analyzing Design Heating Loads in Superinsulated Buildings

    Energy Technology Data Exchange (ETDEWEB)

    Arena, Lois [Consortium for Advanced Residential Buildings, Norwalk, CT (United States)

    2015-06-16

    The U.S. Department of Energy’s Building America research team Consortium for Advanced Residential Buildings (CARB) worked with the EcoVillage cohousing community in Ithaca, New York, on the Third Residential EcoVillage Experience neighborhood. This communityscale project consists of 40 housing units—15 apartments and 25 single-family residences. Units range in size from 450 ft2 to 1,664 ft2 and cost from $80,000 for a studio apartment to $235,000 for a three- or four-bedroom single-family home. For the research component of this project, CARB analyzed current heating system sizing methods for superinsulated homes in cold climates to determine if changes in building load calculation methodology should be recommended. Actual heating energy use was monitored and compared to results from the Air Conditioning Contractors of America’s Manual J8 (MJ8) and the Passive House Planning Package software. Results from that research indicate that MJ8 significantly oversizes heating systems for superinsulated homes and that thermal inertia and internal gains should be considered for more accurate load calculations.

  6. Analyzing the Pension System of the USSR

    Directory of Open Access Journals (Sweden)

    Aleksei V. Pudovkin

    2015-01-01

    Full Text Available The article under the title "ANALYSIS OF THE PENSION SYSTEM OF THE USSR" deals with numerous aspects of development of the pension system of the former USSR. Since the improvement of the Russian pension system is presently high on the agenda, the author believes that analyzing the own historical experience in the first line is essential in order to create a sound and efficient pension system in Russia. The study presented in the article aims to execute an in-depth analysis of legislature on the soviet pension system with the view to recreate the architecture of the pension system of the USSR. In addition, the study also reflects on the official statistics for the said period to make a qualified and fundamental conclusion on the efficiency of the soviet pension system. The evolution of the pension system, based on statistical data evidently proves the efficiently of the soviet pension system. It is highly recommended that the positive aspects of the soviet pension system are taken into consideration when reforming the actual pension system of Russian Federation.

  7. Analyzing Music Services Positioning Through Qualitative Research

    Directory of Open Access Journals (Sweden)

    Manuel Cuadrado

    2015-12-01

    Full Text Available Information technologies have produced new ways of distributing and consuming music, mainly by youth, in relation to both goods and services. In the case of goods, there has been a dramatic shift from traditional ways of buying and listening to music to new digital platforms. There has also been an evolution in relation to music services. In this sense, live music concerts have been losing their audiences over the past few years, as have music radio stations, in favor of streaming platforms. Curious about this phenomenon, we conducted an exploratory research in order to analyze how all these services, both traditional and new ones were perceived. Specifically, we aimed to study youth´s assessment of the three most relevant music service categories: music radio stations, digital streaming platforms, and pop-rock music festivals. To do so, we used the projective technique of image association to gather information. The population of the study consisted of individuals between 18 and 25 years of age. Our results, after using content analysis, were poor due to spontaneous recall. Therefore, we duplicated the study, but in a more focus-oriented way. Information gathered this time allowed us not only to better know how all these organizations are positioned but also to obtain a list of descriptors to be used in a subsequent descriptive research study.

  8. Analyzing the Existing Undergraduate Engineering Leadership Skills

    Directory of Open Access Journals (Sweden)

    Hamed M. Almalki

    2016-12-01

    Full Text Available Purpose: Studying and analyzing the undergraduate engineering students' leadership skills to discover their potential leadership strengths and weaknesses. This study will unveil potential ways to enhance the ways we teach engineering leadership. The research has great insights that might assist engineering programs to improve curricula for the purpose of better engineering preparation to meet industry's demands. Methodology and Findings: 441 undergraduate engineering students have been surveyed in two undergraduate engineering programs to discover their leadership skills. The results in both programs were revealing that undergraduate engineering students are lacking behind in the visionary leadership skills compared to directing, including and cultivating leadership styles. Recommendation: A practical framework has been proposed to enhance the lacking leadership skills by utilizing the Matrix of Change (MOC, and the Balanced Scorecard BSC to capture the best leadership scenarios to design virtual simulation environment as per the lacking leadership skills which is the visionary leadership skills in this case. After that, the virtual simulation will be used to provide an experiential learning by replacing human beings with avatars that can be managed or dramatized by real people to enable the creation of live, practical, measurable, and customizable leadership development programs.

  9. A Methodology to Analyze Photovoltaic Tracker Uptime

    Energy Technology Data Exchange (ETDEWEB)

    Muller, Matthew T [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Ruth, Dan [National Renewable Energy Laboratory (NREL), Golden, CO (United States)

    2018-04-17

    A metric is developed to analyze the daily performance of single-axis photovoltaic (PV) trackers. The metric relies on comparing correlations between the daily time series of the PV power output and an array of simulated plane-of-array irradiances for the given day. Mathematical thresholds and a logic sequence are presented, so the daily tracking metric can be applied in an automated fashion on large-scale PV systems. The results of applying the metric are visually examined against the time series of the power output data for a large number of days and for various systems. The visual inspection results suggest that overall, the algorithm is accurate in identifying stuck or functioning trackers on clear-sky days. Visual inspection also shows that there are days that are not classified by the metric where the power output data may be sufficient to identify a stuck tracker. Based on the daily tracking metric, uptime results are calculated for 83 different inverters at 34 PV sites. The mean tracker uptime is calculated at 99% based on 2 different calculation methods. The daily tracking metric clearly has limitations, but as there is no existing metrics in the literature, it provides a valuable tool for flagging stuck trackers.

  10. GOoDA: The Generic Optimization Data Analyzer

    International Nuclear Information System (INIS)

    Calafiura, P; Vitillo, R A; Eranian, S; Levinthal, D; Kama, S

    2012-01-01

    Modern superscalar, out-of-order microprocessors dominate large scale server computing. Monitoring their activity, during program execution, has become complicated due to the complexity of the microarchitectures and their IO interactions. Recent processors have thousands of performance monitoring events. These are required to actually provide coverage for all of the complex interactions and performance issues that can occur. Knowing which data to collect and how to interpret the results has become an unreasonable burden for code developers whose tasks are already hard enough. It becomes the task of the analysis tool developer to bridge this gap. To address this issue, a generic decomposition of how a microprocessor is using the consumed cycles allows code developers to quickly understand which of the myriad of microarchitectural complexities they are battling, without requiring a detailed knowledge of the microarchitecture. When this approach is intrinsically integrated into a performance data analysis tool, it enables software developers to take advantage of the microarchitectural methodology that has only been available to experts. The Generic Optimization Data Analyzer (GOoDA) project integrates this expertise into a profiling tool in order to lower the required expertise of the user and, being designed from the ground up with large-scale object-oriented applications in mind, it will be particularly useful for large HENP codebases

  11. Developing rapid methods for analyzing upland riparian functions and values.

    Science.gov (United States)

    Hruby, Thomas

    2009-06-01

    Regulators protecting riparian areas need to understand the integrity, health, beneficial uses, functions, and values of this resource. Up to now most methods providing information about riparian areas are based on analyzing condition or integrity. These methods, however, provide little information about functions and values. Different methods are needed that specifically address this aspect of riparian areas. In addition to information on functions and values, regulators have very specific needs that include: an analysis at the site scale, low cost, usability, and inclusion of policy interpretations. To meet these needs a rapid method has been developed that uses a multi-criteria decision matrix to categorize riparian areas in Washington State, USA. Indicators are used to identify the potential of the site to provide a function, the potential of the landscape to support the function, and the value the function provides to society. To meet legal needs fixed boundaries for assessment units are established based on geomorphology, the distance from "Ordinary High Water Mark" and different categories of land uses. Assessment units are first classified based on ecoregions, geomorphic characteristics, and land uses. This simplifies the data that need to be collected at a site, but it requires developing and calibrating a separate model for each "class." The approach to developing methods is adaptable to other locations as its basic structure is not dependent on local conditions.

  12. Analyzing Cyber-Physical Threats on Robotic Platforms.

    Science.gov (United States)

    Ahmad Yousef, Khalil M; AlMajali, Anas; Ghalyon, Salah Abu; Dweik, Waleed; Mohd, Bassam J

    2018-05-21

    Robots are increasingly involved in our daily lives. Fundamental to robots are the communication link (or stream) and the applications that connect the robots to their clients or users. Such communication link and applications are usually supported through client/server network connection. This networking system is amenable of being attacked and vulnerable to the security threats. Ensuring security and privacy for robotic platforms is thus critical, as failures and attacks could have devastating consequences. In this paper, we examine several cyber-physical security threats that are unique to the robotic platforms; specifically the communication link and the applications. Threats target integrity, availability and confidential security requirements of the robotic platforms, which use MobileEyes/arnlServer client/server applications. A robot attack tool (RAT) was developed to perform specific security attacks. An impact-oriented approach was adopted to analyze the assessment results of the attacks. Tests and experiments of attacks were conducted in simulation environment and physically on the robot. The simulation environment was based on MobileSim; a software tool for simulating, debugging and experimenting on MobileRobots/ActivMedia platforms and their environments. The robot platform PeopleBot TM was used for physical experiments. The analysis and testing results show that certain attacks were successful at breaching the robot security. Integrity attacks modified commands and manipulated the robot behavior. Availability attacks were able to cause Denial-of-Service (DoS) and the robot was not responsive to MobileEyes commands. Integrity and availability attacks caused sensitive information on the robot to be hijacked. To mitigate security threats, we provide possible mitigation techniques and suggestions to raise awareness of threats on the robotic platforms, especially when the robots are involved in critical missions or applications.

  13. Analyzing Cyber-Physical Threats on Robotic Platforms †

    Science.gov (United States)

    2018-01-01

    Robots are increasingly involved in our daily lives. Fundamental to robots are the communication link (or stream) and the applications that connect the robots to their clients or users. Such communication link and applications are usually supported through client/server network connection. This networking system is amenable of being attacked and vulnerable to the security threats. Ensuring security and privacy for robotic platforms is thus critical, as failures and attacks could have devastating consequences. In this paper, we examine several cyber-physical security threats that are unique to the robotic platforms; specifically the communication link and the applications. Threats target integrity, availability and confidential security requirements of the robotic platforms, which use MobileEyes/arnlServer client/server applications. A robot attack tool (RAT) was developed to perform specific security attacks. An impact-oriented approach was adopted to analyze the assessment results of the attacks. Tests and experiments of attacks were conducted in simulation environment and physically on the robot. The simulation environment was based on MobileSim; a software tool for simulating, debugging and experimenting on MobileRobots/ActivMedia platforms and their environments. The robot platform PeopleBotTM was used for physical experiments. The analysis and testing results show that certain attacks were successful at breaching the robot security. Integrity attacks modified commands and manipulated the robot behavior. Availability attacks were able to cause Denial-of-Service (DoS) and the robot was not responsive to MobileEyes commands. Integrity and availability attacks caused sensitive information on the robot to be hijacked. To mitigate security threats, we provide possible mitigation techniques and suggestions to raise awareness of threats on the robotic platforms, especially when the robots are involved in critical missions or applications. PMID:29883403

  14. Analyzing Cyber-Physical Threats on Robotic Platforms

    Directory of Open Access Journals (Sweden)

    Khalil M. Ahmad Yousef

    2018-05-01

    Full Text Available Robots are increasingly involved in our daily lives. Fundamental to robots are the communication link (or stream and the applications that connect the robots to their clients or users. Such communication link and applications are usually supported through client/server network connection. This networking system is amenable of being attacked and vulnerable to the security threats. Ensuring security and privacy for robotic platforms is thus critical, as failures and attacks could have devastating consequences. In this paper, we examine several cyber-physical security threats that are unique to the robotic platforms; specifically the communication link and the applications. Threats target integrity, availability and confidential security requirements of the robotic platforms, which use MobileEyes/arnlServer client/server applications. A robot attack tool (RAT was developed to perform specific security attacks. An impact-oriented approach was adopted to analyze the assessment results of the attacks. Tests and experiments of attacks were conducted in simulation environment and physically on the robot. The simulation environment was based on MobileSim; a software tool for simulating, debugging and experimenting on MobileRobots/ActivMedia platforms and their environments. The robot platform PeopleBotTM was used for physical experiments. The analysis and testing results show that certain attacks were successful at breaching the robot security. Integrity attacks modified commands and manipulated the robot behavior. Availability attacks were able to cause Denial-of-Service (DoS and the robot was not responsive to MobileEyes commands. Integrity and availability attacks caused sensitive information on the robot to be hijacked. To mitigate security threats, we provide possible mitigation techniques and suggestions to raise awareness of threats on the robotic platforms, especially when the robots are involved in critical missions or applications.

  15. Climate Model Diagnostic Analyzer Web Service System

    Science.gov (United States)

    Lee, S.; Pan, L.; Zhai, C.; Tang, B.; Kubar, T. L.; Li, J.; Zhang, J.; Wang, W.

    2015-12-01

    Both the National Research Council Decadal Survey and the latest Intergovernmental Panel on Climate Change Assessment Report stressed the need for the comprehensive and innovative evaluation of climate models with the synergistic use of global satellite observations in order to improve our weather and climate simulation and prediction capabilities. The abundance of satellite observations for fundamental climate parameters and the availability of coordinated model outputs from CMIP5 for the same parameters offer a great opportunity to understand and diagnose model biases in climate models. In addition, the Obs4MIPs efforts have created several key global observational datasets that are readily usable for model evaluations. However, a model diagnostic evaluation process requires physics-based multi-variable comparisons that typically involve large-volume and heterogeneous datasets, making them both computationally- and data-intensive. In response, we have developed a novel methodology to diagnose model biases in contemporary climate models and implementing the methodology as a web-service based, cloud-enabled, provenance-supported climate-model evaluation system. The evaluation system is named Climate Model Diagnostic Analyzer (CMDA), which is the product of the research and technology development investments of several current and past NASA ROSES programs. The current technologies and infrastructure of CMDA are designed and selected to address several technical challenges that the Earth science modeling and model analysis community faces in evaluating and diagnosing climate models. In particular, we have three key technology components: (1) diagnostic analysis methodology; (2) web-service based, cloud-enabled technology; (3) provenance-supported technology. The diagnostic analysis methodology includes random forest feature importance ranking, conditional probability distribution function, conditional sampling, and time-lagged correlation map. We have implemented the

  16. Analyzing wildfire exposure on Sardinia, Italy

    Science.gov (United States)

    Salis, Michele; Ager, Alan A.; Arca, Bachisio; Finney, Mark A.; Alcasena, Fermin; Bacciu, Valentina; Duce, Pierpaolo; Munoz Lozano, Olga; Spano, Donatella

    2014-05-01

    We used simulation modeling based on the minimum travel time algorithm (MTT) to analyze wildfire exposure of key ecological, social and economic features on Sardinia, Italy. Sardinia is the second largest island of the Mediterranean Basin, and in the last fifty years experienced large and dramatic wildfires, which caused losses and threatened urban interfaces, forests and natural areas, and agricultural productions. Historical fires and environmental data for the period 1995-2009 were used as input to estimate fine scale burn probability, conditional flame length, and potential fire size in the study area. With this purpose, we simulated 100,000 wildfire events within the study area, randomly drawing from the observed frequency distribution of burn periods and wind directions for each fire. Estimates of burn probability, excluding non-burnable fuels, ranged from 0 to 1.92x10-3, with a mean value of 6.48x10-5. Overall, the outputs provided a quantitative assessment of wildfire exposure at the landscape scale and captured landscape properties of wildfire exposure. We then examined how the exposure profiles varied among and within selected features and assets located on the island. Spatial variation in modeled outputs resulted in a strong effect of fuel models, coupled with slope and weather. In particular, the combined effect of Mediterranean maquis, woodland areas and complex topography on flame length was relevant, mainly in north-east Sardinia, whereas areas with herbaceous fuels and flat areas were in general characterized by lower fire intensity but higher burn probability. The simulation modeling proposed in this work provides a quantitative approach to inform wildfire risk management activities, and represents one of the first applications of burn probability modeling to capture fire risk and exposure profiles in the Mediterranean basin.

  17. Modeling and Analyzing Academic Researcher Behavior

    Directory of Open Access Journals (Sweden)

    Phuc Huu Nguyen

    2016-12-01

    Full Text Available Abstract. This paper suggests a theoretical framework for analyzing the mechanism of the behavior of academic researchers whose interests are tangled and vary widely in academic factors (the intrinsic satisfaction in conducting research, the improvement in individual research ability, etc. or non-academic factors (career rewards, financial rewards, etc.. Furthermore, each researcher also has his/her different academic stances in their preferences about academic freedom and academic entrepreneurship. Understanding the behavior of academic researchers will contribute to nurture young researchers, to improve the standard of research and education as well as to boost collaboration in academia-industry. In particular, as open innovation is increasingly in need of the involvement of university researchers, to establish a successful approach to entice researchers into enterprises’ research, companies must comprehend the behavior of university researchers who have multiple complex motivations. The paper explores academic researchers' behaviors through optimizing their utility functions, i.e. the satisfaction obtained by their research outputs. This paper characterizes these outputs as the results of researchers' 3C: Competence (the ability to implement the research, Commitment (the effort to do the research, and Contribution (finding meaning in the research. Most of the previous research utilized the empirical methods to study researcher's motivation. Without adopting economic theory into the analysis, the past literature could not offer a deeper understanding of researcher's behavior. Our contribution is important both conceptually and practically because it provides the first theoretical framework to study the mechanism of researcher's behavior. Keywords: Academia-Industry, researcher behavior, ulrich model’s 3C.

  18. Nuclear plant analyzer program for Bulgaria

    International Nuclear Information System (INIS)

    Shier, W.; Kennett, R.

    1993-01-01

    An interactive nuclear plant analyzer(NPA) has been developed for use by the Bulgarian technical community in the training of plant personnel, the development and verification of plant operating procedures, and in the analysis of various anticipated operational occurrences and accident scenarios. The current NPA includes models for a VVER-440 Model 230 and a VVER-1000 Model 320 and is operational on an IBM RISC6000 workstation. The RELAP5/MOD2 computer code has been used for the calculation of the reactor responses to the interactive commands initiated by the NPA operator. The interactive capabilities of the NPA have been developed to provide considerable flexibility in the plant actions that can be initiated by the operator. The current capabilities for both the VVER-440 and VVER-1000 models include: (1) scram initiation; (2) reactor coolant pump trip; (3) high pressure safety injection system initiation; (4) low pressure safety injection system initiation; (5) pressurizer safety valve opening; (6) steam generator relief/safety valve opening; (7) feedwater system initiation and trip; (8) turbine trip; and (9) emergency feedwater initiation. The NPA has the capability to display the results of the simulations in various forms that are determined by the model developer. Results displayed on the reactor mask are shown through the user defined, digital display of various plant parameters and through color changes that reflect changes in primary system fluid temperatures, fuel and clad temperatures, and the temperature of other metal structures. In addition, changes in the status of various components and systems can be initiated and/or displayed both numerically and graphically on the mask. This paper provides a description of the structure of the NPA, a discussion of the simulation models used for the VVER-440 and the VVER-1000, and an overview of the NPA capabilities. Typical results obtained using both simulation models will be discussed

  19. Analyzing personalized policies for online biometric verification.

    Science.gov (United States)

    Sadhwani, Apaar; Yang, Yan; Wein, Lawrence M

    2014-01-01

    Motivated by India's nationwide biometric program for social inclusion, we analyze verification (i.e., one-to-one matching) in the case where we possess similarity scores for 10 fingerprints and two irises between a resident's biometric images at enrollment and his biometric images during his first verification. At subsequent verifications, we allow individualized strategies based on these 12 scores: we acquire a subset of the 12 images, get new scores for this subset that quantify the similarity to the corresponding enrollment images, and use the likelihood ratio (i.e., the likelihood of observing these scores if the resident is genuine divided by the corresponding likelihood if the resident is an imposter) to decide whether a resident is genuine or an imposter. We also consider two-stage policies, where additional images are acquired in a second stage if the first-stage results are inconclusive. Using performance data from India's program, we develop a new probabilistic model for the joint distribution of the 12 similarity scores and find near-optimal individualized strategies that minimize the false reject rate (FRR) subject to constraints on the false accept rate (FAR) and mean verification delay for each resident. Our individualized policies achieve the same FRR as a policy that acquires (and optimally fuses) 12 biometrics for each resident, which represents a five (four, respectively) log reduction in FRR relative to fingerprint (iris, respectively) policies previously proposed for India's biometric program. The mean delay is [Formula: see text] sec for our proposed policy, compared to 30 sec for a policy that acquires one fingerprint and 107 sec for a policy that acquires all 12 biometrics. This policy acquires iris scans from 32-41% of residents (depending on the FAR) and acquires an average of 1.3 fingerprints per resident.

  20. Novel topological descriptors for analyzing biological networks

    Directory of Open Access Journals (Sweden)

    Varmuza Kurt K

    2010-06-01

    Full Text Available Abstract Background Topological descriptors, other graph measures, and in a broader sense, graph-theoretical methods, have been proven as powerful tools to perform biological network analysis. However, the majority of the developed descriptors and graph-theoretical methods does not have the ability to take vertex- and edge-labels into account, e.g., atom- and bond-types when considering molecular graphs. Indeed, this feature is important to characterize biological networks more meaningfully instead of only considering pure topological information. Results In this paper, we put the emphasis on analyzing a special type of biological networks, namely bio-chemical structures. First, we derive entropic measures to calculate the information content of vertex- and edge-labeled graphs and investigate some useful properties thereof. Second, we apply the mentioned measures combined with other well-known descriptors to supervised machine learning methods for predicting Ames mutagenicity. Moreover, we investigate the influence of our topological descriptors - measures for only unlabeled vs. measures for labeled graphs - on the prediction performance of the underlying graph classification problem. Conclusions Our study demonstrates that the application of entropic measures to molecules representing graphs is useful to characterize such structures meaningfully. For instance, we have found that if one extends the measures for determining the structural information content of unlabeled graphs to labeled graphs, the uniqueness of the resulting indices is higher. Because measures to structurally characterize labeled graphs are clearly underrepresented so far, the further development of such methods might be valuable and fruitful for solving problems within biological network analysis.

  1. Bicycle: a bioinformatics pipeline to analyze bisulfite sequencing data.

    Science.gov (United States)

    Graña, Osvaldo; López-Fernández, Hugo; Fdez-Riverola, Florentino; González Pisano, David; Glez-Peña, Daniel

    2018-04-15

    High-throughput sequencing of bisulfite-converted DNA is a technique used to measure DNA methylation levels. Although a considerable number of computational pipelines have been developed to analyze such data, none of them tackles all the peculiarities of the analysis together, revealing limitations that can force the user to manually perform additional steps needed for a complete processing of the data. This article presents bicycle, an integrated, flexible analysis pipeline for bisulfite sequencing data. Bicycle analyzes whole genome bisulfite sequencing data, targeted bisulfite sequencing data and hydroxymethylation data. To show how bicycle overtakes other available pipelines, we compared them on a defined number of features that are summarized in a table. We also tested bicycle with both simulated and real datasets, to show its level of performance, and compared it to different state-of-the-art methylation analysis pipelines. Bicycle is publicly available under GNU LGPL v3.0 license at http://www.sing-group.org/bicycle. Users can also download a customized Ubuntu LiveCD including bicycle and other bisulfite sequencing data pipelines compared here. In addition, a docker image with bicycle and its dependencies, which allows a straightforward use of bicycle in any platform (e.g. Linux, OS X or Windows), is also available. ograna@cnio.es or dgpena@uvigo.es. Supplementary data are available at Bioinformatics online.

  2. Analyzing the User Behavior toward Electronic Commerce Stimuli.

    Science.gov (United States)

    Lorenzo-Romero, Carlota; Alarcón-Del-Amo, María-Del-Carmen; Gómez-Borja, Miguel-Ángel

    2016-01-01

    Based on the Stimulus-Organism-Response paradigm this research analyzes the main differences between the effects of two types of web technologies: Verbal web technology (i.e., navigational structure as utilitarian stimulus) versus non-verbal web technology (music and presentation of products as hedonic stimuli). Specific webmosphere stimuli have not been examined yet as separate variables and their impact on internal and behavioral responses seems unknown. Therefore, the objective of this research consists in analyzing the impact of these web technologies -which constitute the web atmosphere or webmosphere of a website- on shopping human behavior (i.e., users' internal states -affective, cognitive, and satisfaction- and behavioral responses - approach responses, and real shopping outcomes-) within the retail online store created by computer, taking into account some mediator variables (i.e., involvement, atmospheric responsiveness, and perceived risk). A 2 ("free" versus "hierarchical" navigational structure) × 2 ("on" versus "off" music) × 2 ("moving" versus "static" images) between-subjects computer experimental design is used to test empirically this research. In addition, an integrated methodology was developed allowing the simulation, tracking and recording of virtual user behavior within an online shopping environment. As main conclusion, this study suggests that the positive responses of online consumers might increase when they are allowed to freely navigate the online stores and their experience is enriched by animate gifts and music background. The effect caused by mediator variables modifies relatively the final shopping human behavior.

  3. Analyzing the user behavior towards Electronic Commerce stimuli

    Directory of Open Access Journals (Sweden)

    Carlota Lorenzo-Romero

    2016-11-01

    Full Text Available Based on the Stimulus-Organism-Response paradigm this research analyzes the main differences between the effects of two types of web technologies: Verbal web technology (i.e. navigational structure as utilitarian stimulus versus nonverbal web technology (music and presentation of products as hedonic stimuli. Specific webmosphere stimuli have not been examined yet as separate variables and their impact on internal and behavioral responses seems unknown. Therefore, the objective of this research consists in analyzing the impact of these web technologies –which constitute the web atmosphere or webmosphere of a website– on shopping human bebaviour (i.e. users’ internal states -affective, cognitive, and satisfaction- and behavioral responses - approach responses, and real shopping outcomes- within the retail online store created by computer, taking into account some mediator variables (i.e. involvement, atmospheric responsiveness, and perceived risk. A 2(free versus hierarchical navigational structure x2(on versus off music x2(moving versus static images between-subjects computer experimental design is used to test empirically this research. In addition, an integrated methodology was developed allowing the simulation, tracking and recording of virtual user behavior within an online shopping environment. As main conclusion, this study suggests that the positive responses of online consumers might increase when they are allowed to freely navigate the online stores and their experience is enriched by animate gifts and music background. The effect caused by mediator variables modifies relatively the final shopping human behavior.

  4. Thromboelastography platelet mapping in healthy dogs using 1 analyzer versus 2 analyzers.

    Science.gov (United States)

    Blois, Shauna L; Banerjee, Amrita; Wood, R Darren; Park, Fiona M

    2013-07-01

    The objective of this study was to describe the results of thromboelastography platelet mapping (TEG-PM) carried out using 2 techniques in 20 healthy dogs. Maximum amplitudes (MA) generated by thrombin (MAthrombin), fibrin (MAfibrin), adenosine diphosphate (ADP) receptor activity (MAADP), and thromboxane A2 (TxA2) receptor activity (stimulated by arachidonic acid, MAAA) were recorded. Thromboelastography platelet mapping was carried out according to the manufacturer's guidelines (2-analyzer technique) and using a variation of this method employing only 1 analyzer (1-analyzer technique) on 2 separate blood samples obtained from each dog. Mean [± standard deviation (SD)] MA values for the 1-analyzer/2-analyzer techniques were: MAthrombin = 51.9 mm (± 7.1)/52.5 mm (± 8.0); MAfibrin = 20.7 mm (± 21.8)/23.0 mm (± 26.1); MAADP = 44.5 mm (± 15.6)/45.6 mm (± 17.0); and MAAA = 45.7 mm (± 11.6)/45.0 mm (± 15.4). Mean (± SD) percentage aggregation due to ADP receptor activity was 70.4% (± 32.8)/67.6% (± 33.7). Mean percentage aggregation due to TxA2 receptor activity was 77.3% (± 31.6)/78.1% (± 50.2). Results of TEG-PM were not significantly different for the 1-analyzer and 2-analyzer methods. High correlation was found between the 2 methods for MAfibrin [concordance correlation coefficient (r) = 0.930]; moderate correlation was found for MAthrombin (r = 0.70) and MAADP (r = 0.57); correlation between the 2 methods for MAAA was lower (r = 0.32). Thromboelastography platelet mapping (TEG-PM) should be further investigated to determine if it is a suitable method for measuring platelet dysfunction in dogs with thrombopathy.

  5. Data analysis in the post-genome-wide association study era

    Directory of Open Access Journals (Sweden)

    Qiao-Ling Wang

    2016-12-01

    Full Text Available Since the first report of a genome-wide association study (GWAS on human age-related macular degeneration, GWAS has successfully been used to discover genetic variants for a variety of complex human diseases and/or traits, and thousands of associated loci have been identified. However, the underlying mechanisms for these loci remain largely unknown. To make these GWAS findings more useful, it is necessary to perform in-depth data mining. The data analysis in the post-GWAS era will include the following aspects: fine-mapping of susceptibility regions to identify susceptibility genes for elucidating the biological mechanism of action; joint analysis of susceptibility genes in different diseases; integration of GWAS, transcriptome, and epigenetic data to analyze expression and methylation quantitative trait loci at the whole-genome level, and find single-nucleotide polymorphisms that influence gene expression and DNA methylation; genome-wide association analysis of disease-related DNA copy number variations. Applying these strategies and methods will serve to strengthen GWAS data to enhance the utility and significance of GWAS in improving understanding of the genetics of complex diseases or traits and translate these findings for clinical applications. Keywords: Genome-wide association study, Data mining, Integrative data analysis, Polymorphism, Copy number variation

  6. Development of turbine cycle performance analyzer using intelligent data mining

    Energy Technology Data Exchange (ETDEWEB)

    Heo, Gyun Young

    2004-02-15

    In recent year, the performance enhancement of turbine cycle in nuclear power plants is being highlighted because of worldwide deregulation environment. Especially the first target of operating plants became the reduction of operating cost to compete other power plants. It is known that overhaul interval is closely related to operating cost Author identified that the rapid and reliable performance tests, analysis, and diagnosis play an important role in the control of overhaul interval through field investigation. First the technical road map was proposed to clearly set up the objectives. The controversial issues were summarized into data gathering, analysis tool, and diagnosis method. Author proposed the integrated solution on the basis of intelligent data mining techniques. For the reliable data gathering, the state analyzer composed of statistical regression, wavelet analysis, and neural network was developed. The role of the state analyzer is to estimate unmeasured data and to increase the reliability of the collected data. For the advanced performance analysis, performance analysis toolbox was developed. The purpose of this tool makes analysis process easier and more accurate by providing three novel heat balance diagrams. This tool includes the state analyzer and turbine cycle simulation code. In diagnosis module, the probabilistic technique based on Bayesian network model and the deterministic technique based on algebraical model are provided together. It compromises the uncertainty in diagnosis process and the pin-point capability. All the modules were validated by simulated data as well as actual test data, and some modules are used as industrial applications. We have a lot of thing to be improved in turbine cycle in order to increase plant availability. This study was accomplished to remind the concern about the importance of turbine cycle and to propose the solutions on the basis of academic as well as industrial needs.

  7. Development of turbine cycle performance analyzer using intelligent data mining

    International Nuclear Information System (INIS)

    Heo, Gyun Young

    2004-02-01

    In recent year, the performance enhancement of turbine cycle in nuclear power plants is being highlighted because of worldwide deregulation environment. Especially the first target of operating plants became the reduction of operating cost to compete other power plants. It is known that overhaul interval is closely related to operating cost Author identified that the rapid and reliable performance tests, analysis, and diagnosis play an important role in the control of overhaul interval through field investigation. First the technical road map was proposed to clearly set up the objectives. The controversial issues were summarized into data gathering, analysis tool, and diagnosis method. Author proposed the integrated solution on the basis of intelligent data mining techniques. For the reliable data gathering, the state analyzer composed of statistical regression, wavelet analysis, and neural network was developed. The role of the state analyzer is to estimate unmeasured data and to increase the reliability of the collected data. For the advanced performance analysis, performance analysis toolbox was developed. The purpose of this tool makes analysis process easier and more accurate by providing three novel heat balance diagrams. This tool includes the state analyzer and turbine cycle simulation code. In diagnosis module, the probabilistic technique based on Bayesian network model and the deterministic technique based on algebraical model are provided together. It compromises the uncertainty in diagnosis process and the pin-point capability. All the modules were validated by simulated data as well as actual test data, and some modules are used as industrial applications. We have a lot of thing to be improved in turbine cycle in order to increase plant availability. This study was accomplished to remind the concern about the importance of turbine cycle and to propose the solutions on the basis of academic as well as industrial needs

  8. A Portable, Field-Deployable Analyzer for Isotopic Water Measurements

    Science.gov (United States)

    Berman, E. S.; Gupta, M.; Huang, Y. W.; Lacelle, D.; McKay, C. P.; Fortson, S.

    2015-12-01

    Water stable isotopes have for many years been used to study the hydrological cycle, catchment hydrology, and polar climate among other applications. Typically, discrete water samples are collected and transported to a laboratory for isotope analysis. Due to the expense and labor associated with such sampling, isotope studies have generally been limited in scope and time-resolution. Field sampling of water isotopes has been shown in recent years to provide dense data sets with the increased time resolution illuminating substantially greater short term variability than is generally observed during discrete sampling. A truly portable instrument also opens the possibility to utilize the instrument as a tool for identifying which water samples would be particularly interesting for further laboratory investigation. To make possible such field measurements of liquid water isotopes, Los Gatos Research has developed a miniaturized, field-deployable liquid water isotope analyzer. The prototype miniature liquid water isotope analyzer (mini-LWIA) uses LGR's patented Off-Axis ICOS (Integrated Cavity Output Spectroscopy) technology in a rugged, Pelican case housing for easy transport and field operations. The analyzer simultaneously measures both δ2H and δ18O from liquid water, with both manual and automatic water introduction options. The laboratory precision for δ2H is 0.6 ‰, and for δ18O is 0.3 ‰. The mini-LWIA was deployed in the high Arctic during the summer of 2015 at Inuvik in the Canadian Northwest Territories. Samples were collected from Sachs Harbor, on the southwest coast of Banks Island, including buried basal ice from the Lurentide Ice Sheet, some ice wedges, and other types of ground ice. Methodology and water analysis results from this extreme field deployment will be presented.

  9. Analyzing the attributes of Indiana's STEM schools

    Science.gov (United States)

    Eltz, Jeremy

    "Primary and secondary schools do not seem able to produce enough students with the interest, motivation, knowledge, and skills they will need to compete and prosper in the emerging world" (National Academy of Sciences [NAS], 2007a, p. 94). This quote indicated that there are changing expectations for today's students which have ultimately led to new models of education, such as charters, online and blended programs, career and technical centers, and for the purposes of this research, STEM schools. STEM education as defined in this study is a non-traditional model of teaching and learning intended to "equip them [students] with critical thinking, problem solving, creative and collaborative skills, and ultimately establishes connections between the school, work place, community and the global economy" (Science Foundation Arizona, 2014, p. 1). Focusing on science, technology, engineering, and math (STEM) education is believed by many educational stakeholders to be the solution for the deficits many students hold as they move on to college and careers. The National Governors Association (NGA; 2011) believes that building STEM skills in the nation's students will lead to the ability to compete globally with a new workforce that has the capacity to innovate and will in turn spur economic growth. In order to accomplish the STEM model of education, a group of educators and business leaders from Indiana developed a comprehensive plan for STEM education as an option for schools to use in order to close this gap. This plan has been promoted by the Indiana Department of Education (IDOE, 2014a) with the goal of increasing STEM schools throughout Indiana. To determine what Indiana's elementary STEM schools are doing, this study analyzed two of the elementary schools that were certified STEM by the IDOE. This qualitative case study described the findings and themes from two elementary STEM schools. Specifically, the research looked at the vital components to accomplish STEM

  10. analyzers in overweight/obese renal patients

    Directory of Open Access Journals (Sweden)

    Mariusz Kusztal

    2015-05-01

    Full Text Available Bioelectrical impedance analysis (BIA is an affordable, non-invasive and fast alternative method to assess body composition. The purpose of this study was to compare two different tetrapolar BIA devices for estimating body fluid volumes and body cell mass (BCM in a clinical setting among patients with kidney failure.All double measurements were performed by multi-frequency (MF and single-frequency (SF BIA analyzers: a Body Composition Monitor (Fresenius Medical Care, Germany and BIA-101 (Akern, Italy, respectively. All procedures were conducted according to the manufacturers’ instructions (dedicated electrodes, measurement sites, positions, etc. Total body water (TBW, extracellular water (ECW, intracellular water (ICW and BCM were compared. The study included 39 chronic kidney disease patients (stage III-V with a mean age of 45.8 ± 8 years (21 men and 18 women who had a wide range of BMI [17-34 kg/m2 (mean 26.6 ±5].A comparison of results from patients with BMI <25 vs ≥25 revealed a significant discrepancy in measurements between the two BIA devices. Namely, in the group with BMI <25 (n=16 acceptable correlations were obtained in TBW (r 0.99; p<0.01, ICW (0.92; p<0.01, BCM (0.68; p<0.01, and ECW (0.96 p<0.05, but those with BMI ≥25 (n=23 showed a discrepancy (lower correlations in TBW (r 0.82; p<0.05, ICW (0.78; p<0.05, BCM (0.52; p<0.05, and ECW (0.76; p<0.01.Since estimates of TBW, ICW and BCM by the present BIA devices do not differ in patients with BMI <25, they might be interchangeable. This does not hold true for overweight/obese renal patients.

  11. Climate Model Diagnostic Analyzer Web Service System

    Science.gov (United States)

    Lee, S.; Pan, L.; Zhai, C.; Tang, B.; Jiang, J. H.

    2014-12-01

    We have developed a cloud-enabled web-service system that empowers physics-based, multi-variable model performance evaluations and diagnoses through the comprehensive and synergistic use of multiple observational data, reanalysis data, and model outputs. We have developed a methodology to transform an existing science application code into a web service using a Python wrapper interface and Python web service frameworks. The web-service system, called Climate Model Diagnostic Analyzer (CMDA), currently supports (1) all the observational datasets from Obs4MIPs and a few ocean datasets from NOAA and Argo, which can serve as observation-based reference data for model evaluation, (2) many of CMIP5 model outputs covering a broad range of atmosphere, ocean, and land variables from the CMIP5 specific historical runs and AMIP runs, and (3) ECMWF reanalysis outputs for several environmental variables in order to supplement observational datasets. Analysis capabilities currently supported by CMDA are (1) the calculation of annual and seasonal means of physical variables, (2) the calculation of time evolution of the means in any specified geographical region, (3) the calculation of correlation between two variables, (4) the calculation of difference between two variables, and (5) the conditional sampling of one physical variable with respect to another variable. A web user interface is chosen for CMDA because it not only lowers the learning curve and removes the adoption barrier of the tool but also enables instantaneous use, avoiding the hassle of local software installation and environment incompatibility. CMDA will be used as an educational tool for the summer school organized by JPL's Center for Climate Science in 2014. In order to support 30+ simultaneous users during the school, we have deployed CMDA to the Amazon cloud environment. The cloud-enabled CMDA will provide each student with a virtual machine while the user interaction with the system will remain the same

  12. The Albuquerque Seismological Laboratory Data Quality Analyzer

    Science.gov (United States)

    Ringler, A. T.; Hagerty, M.; Holland, J.; Gee, L. S.; Wilson, D.

    2013-12-01

    The U.S. Geological Survey's Albuquerque Seismological Laboratory (ASL) has several efforts underway to improve data quality at its stations. The Data Quality Analyzer (DQA) is one such development. The DQA is designed to characterize station data quality in a quantitative and automated manner. Station quality is based on the evaluation of various metrics, such as timing quality, noise levels, sensor coherence, and so on. These metrics are aggregated into a measurable grade for each station. The DQA consists of a website, a metric calculator (Seedscan), and a PostgreSQL database. The website allows the user to make requests for various time periods, review specific networks and stations, adjust weighting of the station's grade, and plot metrics as a function of time. The website dynamically loads all station data from a PostgreSQL database. The database is central to the application; it acts as a hub where metric values and limited station descriptions are stored. Data is stored at the level of one sensor's channel per day. The database is populated by Seedscan. Seedscan reads and processes miniSEED data, to generate metric values. Seedscan, written in Java, compares hashes of metadata and data to detect changes and perform subsequent recalculations. This ensures that the metric values are up to date and accurate. Seedscan can be run in a scheduled task or on demand by way of a config file. It will compute metrics specified in its configuration file. While many metrics are currently in development, some are completed and being actively used. These include: availability, timing quality, gap count, deviation from the New Low Noise Model, deviation from a station's noise baseline, inter-sensor coherence, and data-synthetic fits. In all, 20 metrics are planned, but any number could be added. ASL is actively using the DQA on a daily basis for station diagnostics and evaluation. As Seedscan is scheduled to run every night, data quality analysts are able to then use the

  13. Technology for collecting and analyzing relational data

    Directory of Open Access Journals (Sweden)

    E. N. Fedorova

    2016-01-01

    summarize the information there is a mechanism of data grouping, which provides general data of the number of entries, maximum, minimum, average values for different groups of records.Results. This technology has been tested in the monitoring requirements of the services of additional professional education and the definition of the educational needs of teachers and executives of educational organizations of the Irkutsk region. The survey has involved 2,780 respondents in 36 municipalities. Creating the data model took several hours. The survey was conducted during the month.Conclusion. The proposed technology allows a short time to collect the information in relational form, and then analyze it without the need for programming with flexible assignment of the operating logic for form.

  14. Interorganisational Integration

    DEFF Research Database (Denmark)

    Lyngsø, Anne Marie; Godtfredsen, Nina Skavlan; Frølich, Anne

    2016-01-01

    INTRODUCTION: Despite many initiatives to improve coordination of patient pathways and intersectoral cooperation, Danish health care is still fragmented, lacking intra- and interorganisational integration. This study explores barriers to and facilitators of interorganisational integration...... at a university hospital in the Capital Region of Denmark. RESULTS AND DISCUSSION: Our results can be grouped into five influencing areas for interorganisational integration: communication/information transfer, committed leadership, patient engagement, the role and competencies of the general practitioner...... and organisational culture. Proposed solutions to barriers in each area hold the potential to improve care integration as experienced by individuals responsible for supporting and facilitating it. Barriers and facilitators to integrating care relate to clinical, professional, functional and normative integration...

  15. Vertical integration

    International Nuclear Information System (INIS)

    Antill, N.

    1999-01-01

    This paper focuses on the trend in international energy companies towards vertical integration in the gas chain from wellhead to power generation, horizontal integration in refining and marketing businesses, and the search for larger projects with lower upstream costs. The shape of the petroleum industry in the next millennium, the creation of super-major oil companies, and the relationship between size and risk are discussed. The dynamics of vertical integration, present events and future developments are considered. (UK)

  16. Analyzers Measure Greenhouse Gases, Airborne Pollutants

    Science.gov (United States)

    2012-01-01

    In complete darkness, a NASA observatory waits. When an eruption of boiling water billows from a nearby crack in the ground, the observatory s sensors seek particles in the fluid, measure shifts in carbon isotopes, and analyze samples for biological signatures. NASA has landed the observatory in this remote location, far removed from air and sunlight, to find life unlike any that scientists have ever seen. It might sound like a scene from a distant planet, but this NASA mission is actually exploring an ocean floor right here on Earth. NASA established a formal exobiology program in 1960, which expanded into the present-day Astrobiology Program. The program, which celebrated its 50th anniversary in 2010, not only explores the possibility of life elsewhere in the universe, but also examines how life begins and evolves, and what the future may hold for life on Earth and other planets. Answers to these questions may be found not only by launching rockets skyward, but by sending probes in the opposite direction. Research here on Earth can revise prevailing concepts of life and biochemistry and point to the possibilities for life on other planets, as was demonstrated in December 2010, when NASA researchers discovered microbes in Mono Lake in California that subsist and reproduce using arsenic, a toxic chemical. The Mono Lake discovery may be the first of many that could reveal possible models for extraterrestrial life. One primary area of interest for NASA astrobiologists lies with the hydrothermal vents on the ocean floor. These vents expel jets of water heated and enriched with chemicals from off-gassing magma below the Earth s crust. Also potentially within the vents: microbes that, like the Mono Lake microorganisms, defy the common characteristics of life on Earth. Basically all organisms on our planet generate energy through the Krebs Cycle, explains Mike Flynn, research scientist at NASA s Ames Research Center. This metabolic process breaks down sugars for energy

  17. Integral equations

    CERN Document Server

    Moiseiwitsch, B L

    2005-01-01

    Two distinct but related approaches hold the solutions to many mathematical problems--the forms of expression known as differential and integral equations. The method employed by the integral equation approach specifically includes the boundary conditions, which confers a valuable advantage. In addition, the integral equation approach leads naturally to the solution of the problem--under suitable conditions--in the form of an infinite series.Geared toward upper-level undergraduate students, this text focuses chiefly upon linear integral equations. It begins with a straightforward account, acco

  18. Analyzing Systems Integration Best Practices and Assessment in DoD Space Systems Acquisition

    Science.gov (United States)

    2009-12-01

    AFIT/GLM/LAL/93S-1, 1993. 2. Adoption of ISO /IEC 15288:2002 Systems Engineering – System Life Cycle Process. Institute of Electrical and Electronic...Air Force. 40. Pennel, L.W. and Knight, F.L (Eds). TOR-2005( 8583 )-3, Systems Engineering. The Aerospace Corporation, 2005. 41. Roche, James G

  19. Biologically inspired autonomous agent navigation using an integrated polarization analyzing CMOS image sensor

    NARCIS (Netherlands)

    Sarkaer, M.; San Segundo Bello, D.; Van Hoof, C.; Theuwissen, A.

    2010-01-01

    The navigational strategies of insects using skylight polarization are interesting for applications in autonomous agent navigation because they rely on very little information for navigation. A polarization navigation sensor using the Stokes parameters to determine the orientation is presented. The

  20. Integrated Autonomous Network Management (IANM) Multi-Topology Route Manager and Analyzer

    National Research Council Canada - National Science Library

    Henderson, Thomas R; Bae, Kyle; Fang, Jin; Kushi, David M

    2008-01-01

    .... In a previous ONR research effort, Boeing and Cisco Systems had studied the applicability of MTR in the context of Navy network scenarios, and Boeing had produced a Linux-based prototype of MTR...

  1. Automated mineralogy and petrology - applications of TESCAN Integrated Mineral Analyzer (TIMA)

    Czech Academy of Sciences Publication Activity Database

    Hrstka, Tomáš; Gottlieb, P.; Skála, Roman; Breiter, Karel; Motl, D.

    2018-01-01

    Roč. 63, č. 1 (2018), s. 47-63 ISSN 1802-6222 Grant - others:AV ČR(CZ) StrategieAV21/4 Program:StrategieAV Institutional support: RVO:67985831 Keywords : TIMA * Automated SEM/EDS * applied mineralogy * modal analysis * artificial intelligence * neural networks Subject RIV: DB - Geology ; Mineralogy OBOR OECD: Mineralogy Impact factor: 0.609, year: 2016

  2. DMET-analyzer: automatic analysis of Affymetrix DMET data.

    Science.gov (United States)

    Guzzi, Pietro Hiram; Agapito, Giuseppe; Di Martino, Maria Teresa; Arbitrio, Mariamena; Tassone, Pierfrancesco; Tagliaferri, Pierosandro; Cannataro, Mario

    2012-10-05

    Clinical Bioinformatics is currently growing and is based on the integration of clinical and omics data aiming at the development of personalized medicine. Thus the introduction of novel technologies able to investigate the relationship among clinical states and biological machineries may help the development of this field. For instance the Affymetrix DMET platform (drug metabolism enzymes and transporters) is able to study the relationship among the variation of the genome of patients and drug metabolism, detecting SNPs (Single Nucleotide Polymorphism) on genes related to drug metabolism. This may allow for instance to find genetic variants in patients which present different drug responses, in pharmacogenomics and clinical studies. Despite this, there is currently a lack in the development of open-source algorithms and tools for the analysis of DMET data. Existing software tools for DMET data generally allow only the preprocessing of binary data (e.g. the DMET-Console provided by Affymetrix) and simple data analysis operations, but do not allow to test the association of the presence of SNPs with the response to drugs. We developed DMET-Analyzer a tool for the automatic association analysis among the variation of the patient genomes and the clinical conditions of patients, i.e. the different response to drugs. The proposed system allows: (i) to automatize the workflow of analysis of DMET-SNP data avoiding the use of multiple tools; (ii) the automatic annotation of DMET-SNP data and the search in existing databases of SNPs (e.g. dbSNP), (iii) the association of SNP with pathway through the search in PharmaGKB, a major knowledge base for pharmacogenomic studies. DMET-Analyzer has a simple graphical user interface that allows users (doctors/biologists) to upload and analyse DMET files produced by Affymetrix DMET-Console in an interactive way. The effectiveness and easy use of DMET Analyzer is demonstrated through different case studies regarding the analysis of

  3. DMET-Analyzer: automatic analysis of Affymetrix DMET Data

    Directory of Open Access Journals (Sweden)

    Guzzi Pietro

    2012-10-01

    Full Text Available Abstract Background Clinical Bioinformatics is currently growing and is based on the integration of clinical and omics data aiming at the development of personalized medicine. Thus the introduction of novel technologies able to investigate the relationship among clinical states and biological machineries may help the development of this field. For instance the Affymetrix DMET platform (drug metabolism enzymes and transporters is able to study the relationship among the variation of the genome of patients and drug metabolism, detecting SNPs (Single Nucleotide Polymorphism on genes related to drug metabolism. This may allow for instance to find genetic variants in patients which present different drug responses, in pharmacogenomics and clinical studies. Despite this, there is currently a lack in the development of open-source algorithms and tools for the analysis of DMET data. Existing software tools for DMET data generally allow only the preprocessing of binary data (e.g. the DMET-Console provided by Affymetrix and simple data analysis operations, but do not allow to test the association of the presence of SNPs with the response to drugs. Results We developed DMET-Analyzer a tool for the automatic association analysis among the variation of the patient genomes and the clinical conditions of patients, i.e. the different response to drugs. The proposed system allows: (i to automatize the workflow of analysis of DMET-SNP data avoiding the use of multiple tools; (ii the automatic annotation of DMET-SNP data and the search in existing databases of SNPs (e.g. dbSNP, (iii the association of SNP with pathway through the search in PharmaGKB, a major knowledge base for pharmacogenomic studies. DMET-Analyzer has a simple graphical user interface that allows users (doctors/biologists to upload and analyse DMET files produced by Affymetrix DMET-Console in an interactive way. The effectiveness and easy use of DMET Analyzer is demonstrated through different

  4. Integrated Design

    DEFF Research Database (Denmark)

    Lenau, Torben Anker

    1999-01-01

    A homepage on the internet with course material, lecture plan, student exercises, etc. Continuesly updated during the course Integrated Design (80402, 80403)......A homepage on the internet with course material, lecture plan, student exercises, etc. Continuesly updated during the course Integrated Design (80402, 80403)...

  5. Organising integration

    DEFF Research Database (Denmark)

    Axelsson, Runo

    2013-01-01

    Background: In Sweden, as in many other countries, there has been a succession of trends in the organisation of health care and other welfare services. These trends have had different implications for the integration of services in the health and welfare system. Aims: One aim is to discuss...... the implications of different organisational trends for the integration of health and welfare services. Another aim is to introduce a Swedish model of financial coordination as a flexible way to organise integration. Organisational trends: In the 1960’s there was an expansion of health and welfare services leading...... an increasing lack of integration in the health and welfare system. In the 2000’s, there has been a re-centralisation through mergers of hospitals, regions and state agencies. It has become clear, however, that mergers do not promote integration but rather increase the bureaucratisation of the system. Model...

  6. The integration of immigrants

    OpenAIRE

    Bauböck, Rainer

    1995-01-01

    from the Table of Contents: Migration and integration - Basic concepts and definitions; Immigration and Integration policies; The legal framework for integration; Dimension of social integration; Cultural integration; Conclusions;

  7. Noise and analyzer-crystal angular position analysis for analyzer-based phase-contrast imaging

    Science.gov (United States)

    Majidi, Keivan; Li, Jun; Muehleman, Carol; Brankov, Jovan G.

    2014-04-01

    The analyzer-based phase-contrast x-ray imaging (ABI) method is emerging as a potential alternative to conventional radiography. Like many of the modern imaging techniques, ABI is a computed imaging method (meaning that images are calculated from raw data). ABI can simultaneously generate a number of planar parametric images containing information about absorption, refraction, and scattering properties of an object. These images are estimated from raw data acquired by measuring (sampling) the angular intensity profile of the x-ray beam passed through the object at different angular positions of the analyzer crystal. The noise in the estimated ABI parametric images depends upon imaging conditions like the source intensity (flux), measurements angular positions, object properties, and the estimation method. In this paper, we use the Cramér-Rao lower bound (CRLB) to quantify the noise properties in parametric images and to investigate the effect of source intensity, different analyzer-crystal angular positions and object properties on this bound, assuming a fixed radiation dose delivered to an object. The CRLB is the minimum bound for the variance of an unbiased estimator and defines the best noise performance that one can obtain regardless of which estimation method is used to estimate ABI parametric images. The main result of this paper is that the variance (hence the noise) in parametric images is directly proportional to the source intensity and only a limited number of analyzer-crystal angular measurements (eleven for uniform and three for optimal non-uniform) are required to get the best parametric images. The following angular measurements only spread the total dose to the measurements without improving or worsening CRLB, but the added measurements may improve parametric images by reducing estimation bias. Next, using CRLB we evaluate the multiple-image radiography, diffraction enhanced imaging and scatter diffraction enhanced imaging estimation techniques

  8. Noise and analyzer-crystal angular position analysis for analyzer-based phase-contrast imaging

    International Nuclear Information System (INIS)

    Majidi, Keivan; Brankov, Jovan G; Li, Jun; Muehleman, Carol

    2014-01-01

    The analyzer-based phase-contrast x-ray imaging (ABI) method is emerging as a potential alternative to conventional radiography. Like many of the modern imaging techniques, ABI is a computed imaging method (meaning that images are calculated from raw data). ABI can simultaneously generate a number of planar parametric images containing information about absorption, refraction, and scattering properties of an object. These images are estimated from raw data acquired by measuring (sampling) the angular intensity profile of the x-ray beam passed through the object at different angular positions of the analyzer crystal. The noise in the estimated ABI parametric images depends upon imaging conditions like the source intensity (flux), measurements angular positions, object properties, and the estimation method. In this paper, we use the Cramér–Rao lower bound (CRLB) to quantify the noise properties in parametric images and to investigate the effect of source intensity, different analyzer-crystal angular positions and object properties on this bound, assuming a fixed radiation dose delivered to an object. The CRLB is the minimum bound for the variance of an unbiased estimator and defines the best noise performance that one can obtain regardless of which estimation method is used to estimate ABI parametric images. The main result of this paper is that the variance (hence the noise) in parametric images is directly proportional to the source intensity and only a limited number of analyzer-crystal angular measurements (eleven for uniform and three for optimal non-uniform) are required to get the best parametric images. The following angular measurements only spread the total dose to the measurements without improving or worsening CRLB, but the added measurements may improve parametric images by reducing estimation bias. Next, using CRLB we evaluate the multiple-image radiography, diffraction enhanced imaging and scatter diffraction enhanced imaging estimation techniques

  9. Integrative psychotherapy.

    Science.gov (United States)

    Kozarić-Kovacić, Dragica

    2008-09-01

    The main purposes of the article are to present the history of integration in psychotherapy, the reasons of the development integrative approaches, and the approaches to integration in psychotherapy. Three approaches to integration in psychotherapy exist: theoretical integration, theoretical eclecticism, and common factors in different psychotherapeutic trends. In integrative psychotherapy, the basic epistemology, theory, and clinical practice are based on the phenomenology, field theory, holism, dialogue, and co-creation of dialogue in the therapeutic relationship. The main criticism is that integrative psychotherapy suffers from confusion and many unresolved controversies. It is difficult to theoretically and methodologically define the clinically applied model that is based on such a different epistemological and theoretical presumptions. Integrative psychotherapy is a synthesis of humanistic psychotherapy, object relations theory, and psychoanalytical self psychology. It focuses on the dynamics and potentials of human relationships, with a goal of changing the relations and understanding internal and external resistances. The process of integrative psychotherapy is primarily focused on the developmental-relational model and co-creation of psychotherapeutic relationship as a single interactive event, which is not unilateral, but rather a joint endeavor by both the therapist and the patient/client. The need for a relationship is an important human need and represents a process of attunement that occurs as a response to the need for a relationship, a unique interpersonal contact between two people. If this need is not met, it manifests with the different feelings and various defenses. To meet this need, we need to have another person with whom we can establish a sensitive, attuned relationship. Thus, the therapist becomes this person who tries to supplement what the person did not receive. Neuroscience can be a source of integration through different therapies. We

  10. Integration of Chandrasekhar's integral equation

    International Nuclear Information System (INIS)

    Tanaka, Tasuku

    2003-01-01

    We solve Chandrasekhar's integration equation for radiative transfer in the plane-parallel atmosphere by iterative integration. The primary thrust in radiative transfer has been to solve the forward problem, i.e., to evaluate the radiance, given the optical thickness and the scattering phase function. In the area of satellite remote sensing, our problem is the inverse problem: to retrieve the surface reflectance and the optical thickness of the atmosphere from the radiance measured by satellites. In order to retrieve the optical thickness and the surface reflectance from the radiance at the top-of-the atmosphere (TOA), we should express the radiance at TOA 'explicitly' in the optical thickness and the surface reflectance. Chandrasekhar formalized radiative transfer in the plane-parallel atmosphere in a simultaneous integral equation, and he obtained the second approximation. Since then no higher approximation has been reported. In this paper, we obtain the third approximation of the scattering function. We integrate functions derived from the second approximation in the integral interval from 1 to ∞ of the inverse of the cos of zenith angles. We can obtain the indefinite integral rather easily in the form of a series expansion. However, the integrals at the upper limit, ∞, are not yet known to us. We can assess the converged values of those series expansions at ∞ through calculus. For integration, we choose coupling pairs to avoid unnecessary terms in the outcome of integral and discover that the simultaneous integral equation can be deduced to the mere integral equation. Through algebraic calculation, we obtain the third approximation as a polynomial of the third degree in the atmospheric optical thickness

  11. Comparative evaluation of Plateletworks, Multiplate analyzer and Platelet function analyzer-200 in cardiology patients.

    Science.gov (United States)

    Kim, Jeeyong; Cho, Chi Hyun; Jung, Bo Kyeung; Nam, Jeonghun; Seo, Hong Seog; Shin, Sehyun; Lim, Chae Seung

    2018-04-14

    The objective of this study was to comparatively evaluate three commercial whole-blood platelet function analyzer systems: Platelet Function Analyzer-200 (PFA; Siemens Canada, Mississauga, Ontario, Canada), Multiplate analyzer (MP; Roche Diagnostics International Ltd., Rotkreuz, Switzerland), and Plateletworks Combo-25 kit (PLW; Helena Laboratories, Beaumont, TX, USA). Venipuncture was performed on 160 patients who visited a department of cardiology. Pairwise agreement among the three platelet function assays was assessed using Cohen's kappa coefficient and percent agreement within the reference limit. Kappa values with the same agonists were poor between PFA-collagen (COL; agonist)/adenosine diphosphate (ADP) and MP-ADP (-0.147), PFA-COL/ADP and PLW-ADP (0.089), MP-ADP and PLW-ADP (0.039), PFA-COL/ADP and MP-COL (-0.039), and between PFA-COL/ADP and PLW-COL (-0.067). Nonetheless, kappa values for the same assay principle with a different agonist were slightly higher between PFA-COL/ADP and PFA-COL/EPI (0.352), MP-ADP and MP-COL (0.235), and between PLW-ADP and PLW-COL (0.247). The range of percent agreement values was 38.7% to 73.8%. Therefore, various measurements of platelet function by more than one method were needed to obtain a reliable interpretation of platelet function considering low kappa coefficient and modest percent agreement rates among 3 different platelet function tests.

  12. Micro-Analyzer: automatic preprocessing of Affymetrix microarray data.

    Science.gov (United States)

    Guzzi, Pietro Hiram; Cannataro, Mario

    2013-08-01

    A current trend in genomics is the investigation of the cell mechanism using different technologies, in order to explain the relationship among genes, molecular processes and diseases. For instance, the combined use of gene-expression arrays and genomic arrays has been demonstrated as an effective instrument in clinical practice. Consequently, in a single experiment different kind of microarrays may be used, resulting in the production of different types of binary data (images and textual raw data). The analysis of microarray data requires an initial preprocessing phase, that makes raw data suitable for use on existing analysis platforms, such as the TIGR M4 (TM4) Suite. An additional challenge to be faced by emerging data analysis platforms is the ability to treat in a combined way those different microarray formats coupled with clinical data. In fact, resulting integrated data may include both numerical and symbolic data (e.g. gene expression and SNPs regarding molecular data), as well as temporal data (e.g. the response to a drug, time to progression and survival rate), regarding clinical data. Raw data preprocessing is a crucial step in analysis but is often performed in a manual and error prone way using different software tools. Thus novel, platform independent, and possibly open source tools enabling the semi-automatic preprocessing and annotation of different microarray data are needed. The paper presents Micro-Analyzer (Microarray Analyzer), a cross-platform tool for the automatic normalization, summarization and annotation of Affymetrix gene expression and SNP binary data. It represents the evolution of the μ-CS tool, extending the preprocessing to SNP arrays that were not allowed in μ-CS. The Micro-Analyzer is provided as a Java standalone tool and enables users to read, preprocess and analyse binary microarray data (gene expression and SNPs) by invoking TM4 platform. It avoids: (i) the manual invocation of external tools (e.g. the Affymetrix Power

  13. The Size Spectrum as Tool for Analyzing Marine Plastic Pollution

    KAUST Repository

    Martí, E.

    2016-12-02

    Marine plastic debris spans over six orders of magnitude in lineal size, from microns to meters. The broad range of plastic sizes mainly arises from the continuous photodegradation and fragmentation affecting the plastic objects. Interestingly, this time-dependent process links, to some degree, the size to the age of the debris. The variety of plastic sizes gives the possibility to marine biota to interact and possible take up microplastics through numerous pathways. Physical processes such as sinking and wind-induced transport or the chemical adsorption of contaminants are also closely related to the size and shape of the plastic items. Likewise, available sampling techniques should be considered as partial views of the marine plastic size range. This being so and given that the size is one of the most easily measurable plastic traits, the size spectrum appears as an ideal frame to arrange, integrate, and analyze plastic data of diverse nature. In this work, we examined tens of thousands of plastic items sampled from across the world with the aim of (1) developing and standardizing the size-spectrum tool to study marine plastics, and (2) assembling a global plastic size spectrum (GPSS) database, relating individual size measurements to abundance, color (129 tons), polymer type, and category (rigid fragments, films, threads, foam, pellets, and microbeads). Using GPSS database, we show for instance the dependence of plastic composition on the item size, with high diversity of categories for items larger than 1 cm and a clear dominance (~90%) of hard fragments below, except for the size interval corresponding to microbeads (around 0.5 mm). GPSS database depicts a comprehensive size-based framework for analyzing the marine plastic pollution, enabling the comparison of size-related studies or the testing of hypothesis.

  14. Polarized 3He Gas Circulating Technologies for Neutron Analyzers

    Energy Technology Data Exchange (ETDEWEB)

    Watt, David [Xemed LLC, Durham, NH (United States); Hersman, Bill [Xemed LLC, Durham, NH (United States)

    2014-12-10

    We describe the development of an integrated system for quasi-continuous operation of a large volume neutron analyzer. The system consists of a non-magnetic diaphragm compressor, a prototype large volume helium polarizer, a surrogate neutron analyzer, a non-depolarizing gas storage reservoir, a non-ferrous valve manifold for handling gas distribution, a custom rubidium-vapor gas return purifier, and wire-wound transfer lines, all of which are immersed in a two-meter external magnetic field. Over the Phase II period we focused on three major tasks required for the successful deployment of these types of systems: 1) design and implementation of gas handling hardware, 2) automation for long-term operation, and 3) improvements in polarizer performance, specifically fabrication of aluminosilicate optical pumping cells. In this report we describe the design, implementation, and testing of the gas handling hardware. We describe improved polarizer performance resulting from improved cell materials and fabrication methods. These improvements yielded valved 8.5 liter cells with relaxation times greater than 12 hours. Pumping this cell with 1500W laser power with 1.25nm linewidth yielded peak polarizations of 60%, measured both inside and outside the polarizer. Fully narrowing this laser to 0.25nm, demonstrated separately on one stack of the four, would have allowed 70% polarization with this cell. We demonstrated the removal of 5 liters of polarized helium from the polarizer with no measured loss of polarization. We circulated the gas through a titanium-clad compressor with polarization loss below 3% per pass. We also prepared for the next phase of development by refining the design of the polarizer so that it can be engineer-certified for pressurized operation. The performance of our system far exceeds comparable efforts elsewhere.

  15. Analyzing the User Behavior toward Electronic Commerce Stimuli

    Science.gov (United States)

    Lorenzo-Romero, Carlota; Alarcón-del-Amo, María-del-Carmen; Gómez-Borja, Miguel-Ángel

    2016-01-01

    Based on the Stimulus-Organism-Response paradigm this research analyzes the main differences between the effects of two types of web technologies: Verbal web technology (i.e., navigational structure as utilitarian stimulus) versus non-verbal web technology (music and presentation of products as hedonic stimuli). Specific webmosphere stimuli have not been examined yet as separate variables and their impact on internal and behavioral responses seems unknown. Therefore, the objective of this research consists in analyzing the impact of these web technologies –which constitute the web atmosphere or webmosphere of a website– on shopping human behavior (i.e., users’ internal states -affective, cognitive, and satisfaction- and behavioral responses – approach responses, and real shopping outcomes-) within the retail online store created by computer, taking into account some mediator variables (i.e., involvement, atmospheric responsiveness, and perceived risk). A 2 (“free” versus “hierarchical” navigational structure) × 2 (“on” versus “off” music) × 2 (“moving” versus “static” images) between-subjects computer experimental design is used to test empirically this research. In addition, an integrated methodology was developed allowing the simulation, tracking and recording of virtual user behavior within an online shopping environment. As main conclusion, this study suggests that the positive responses of online consumers might increase when they are allowed to freely navigate the online stores and their experience is enriched by animate gifts and music background. The effect caused by mediator variables modifies relatively the final shopping human behavior. PMID:27965549

  16. Integrated services

    International Nuclear Information System (INIS)

    Chafcouloff, S.; Michel, G.; Trice, M.; Clark, G.; Cosad, C.; Forbes, K.

    1995-01-01

    Integrated services is the name given to several services grouped together under a single contract. Four key factors determine the success of integrated services projects: teamwork, common objectives, technology, and shared benefits. For oil companies, integration means smoother, more efficient operations by bringing service companies on board as part of the team. For the service industry, it means a radical change in the way business is conducted, taking on more responsibility in return for greater incentives. This article reviews the need for change and the approach Schlumberger has adopted to meet this challenge. 20 figs., 20 refs

  17. Integrated services

    Energy Technology Data Exchange (ETDEWEB)

    Chafcouloff, S.; Michel, G.; Trice, M. [Schlumberger Integrated Project Management Group, Montrouge (France); Clark, G. [Schlumberger Testing Services, Aberdeen (United Kingdom); Cosad, C.; Forbes, K. [Schlumberger Integrated Project Management Group, Aberdeen (United Kingdom)

    1995-12-31

    Integrated services is the name given to several services grouped together under a single contract. Four key factors determine the success of integrated services projects: teamwork, common objectives, technology, and shared benefits. For oil companies, integration means smoother, more efficient operations by bringing service companies on board as part of the team. For the service industry, it means a radical change in the way business is conducted, taking on more responsibility in return for greater incentives. This article reviews the need for change and the approach Schlumberger has adopted to meet this challenge. 20 figs., 20 refs

  18. Integrated mobile robot control

    Science.gov (United States)

    Amidi, Omead; Thorpe, Chuck E.

    1991-03-01

    This paper describes the strucwre implementation and operation of a real-time mobile robot controller which integrates capabilities such as: position estimation path specification and hacking human interfaces fast communication and multiple client support The benefits of such high-level capabilities in a low-level controller was shown by its implementation for the Naviab autonomous vehicle. In addition performance results from positioning and tracking systems are reported and analyzed.

  19. Integrated Microwave Photonics

    OpenAIRE

    Marpaung, David; Roeloffzen, Chris; Heideman, René; Leinse, Arne; Sales Maicas, Salvador; Capmany Francoy, José

    2013-01-01

    Microwave photonics (MWP) is an emerging field in which radio frequency (RF) signals are generated, distributed, processed and analyzed using the strength of photonic techniques. It is a technology that enables various functionalities which are not feasible to achieve only in the microwave domain. A particular aspect that recently gains significant interests is the use of photonic integrated circuit (PIC) technology in the MWP field for enhanced functionalities and robustness as well as the r...

  20. FRAPCON-3: Integral assessment

    Energy Technology Data Exchange (ETDEWEB)

    Lanning, D.D.; Berna, G.A.; Berna, G.A.

    1997-12-01

    An integral assessment has been performed for the U.S. Nuclear Regulatory Commission by Pacific Northwest National Laboratory to quantify the predictive capabilities of FRAPCON-3, a steady-state fuel behavior code designed to analyze fuel behavior from beginning-of-life to burnup levels of 65 GWd/MTU. FRAPCON-3 code calculations are shown to compare satisfactorily to a pre-selected set of experimental data with steady-state operating conditions. 30 refs., 27 figs., 18 tabs.