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Sample records for large-scale genetic studies

  1. Spitting for Science: Danish High School Students Commit to a Large-Scale Self-Reported Genetic Study

    PubMed Central

    Athanasiadis, Georgios; Jørgensen, Frank G.; Cheng, Jade Y.; Kjærgaard, Peter C.; Schierup, Mikkel H.; Mailund, Thomas

    2016-01-01

    Scientific outreach delivers science to the people. But it can also deliver people to the science. In this work, we report our experience from a large-scale public engagement project promoting genomic literacy among Danish high school students with the additional benefit of collecting data for studying the genetic makeup of the Danish population. Not only did we confirm that students have a great interest in their genetic past, but we were also gratified to see that, with the right motivation, adolescents can provide high-quality data for genetic studies. PMID:27571202

  2. Spitting for Science: Danish High School Students Commit to a Large-Scale Self-Reported Genetic Study.

    PubMed

    Athanasiadis, Georgios; Jørgensen, Frank G; Cheng, Jade Y; Kjærgaard, Peter C; Schierup, Mikkel H; Mailund, Thomas

    2016-01-01

    Scientific outreach delivers science to the people. But it can also deliver people to the science. In this work, we report our experience from a large-scale public engagement project promoting genomic literacy among Danish high school students with the additional benefit of collecting data for studying the genetic makeup of the Danish population. Not only did we confirm that students have a great interest in their genetic past, but we were also gratified to see that, with the right motivation, adolescents can provide high-quality data for genetic studies. PMID:27571202

  3. Discovering Genetic Interactions in Large-Scale Association Studies by Stage-wise Likelihood Ratio Tests.

    PubMed

    Frånberg, Mattias; Gertow, Karl; Hamsten, Anders; Lagergren, Jens; Sennblad, Bengt

    2015-09-01

    Despite the success of genome-wide association studies in medical genetics, the underlying genetics of many complex diseases remains enigmatic. One plausible reason for this could be the failure to account for the presence of genetic interactions in current analyses. Exhaustive investigations of interactions are typically infeasible because the vast number of possible interactions impose hard statistical and computational challenges. There is, therefore, a need for computationally efficient methods that build on models appropriately capturing interaction. We introduce a new methodology where we augment the interaction hypothesis with a set of simpler hypotheses that are tested, in order of their complexity, against a saturated alternative hypothesis representing interaction. This sequential testing provides an efficient way to reduce the number of non-interacting variant pairs before the final interaction test. We devise two different methods, one that relies on a priori estimated numbers of marginally associated variants to correct for multiple tests, and a second that does this adaptively. We show that our methodology in general has an improved statistical power in comparison to seven other methods, and, using the idea of closed testing, that it controls the family-wise error rate. We apply our methodology to genetic data from the PROCARDIS coronary artery disease case/control cohort and discover three distinct interactions. While analyses on simulated data suggest that the statistical power may suffice for an exhaustive search of all variant pairs in ideal cases, we explore strategies for a priori selecting subsets of variant pairs to test. Our new methodology facilitates identification of new disease-relevant interactions from existing and future genome-wide association data, which may involve genes with previously unknown association to the disease. Moreover, it enables construction of interaction networks that provide a systems biology view of complex

  4. Discovering Genetic Interactions in Large-Scale Association Studies by Stage-wise Likelihood Ratio Tests

    PubMed Central

    Frånberg, Mattias; Gertow, Karl; Hamsten, Anders; Lagergren, Jens; Sennblad, Bengt

    2015-01-01

    Despite the success of genome-wide association studies in medical genetics, the underlying genetics of many complex diseases remains enigmatic. One plausible reason for this could be the failure to account for the presence of genetic interactions in current analyses. Exhaustive investigations of interactions are typically infeasible because the vast number of possible interactions impose hard statistical and computational challenges. There is, therefore, a need for computationally efficient methods that build on models appropriately capturing interaction. We introduce a new methodology where we augment the interaction hypothesis with a set of simpler hypotheses that are tested, in order of their complexity, against a saturated alternative hypothesis representing interaction. This sequential testing provides an efficient way to reduce the number of non-interacting variant pairs before the final interaction test. We devise two different methods, one that relies on a priori estimated numbers of marginally associated variants to correct for multiple tests, and a second that does this adaptively. We show that our methodology in general has an improved statistical power in comparison to seven other methods, and, using the idea of closed testing, that it controls the family-wise error rate. We apply our methodology to genetic data from the PROCARDIS coronary artery disease case/control cohort and discover three distinct interactions. While analyses on simulated data suggest that the statistical power may suffice for an exhaustive search of all variant pairs in ideal cases, we explore strategies for a priori selecting subsets of variant pairs to test. Our new methodology facilitates identification of new disease-relevant interactions from existing and future genome-wide association data, which may involve genes with previously unknown association to the disease. Moreover, it enables construction of interaction networks that provide a systems biology view of complex

  5. Assessing the Probability that a Finding Is Genuine for Large-Scale Genetic Association Studies

    PubMed Central

    Kuo, Chia-Ling; Vsevolozhskaya, Olga A.; Zaykin, Dmitri V.

    2015-01-01

    Genetic association studies routinely involve massive numbers of statistical tests accompanied by P-values. Whole genome sequencing technologies increased the potential number of tested variants to tens of millions. The more tests are performed, the smaller P-value is required to be deemed significant. However, a small P-value is not equivalent to small chances of a spurious finding and significance thresholds may fail to serve as efficient filters against false results. While the Bayesian approach can provide a direct assessment of the probability that a finding is spurious, its adoption in association studies has been slow, due in part to the ubiquity of P-values and the automated way they are, as a rule, produced by software packages. Attempts to design simple ways to convert an association P-value into the probability that a finding is spurious have been met with difficulties. The False Positive Report Probability (FPRP) method has gained increasing popularity. However, FPRP is not designed to estimate the probability for a particular finding, because it is defined for an entire region of hypothetical findings with P-values at least as small as the one observed for that finding. Here we propose a method that lets researchers extract probability that a finding is spurious directly from a P-value. Considering the counterpart of that probability, we term this method POFIG: the Probability that a Finding is Genuine. Our approach shares FPRP's simplicity, but gives a valid probability that a finding is spurious given a P-value. In addition to straightforward interpretation, POFIG has desirable statistical properties. The POFIG average across a set of tentative associations provides an estimated proportion of false discoveries in that set. POFIGs are easily combined across studies and are immune to multiple testing and selection bias. We illustrate an application of POFIG method via analysis of GWAS associations with Crohn's disease. PMID:25955023

  6. Discovering epistasis in large scale genetic association studies by exploiting graphics cards.

    PubMed

    Chen, Gary K; Guo, Yunfei

    2013-01-01

    Despite the enormous investments made in collecting DNA samples and generating germline variation data across thousands of individuals in modern genome-wide association studies (GWAS), progress has been frustratingly slow in explaining much of the heritability in common disease. Today's paradigm of testing independent hypotheses on each single nucleotide polymorphism (SNP) marker is unlikely to adequately reflect the complex biological processes in disease risk. Alternatively, modeling risk as an ensemble of SNPs that act in concert in a pathway, and/or interact non-additively on log risk for example, may be a more sensible way to approach gene mapping in modern studies. Implementing such analyzes genome-wide can quickly become intractable due to the fact that even modest size SNP panels on modern genotype arrays (500k markers) pose a combinatorial nightmare, require tens of billions of models to be tested for evidence of interaction. In this article, we provide an in-depth analysis of programs that have been developed to explicitly overcome these enormous computational barriers through the use of processors on graphics cards known as Graphics Processing Units (GPU). We include tutorials on GPU technology, which will convey why they are growing in appeal with today's numerical scientists. One obvious advantage is the impressive density of microprocessor cores that are available on only a single GPU. Whereas high end servers feature up to 24 Intel or AMD CPU cores, the latest GPU offerings from nVidia feature over 2600 cores. Each compute node may be outfitted with up to 4 GPU devices. Success on GPUs varies across problems. However, epistasis screens fare well due to the high degree of parallelism exposed in these problems. Papers that we review routinely report GPU speedups of over two orders of magnitude (>100x) over standard CPU implementations. PMID:24348518

  7. Discovering epistasis in large scale genetic association studies by exploiting graphics cards

    PubMed Central

    Chen, Gary K.; Guo, Yunfei

    2013-01-01

    Despite the enormous investments made in collecting DNA samples and generating germline variation data across thousands of individuals in modern genome-wide association studies (GWAS), progress has been frustratingly slow in explaining much of the heritability in common disease. Today's paradigm of testing independent hypotheses on each single nucleotide polymorphism (SNP) marker is unlikely to adequately reflect the complex biological processes in disease risk. Alternatively, modeling risk as an ensemble of SNPs that act in concert in a pathway, and/or interact non-additively on log risk for example, may be a more sensible way to approach gene mapping in modern studies. Implementing such analyzes genome-wide can quickly become intractable due to the fact that even modest size SNP panels on modern genotype arrays (500k markers) pose a combinatorial nightmare, require tens of billions of models to be tested for evidence of interaction. In this article, we provide an in-depth analysis of programs that have been developed to explicitly overcome these enormous computational barriers through the use of processors on graphics cards known as Graphics Processing Units (GPU). We include tutorials on GPU technology, which will convey why they are growing in appeal with today's numerical scientists. One obvious advantage is the impressive density of microprocessor cores that are available on only a single GPU. Whereas high end servers feature up to 24 Intel or AMD CPU cores, the latest GPU offerings from nVidia feature over 2600 cores. Each compute node may be outfitted with up to 4 GPU devices. Success on GPUs varies across problems. However, epistasis screens fare well due to the high degree of parallelism exposed in these problems. Papers that we review routinely report GPU speedups of over two orders of magnitude (>100x) over standard CPU implementations. PMID:24348518

  8. Genetic influences on schizophrenia and subcortical brain volumes: large-scale proof-of-concept and roadmap for future studies

    PubMed Central

    Anttila, Verneri; Hibar, Derrek P; van Hulzen, Kimm J E; Arias-Vasquez, Alejandro; Smoller, Jordan W; Nichols, Thomas E; Neale, Michael C; McIntosh, Andrew M; Lee, Phil; McMahon, Francis J; Meyer-Lindenberg, Andreas; Mattheisen, Manuel; Andreassen, Ole A; Gruber, Oliver; Sachdev, Perminder S; Roiz-Santiañez, Roberto; Saykin, Andrew J; Ehrlich, Stefan; Mather, Karen A; Turner, Jessica A; Schwarz, Emanuel; Thalamuthu, Anbupalam; Shugart, Yin Yao; Ho, Yvonne YW; Martin, Nicholas G; Wright, Margaret J

    2016-01-01

    Schizophrenia is a devastating psychiatric illness with high heritability. Brain structure and function differ, on average, between schizophrenia cases and healthy individuals. As common genetic associations are emerging for both schizophrenia and brain imaging phenotypes, we can now use genome-wide data to investigate genetic overlap. Here we integrated results from common variant studies of schizophrenia (33,636 cases, 43,008 controls) and volumes of several (mainly subcortical) brain structures (11,840 subjects). We did not find evidence of genetic overlap between schizophrenia risk and subcortical volume measures either at the level of common variant genetic architecture or for single genetic markers. The current study provides proof-of-concept (albeit based on a limited set of structural brain measures), and defines a roadmap for future studies investigating the genetic covariance between structural/functional brain phenotypes and risk for psychiatric disorders. PMID:26854805

  9. A Large-Scale Rheumatoid Arthritis Genetic Study Identifies Association at Chromosome 9q33.2

    PubMed Central

    Chang, Monica; Rowland, Charles M.; Garcia, Veronica E.; Schrodi, Steven J.; Catanese, Joseph J.; van der Helm-van Mil, Annette H. M.; Ardlie, Kristin G.; Amos, Christopher I.; Criswell, Lindsey A.; Kastner, Daniel L.; Gregersen, Peter K.; Kurreeman, Fina A. S.; Toes, Rene E. M.; Huizinga, Tom W. J.; Seldin, Michael F.; Begovich, Ann B.

    2008-01-01

    Rheumatoid arthritis (RA) is a chronic, systemic autoimmune disease affecting both joints and extra-articular tissues. Although some genetic risk factors for RA are well-established, most notably HLA-DRB1 and PTPN22, these markers do not fully account for the observed heritability. To identify additional susceptibility loci, we carried out a multi-tiered, case-control association study, genotyping 25,966 putative functional SNPs in 475 white North American RA patients and 475 matched controls. Significant markers were genotyped in two additional, independent, white case-control sample sets (661 cases/1322 controls from North America and 596 cases/705 controls from The Netherlands) identifying a SNP, rs1953126, on chromosome 9q33.2 that was significantly associated with RA (ORcommon = 1.28, trend Pcomb = 1.45E-06). Through a comprehensive fine-scale-mapping SNP-selection procedure, 137 additional SNPs in a 668 kb region from MEGF9 to STOM on 9q33.2 were chosen for follow-up genotyping in a staged-approach. Significant single marker results (Pcomb<0.01) spanned a large 525 kb region from FBXW2 to GSN. However, a variety of analyses identified SNPs in a 70 kb region extending from the third intron of PHF19 across TRAF1 into the TRAF1-C5 intergenic region, but excluding the C5 coding region, as the most interesting (trend Pcomb: 1.45E-06 → 5.41E-09). The observed association patterns for these SNPs had heightened statistical significance and a higher degree of consistency across sample sets. In addition, the allele frequencies for these SNPs displayed reduced variability between control groups when compared to other SNPs. Lastly, in combination with the other two known genetic risk factors, HLA-DRB1 and PTPN22, the variants reported here generate more than a 45-fold RA-risk differential. PMID:18648537

  10. Genetic Association of CD247 (CD3ζ) with SLE in a Large-Scale Multiethnic Study

    PubMed Central

    Martins, Madalena; Williams, Adrienne H.; Comeau, Mary; Marion, Miranda; Ziegler, Julie T.; Freedman, Barry I.; Merrill, Joan T.; Glenn, Stuart B.; Kelly, Jennifer A.; Sivils, Kathy M.; James, Judith A.; Guthridge, Joel M.; Alarcón-Riquelme, Marta E.; Bae, Sang-Cheol; Kim, Jae-Hoon; Kim, Dam; Anaya, Juan-Manuel; Boackle, Susan A.; Criswell, Lindsey A.; Kimberly, Robert P.; Alarcón, Graciela S.; Brown, Elizabeth E.; Vilá, Luis M.; Petri, Michelle A.; Ramsey-Goldman, Rosalind; Niewold, Timothy B.; Tsao, Betty P.; Gilkeson, Gary S.; Kamen, Diane L.; Jacob, Chaim O.; Stevens, Anne M.; Gaffney, Patrick M.; Harley, John B.; Langefeld, Carl D.; Fesel, Constantin

    2015-01-01

    A classic T-cell phenotype in Systemic lupus erythematosus (SLE) is the downregulation and replacement of the CD3ζ chain that alters TCR signaling. However, genetic associations with SLE in the human CD247 locus that encodes CD3ζ are not well established and require replication in independent cohorts. Our aim was therefore to examine, localize and validate CD247-SLE association in a large multi-ethnic population. We typed 44 contiguous CD247 SNPs in 8 922 SLE patients and 8 077 controls from four ethnically distinct populations. The strongest associations were found in the Asian population (11 SNPs in intron 1, 4.99×10−4genetic model adjusted for population proportions, showed 5 SNPs with significant P-values (1.40×10−3study independently confirms and extends the association of SLE with CD247, which is shared by various autoimmune disorders and supports a common T cell-mediated mechanism. PMID:25569266

  11. Genetic variants determining survival and fertility in an adverse African environment: a population-based large-scale candidate gene association study

    PubMed Central

    Koopman, Jacob J.E.; Pijpe, Jeroen; Böhringer, Stefan; van Bodegom, David; Eriksson, Ulrika K.; Sanchez-Faddeev, Hernando; Ziem, Juventus B.; Zwaan, Bas; Slagboom, P. Eline; de Knijff, Peter; Westendorp, Rudi G.J.

    2016-01-01

    Human survival probability and fertility decline strongly with age. These life history traits have been shaped by evolution. However, research has failed to uncover a consistent genetic determination of variation in survival and fertility. As an explanation, such genetic determinants have been selected in adverse environments, in which humans have lived during most of their history, but are almost exclusively studied in populations in modern affluent environments. Here, we present a large-scale candidate gene association study in a rural African population living in an adverse environment. In 4387 individuals, we studied 4052 SNPs in 148 genes that have previously been identified as possible determinants of survival or fertility in animals or humans. We studied their associations with survival comparing newborns, middle-age adults, and old individuals. In women, we assessed their associations with reported and observed numbers of children. We found no statistically significant associations of these SNPs with survival between the three age groups nor with women's reported and observed fertility. Population stratification was unlikely to explain these results. Apart from a lack of power, we hypothesise that genetic heterogeneity of complex phenotypes and gene-environment interactions prevent the identification of genetic variants explaining variation in survival and fertility in humans. PMID:27356285

  12. Large-Scale PV Integration Study

    SciTech Connect

    Lu, Shuai; Etingov, Pavel V.; Diao, Ruisheng; Ma, Jian; Samaan, Nader A.; Makarov, Yuri V.; Guo, Xinxin; Hafen, Ryan P.; Jin, Chunlian; Kirkham, Harold; Shlatz, Eugene; Frantzis, Lisa; McClive, Timothy; Karlson, Gregory; Acharya, Dhruv; Ellis, Abraham; Stein, Joshua; Hansen, Clifford; Chadliev, Vladimir; Smart, Michael; Salgo, Richard; Sorensen, Rahn; Allen, Barbara; Idelchik, Boris

    2011-07-29

    This research effort evaluates the impact of large-scale photovoltaic (PV) and distributed generation (DG) output on NV Energy’s electric grid system in southern Nevada. It analyzes the ability of NV Energy’s generation to accommodate increasing amounts of utility-scale PV and DG, and the resulting cost of integrating variable renewable resources. The study was jointly funded by the United States Department of Energy and NV Energy, and conducted by a project team comprised of industry experts and research scientists from Navigant Consulting Inc., Sandia National Laboratories, Pacific Northwest National Laboratory and NV Energy.

  13. Robust regression for large-scale neuroimaging studies.

    PubMed

    Fritsch, Virgile; Da Mota, Benoit; Loth, Eva; Varoquaux, Gaël; Banaschewski, Tobias; Barker, Gareth J; Bokde, Arun L W; Brühl, Rüdiger; Butzek, Brigitte; Conrod, Patricia; Flor, Herta; Garavan, Hugh; Lemaitre, Hervé; Mann, Karl; Nees, Frauke; Paus, Tomas; Schad, Daniel J; Schümann, Gunter; Frouin, Vincent; Poline, Jean-Baptiste; Thirion, Bertrand

    2015-05-01

    Multi-subject datasets used in neuroimaging group studies have a complex structure, as they exhibit non-stationary statistical properties across regions and display various artifacts. While studies with small sample sizes can rarely be shown to deviate from standard hypotheses (such as the normality of the residuals) due to the poor sensitivity of normality tests with low degrees of freedom, large-scale studies (e.g. >100 subjects) exhibit more obvious deviations from these hypotheses and call for more refined models for statistical inference. Here, we demonstrate the benefits of robust regression as a tool for analyzing large neuroimaging cohorts. First, we use an analytic test based on robust parameter estimates; based on simulations, this procedure is shown to provide an accurate statistical control without resorting to permutations. Second, we show that robust regression yields more detections than standard algorithms using as an example an imaging genetics study with 392 subjects. Third, we show that robust regression can avoid false positives in a large-scale analysis of brain-behavior relationships with over 1500 subjects. Finally we embed robust regression in the Randomized Parcellation Based Inference (RPBI) method and demonstrate that this combination further improves the sensitivity of tests carried out across the whole brain. Altogether, our results show that robust procedures provide important advantages in large-scale neuroimaging group studies. PMID:25731989

  14. Software for large scale tracking studies

    SciTech Connect

    Niederer, J.

    1984-05-01

    Over the past few years, Brookhaven accelerator physicists have been adapting particle tracking programs in planning local storage rings, and lately for SSC reference designs. In addition, the Laboratory is actively considering upgrades to its AGS capabilities aimed at higher proton intensity, polarized proton beams, and heavy ion acceleration. Further activity concerns heavy ion transfer, a proposed booster, and most recently design studies for a heavy ion collider to join to this complex. Circumstances have thus encouraged a search for common features among design and modeling programs and their data, and the corresponding controls efforts among present and tentative machines. Using a version of PATRICIA with nonlinear forces as a vehicle, we have experimented with formal ways to describe accelerator lattice problems to computers as well as to speed up the calculations for large storage ring models. Code treated by straightforward reorganization has served for SSC explorations. The representation work has led to a relational data base centered program, LILA, which has desirable properties for dealing with the many thousands of rapidly changing variables in tracking and other model programs. 13 references.

  15. The Genetic Etiology of Tourette Syndrome: Large-Scale Collaborative Efforts on the Precipice of Discovery.

    PubMed

    Georgitsi, Marianthi; Willsey, A Jeremy; Mathews, Carol A; State, Matthew; Scharf, Jeremiah M; Paschou, Peristera

    2016-01-01

    Gilles de la Tourette Syndrome (TS) is a childhood-onset neurodevelopmental disorder that is characterized by multiple motor and phonic tics. It has a complex etiology with multiple genes likely interacting with environmental factors to lead to the onset of symptoms. The genetic basis of the disorder remains elusive. However, multiple resources and large-scale projects are coming together, launching a new era in the field and bringing us on the verge of discovery. The large-scale efforts outlined in this report are complementary and represent a range of different approaches to the study of disorders with complex inheritance. The Tourette Syndrome Association International Consortium for Genetics (TSAICG) has focused on large families, parent-proband trios and cases for large case-control designs such as genomewide association studies (GWAS), copy number variation (CNV) scans, and exome/genome sequencing. TIC Genetics targets rare, large effect size mutations in simplex trios, and multigenerational families. The European Multicentre Tics in Children Study (EMTICS) seeks to elucidate gene-environment interactions including the involvement of infection and immune mechanisms in TS etiology. Finally, TS-EUROTRAIN, a Marie Curie Initial Training Network, aims to act as a platform to unify large-scale projects in the field and to educate the next generation of experts. Importantly, these complementary large-scale efforts are joining forces to uncover the full range of genetic variation and environmental risk factors for TS, holding great promise for identifying definitive TS susceptibility genes and shedding light into the complex pathophysiology of this disorder. PMID:27536211

  16. The Genetic Etiology of Tourette Syndrome: Large-Scale Collaborative Efforts on the Precipice of Discovery

    PubMed Central

    Georgitsi, Marianthi; Willsey, A. Jeremy; Mathews, Carol A.; State, Matthew; Scharf, Jeremiah M.; Paschou, Peristera

    2016-01-01

    Gilles de la Tourette Syndrome (TS) is a childhood-onset neurodevelopmental disorder that is characterized by multiple motor and phonic tics. It has a complex etiology with multiple genes likely interacting with environmental factors to lead to the onset of symptoms. The genetic basis of the disorder remains elusive. However, multiple resources and large-scale projects are coming together, launching a new era in the field and bringing us on the verge of discovery. The large-scale efforts outlined in this report are complementary and represent a range of different approaches to the study of disorders with complex inheritance. The Tourette Syndrome Association International Consortium for Genetics (TSAICG) has focused on large families, parent-proband trios and cases for large case-control designs such as genomewide association studies (GWAS), copy number variation (CNV) scans, and exome/genome sequencing. TIC Genetics targets rare, large effect size mutations in simplex trios, and multigenerational families. The European Multicentre Tics in Children Study (EMTICS) seeks to elucidate gene-environment interactions including the involvement of infection and immune mechanisms in TS etiology. Finally, TS-EUROTRAIN, a Marie Curie Initial Training Network, aims to act as a platform to unify large-scale projects in the field and to educate the next generation of experts. Importantly, these complementary large-scale efforts are joining forces to uncover the full range of genetic variation and environmental risk factors for TS, holding great promise for identifying definitive TS susceptibility genes and shedding light into the complex pathophysiology of this disorder. PMID:27536211

  17. The Influence of Age and Sex on Genetic Associations with Adult Body Size and Shape: A Large-Scale Genome-Wide Interaction Study.

    PubMed

    Winkler, Thomas W; Justice, Anne E; Graff, Mariaelisa; Barata, Llilda; Feitosa, Mary F; Chu, Su; Czajkowski, Jacek; Esko, Tõnu; Fall, Tove; Kilpeläinen, Tuomas O; Lu, Yingchang; Mägi, Reedik; Mihailov, Evelin; Pers, Tune H; Rüeger, Sina; Teumer, Alexander; Ehret, Georg B; Ferreira, Teresa; Heard-Costa, Nancy L; Karjalainen, Juha; Lagou, Vasiliki; Mahajan, Anubha; Neinast, Michael D; Prokopenko, Inga; Simino, Jeannette; Teslovich, Tanya M; Jansen, Rick; Westra, Harm-Jan; White, Charles C; Absher, Devin; Ahluwalia, Tarunveer S; Ahmad, Shafqat; Albrecht, Eva; Alves, Alexessander Couto; Bragg-Gresham, Jennifer L; de Craen, Anton J M; Bis, Joshua C; Bonnefond, Amélie; Boucher, Gabrielle; Cadby, Gemma; Cheng, Yu-Ching; Chiang, Charleston W K; Delgado, Graciela; Demirkan, Ayse; Dueker, Nicole; Eklund, Niina; Eiriksdottir, Gudny; Eriksson, Joel; Feenstra, Bjarke; Fischer, Krista; Frau, Francesca; Galesloot, Tessel E; Geller, Frank; Goel, Anuj; Gorski, Mathias; Grammer, Tanja B; Gustafsson, Stefan; Haitjema, Saskia; Hottenga, Jouke-Jan; Huffman, Jennifer E; Jackson, Anne U; Jacobs, Kevin B; Johansson, Åsa; Kaakinen, Marika; Kleber, Marcus E; Lahti, Jari; Mateo Leach, Irene; Lehne, Benjamin; Liu, Youfang; Lo, Ken Sin; Lorentzon, Mattias; Luan, Jian'an; Madden, Pamela A F; Mangino, Massimo; McKnight, Barbara; Medina-Gomez, Carolina; Monda, Keri L; Montasser, May E; Müller, Gabriele; Müller-Nurasyid, Martina; Nolte, Ilja M; Panoutsopoulou, Kalliope; Pascoe, Laura; Paternoster, Lavinia; Rayner, Nigel W; Renström, Frida; Rizzi, Federica; Rose, Lynda M; Ryan, Kathy A; Salo, Perttu; Sanna, Serena; Scharnagl, Hubert; Shi, Jianxin; Smith, Albert Vernon; Southam, Lorraine; Stančáková, Alena; Steinthorsdottir, Valgerdur; Strawbridge, Rona J; Sung, Yun Ju; Tachmazidou, Ioanna; Tanaka, Toshiko; Thorleifsson, Gudmar; Trompet, Stella; Pervjakova, Natalia; Tyrer, Jonathan P; Vandenput, Liesbeth; van der Laan, Sander W; van der Velde, Nathalie; van Setten, Jessica; van Vliet-Ostaptchouk, Jana V; Verweij, Niek; Vlachopoulou, Efthymia; Waite, Lindsay L; Wang, Sophie R; Wang, Zhaoming; Wild, Sarah H; Willenborg, Christina; Wilson, James F; Wong, Andrew; Yang, Jian; Yengo, Loïc; Yerges-Armstrong, Laura M; Yu, Lei; Zhang, Weihua; Zhao, Jing Hua; Andersson, Ehm A; Bakker, Stephan J L; Baldassarre, Damiano; Banasik, Karina; Barcella, Matteo; Barlassina, Cristina; Bellis, Claire; Benaglio, Paola; Blangero, John; Blüher, Matthias; Bonnet, Fabrice; Bonnycastle, Lori L; Boyd, Heather A; Bruinenberg, Marcel; Buchman, Aron S; Campbell, Harry; Chen, Yii-Der Ida; Chines, Peter S; Claudi-Boehm, Simone; Cole, John; Collins, Francis S; de Geus, Eco J C; de Groot, Lisette C P G M; Dimitriou, Maria; Duan, Jubao; Enroth, Stefan; Eury, Elodie; Farmaki, Aliki-Eleni; Forouhi, Nita G; Friedrich, Nele; Gejman, Pablo V; Gigante, Bruna; Glorioso, Nicola; Go, Alan S; Gottesman, Omri; Gräßler, Jürgen; Grallert, Harald; Grarup, Niels; Gu, Yu-Mei; Broer, Linda; Ham, Annelies C; Hansen, Torben; Harris, Tamara B; Hartman, Catharina A; Hassinen, Maija; Hastie, Nicholas; Hattersley, Andrew T; Heath, Andrew C; Henders, Anjali K; Hernandez, Dena; Hillege, Hans; Holmen, Oddgeir; Hovingh, Kees G; Hui, Jennie; Husemoen, Lise L; Hutri-Kähönen, Nina; Hysi, Pirro G; Illig, Thomas; De Jager, Philip L; Jalilzadeh, Shapour; Jørgensen, Torben; Jukema, J Wouter; Juonala, Markus; Kanoni, Stavroula; Karaleftheri, Maria; Khaw, Kay Tee; Kinnunen, Leena; Kittner, Steven J; Koenig, Wolfgang; Kolcic, Ivana; Kovacs, Peter; Krarup, Nikolaj T; Kratzer, Wolfgang; Krüger, Janine; Kuh, Diana; Kumari, Meena; Kyriakou, Theodosios; Langenberg, Claudia; Lannfelt, Lars; Lanzani, Chiara; Lotay, Vaneet; Launer, Lenore J; Leander, Karin; Lindström, Jaana; Linneberg, Allan; Liu, Yan-Ping; Lobbens, Stéphane; Luben, Robert; Lyssenko, Valeriya; Männistö, Satu; Magnusson, Patrik K; McArdle, Wendy L; Menni, Cristina; Merger, Sigrun; Milani, Lili; Montgomery, Grant W; Morris, Andrew P; Narisu, Narisu; Nelis, Mari; Ong, Ken K; Palotie, Aarno; Pérusse, Louis; Pichler, Irene; Pilia, Maria G; Pouta, Anneli; Rheinberger, Myriam; Ribel-Madsen, Rasmus; Richards, Marcus; Rice, Kenneth M; Rice, Treva K; Rivolta, Carlo; Salomaa, Veikko; Sanders, Alan R; Sarzynski, Mark A; Scholtens, Salome; Scott, Robert A; Scott, William R; Sebert, Sylvain; Sengupta, Sebanti; Sennblad, Bengt; Seufferlein, Thomas; Silveira, Angela; Slagboom, P Eline; Smit, Jan H; Sparsø, Thomas H; Stirrups, Kathleen; Stolk, Ronald P; Stringham, Heather M; Swertz, Morris A; Swift, Amy J; Syvänen, Ann-Christine; Tan, Sian-Tsung

    2015-10-01

    Genome-wide association studies (GWAS) have identified more than 100 genetic variants contributing to BMI, a measure of body size, or waist-to-hip ratio (adjusted for BMI, WHRadjBMI), a measure of body shape. Body size and shape change as people grow older and these changes differ substantially between men and women. To systematically screen for age- and/or sex-specific effects of genetic variants on BMI and WHRadjBMI, we performed meta-analyses of 114 studies (up to 320,485 individuals of European descent) with genome-wide chip and/or Metabochip data by the Genetic Investigation of Anthropometric Traits (GIANT) Consortium. Each study tested the association of up to ~2.8M SNPs with BMI and WHRadjBMI in four strata (men ≤50y, men >50y, women ≤50y, women >50y) and summary statistics were combined in stratum-specific meta-analyses. We then screened for variants that showed age-specific effects (G x AGE), sex-specific effects (G x SEX) or age-specific effects that differed between men and women (G x AGE x SEX). For BMI, we identified 15 loci (11 previously established for main effects, four novel) that showed significant (FDR<5%) age-specific effects, of which 11 had larger effects in younger (<50y) than in older adults (≥50y). No sex-dependent effects were identified for BMI. For WHRadjBMI, we identified 44 loci (27 previously established for main effects, 17 novel) with sex-specific effects, of which 28 showed larger effects in women than in men, five showed larger effects in men than in women, and 11 showed opposite effects between sexes. No age-dependent effects were identified for WHRadjBMI. This is the first genome-wide interaction meta-analysis to report convincing evidence of age-dependent genetic effects on BMI. In addition, we confirm the sex-specificity of genetic effects on WHRadjBMI. These results may provide further insights into the biology that underlies weight change with age or the sexually dimorphism of body shape. PMID:26426971

  18. The Influence of Age and Sex on Genetic Associations with Adult Body Size and Shape: A Large-Scale Genome-Wide Interaction Study

    PubMed Central

    Feitosa, Mary F.; Chu, Su; Czajkowski, Jacek; Esko, Tõnu; Fall, Tove; Kilpeläinen, Tuomas O.; Lu, Yingchang; Mägi, Reedik; Mihailov, Evelin; Pers, Tune H.; Rüeger, Sina; Teumer, Alexander; Ehret, Georg B.; Ferreira, Teresa; Heard-Costa, Nancy L.; Karjalainen, Juha; Lagou, Vasiliki; Mahajan, Anubha; Neinast, Michael D.; Prokopenko, Inga; Simino, Jeannette; Teslovich, Tanya M.; Jansen, Rick; Westra, Harm-Jan; White, Charles C.; Absher, Devin; Ahluwalia, Tarunveer S.; Ahmad, Shafqat; Albrecht, Eva; Alves, Alexessander Couto; Bragg-Gresham, Jennifer L.; de Craen, Anton J. M.; Bis, Joshua C.; Bonnefond, Amélie; Boucher, Gabrielle; Cadby, Gemma; Cheng, Yu-Ching; Chiang, Charleston W. K.; Delgado, Graciela; Demirkan, Ayse; Dueker, Nicole; Eklund, Niina; Eiriksdottir, Gudny; Eriksson, Joel; Feenstra, Bjarke; Fischer, Krista; Frau, Francesca; Galesloot, Tessel E.; Geller, Frank; Goel, Anuj; Gorski, Mathias; Grammer, Tanja B.; Gustafsson, Stefan; Haitjema, Saskia; Hottenga, Jouke-Jan; Huffman, Jennifer E.; Jackson, Anne U.; Jacobs, Kevin B.; Johansson, Åsa; Kaakinen, Marika; Kleber, Marcus E.; Lahti, Jari; Leach, Irene Mateo; Lehne, Benjamin; Liu, Youfang; Lo, Ken Sin; Lorentzon, Mattias; Luan, Jian'an; Madden, Pamela A. F.; Mangino, Massimo; McKnight, Barbara; Medina-Gomez, Carolina; Monda, Keri L.; Montasser, May E.; Müller, Gabriele; Müller-Nurasyid, Martina; Nolte, Ilja M.; Panoutsopoulou, Kalliope; Pascoe, Laura; Paternoster, Lavinia; Rayner, Nigel W.; Renström, Frida; Rizzi, Federica; Rose, Lynda M.; Ryan, Kathy A.; Salo, Perttu; Sanna, Serena; Scharnagl, Hubert; Shi, Jianxin; Smith, Albert Vernon; Southam, Lorraine; Stančáková, Alena; Steinthorsdottir, Valgerdur; Strawbridge, Rona J.; Sung, Yun Ju; Tachmazidou, Ioanna; Tanaka, Toshiko; Thorleifsson, Gudmar; Trompet, Stella; Pervjakova, Natalia; Tyrer, Jonathan P.; Vandenput, Liesbeth; van der Laan, Sander W; van der Velde, Nathalie; van Setten, Jessica; van Vliet-Ostaptchouk, Jana V.; Verweij, Niek; Vlachopoulou, Efthymia; Waite, Lindsay L.; Wang, Sophie R.; Wang, Zhaoming; Wild, Sarah H.; Willenborg, Christina; Wilson, James F.; Wong, Andrew; Yang, Jian; Yengo, Loïc; Yerges-Armstrong, Laura M.; Yu, Lei; Zhang, Weihua; Zhao, Jing Hua; Andersson, Ehm A.; Bakker, Stephan J. L.; Baldassarre, Damiano; Banasik, Karina; Barcella, Matteo; Barlassina, Cristina; Bellis, Claire; Benaglio, Paola; Blangero, John; Blüher, Matthias; Bonnet, Fabrice; Bonnycastle, Lori L.; Boyd, Heather A.; Bruinenberg, Marcel; Buchman, Aron S; Campbell, Harry; Chen, Yii-Der Ida; Chines, Peter S.; Claudi-Boehm, Simone; Cole, John; Collins, Francis S.; de Geus, Eco J. C.; de Groot, Lisette C. P. G. M.; Dimitriou, Maria; Duan, Jubao; Enroth, Stefan; Eury, Elodie; Farmaki, Aliki-Eleni; Forouhi, Nita G.; Friedrich, Nele; Gejman, Pablo V.; Gigante, Bruna; Glorioso, Nicola; Go, Alan S.; Gottesman, Omri; Gräßler, Jürgen; Grallert, Harald; Grarup, Niels; Gu, Yu-Mei; Broer, Linda; Ham, Annelies C.; Hansen, Torben; Harris, Tamara B.; Hartman, Catharina A.; Hassinen, Maija; Hastie, Nicholas; Hattersley, Andrew T.; Heath, Andrew C.; Henders, Anjali K.; Hernandez, Dena; Hillege, Hans; Holmen, Oddgeir; Hovingh, Kees G; Hui, Jennie; Husemoen, Lise L.; Hutri-Kähönen, Nina; Hysi, Pirro G.; Illig, Thomas; De Jager, Philip L.; Jalilzadeh, Shapour; Jørgensen, Torben; Jukema, J. Wouter; Juonala, Markus; Kanoni, Stavroula; Karaleftheri, Maria; Khaw, Kay Tee; Kinnunen, Leena; Kittner, Steven J.; Koenig, Wolfgang; Kolcic, Ivana; Kovacs, Peter; Krarup, Nikolaj T.; Kratzer, Wolfgang; Krüger, Janine; Kuh, Diana; Kumari, Meena; Kyriakou, Theodosios; Langenberg, Claudia; Lannfelt, Lars; Lanzani, Chiara; Lotay, Vaneet; Launer, Lenore J.; Leander, Karin; Lindström, Jaana; Linneberg, Allan; Liu, Yan-Ping; Lobbens, Stéphane; Luben, Robert; Lyssenko, Valeriya; Männistö, Satu; Magnusson, Patrik K.; McArdle, Wendy L.; Menni, Cristina; Merger, Sigrun; Milani, Lili; Montgomery, Grant W.; Morris, Andrew P.; Narisu, Narisu; Nelis, Mari; Ong, Ken K.; Palotie, Aarno; Pérusse, Louis; Pichler, Irene; Pilia, Maria G.; Pouta, Anneli; Rheinberger, Myriam; Ribel-Madsen, Rasmus; Richards, Marcus; Rice, Kenneth M.; Rice, Treva K.; Rivolta, Carlo; Salomaa, Veikko; Sanders, Alan R.; Sarzynski, Mark A.; Scholtens, Salome; Scott, Robert A.; Scott, William R.; Sebert, Sylvain; Sengupta, Sebanti; Sennblad, Bengt; Seufferlein, Thomas; Silveira, Angela; Slagboom, P. Eline; Smit, Jan H.; Sparsø, Thomas H.

    2015-01-01

    Genome-wide association studies (GWAS) have identified more than 100 genetic variants contributing to BMI, a measure of body size, or waist-to-hip ratio (adjusted for BMI, WHRadjBMI), a measure of body shape. Body size and shape change as people grow older and these changes differ substantially between men and women. To systematically screen for age- and/or sex-specific effects of genetic variants on BMI and WHRadjBMI, we performed meta-analyses of 114 studies (up to 320,485 individuals of European descent) with genome-wide chip and/or Metabochip data by the Genetic Investigation of Anthropometric Traits (GIANT) Consortium. Each study tested the association of up to ~2.8M SNPs with BMI and WHRadjBMI in four strata (men ≤50y, men >50y, women ≤50y, women >50y) and summary statistics were combined in stratum-specific meta-analyses. We then screened for variants that showed age-specific effects (G x AGE), sex-specific effects (G x SEX) or age-specific effects that differed between men and women (G x AGE x SEX). For BMI, we identified 15 loci (11 previously established for main effects, four novel) that showed significant (FDR<5%) age-specific effects, of which 11 had larger effects in younger (<50y) than in older adults (≥50y). No sex-dependent effects were identified for BMI. For WHRadjBMI, we identified 44 loci (27 previously established for main effects, 17 novel) with sex-specific effects, of which 28 showed larger effects in women than in men, five showed larger effects in men than in women, and 11 showed opposite effects between sexes. No age-dependent effects were identified for WHRadjBMI. This is the first genome-wide interaction meta-analysis to report convincing evidence of age-dependent genetic effects on BMI. In addition, we confirm the sex-specificity of genetic effects on WHRadjBMI. These results may provide further insights into the biology that underlies weight change with age or the sexually dimorphism of body shape. PMID:26426971

  19. Acoustic Studies of the Large Scale Ocean Circulation

    NASA Technical Reports Server (NTRS)

    Menemenlis, Dimitris

    1999-01-01

    Detailed knowledge of ocean circulation and its transport properties is prerequisite to an understanding of the earth's climate and of important biological and chemical cycles. Results from two recent experiments, THETIS-2 in the Western Mediterranean and ATOC in the North Pacific, illustrate the use of ocean acoustic tomography for studies of the large scale circulation. The attraction of acoustic tomography is its ability to sample and average the large-scale oceanic thermal structure, synoptically, along several sections, and at regular intervals. In both studies, the acoustic data are compared to, and then combined with, general circulation models, meteorological analyses, satellite altimetry, and direct measurements from ships. Both studies provide complete regional descriptions of the time-evolving, three-dimensional, large scale circulation, albeit with large uncertainties. The studies raise serious issues about existing ocean observing capability and provide guidelines for future efforts.

  20. Improving AFLP analysis of large-scale patterns of genetic variation--a case study with the Central African lianas Haumania spp (Marantaceae) showing interspecific gene flow.

    PubMed

    Ley, A C; Hardy, O J

    2013-04-01

    AFLP markers are often used to study patterns of population genetic variation and gene flow because they offer a good coverage of the nuclear genome, but the reliability of AFLP scoring is critical. To assess interspecific gene flow in two African rainforest liana species (Haumania danckelmaniana, H. liebrechtsiana) where previous evidence of chloroplast captures questioned the importance of hybridization and species boundaries, we developed new AFLP markers and a novel approach to select reliable bands from their degree of reproducibility. The latter is based on the estimation of the broad-sense heritability of AFLP phenotypes, an improvement over classical scoring error rates, which showed that the polymorphism of most AFLP bands was affected by a substantial nongenetic component. Therefore, using a quantitative genetics framework, we also modified an existing estimator of pairwise kinship coefficient between individuals correcting for the limited heritability of markers. Bayesian clustering confirms the recognition of the two Haumania species. Nevertheless, the decay of the relatedness between individuals of distinct species with geographic distance demonstrates that hybridization affects the nuclear genome. In conclusion, although we showed that AFLP markers might be substantially affected by nongenetic factors, their analysis using the new methods developed considerably advanced our understanding of the pattern of gene flow in our model species. PMID:23398575

  1. Exploring the Performance of Multifactor Dimensionality Reduction in Large Scale SNP Studies and in the Presence of Genetic Heterogeneity among Epistatic Disease Models

    PubMed Central

    Edwards, Todd L.; Lewis, Kenneth; Velez, Digna R.; Dudek, Scott; Ritchie, Marylyn D.

    2009-01-01

    Background/Aims In genetic studies of complex disease a consideration for the investigator is detection of joint effects. The Multifactor Dimensionality Reduction (MDR) algorithm searches for these effects with an exhaustive approach. Previously unknown aspects of MDR performance were the power to detect interactive effects given large numbers of non-model loci or varying degrees of heterogeneity among multiple epistatic disease models. Methods To address the performance with many non-model loci, datasets of 500 cases and 500 controls with 100 to 10,000 SNPs were simulated for two-locus models, and one hundred 500-case/500-control datasets with 100 and 500 SNPs were simulated for three-locus models. Multiple levels of locus heterogeneity were simulated in several sample sizes. Results These results show MDR is robust to locus heterogeneity when the definition of power is not as conservative as in previous simulation studies where all model loci were required to be found by the method. The results also indicate that MDR performance is related more strongly to broad-sense heritability than sample size and is not greatly affected by non-model loci. Conclusions A study in which a population with high heritability estimates is sampled predisposes the MDR study to success more than a larger ascertainment in a population with smaller estimates. PMID:19077437

  2. FVGWAS: Fast voxelwise genome wide association analysis of large-scale imaging genetic data.

    PubMed

    Huang, Meiyan; Nichols, Thomas; Huang, Chao; Yu, Yang; Lu, Zhaohua; Knickmeyer, Rebecca C; Feng, Qianjin; Zhu, Hongtu

    2015-09-01

    More and more large-scale imaging genetic studies are being widely conducted to collect a rich set of imaging, genetic, and clinical data to detect putative genes for complexly inherited neuropsychiatric and neurodegenerative disorders. Several major big-data challenges arise from testing genome-wide (NC>12 million known variants) associations with signals at millions of locations (NV~10(6)) in the brain from thousands of subjects (n~10(3)). The aim of this paper is to develop a Fast Voxelwise Genome Wide Association analysiS (FVGWAS) framework to efficiently carry out whole-genome analyses of whole-brain data. FVGWAS consists of three components including a heteroscedastic linear model, a global sure independence screening (GSIS) procedure, and a detection procedure based on wild bootstrap methods. Specifically, for standard linear association, the computational complexity is O (nNVNC) for voxelwise genome wide association analysis (VGWAS) method compared with O ((NC+NV)n(2)) for FVGWAS. Simulation studies show that FVGWAS is an efficient method of searching sparse signals in an extremely large search space, while controlling for the family-wise error rate. Finally, we have successfully applied FVGWAS to a large-scale imaging genetic data analysis of ADNI data with 708 subjects, 193,275voxels in RAVENS maps, and 501,584 SNPs, and the total processing time was 203,645s for a single CPU. Our FVGWAS may be a valuable statistical toolbox for large-scale imaging genetic analysis as the field is rapidly advancing with ultra-high-resolution imaging and whole-genome sequencing. PMID:26025292

  3. Lessons from Large-Scale Renewable Energy Integration Studies: Preprint

    SciTech Connect

    Bird, L.; Milligan, M.

    2012-06-01

    In general, large-scale integration studies in Europe and the United States find that high penetrations of renewable generation are technically feasible with operational changes and increased access to transmission. This paper describes other key findings such as the need for fast markets, large balancing areas, system flexibility, and the use of advanced forecasting.

  4. The ENIGMA Consortium: large-scale collaborative analyses of neuroimaging and genetic data.

    PubMed

    Thompson, Paul M; Stein, Jason L; Medland, Sarah E; Hibar, Derrek P; Vasquez, Alejandro Arias; Renteria, Miguel E; Toro, Roberto; Jahanshad, Neda; Schumann, Gunter; Franke, Barbara; Wright, Margaret J; Martin, Nicholas G; Agartz, Ingrid; Alda, Martin; Alhusaini, Saud; Almasy, Laura; Almeida, Jorge; Alpert, Kathryn; Andreasen, Nancy C; Andreassen, Ole A; Apostolova, Liana G; Appel, Katja; Armstrong, Nicola J; Aribisala, Benjamin; Bastin, Mark E; Bauer, Michael; Bearden, Carrie E; Bergmann, Orjan; Binder, Elisabeth B; Blangero, John; Bockholt, Henry J; Bøen, Erlend; Bois, Catherine; Boomsma, Dorret I; Booth, Tom; Bowman, Ian J; Bralten, Janita; Brouwer, Rachel M; Brunner, Han G; Brohawn, David G; Buckner, Randy L; Buitelaar, Jan; Bulayeva, Kazima; Bustillo, Juan R; Calhoun, Vince D; Cannon, Dara M; Cantor, Rita M; Carless, Melanie A; Caseras, Xavier; Cavalleri, Gianpiero L; Chakravarty, M Mallar; Chang, Kiki D; Ching, Christopher R K; Christoforou, Andrea; Cichon, Sven; Clark, Vincent P; Conrod, Patricia; Coppola, Giovanni; Crespo-Facorro, Benedicto; Curran, Joanne E; Czisch, Michael; Deary, Ian J; de Geus, Eco J C; den Braber, Anouk; Delvecchio, Giuseppe; Depondt, Chantal; de Haan, Lieuwe; de Zubicaray, Greig I; Dima, Danai; Dimitrova, Rali; Djurovic, Srdjan; Dong, Hongwei; Donohoe, Gary; Duggirala, Ravindranath; Dyer, Thomas D; Ehrlich, Stefan; Ekman, Carl Johan; Elvsåshagen, Torbjørn; Emsell, Louise; Erk, Susanne; Espeseth, Thomas; Fagerness, Jesen; Fears, Scott; Fedko, Iryna; Fernández, Guillén; Fisher, Simon E; Foroud, Tatiana; Fox, Peter T; Francks, Clyde; Frangou, Sophia; Frey, Eva Maria; Frodl, Thomas; Frouin, Vincent; Garavan, Hugh; Giddaluru, Sudheer; Glahn, David C; Godlewska, Beata; Goldstein, Rita Z; Gollub, Randy L; Grabe, Hans J; Grimm, Oliver; Gruber, Oliver; Guadalupe, Tulio; Gur, Raquel E; Gur, Ruben C; Göring, Harald H H; Hagenaars, Saskia; Hajek, Tomas; Hall, Geoffrey B; Hall, Jeremy; Hardy, John; Hartman, Catharina A; Hass, Johanna; Hatton, Sean N; Haukvik, Unn K; Hegenscheid, Katrin; Heinz, Andreas; Hickie, Ian B; Ho, Beng-Choon; Hoehn, David; Hoekstra, Pieter J; Hollinshead, Marisa; Holmes, Avram J; Homuth, Georg; Hoogman, Martine; Hong, L Elliot; Hosten, Norbert; Hottenga, Jouke-Jan; Hulshoff Pol, Hilleke E; Hwang, Kristy S; Jack, Clifford R; Jenkinson, Mark; Johnston, Caroline; Jönsson, Erik G; Kahn, René S; Kasperaviciute, Dalia; Kelly, Sinead; Kim, Sungeun; Kochunov, Peter; Koenders, Laura; Krämer, Bernd; Kwok, John B J; Lagopoulos, Jim; Laje, Gonzalo; Landen, Mikael; Landman, Bennett A; Lauriello, John; Lawrie, Stephen M; Lee, Phil H; Le Hellard, Stephanie; Lemaître, Herve; Leonardo, Cassandra D; Li, Chiang-Shan; Liberg, Benny; Liewald, David C; Liu, Xinmin; Lopez, Lorna M; Loth, Eva; Lourdusamy, Anbarasu; Luciano, Michelle; Macciardi, Fabio; Machielsen, Marise W J; Macqueen, Glenda M; Malt, Ulrik F; Mandl, René; Manoach, Dara S; Martinot, Jean-Luc; Matarin, Mar; Mather, Karen A; Mattheisen, Manuel; Mattingsdal, Morten; Meyer-Lindenberg, Andreas; McDonald, Colm; McIntosh, Andrew M; McMahon, Francis J; McMahon, Katie L; Meisenzahl, Eva; Melle, Ingrid; Milaneschi, Yuri; Mohnke, Sebastian; Montgomery, Grant W; Morris, Derek W; Moses, Eric K; Mueller, Bryon A; Muñoz Maniega, Susana; Mühleisen, Thomas W; Müller-Myhsok, Bertram; Mwangi, Benson; Nauck, Matthias; Nho, Kwangsik; Nichols, Thomas E; Nilsson, Lars-Göran; Nugent, Allison C; Nyberg, Lars; Olvera, Rene L; Oosterlaan, Jaap; Ophoff, Roel A; Pandolfo, Massimo; Papalampropoulou-Tsiridou, Melina; Papmeyer, Martina; Paus, Tomas; Pausova, Zdenka; Pearlson, Godfrey D; Penninx, Brenda W; Peterson, Charles P; Pfennig, Andrea; Phillips, Mary; Pike, G Bruce; Poline, Jean-Baptiste; Potkin, Steven G; Pütz, Benno; Ramasamy, Adaikalavan; Rasmussen, Jerod; Rietschel, Marcella; Rijpkema, Mark; Risacher, Shannon L; Roffman, Joshua L; Roiz-Santiañez, Roberto; Romanczuk-Seiferth, Nina; Rose, Emma J; Royle, Natalie A; Rujescu, Dan; Ryten, Mina; Sachdev, Perminder S; Salami, Alireza; Satterthwaite, Theodore D; Savitz, Jonathan; Saykin, Andrew J; Scanlon, Cathy; Schmaal, Lianne; Schnack, Hugo G; Schork, Andrew J; Schulz, S Charles; Schür, Remmelt; Seidman, Larry; Shen, Li; Shoemaker, Jody M; Simmons, Andrew; Sisodiya, Sanjay M; Smith, Colin; Smoller, Jordan W; Soares, Jair C; Sponheim, Scott R; Sprooten, Emma; Starr, John M; Steen, Vidar M; Strakowski, Stephen; Strike, Lachlan; Sussmann, Jessika; Sämann, Philipp G; Teumer, Alexander; Toga, Arthur W; Tordesillas-Gutierrez, Diana; Trabzuni, Daniah; Trost, Sarah; Turner, Jessica; Van den Heuvel, Martijn

    2014-06-01

    The Enhancing NeuroImaging Genetics through Meta-Analysis (ENIGMA) Consortium is a collaborative network of researchers working together on a range of large-scale studies that integrate data from 70 institutions worldwide. Organized into Working Groups that tackle questions in neuroscience, genetics, and medicine, ENIGMA studies have analyzed neuroimaging data from over 12,826 subjects. In addition, data from 12,171 individuals were provided by the CHARGE consortium for replication of findings, in a total of 24,997 subjects. By meta-analyzing results from many sites, ENIGMA has detected factors that affect the brain that no individual site could detect on its own, and that require larger numbers of subjects than any individual neuroimaging study has currently collected. ENIGMA's first project was a genome-wide association study identifying common variants in the genome associated with hippocampal volume or intracranial volume. Continuing work is exploring genetic associations with subcortical volumes (ENIGMA2) and white matter microstructure (ENIGMA-DTI). Working groups also focus on understanding how schizophrenia, bipolar illness, major depression and attention deficit/hyperactivity disorder (ADHD) affect the brain. We review the current progress of the ENIGMA Consortium, along with challenges and unexpected discoveries made on the way. PMID:24399358

  5. Large-Scale Genetic Structuring of a Widely Distributed Carnivore - The Eurasian Lynx (Lynx lynx)

    PubMed Central

    Rueness, Eli K.; Naidenko, Sergei; Trosvik, Pål; Stenseth, Nils Chr.

    2014-01-01

    Over the last decades the phylogeography and genetic structure of a multitude of species inhabiting Europe and North America have been described. The flora and fauna of the vast landmasses of north-eastern Eurasia are still largely unexplored in this respect. The Eurasian lynx is a large felid that is relatively abundant over much of the Russian sub-continent and the adjoining countries. Analyzing 148 museum specimens collected throughout its range over the last 150 years we have described the large-scale genetic structuring in this highly mobile species. We have investigated the spatial genetic patterns using mitochondrial DNA sequences (D-loop and cytochrome b) and 11 microsatellite loci, and describe three phylogenetic clades and a clear structuring along an east-west gradient. The most likely scenario is that the contemporary Eurasian lynx populations originated in central Asia and that parts of Europe were inhabited by lynx during the Pleistocene. After the Last Glacial Maximum (LGM) range expansions lead to colonization of north-western Siberia and Scandinavia from the Caucasus and north-eastern Siberia from a refugium further east. No evidence of a Berinigan refugium could be detected in our data. We observed restricted gene flow and suggest that future studies of the Eurasian lynx explore to what extent the contemporary population structure may be explained by ecological variables. PMID:24695745

  6. Large-scale replication and heterogeneity in Parkinson disease genetic loci

    PubMed Central

    Ioannidis, John P.A.; Aasly, Jan O.; Annesi, Grazia; Brice, Alexis; Van Broeckhoven, Christine; Bertram, Lars; Bozi, Maria; Crosiers, David; Clarke, Carl; Facheris, Maurizio; Farrer, Matthew; Garraux, Gaetan; Gispert, Suzana; Auburger, Georg; Vilariño-Güell, Carles; Hadjigeorgiou, Georgios M.; Hicks, Andrew A.; Hattori, Nobutaka; Jeon, Beom; Lesage, Suzanne; Lill, Christina M.; Lin, Juei-Jueng; Lynch, Timothy; Lichtner, Peter; Lang, Anthony E.; Mok, Vincent; Jasinska-Myga, Barbara; Mellick, George D.; Morrison, Karen E.; Opala, Grzegorz; Pramstaller, Peter P.; Pichler, Irene; Park, Sung Sup; Quattrone, Aldo; Rogaeva, Ekaterina; Ross, Owen A.; Stefanis, Leonidas; Stockton, Joanne D.; Satake, Wataru; Silburn, Peter A.; Theuns, Jessie; Tan, Eng-King; Toda, Tatsushi; Tomiyama, Hiroyuki; Uitti, Ryan J.; Wirdefeldt, Karin; Wszolek, Zbigniew; Xiromerisiou, Georgia; Yueh, Kuo-Chu; Zhao, Yi; Gasser, Thomas; Maraganore, Demetrius; Krüger, Rejko

    2012-01-01

    Objective: Eleven genetic loci have reached genome-wide significance in a recent meta-analysis of genome-wide association studies in Parkinson disease (PD) based on populations of Caucasian descent. The extent to which these genetic effects are consistent across different populations is unknown. Methods: Investigators from the Genetic Epidemiology of Parkinson's Disease Consortium were invited to participate in the study. A total of 11 SNPs were genotyped in 8,750 cases and 8,955 controls. Fixed as well as random effects models were used to provide the summary risk estimates for these variants. We evaluated between-study heterogeneity and heterogeneity between populations of different ancestry. Results: In the overall analysis, single nucleotide polymorphisms (SNPs) in 9 loci showed significant associations with protective per-allele odds ratios of 0.78–0.87 (LAMP3, BST1, and MAPT) and susceptibility per-allele odds ratios of 1.14–1.43 (STK39, GAK, SNCA, LRRK2, SYT11, and HIP1R). For 5 of the 9 replicated SNPs there was nominally significant between-site heterogeneity in the effect sizes (I2 estimates ranged from 39% to 48%). Subgroup analysis by ethnicity showed significantly stronger effects for the BST1 (rs11724635) in Asian vs Caucasian populations and similar effects for SNCA, LRRK2, LAMP3, HIP1R, and STK39 in Asian and Caucasian populations, while MAPT rs2942168 and SYT11 rs34372695 were monomorphic in the Asian population, highlighting the role of population-specific heterogeneity in PD. Conclusion: Our study allows insight to understand the distribution of newly identified genetic factors contributing to PD and shows that large-scale evaluation in diverse populations is important to understand the role of population-specific heterogeneity. Neurology® 2012;79:659–667 PMID:22786590

  7. Compromising genetic diversity in the wild: unmonitored large-scale release of plants and animals.

    PubMed

    Laikre, Linda; Schwartz, Michael K; Waples, Robin S; Ryman, Nils

    2010-09-01

    Large-scale exploitation of wild animals and plants through fishing, hunting and logging often depends on augmentation through releases of translocated or captively raised individuals. Such releases are performed worldwide in vast numbers. Augmentation can be demographically and economically beneficial but can also cause four types of adverse genetic change to wild populations: (1) loss of genetic variation, (2) loss of adaptations, (3) change of population composition, and (4) change of population structure. While adverse genetic impacts are recognized and documented in fisheries, little effort is devoted to actually monitoring them. In forestry and wildlife management, genetic risks associated with releases are largely neglected. We outline key features of programs to effectively monitor consequences of such releases on natural populations. PMID:20688414

  8. Prediction of monthly rainfall on homogeneous monsoon regions of India based on large scale circulation patterns using Genetic Programming

    NASA Astrophysics Data System (ADS)

    Kashid, Satishkumar S.; Maity, Rajib

    2012-08-01

    SummaryPrediction of Indian Summer Monsoon Rainfall (ISMR) is of vital importance for Indian economy, and it has been remained a great challenge for hydro-meteorologists due to inherent complexities in the climatic systems. The Large-scale atmospheric circulation patterns from tropical Pacific Ocean (ENSO) and those from tropical Indian Ocean (EQUINOO) are established to influence the Indian Summer Monsoon Rainfall. The information of these two large scale atmospheric circulation patterns in terms of their indices is used to model the complex relationship between Indian Summer Monsoon Rainfall and the ENSO as well as EQUINOO indices. However, extracting the signal from such large-scale indices for modeling such complex systems is significantly difficult. Rainfall predictions have been done for 'All India' as one unit, as well as for five 'homogeneous monsoon regions of India', defined by Indian Institute of Tropical Meteorology. Recent 'Artificial Intelligence' tool 'Genetic Programming' (GP) has been employed for modeling such problem. The Genetic Programming approach is found to capture the complex relationship between the monthly Indian Summer Monsoon Rainfall and large scale atmospheric circulation pattern indices - ENSO and EQUINOO. Research findings of this study indicate that GP-derived monthly rainfall forecasting models, that use large-scale atmospheric circulation information are successful in prediction of All India Summer Monsoon Rainfall with correlation coefficient as good as 0.866, which may appears attractive for such a complex system. A separate analysis is carried out for All India Summer Monsoon rainfall for India as one unit, and five homogeneous monsoon regions, based on ENSO and EQUINOO indices of months of March, April and May only, performed at end of month of May. In this case, All India Summer Monsoon Rainfall could be predicted with 0.70 as correlation coefficient with somewhat lesser Correlation Coefficient (C.C.) values for different

  9. Large-Scale periodic solar velocities: An observational study

    NASA Technical Reports Server (NTRS)

    Dittmer, P. H.

    1977-01-01

    Observations of large-scale solar velocities were made using the mean field telescope and Babcock magnetograph of the Stanford Solar Observatory. Observations were made in the magnetically insensitive ion line at 5124 A, with light from the center (limb) of the disk right (left) circularly polarized, so that the magnetograph measures the difference in wavelength between center and limb. Computer calculations are made of the wavelength difference produced by global pulsations for spherical harmonics up to second order and of the signal produced by displacing the solar image relative to polarizing optics or diffraction grating.

  10. A new way to protect privacy in large-scale genome-wide association studies

    PubMed Central

    Kamm, Liina; Bogdanov, Dan; Laur, Sven; Vilo, Jaak

    2013-01-01

    Motivation: Increased availability of various genotyping techniques has initiated a race for finding genetic markers that can be used in diagnostics and personalized medicine. Although many genetic risk factors are known, key causes of common diseases with complex heritage patterns are still unknown. Identification of such complex traits requires a targeted study over a large collection of data. Ideally, such studies bring together data from many biobanks. However, data aggregation on such a large scale raises many privacy issues. Results: We show how to conduct such studies without violating privacy of individual donors and without leaking the data to third parties. The presented solution has provable security guarantees. Contact: jaak.vilo@ut.ee Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23413435

  11. Evaluation of Penalized and Nonpenalized Methods for Disease Prediction with Large-Scale Genetic Data

    PubMed Central

    Won, Sungho; Choi, Hosik; Park, Suyeon; Lee, Juyoung; Park, Changyi; Kwon, Sunghoon

    2015-01-01

    Owing to recent improvement of genotyping technology, large-scale genetic data can be utilized to identify disease susceptibility loci and this successful finding has substantially improved our understanding of complex diseases. However, in spite of these successes, most of the genetic effects for many complex diseases were found to be very small, which have been a big hurdle to build disease prediction model. Recently, many statistical methods based on penalized regressions have been proposed to tackle the so-called “large P and small N” problem. Penalized regressions including least absolute selection and shrinkage operator (LASSO) and ridge regression limit the space of parameters, and this constraint enables the estimation of effects for very large number of SNPs. Various extensions have been suggested, and, in this report, we compare their accuracy by applying them to several complex diseases. Our results show that penalized regressions are usually robust and provide better accuracy than the existing methods for at least diseases under consideration. PMID:26346893

  12. Caught you: threats to confidentiality due to the public release of large-scale genetic data sets

    PubMed Central

    2010-01-01

    Background Large-scale genetic data sets are frequently shared with other research groups and even released on the Internet to allow for secondary analysis. Study participants are usually not informed about such data sharing because data sets are assumed to be anonymous after stripping off personal identifiers. Discussion The assumption of anonymity of genetic data sets, however, is tenuous because genetic data are intrinsically self-identifying. Two types of re-identification are possible: the "Netflix" type and the "profiling" type. The "Netflix" type needs another small genetic data set, usually with less than 100 SNPs but including a personal identifier. This second data set might originate from another clinical examination, a study of leftover samples or forensic testing. When merged to the primary, unidentified set it will re-identify all samples of that individual. Even with no second data set at hand, a "profiling" strategy can be developed to extract as much information as possible from a sample collection. Starting with the identification of ethnic subgroups along with predictions of body characteristics and diseases, the asthma kids case as a real-life example is used to illustrate that approach. Summary Depending on the degree of supplemental information, there is a good chance that at least a few individuals can be identified from an anonymized data set. Any re-identification, however, may potentially harm study participants because it will release individual genetic disease risks to the public. PMID:21190545

  13. Genetic influences on schizophrenia and subcortical brain volumes: large-scale proof of concept.

    PubMed

    Franke, Barbara; Stein, Jason L; Ripke, Stephan; Anttila, Verneri; Hibar, Derrek P; van Hulzen, Kimm J E; Arias-Vasquez, Alejandro; Smoller, Jordan W; Nichols, Thomas E; Neale, Michael C; McIntosh, Andrew M; Lee, Phil; McMahon, Francis J; Meyer-Lindenberg, Andreas; Mattheisen, Manuel; Andreassen, Ole A; Gruber, Oliver; Sachdev, Perminder S; Roiz-Santiañez, Roberto; Saykin, Andrew J; Ehrlich, Stefan; Mather, Karen A; Turner, Jessica A; Schwarz, Emanuel; Thalamuthu, Anbupalam; Yao, Yin; Ho, Yvonne Y W; Martin, Nicholas G; Wright, Margaret J; O'Donovan, Michael C; Thompson, Paul M; Neale, Benjamin M; Medland, Sarah E; Sullivan, Patrick F

    2016-03-01

    Schizophrenia is a devastating psychiatric illness with high heritability. Brain structure and function differ, on average, between people with schizophrenia and healthy individuals. As common genetic associations are emerging for both schizophrenia and brain imaging phenotypes, we can now use genome-wide data to investigate genetic overlap. Here we integrated results from common variant studies of schizophrenia (33,636 cases, 43,008 controls) and volumes of several (mainly subcortical) brain structures (11,840 subjects). We did not find evidence of genetic overlap between schizophrenia risk and subcortical volume measures either at the level of common variant genetic architecture or for single genetic markers. These results provide a proof of concept (albeit based on a limited set of structural brain measures) and define a roadmap for future studies investigating the genetic covariance between structural or functional brain phenotypes and risk for psychiatric disorders. PMID:26854805

  14. Evaluating Large-Scale Studies to Accurately Appraise Children's Performance

    ERIC Educational Resources Information Center

    Ernest, James M.

    2012-01-01

    Educational policy is often developed using a top-down approach. Recently, there has been a concerted shift in policy for educators to develop programs and research proposals that evolve from "scientific" studies and focus less on their intuition, aided by professional wisdom. This article analyzes several national and international educational…

  15. Studies relating to temperature control of a large scale telescope

    NASA Technical Reports Server (NTRS)

    Katzoff, S.

    1973-01-01

    Analytical methods are developed for estimating the circumferential and longitudinal temperature distributions in a large space telescope, idealized as a simple insulated tube with a flat mirror across one end. The effects of wall conduction, multilayer insulation, thermal coatings, heat pipes, and heated collars are analyzed, with numerical examples. For most of the study, the only thermal input to the tube was assumed to be from steady solar irradiation from one side, as in a geosynchronous orbit. Unsteady heat flow through the insulation, as in alternating sunlight and shadow of a low orbit, is briefly discussed.

  16. The Study of Clusters of Galaxies and Large Scale Structures

    NASA Technical Reports Server (NTRS)

    1998-01-01

    Many research projects have been initiated and completed under support of this program. The results are summarized below. The work on the ROSAT Deep Survey has been successfully completed. A number of interesting results have been established within this joint MPE, Cal Tech, JHU, ST ScI, ESO collaboration. First, a very large fraction, 70-80 percent, of the X-ray background has been directly resolved into point sources. We have derived a new log N-log S for X-ray sources and have measured a source density of 970 sources per square degree at a limiting flux level. Care was taken in these studies to accurately model and measure the effects of sources confusion. This was possible because of our observing strategy which included both deep PSPC and HRI observations. No evidence of a population of narrow emission line galaxies has been established but some evidence for the evolution of low luminosity AGN (Seyfert galaxies) has been reported. The work on the ROSAT All Sky Survey Northern Cluster Survey has been substantially concluded but the publication of the list has been held up by the need to analyze newly re-calibrated data. This should result in publication over the next year. During the past year we have submitted a paper to the Astrophysical Journal which utilized a sample of clusters originally selected from the ROSAT All-sky survey at redshifts greater than 0.3. This sample was studied with ASCA to determine temperature and luminosity.

  17. A large scale flume for hydro-environmental studies

    NASA Astrophysics Data System (ADS)

    Gomez, Jose Alfonso; Giráldez, Juan Vicente; Castro-Orgaz, Oscar; Casalí, Javier; Hermosín, Maria del Carmen; Mateos, Luciano

    2013-04-01

    The understanding of key hydrologic processes such as, water erosion, rill network development or agrochemical transport, requires controlled experiments at the appropriate scale. This is the reason for experimentation at flume scale in hydro-environmental research, used for many decades in this field. This communication presents a research infrastructure, recently completed in its first stage, consisting of a large flume for studying soil water erosion, sediment transport, and environmental processes such as the transport of different substances (salts, fertilizers, herbicides, carbon, …) rather dissolved or absorbed with the sediment. It is located at the Institute for Sustainable Agriculture (CSIC) in Córdoba, Spain. The flume is 0.6 m deep, 12 m long, and 6 m wide. It may be divided longitudinally into three channels (6 m long, 1 m wide). The slope of the flume can be regulated from 0 % to 20 %. The device allows studying free surface flows over movable beds with different conditions of sediment transport by supplying clear or sediment-laden water from its head system. The head system consists of three triangular weirs for accurate measurement of water flow, three stilling tanks at the entrance of the flume, and three vibratory hoppers for applying sediments at pre-set rates. The water can be re-circulated, the maximum inflow is then about 30 l s-1, or evacuated, then the inflow is limited to about 20 l s-1. The infrastructure is within a shelter with an area of 400 m2 and height 8.7 m. The area of the shelter allows in-door mechanical preparation of soil and sediments. The height of the shelter will allow the installation of the rainfall simulator and a light rail crane in a second stage, not started yet. Several experiments have been planned at IAS-CSIC already, particularly investigation of the water erosion and sediment transport processes in concentrated flows under different soil conditions, as well as hydrodynamics aspects of suspended and bed

  18. The Study of Clusters of Galaxies and Large Scale Structures

    NASA Technical Reports Server (NTRS)

    1998-01-01

    The work on the ROSAT Deep Survey has been successfully completed. A number of interesting results have been established within this joint MPE, Cal Tech, JHU, ST Scl, ESO collaboration. First, a very large fraction, 70-80 percent, of the X-ray background has been directly resolved into point sources. We have derived a new log N-log S for X- ray sources and have measured a source density of 970 sources per square degree at a limiting flux level of 10(exp -15)/erg s sq cm (0.5-2.0 keV). Care was taken in these studies to accurately model and measure the effects of sources confusion. This was possible because of our observing strategy which included both deep PSPC and HRI observations. In the last year we initiated work in the design and development of the Next Generation Space Telescope.

  19. Discovery and mapping of a new expressed sequence tag-single nucleotide polymorphism and simple sequence repeat panel for large-scale genetic studies and breeding of Theobroma cacao L.

    PubMed Central

    Allegre, Mathilde; Argout, Xavier; Boccara, Michel; Fouet, Olivier; Roguet, Yolande; Bérard, Aurélie; Thévenin, Jean Marc; Chauveau, Aurélie; Rivallan, Ronan; Clement, Didier; Courtois, Brigitte; Gramacho, Karina; Boland-Augé, Anne; Tahi, Mathias; Umaharan, Pathmanathan; Brunel, Dominique; Lanaud, Claire

    2012-01-01

    Theobroma cacao is an economically important tree of several tropical countries. Its genetic improvement is essential to provide protection against major diseases and improve chocolate quality. We discovered and mapped new expressed sequence tag-single nucleotide polymorphism (EST-SNP) and simple sequence repeat (SSR) markers and constructed a high-density genetic map. By screening 149 650 ESTs, 5246 SNPs were detected in silico, of which 1536 corresponded to genes with a putative function, while 851 had a clear polymorphic pattern across a collection of genetic resources. In addition, 409 new SSR markers were detected on the Criollo genome. Lastly, 681 new EST-SNPs and 163 new SSRs were added to the pre-existing 418 co-dominant markers to construct a large consensus genetic map. This high-density map and the set of new genetic markers identified in this study are a milestone in cocoa genomics and for marker-assisted breeding. The data are available at http://tropgenedb.cirad.fr. PMID:22210604

  20. Ethnography and Case Study Methodology: An Approach to Large-Scale Policy Studies of Federal Programs.

    ERIC Educational Resources Information Center

    Deslonde, James L.

    Studies of the use of ethnography as an evaluation tool in large-scale contract research studies were reviewed before data collection and design decisions were finalized in response to a Request for Proposal (RFP). Five tasks had to be accomplished before data collection could begin: study sites were selected, a system for data collection was…

  1. A large-scale genetic screen for mutants with altered salicylic acid accumulation in Arabidopsis

    PubMed Central

    Ding, Yezhang; Shaholli, Danjela; Mou, Zhonglin

    2014-01-01

    Salicylic acid (SA) is a key defense signal molecule against biotrophic and hemibiotrophic pathogens in plants, but how SA is synthesized in plant cells still remains elusive. Identification of new components involved in pathogen-induced SA accumulation would help address this question. To this end, we performed a large-scale genetic screen for mutants with altered SA accumulation during pathogen infection in Arabidopsis using a bacterial biosensor Acinetobacter sp. ADPWH_lux-based SA quantification method. A total of 35,000 M2 plants in the npr1-3 mutant background have been individually analyzed for the bacterial pathogen Pseudomonas syringae pv. maculicola (Psm) ES4326-induced SA accumulation. Among the mutants isolated, 19 had SA levels lower than npr1 (sln) and two exhibited increased SA accumulation in npr1 (isn). Complementation tests revealed that seven of the sln mutants are new alleles of eds5/sid1, two are sid2/eds16 alleles, one is allelic to pad4, and the remaining seven sln and two isn mutants are new non-allelic SA accumulation mutants. Interestingly, a large group of mutants (in the npr1-3 background), in which Psm ES4326-induced SA levels were similar to those in the wild-type Columbia plants, were identified, suggesting that the signaling network fine-tuning pathogen-induced SA accumulation is complex. We further characterized the sln1 single mutant and found that Psm ES4326-induced defense responses were compromised in this mutant. These defense response defects could be rescued by exogenous SA, suggesting that SLN1 functions upstream of SA. The sln1 mutation was mapped to a region on the north arm of chromosome I, which contains no known genes regulating pathogen-induced SA accumulation, indicating that SLN1 likely encodes a new regulator of SA biosynthesis. Thus, the new sln and isn mutants identified in this genetic screen are valuable for dissecting the molecular mechanisms underlying pathogen-induced SA accumulation in plants. PMID:25610446

  2. Effects of Large-Scale Releases on the Genetic Structure of Red Sea Bream (Pagrus major, Temminck et Schlegel) Populations in Japan

    PubMed Central

    Blanco Gonzalez, Enrique; Aritaki, Masato; Knutsen, Halvor; Taniguchi, Nobuhiko

    2015-01-01

    Large-scale hatchery releases are carried out for many marine fish species worldwide; nevertheless, the long-term effects of this practice on the genetic structure of natural populations remains unclear. The lack of knowledge is especially evident when independent stock enhancement programs are conducted simultaneously on the same species at different geographical locations, as occurs with red sea bream (Pagrus major, Temminck et Schlegel) in Japan. In this study, we examined the putative effects of intensive offspring releases on the genetic structure of red sea bream populations along the Japanese archipelago by genotyping 848 fish at fifteen microsatellite loci. Our results suggests weak but consistent patterns of genetic divergence (FST = 0.002, p < 0.001). Red sea bream in Japan appeared spatially structured with several patches of distinct allelic composition, which corresponded to areas receiving an important influx of fish of hatchery origin, either released intentionally or from unintentional escapees from aquaculture operations. In addition to impacts upon local populations inhabiting semi-enclosed embayments, large-scale releases (either intentionally or from unintentional escapes) appeared also to have perturbed genetic structure in open areas. Hence, results of the present study suggest that independent large-scale marine stock enhancement programs conducted simultaneously on one species at different geographical locations may compromise native genetic structure and lead to patchy patterns in population genetic structure. PMID:25993089

  3. Large-scale natural disturbance alters genetic population structure of the sailfin molly, Poecilia latipinna.

    PubMed

    Apodaca, Joseph J; Trexler, Joel C; Jue, Nathaniel K; Schrader, Matthew; Travis, Joseph

    2013-02-01

    Many inferences about contemporary rates of gene flow are based on the assumption that the observed genetic structure among populations is stable. Recent studies have uncovered several cases in which this assumption is tenuous. Most of those studies have focused on the effects that regular environmental fluctuations can have on genetic structure and gene flow patterns. Occasional catastrophic disturbances could also alter either the distribution of habitat or the spatial distribution of organisms in a way that affects population structure. However, evidence of such effects is sparse in the literature because it is difficult to obtain. Hurricanes, in particular, have the potential to exert dramatic effects on population structure of organisms found on islands or coral reefs or in near shore and coastal habitats. Here we draw on a historic genetic data set and new data to suggest that the genetic structure of sailfin molly (Poecilia latipinna) populations in north Florida was altered dramatically by an unusually large and uncommon type of storm surge associated with Hurricane Dennis in 2005. We compare the spatial pattern of genetic variation in these populations after Hurricane Dennis to the patterns described in an earlier study in this same area. We use comparable genetic data from another region of Florida, collected in the same two periods, to estimate the amount of change expected from typical temporal variation in population structure. The comparative natural history of sailfin mollies in these two regions indicates that the change in population structure produced by the storm surge is not the result of many local extinctions with recolonization from a few refugia but emerged from a pattern of mixing and redistribution. PMID:23348779

  4. Large-scale discovery of novel genetic causes of developmental disorders.

    PubMed

    2015-03-12

    Despite three decades of successful, predominantly phenotype-driven discovery of the genetic causes of monogenic disorders, up to half of children with severe developmental disorders of probable genetic origin remain without a genetic diagnosis. Particularly challenging are those disorders rare enough to have eluded recognition as a discrete clinical entity, those with highly variable clinical manifestations, and those that are difficult to distinguish from other, very similar, disorders. Here we demonstrate the power of using an unbiased genotype-driven approach to identify subsets of patients with similar disorders. By studying 1,133 children with severe, undiagnosed developmental disorders, and their parents, using a combination of exome sequencing and array-based detection of chromosomal rearrangements, we discovered 12 novel genes associated with developmental disorders. These newly implicated genes increase by 10% (from 28% to 31%) the proportion of children that could be diagnosed. Clustering of missense mutations in six of these newly implicated genes suggests that normal development is being perturbed by an activating or dominant-negative mechanism. Our findings demonstrate the value of adopting a comprehensive strategy, both genome-wide and nationwide, to elucidate the underlying causes of rare genetic disorders. PMID:25533962

  5. Genetic effects of a large-scale Spartina alterniflora (smooth cordgrass) dieback and recovery in the northern Gulf of Mexico

    USGS Publications Warehouse

    Edwards, K.R.; Travis, S.E.; Proffitt, C.E.

    2005-01-01

    A large-scale dieback event struck marshes along the northwestern Gulf of Mexico coast during summer 2000, in apparent response to a prolonged and severe drought. Along the Louisiana coast, large areas of the dominant marsh species, Spartina alterniflora, turned brown, followed by death of at least the aboveground structures or entire plant mortality. Key ecological and genetic measures were studied in a dieback-affected marsh in southwest Louisiana (C83 marsh, Sabine National Wildlife Refuge), for which existed predieback ecologic and genetic datasets. Effects on genetic diversity only were studied in a second set of sites in southeastern Louisiana (near Bay Junop), where the dieback was more widespread. We hypothesized that stem density, live aboveground biomass, and genetic diversity would be significantly reduced compared to predieback conditions and to nearby unaffected marshes. Stem densities and biomass levels approached predieback conditions 14 months after first observance of the dieback in the Sabine marsh and were similar to or exceeded the same measures for a nearby unaffected marsh. DNA extracted from leaf samples in the Sabine and Bay Junop sites was used to construct genotype profiles using AFLPs and analyzed using the complement of Simpson's Index (1-D), the richness measure G/N, average heterozygosity ???H???, and the estimated proportion of polymorphic genes ???P???. Genetic diversity was relatively unaffected by the dieback at either the Sabine or Bay Junop sites. Evidence from field observations and the results of the genetic analyses suggest that seedling recruitment is an important factor in the recovery of both the Bay Junop and C83 sites, although re-growth from surviving below-ground rhizomes appeared to dominate recovery at the latter site. Survival of below-ground structures, leading to the rapid recovery observed, indicates a high level of resilience of the Sabine marsh to drought-induced stress. Still, the genetic diversity of S

  6. Genetic diversity and molecular phylogeography of Chinese domestic goats by large-scale mitochondrial DNA analysis.

    PubMed

    Zhao, Yongju; Zhao, Runze; Zhao, Zhongquan; Xu, Huizhong; Zhao, Erhu; Zhang, Jiahua

    2014-06-01

    Mitochondrial DNA (mtDNA) D-loop sequences of 666 individuals (including 109 new individuals, 557 individuals retrieved from GenBank) from 33 Chinese domestic goat breeds throughout China were used to investigate their mtDNA variability and molecular phylogeography. The results showed that all goat breeds in this study proved to be extremely diverse, and the average haplotype diversity and nucleotide diversity were 0.990 ± 0.001 and 0.032 ± 0.001, respectively. The 666 sequences gave 326 different haplotypes. Phylogenetic analyses revealed that there were 4 mtDNA haplogroups identified in Chinese domestic goats, in which haplogroup A was predominant and widely distributed. Our finding was consistent with archaeological data and other genetic diversity studies. Amova analysis showed there was significant geographical structuring. Almost 84.31% of genetic variation was included in the within-breed variance component and only 4.69% was observed among the geographic distributions. This genetic diversity results further supported the previous view of multiple maternal origins of Chinese domestic goats, and the results on the phylogenetic relationship contributed to a better understanding of the history of goat domestication and modern production of domestic goats. PMID:24532161

  7. Systematic large-scale study of the inheritance mode of Mendelian disorders provides new insight into human diseasome

    PubMed Central

    Hao, Dapeng; Wang, Guangyu; Yin, Zuojing; Li, Chuanxing; Cui, Yan; Zhou, Meng

    2014-01-01

    One important piece of information about the human Mendelian disorders is the mode of inheritance. Recent studies of human genetic diseases on a large scale have provided many novel insights into the underlying molecular mechanisms. However, most successful analyses ignored the mode of inheritance of diseases, which severely limits our understanding of human disease mechanisms relating to the mode of inheritance at the large scale. Therefore, we here conducted a systematic large-scale study of the inheritance mode of Mendelian disorders, to bring new insight into human diseases. Our analyses include the comparison between dominant and recessive disease genes on both genomic and proteomic characteristics, Mendelian mutations, protein network properties and disease connections on both the genetic and the population levels. We found that dominant disease genes are more functionally central, topological central and more sensitive to disease outcome. On the basis of these findings, we suggested that dominant diseases should have higher genetic heterogeneity and should have more comprehensive connections with each other compared with recessive diseases, a prediction we confirm by disease network and disease comorbidity. PMID:24448549

  8. CYP1A1, GSTM1 and GSTT1 genetic polymorphisms and gastric cancer risk among Japanese: A nested case-control study within a large-scale population-based prospective study.

    PubMed

    Hidaka, Akihisa; Sasazuki, Shizuka; Matsuo, Keitaro; Ito, Hidemi; Charvat, Hadrien; Sawada, Norie; Shimazu, Taichi; Yamaji, Taiki; Iwasaki, Motoki; Inoue, Manami; Tsugane, Shoichiro

    2016-08-15

    Cytochrome P450 (CYP) 1A1 and glutathione S-transferases (GST) M1 and T1 are major enzymes in the carcinogen metabolizing pathway. We examined the association between single nucleotide polymorphisms (SNPs) of CYP1A1 (rs4646421, rs4646422 and rs1048943), GSTM1 and GSTT1 and gastric cancer risk in Japan. This is a nested case-control study (457 cases and 457 matched controls) of our population-based cohort involving 36,745 subjects who answered a baseline questionnaire and supplied blood samples. The odds ratios (ORs) and their corresponding 95% confidence intervals (CIs) were calculated using conditional logistic regression models. We found that CYP1A1 (rs4646422) variant allele was associated with a statistically significant increased risk of gastric cancer compared with the homozygous wild-type genotype (OR = 1.65; 95% CI = 1.17-2.32). GSTM1 null, GSTT1 null and GSTM1/T1 both or either null genotypes were associated with increased risk, but not statistically significantly. Combination of the CYP1A1 (rs4646422) variant allele and GSTM1/T1 both or either null genotypes was associated with a statistically significant increased risk compared with the combination of the CYP1A1 homozygous wild-type genotype and the GSTM1/T1 both active genotypes. In addition, compared with CYP1A1 (rs4646422) homozygous wild-type genotypes in those who were never-smokers, CYP1A1 variant alleles in those who smoked ≥30 pack-years were associated with an increased risk; neither gene-gene nor gene-environment interactions were significant. The CYP1A1 (rs4646422) polymorphism might be involved in gastric carcinogenesis among the Japanese population. PMID:27062139

  9. Large Scale Interventions: An Historical Case Study of Florida Schoolyear, 2000.

    ERIC Educational Resources Information Center

    Russo-Converso, Judith A.

    This research study focuses an historical case study on a large-scale intervention called Florida SchoolYear (SY2000), which was a visionary example of how the state of Florida tried to design and develop a means for delivering quality education. By studying the Florida SY2000 Initiative, this research study examined issue-oriented questions…

  10. Genetically encoded voltage indicators for large scale cortical imaging come of age.

    PubMed

    Knöpfel, Thomas; Gallero-Salas, Yasir; Song, Chenchen

    2015-08-01

    Electrical signals are fundamental to cellular sensing, communication and motility. In the nervous system, information is represented as receptor, synaptic and action potentials. Understanding how brain functions emerge from these electrical signals is one of the ultimate challenges in neuroscience and requires a methodology to monitor membrane voltage transients from large numbers of cells at high spatio-temporal resolution. Optical voltage imaging holds longstanding promises to achieve this, and has gained a fresh powerful momentum with the development of genetically encoded voltage indicators (GEVIs). With a focus on neuroimaging studies on intact mouse brains, we highlight recent advances in this field. PMID:26115448

  11. Rare Variants Association Analysis in Large-Scale Sequencing Studies at the Single Locus Level

    PubMed Central

    Lu, Wenbin; Tzeng, Jung-Ying

    2016-01-01

    Genetic association analyses of rare variants in next-generation sequencing (NGS) studies are fundamentally challenging due to the presence of a very large number of candidate variants at extremely low minor allele frequencies. Recent developments often focus on pooling multiple variants to provide association analysis at the gene instead of the locus level. Nonetheless, pinpointing individual variants is a critical goal for genomic researches as such information can facilitate the precise delineation of molecular mechanisms and functions of genetic factors on diseases. Due to the extreme rarity of mutations and high-dimensionality, significances of causal variants cannot easily stand out from those of noncausal ones. Consequently, standard false-positive control procedures, such as the Bonferroni and false discovery rate (FDR), are often impractical to apply, as a majority of the causal variants can only be identified along with a few but unknown number of noncausal variants. To provide informative analysis of individual variants in large-scale sequencing studies, we propose the Adaptive False-Negative Control (AFNC) procedure that can include a large proportion of causal variants with high confidence by introducing a novel statistical inquiry to determine those variants that can be confidently dispatched as noncausal. The AFNC provides a general framework that can accommodate for a variety of models and significance tests. The procedure is computationally efficient and can adapt to the underlying proportion of causal variants and quality of significance rankings. Extensive simulation studies across a plethora of scenarios demonstrate that the AFNC is advantageous for identifying individual rare variants, whereas the Bonferroni and FDR are exceedingly over-conservative for rare variants association studies. In the analyses of the CoLaus dataset, AFNC has identified individual variants most responsible for gene-level significances. Moreover, single-variant results

  12. Large-scale genetic survey provides insights into the captive management and reintroduction of giant pandas.

    PubMed

    Shan, Lei; Hu, Yibo; Zhu, Lifeng; Yan, Li; Wang, Chengdong; Li, Desheng; Jin, Xuelin; Zhang, Chenglin; Wei, Fuwen

    2014-10-01

    The captive genetic management of threatened species strives to preserve genetic diversity and avoid inbreeding to ensure populations remain available, healthy, and viable for future reintroduction. Determining and responding to the genetic status of captive populations is therefore paramount to these programs. Here, we genotyped 19 microsatellite loci for 240 captive giant pandas (Ailuropoda melanoleuca) (∼64% of the captive population) from four breeding centers, Wolong (WL), Chengdu (CD), Louguantai (LGT), and Beijing (BJ), and analyzed 655 bp of mitochondrial DNA control region sequence for 220 of these animals. High levels of genetic diversity and low levels of inbreeding were estimated in the breeding centers, indicating that the captive population is genetically healthy and deliberate further genetic input from wild animals is unnecessary. However, the LGT population faces a higher risk of inbreeding, and significant genetic structure was detected among breeding centers, with LGT-CD and WL-BJ clustering separately. Based on these findings, we highlight that: 1) the LGT population should be managed as an independent captive population to resemble the genetic distinctness of their Qinling Mountain origins; 2) exchange between CD and WL should be encouraged because of similar wild founder sources; 3) the selection of captive individuals for reintroduction should consider their geographic origin, genetic background, and genetic contribution to wild populations; and 4) combining our molecular genetic data with existing pedigree data will better guide giant panda breeding and further reduce inbreeding into the future. PMID:25015646

  13. A Large-Scale Study of the Characteristics of Asperger Syndrome

    ERIC Educational Resources Information Center

    Myles, Brenda Smith; Lee, Hyo Jung; Smith, Sheila M.; Tien, Kai-Chien; Chou, Yu-Chi; Swanson, Terri Cooper; Hudson, Jill

    2007-01-01

    This article presents the results of a large-scale study of the characteristics of 156 individuals with Asperger Syndrome (AS) ages 12 to 18. Specifically, cognitive (intellectual, empathizing, systemizing), adaptive behavior, behavior, temperament, and sensory profiles of study participants are overviewed. These characteristics are discussed as…

  14. A Fundamental Study for Efficient Implementaion of Online Collaborative Activities in Large-Scale Classes

    ERIC Educational Resources Information Center

    Matsuba, Ryuichi; Suzuki, Yusei; Kubota, Shin-Ichiro; Miyazaki, Makoto

    2015-01-01

    We study tactics for writing skills development through cross-disciplinary learning in online large-scale classes, and particularly are interested in implementation of online collaborative activities such as peer reviewing of writing. The goal of our study is to carry out collaborative works efficiently via online effectively in large-scale…

  15. Nurture Groups: A Large-Scale, Controlled Study of Effects on Development and Academic Attainment

    ERIC Educational Resources Information Center

    Reynolds, Sue; MacKay, Tommy; Kearney, Maura

    2009-01-01

    Nurture groups have contributed to inclusive practices in primary schools in the UK for some time now and have frequently been the subject of articles in this journal. This large-scale, controlled study of nurture groups across 32 schools in the City of Glasgow provides further evidence for their effectiveness in addressing the emotional…

  16. Soil physical properties of agricultural systems in a large-scale study

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A large-scale field study was performed to determine the effects of agricultural management systems on soil physical properties, including their spatial and temporal variations. Replicates were established in 1998 at the Center for Environmental Farming Systems, Goldsboro, North Carolina; replicates...

  17. LARGE SCALE CARCINOGEN DOSE RESPONSE STUDIES WITH JAPANESE MEDAKA (ORYZIAS LATIPES)

    EPA Science Inventory

    To investigate the responses to low carcinogen doses in animal models, large sample sizes are needed and it is an advantage if the model has a low spontaneous tumor rate. Three large scale dose response studies were conducted using Japanese medaka and the carcinogen diethylnitros...

  18. Using DNA barcoding and phylogenetics to identify Antarctic invertebrate larvae: Lessons from a large scale study.

    PubMed

    Heimeier, Dorothea; Lavery, Shane; Sewell, Mary A

    2010-01-01

    Ecological studies of the diversity and distribution of marine planktonic larvae are increasingly depending on molecular methods for accurate taxonomic identification. The greater coverage of reference marine species on genetic databases such as GenBank and BoLD (Barcoding of Life Data Systems; www.boldystems.org); together with the decreasing costs for DNA sequencing have made large scale larval identification studies using molecular methods more feasible. Here, we present the development and implementation of a practical molecular approach to identify over 2000 individual marine invertebrate larvae that were collected in the Ross Sea, Antarctica, during the austral summer over five years (2002-2007) as part of the LGP (Latitudinal Gradient Project). Larvae for molecular ID were morphologically identified to belong to the Phyla Mollusca, Echinodermata, Nemertea and Annelida (Class Polychaeta), but also included unidentified early developmental stages which could not be assigned a specific taxon (e.g., eggs, blastulae). The use of a 100μm mesh plankton net makes this one of the first larval identification studies to simultaneously consider both embryos and larvae. Molecular identification methods included amplification of up to three molecular loci for each specimen, a pre-identification step using BLAST with GenBank, phylogenetic reconstructions and cross-validation of assigned Molecular Operational Taxonomic Units (MOTUs). This combined approach of morphological and molecular methods assigned about 700 individuals to 53 MOTUs, which were identified to the lowest possible taxonomic level. During the course of this long-term study we identified several procedural difficulties, including issues with the collection of larvae, locus amplification, contamination, assignment and validation of MOTUs. The practical guidelines that we describe here should greatly assist other researchers to conduct reliable molecular identification studies of larvae in the future. PMID

  19. Large-scale spatial and temporal genetic diversity of feline calicivirus.

    PubMed

    Coyne, Karen P; Christley, Rob M; Pybus, Oliver G; Dawson, Susan; Gaskell, Rosalind M; Radford, Alan D

    2012-10-01

    Feline calicivirus (FCV) is an important pathogen of domestic cats and a frequently used model of human caliciviruses. Here we use an epidemiologically rigorous sampling framework to describe for the first time the phylodynamics of a calicivirus at regional and national scales. A large number of FCV strains cocirculated in the United Kingdom at the national and community levels, with no strain comprising more than 5% and 14% of these populations, respectively. The majority of strains exhibited a relatively restricted geographical range, with only two strains (one field virus and one vaccine virus) spreading further than 100 km. None of the field strains were identified outside the United Kingdom. Temporally, while some strains persisted locally for the majority of the study, others may have become locally extinct. Evolutionary analysis revealed a radial phylogeny with little bootstrap support for nodes above the strain level. In most cases, spatially and temporally diverse strains intermingled in the phylogeny. Together, these data suggest that current FCV evolution is not associated with selective competition among strains. Rather, the genetic and antigenic landscape in each geographical location is highly complex, with many strains cocirculating. These variants likely exist at the community level by a combination of de novo evolution and occasional gene flow from the wider national population. This complexity provides a benchmark, for the first time, against which vaccine cross-protection at both local and national levels can be judged. PMID:22855496

  20. Large-scale risk prediction applied to Genetic Analysis Workshop 17 mini-exome sequence data

    PubMed Central

    2011-01-01

    We consider the application of Efron’s empirical Bayes classification method to risk prediction in a genome-wide association study using the Genetic Analysis Workshop 17 (GAW17) data. A major advantage of using this method is that the effect size distribution for the set of possible features is empirically estimated and that all subsequent parameter estimation and risk prediction is guided by this distribution. Here, we generalize Efron’s method to allow for some of the peculiarities of the GAW17 data. In particular, we introduce two ways to extend Efron’s model: a weighted empirical Bayes model and a joint covariance model that allows the model to properly incorporate the annotation information of single-nucleotide polymorphisms (SNPs). In the course of our analysis, we examine several aspects of the possible simulation model, including the identity of the most important genes, the differing effects of synonymous and nonsynonymous SNPs, and the relative roles of covariates and genes in conferring disease risk. Finally, we compare the three methods to each other and to other classifiers (random forest and neural network). PMID:22373389

  1. A large-scale genetic screen in Arabidopsis to identify genes involved in pollen exine production.

    PubMed

    Dobritsa, Anna A; Geanconteri, Aliza; Shrestha, Jay; Carlson, Ann; Kooyers, Nicholas; Coerper, Daniel; Urbanczyk-Wochniak, Ewa; Bench, Bennie J; Sumner, Lloyd W; Swanson, Robert; Preuss, Daphne

    2011-10-01

    Exine, the outer plant pollen wall, has elaborate species-specific patterns, provides a protective barrier for male gametophytes, and serves as a mediator of strong and species-specific pollen-stigma adhesion. Exine is made of sporopollenin, a material remarkable for its strength, elasticity, and chemical durability. The chemical nature of sporopollenin, as well as the developmental mechanisms that govern its assembly into diverse patterns in different species, are poorly understood. Here, we describe a simple yet effective genetic screen in Arabidopsis (Arabidopsis thaliana) that was undertaken to advance our understanding of sporopollenin synthesis and exine assembly. This screen led to the recovery of mutants with a variety of defects in exine structure, including multiple mutants with novel phenotypes. Fifty-six mutants were selected for further characterization and are reported here. In 14 cases, we have mapped defects to specific genes, including four with previously demonstrated or suggested roles in exine development (MALE STERILITY2, CYP703A2, ANTHER-SPECIFIC PROTEIN6, TETRAKETIDE α-PYRONE REDUCTASE/DIHYDROFLAVONOL-4-REDUCTASE-LIKE1), and a number of genes that have not been implicated in exine production prior to this screen (among them, fatty acid ω-hydroxylase CYP704B1, putative glycosyl transferases At1g27600 and At1g33430, 4-coumarate-coenzyme A ligase 4CL3, polygalacturonase QUARTET3, novel gene At5g58100, and nucleotide-sugar transporter At5g65000). Our study illustrates that morphological screens of pollen can be extremely fruitful in identifying previously unknown exine genes and lays the foundation for biochemical, developmental, and evolutionary studies of exine production. PMID:21849515

  2. A large scale analysis of genetic variants within putative miRNA binding sites in prostate cancer

    PubMed Central

    Stegeman, Shane; Amankwah, Ernest; Klein, Kerenaftali; O’Mara, Tracy A.; Kim, Donghwa; Lin, Hui-Yi; Permuth-Wey, Jennifer; Sellers, Thomas A.; Srinivasan, Srilakshmi; Eeles, Rosalind; Easton, Doug; Kote-Jarai, Zsofia; Olama, Ali Amin Al; Benlloch, Sara; Muir, Kenneth; Giles, Graham G.; Wiklund, Fredrik; Gronberg, Henrik; Haiman, Christopher A.; Schleutker, Johanna; Nordestgaard, Børge G.; Travis, Ruth C.; Neal, David; Pharoah, Paul; Khaw, Kay-Tee; Stanford, Janet L.; Blot, William J.; Thibodeau, Stephen; Maier, Christiane; Kibel, Adam S.; Cybulski, Cezary; Cannon-Albright, Lisa; Brenner, Hermann; Kaneva, Radka; Teixeira, Manuel R.; Consortium, PRACTICAL; Spurdle, Amanda B.; Clements, Judith A.; Park, Jong Y.; Batra, Jyotsna

    2015-01-01

    Prostate cancer is the second most common malignancy among men worldwide. Genome-wide association studies (GWAS) have identified 100 risk variants for prostate cancer, which can explain ~33% of the familial risk of the disease. We hypothesized that a comprehensive analysis of genetic variations found within the 3′ UTR of genes predicted to affect miRNA binding (miRSNPs) can identify additional prostate cancer risk variants. We investigated the association between 2,169 miRSNPs and prostate cancer risk in a large-scale analysis of 22,301 cases and 22,320 controls of European ancestry from 23 participating studies. Twenty-two miRSNPs were associated (p<2.3×10−5) with risk of prostate cancer, 10 of which were within the 7 genes previously not mapped by GWASs. Further, using miRNA mimics and reporter gene assays, we showed that miR-3162-5p has specific affinity for the KLK3 rs1058205 miRSNP T-allele whilst miR-370 has greater affinity for the VAMP8 rs1010 miRSNP A-allele, validating their functional role. Significance Findings from this large association study suggest that a focus on miRSNPs, including functional evaluation, can identify candidate risk loci below currently accepted statistical levels of genome-wide significance. Studies of miRNAs and their interactions with SNPs could provide further insights into the mechanisms of prostate cancer risk. PMID:25691096

  3. Impacts of Large-Scale Circulation on Convection: A 2-D Cloud Resolving Model Study

    NASA Technical Reports Server (NTRS)

    Li, X; Sui, C.-H.; Lau, K.-M.

    1999-01-01

    Studies of impacts of large-scale circulation on convection, and the roles of convection in heat and water balances over tropical region are fundamentally important for understanding global climate changes. Heat and water budgets over warm pool (SST=29.5 C) and cold pool (SST=26 C) were analyzed based on simulations of the two-dimensional cloud resolving model. Here the sensitivity of heat and water budgets to different sizes of warm and cold pools is examined.

  4. Ethical and practical challenges to studying patients who opt out of large-scale biorepository research

    PubMed Central

    Rosenbloom, S Trent; Madison, Jennifer L; Brothers, Kyle B; Bowton, Erica A; Clayton, Ellen Wright; Malin, Bradley A; Roden, Dan M; Pulley, Jill

    2013-01-01

    Large-scale biorepositories that couple biologic specimens with electronic health records containing documentation of phenotypic expression can accelerate scientific research and discovery. However, differences between those subjects who participate in biorepository-based research and the population from which they are drawn may influence research validity. While an opt-out approach to biorepository-based research enhances inclusiveness, empirical research evaluating voluntariness, risk, and the feasibility of an opt-out approach is sparse, and factors influencing patients’ decisions to opt out are understudied. Determining why patients choose to opt out may help to improve voluntariness, however there may be ethical and logistical challenges to studying those who opt out. In this perspective paper, the authors explore what is known about research based on the opt-out model, describe a large-scale biorepository that leverages the opt-out model, and review specific ethical and logistical challenges to bridging the research gaps that remain. PMID:23886923

  5. Large-Scale Single-Guide RNA Library Construction and Use for Genetic Screens

    PubMed Central

    Wang, Tim; Lander, Eric S.; Sabatini, David M.

    2016-01-01

    The ability to systematically disrupt genes serves as a powerful tool for understanding their function. The programmable Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein 9 (CRISPR/Cas9) system enables efficient targeting of large numbers of genes through the use of single-guide RNA (sgRNA) libraries. In cultured mammalian cells, collections of knockout mutants can be readily generated via transduction of Cas9/sgRNA lentiviral pools, screened for a phenotype of interest, and tracked using high-throughput DNA sequencing. This technique represents the first general method for undertaking systematic loss-of-function genetic screens in mammalian cells. In this chapter, we outline the steps for conducting CRISPR-based screens from the initial library design to final data analysis and provide guidelines for developing an appropriate screening strategy. PMID:26933254

  6. Large-scale diversification without genetic isolation in nematode symbionts of figs

    PubMed Central

    Susoy, Vladislav; Herrmann, Matthias; Kanzaki, Natsumi; Kruger, Meike; Nguyen, Chau N.; Rödelsperger, Christian; Röseler, Waltraud; Weiler, Christian; Giblin-Davis, Robin M.; Ragsdale, Erik J.; Sommer, Ralf J.

    2016-01-01

    Diversification is commonly understood to be the divergence of phenotypes accompanying that of lineages. In contrast, alternative phenotypes arising from a single genotype are almost exclusively limited to dimorphism in nature. We report a remarkable case of macroevolutionary-scale diversification without genetic divergence. Upon colonizing the island-like microecosystem of individual figs, symbiotic nematodes of the genus Pristionchus accumulated a polyphenism with up to five discrete adult morphotypes per species. By integrating laboratory and field experiments with extensive genotyping of individuals, including the analysis of 49 genomes from a single species, we show that rapid filling of potential ecological niches is possible without diversifying selection on genotypes. This uncoupling of morphological diversification and speciation in fig-associated nematodes has resulted from a remarkable expansion of discontinuous developmental plasticity. PMID:26824073

  7. Large-scale diversification without genetic isolation in nematode symbionts of figs.

    PubMed

    Susoy, Vladislav; Herrmann, Matthias; Kanzaki, Natsumi; Kruger, Meike; Nguyen, Chau N; Rödelsperger, Christian; Röseler, Waltraud; Weiler, Christian; Giblin-Davis, Robin M; Ragsdale, Erik J; Sommer, Ralf J

    2016-01-01

    Diversification is commonly understood to be the divergence of phenotypes accompanying that of lineages. In contrast, alternative phenotypes arising from a single genotype are almost exclusively limited to dimorphism in nature. We report a remarkable case of macroevolutionary-scale diversification without genetic divergence. Upon colonizing the island-like microecosystem of individual figs, symbiotic nematodes of the genus Pristionchus accumulated a polyphenism with up to five discrete adult morphotypes per species. By integrating laboratory and field experiments with extensive genotyping of individuals, including the analysis of 49 genomes from a single species, we show that rapid filling of potential ecological niches is possible without diversifying selection on genotypes. This uncoupling of morphological diversification and speciation in fig-associated nematodes has resulted from a remarkable expansion of discontinuous developmental plasticity. PMID:26824073

  8. Solving large-scale real-world telecommunication problems using a grid-based genetic algorithm

    NASA Astrophysics Data System (ADS)

    Luna, Francisco; Nebro, Antonio; Alba, Enrique; Durillo, Juan

    2008-11-01

    This article analyses the use of a grid-based genetic algorithm (GrEA) to solve a real-world instance of a problem from the telecommunication domain. The problem, known as automatic frequency planning (AFP), is used in a global system for mobile communications (GSM) networks to assign a number of fixed frequencies to a set of GSM transceivers located in the antennae of a cellular phone network. Real data instances of the AFP are very difficult to solve owing to the NP-hard nature of the problem, so combining grid computing and metaheuristics turns out to be a way to provide satisfactory solutions in a reasonable amount of time. GrEA has been deployed on a grid with up to 300 processors to solve an AFP instance of 2612 transceivers. The results not only show that significant running time reductions are achieved, but that the search capability of GrEA clearly outperforms that of the equivalent non-grid algorithm.

  9. What drivers phenotypic divergence in Leymus chinensis (Poaceae) on large-scale gradient, climate or genetic differentiation?

    NASA Astrophysics Data System (ADS)

    Yuan, Shan; Ma, Linna; Guo, Chengyuan; Wang, Renzhong

    2016-05-01

    Elucidating the driving factors among-population divergence is an important task in evolutionary biology, however the relative contribution from natural selection and neutral genetic differentiation has been less debated. A manipulation experiment was conducted to examine whether the phenotypic divergence of Leymus chinensis depended on climate variations or genetic differentiations at 18 wild sites along a longitudinal gradient from 114 to 124°E in northeast China and at common garden condition of transplantation. Demographical, morphological and physiological phenotypes of 18 L. chinensis populations exhibited significant divergence along the gradient, but these divergent variations narrowed significantly at the transplantation. Moreover, most of the phenotypes were significantly correlated with mean annual precipitation and temperature in wild sites, suggesting that climatic variables played vital roles in phenotypic divergence of the species. Relative greater heterozygosity (HE), genotype evenness (E) and Shannon-Wiener diversity (I) in western group of populations suggested that genetic differentiation also drove phenotypic divergence of the species. However, neutral genetic differentiation (FST = 0.041) was greatly lower than quantitative differentiation (QST = 0.199), indicating that divergent selection/climate variable was the main factor in determining the phenotypic divergence of the species along the large-scale gradient.

  10. What drivers phenotypic divergence in Leymus chinensis (Poaceae) on large-scale gradient, climate or genetic differentiation?

    PubMed Central

    Yuan, Shan; Ma, Linna; Guo, Chengyuan; Wang, Renzhong

    2016-01-01

    Elucidating the driving factors among-population divergence is an important task in evolutionary biology, however the relative contribution from natural selection and neutral genetic differentiation has been less debated. A manipulation experiment was conducted to examine whether the phenotypic divergence of Leymus chinensis depended on climate variations or genetic differentiations at 18 wild sites along a longitudinal gradient from 114 to 124°E in northeast China and at common garden condition of transplantation. Demographical, morphological and physiological phenotypes of 18 L. chinensis populations exhibited significant divergence along the gradient, but these divergent variations narrowed significantly at the transplantation. Moreover, most of the phenotypes were significantly correlated with mean annual precipitation and temperature in wild sites, suggesting that climatic variables played vital roles in phenotypic divergence of the species. Relative greater heterozygosity (HE), genotype evenness (E) and Shannon-Wiener diversity (I) in western group of populations suggested that genetic differentiation also drove phenotypic divergence of the species. However, neutral genetic differentiation (FST = 0.041) was greatly lower than quantitative differentiation (QST = 0.199), indicating that divergent selection/climate variable was the main factor in determining the phenotypic divergence of the species along the large-scale gradient. PMID:27195668

  11. Coalescent-based method for learning parameters of admixture events from large-scale genetic variation data.

    PubMed

    Tsai, Ming-Chi; Blelloch, Guy; Ravi, R; Schwartz, Russell

    2013-01-01

    Detecting and quantifying the timing and the genetic contributions of parental populations to a hybrid population is an important but challenging problem in reconstructing evolutionary histories from genetic variation data. With the advent of high throughput genotyping technologies, new methods suitable for large-scale data are especially needed. Furthermore, existing methods typically assume the assignment of individuals into subpopulations is known, when that itself is a difficult problem often unresolved for real data. Here, we propose a novel method that combines prior work for inferring non reticulate population structures with an MCMC scheme for sampling over admixture scenarios to both identify population assignments and learn divergence times and admixture proportions for those populations using genome-scale admixed genetic variation data. We validated our method using coalescent simulations and a collection of real bovine and human variation data. On simulated sequences, our methods show better accuracy and faster run time than leading competitive methods in estimating admixture fractions and divergence times. Analysis on the real data further shows our methods to be effective at matching our best current knowledge about the relevant populations. PMID:23959633

  12. Constructing large-scale genetic maps using an evolutionary strategy algorithm.

    PubMed Central

    Mester, D; Ronin, Y; Minkov, D; Nevo, E; Korol, A

    2003-01-01

    This article is devoted to the problem of ordering in linkage groups with many dozens or even hundreds of markers. The ordering problem belongs to the field of discrete optimization on a set of all possible orders, amounting to n!/2 for n loci; hence it is considered an NP-hard problem. Several authors attempted to employ the methods developed in the well-known traveling salesman problem (TSP) for multilocus ordering, using the assumption that for a set of linked loci the true order will be the one that minimizes the total length of the linkage group. A novel, fast, and reliable algorithm developed for the TSP and based on evolution-strategy discrete optimization was applied in this study for multilocus ordering on the basis of pairwise recombination frequencies. The quality of derived maps under various complications (dominant vs. codominant markers, marker misclassification, negative and positive interference, and missing data) was analyzed using simulated data with approximately 50-400 markers. High performance of the employed algorithm allows systematic treatment of the problem of verification of the obtained multilocus orders on the basis of computing-intensive bootstrap and/or jackknife approaches for detecting and removing questionable marker scores, thereby stabilizing the resulting maps. Parallel calculation technology can easily be adopted for further acceleration of the proposed algorithm. Real data analysis (on maize chromosome 1 with 230 markers) is provided to illustrate the proposed methodology. PMID:14704202

  13. A Feasibility Study on Operating Large Scale Compressed Air Energy Storage in Porous Formations

    NASA Astrophysics Data System (ADS)

    Wang, B.; Pfeiffer, W. T.; Li, D.; Bauer, S.

    2015-12-01

    Compressed air energy storage (CAES) in porous formations has been considered as one promising option of large scale energy storage for decades. This study, hereby, aims at analyzing the feasibility of operating large scale CAES in porous formations and evaluating the performance of underground porous gas reservoirs. To address these issues quantitatively, a hypothetic CAES scenario with a typical anticline structure in northern Germany was numerically simulated. Because of the rapid growth in photovoltaics, the period of extraction in a daily cycle was set to the early morning and the late afternoon in order to bypass the massive solar energy production around noon. The gas turbine scenario was defined referring to the specifications of the Huntorf CAES power plant. The numerical simulations involved two stages, i.e. initial fill and cyclic operation, and both were carried out using the Eclipse E300 simulator (Schlumberger). Pressure loss in the gas wells was post analyzed using an analytical solution. The exergy concept was applied to evaluate the potential energy amount stored in the specific porous formation. The simulation results show that porous formations prove to be a feasible solution of large scale CAES. The initial fill with shut-in periods determines the spatial distribution of the gas phase and helps to achieve higher gas saturation around the wells, and thus higher deliverability. The performance evaluation shows that the overall exergy flow of stored compressed air is also determined by the permeability, which directly affects the deliverability of the gas reservoir and thus the number of wells required.

  14. Study on tsunami generation and propagation in a large scale wave flume

    NASA Astrophysics Data System (ADS)

    Schimmels, Stefan; Venkatachalam, Sriram; Didenkulova, Ira

    2015-04-01

    In this paper we study very long, i.e. real tsunami-like wave generation in a large scale wave flume using a piston type wave maker. Waves of periods between 30 s and more than 100 s were generated at 1 m water depth using two different approaches: (i) deriving the wave board motion directly by integration of the water surface elevation, composed of a different number of solitons (sech2 waves) and (ii) using an iterative self correcting method (SCM). The importance of very long wave generation instead of solitary waves and the necessity for long testing facilities is discussed and results from GWK experiments are presented for single pulses (elongated solitons), N-waves and real tsunami records, either approximated as a combination of solitons or applying the SCM to the time series directly. The possibility to study propagation, shoaling and run-up of these waves over a slope in a 300-meter long large wave flume (GWK), Hannover is dicsussed. Experimental data of long wave propagation in the flume are compared with numerical simulations performed within the fully nonlinear potential flow theory and KdV equations. Shoaling and run-up of waves on different mild slopes is studied hypothetically using nonlinear shallow water theory. The paper ends with the conclusions about the feasibility of using large scale experimental facility (GWK) to study tsunami wave propagation and run-up.

  15. Studying populations of eclipsing binaries using large scale multi-epoch photometric surveys

    NASA Astrophysics Data System (ADS)

    Mowlavi, Nami; Barblan, Fabio; Holl, Berry; Rimoldini, Lorenzo; Lecoeur-Taïbi, Isabelle; Süveges, Maria; Eyer, Laurent; Guy, Leanne; Nienartowicz, Krzysztof; Ordonez, Diego; Charnas, Jonathan; Jévardat de Fombelle, Grégory

    2015-08-01

    Large scale multi-epoch photometric surveys provide unique opportunities to study populations of binary stars through the study of eclipsing binaries, provided the basic properties of binary systems can be derived from their light curves without the need to fully model the binary system. Those systems can then be classified into various types from, for example, close to wide systems, from circular to highly elliptical systems, or from systems with similar components to highly asymmetric systems. The challenge is to extract physically relevant information from the light curve geometry.In this contribution, we present the study of eclipsing binaries in the Large Magellanic Clouds (LMC) from the OGLE-III survey. The study is based on the analysis of the geometry of their light curves parameterized using a two-Gaussian model. We show what physical parameters could be extracted from such an analysis, and the results for the LMC eclipsing binaries. The method is very well adapted to process large-scale surveys containing millions of eclipsing binaries, such as is expected from the current Gaia mission or the future LSST survey.

  16. Scaling up explanation generation: Large-scale knowledge bases and empirical studies

    SciTech Connect

    Lester, J.C.; Porter, B.W.

    1996-12-31

    To explain complex phenomena, an explanation system must be able to select information from a formal representation of domain knowledge, organize the selected information into multisentential discourse plans, and realize the discourse plans in text. Although recent years have witnessed significant progress in the development of sophisticated computational mechanisms for explanation, empirical results have been limited. This paper reports on a seven year effort to empirically study explanation generation from semantically rich, large-scale knowledge bases. We first describe Knight, a robust explanation system that constructs multi-sentential and multi-paragraph explanations from the Biology Knowledge Base, a large-scale knowledge base in the domain of botanical anatomy, physiology, and development. We then introduce the Two Panel evaluation methodology and describe how Knight`s performance was assessed with this methodology in the most extensive empirical evaluation conducted on an explanation system. In this evaluation, Knight scored within {open_quotes}half a grade{close_quote} of domain experts, and its performance exceeded that of one of the domain experts.

  17. Flaglets for studying the large-scale structure of the Universe

    NASA Astrophysics Data System (ADS)

    Leistedt, Boris; Peiris, Hiranya V.; McEwen, Jason D.

    2013-09-01

    Pressing questions in cosmology such as the nature of dark matter and dark energy can be addressed using large galaxy surveys, which measure the positions, properties and redshifts of galaxies in order to map the large-scale structure of the Universe. We review the Fourier-Laguerre transform, a novel transform in 3D spherical coordinates which is based on spherical harmonics combined with damped Laguerre polynomials and appropriate for analysing galaxy surveys. We also recall the construction of aglets, 3D wavelets obtained through a tiling of the Fourier-Laguerre space, which can be used to extract scale-dependent, spatially localised features on the ball. We exploit a sampling theorem to obtain exact Fourier-Laguerre and aglet transforms, such that band-limited signals can analysed and reconstructed at oating point accuracy on a nite number of voxels on the ball. We present a potential application of the aglet transform for nding voids in galaxy surveys and studying the large-scale structure of the Universe.

  18. Case Study: Commercialization of sweet sorghum juice clarification for large-scale syrup manufacture

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The precipitation and burning of insoluble granules of starch from sweet sorghum juice on heating coils prevented the large scale manufacture of syrup at a new industrial plant in Missouri, USA. To remove insoluble starch granules, a series of small and large-scale experiments were conducted at the...

  19. Transport of iron oxide nanoparticles in saturated porous media: a large-scale 3D study

    NASA Astrophysics Data System (ADS)

    Velimirovic, Milica; Schmid, Doris; Micić, Vesna; Miyajima, Kumiko; Klaas, Norbert; Braun, Jürgen; Bosch, Julian; Meckenstock, Rainer; von der Kammer, Frank; Hofmann, Thilo

    2016-04-01

    Iron oxide nanoparticles (FeOxNp) have a high potential as electron acceptor for in situ microbial oxidation of a wide range of recalcitrant groundwater contaminants (Bosch et al., 2010). Tosco et al. (2012) reported on high colloidal stability of FeOxNp dispersed in water, their low deposition behavior, and consequently improved transport in column experiments compared to extensively studied zerovalent iron nanoparticles. However, determination of FeOxNp transport behavior at the field-relevant conditions has not been done before. The present work is aimed to evaluate different complementary methods for detection, quantification and transport characterization of FeOxNp in a large-scale three-dimensional (3D) model aquifer. Prior to that, batch-scale experiments were performed in order to elucidate the potential of the selected methods for direct and indirect characterization and detection of FeOxNp. Direct methods included measurements of particle size distribution, particle concentration, Fetot content and turbidity of the FeOxNp suspension. Indirect methods included measurements of particle zeta potential, as well as TOC content and pH of the FeOxNp suspension. The results of the batch experiments indicated that the most suitable approach for detecting and quantifying FeOxNp was measuring Fetot content and suspension turbidity, as well as particle size determined using dynamic light scattering principle. These complementary methods were further applied in a large-scale 3D study containing medium and coarse sand in order to 1) assess the transport of FeOxNp in saturated porous medium during injection (VFeOx = 6 m3, cparticle = 20 g/L, Qinj = 0.7 m3/h), and 2) illustrate their spatial distribution after injection. The outcomes of the large-scale 3D study confirmed that FeOxNp transport can be successfully investigated applying complementary methods. Monitoring data including Fetot content, turbidity and particle size showed the transport of particles towards the

  20. A large-scale study of epilepsy in Ecuador: methodological aspects.

    PubMed

    Placencia, M; Suarez, J; Crespo, F; Sander, J W; Shorvon, S D; Ellison, R H; Cascante, S M

    1992-01-01

    The methodology is presented of a large-scale study of epilepsy carried out in a highland area in northern Ecuador, South America, covering a population of 72,121 people; The study was carried out in two phases, the first, a cross-sectional phase, consisted of a house-to-house survey of all persons in this population, screening for epileptic seizures using a specially designed questionnaire. Possible cases identified in screening were assessed in a cascade diagnostic procedure applied by general doctors and neurologists. Its objectives were: to establish a comprehensive epidemiological profile of epileptic seizures; to describe the clinical phenomenology of this condition in the community; to validate methods for diagnosis and classification of epileptic seizures by a non-specialised team; and to ascertain the community's knowledge, attitudes and practices regarding epilepsy. A sample was selected in this phase in order to study the social aspects of epilepsy in this community. The second phase, which was longitudinal, assessed the ability of non-specialist care in the treatment of epilepsy. It consisted of a prospective clinical trial of antiepileptic therapy in untreated patients using two standard anti-epileptic drugs. Patients were followed for 12 months by a multidisciplinary team consisting of a primary health worker, rural doctor, neurologist, anthropologist, and psychologist. Standardised, reproducible instruments and methods were used. This study was carried out through co-operation between the medical profession, political agencies and the pharmaceutical industry, at an international level. We consider this a model for further large-scale studies of this type. PMID:1495577

  1. Large-scale shell model study of the newly found isomer in 136La

    NASA Astrophysics Data System (ADS)

    Teruya, E.; Yoshinaga, N.; Higashiyama, K.; Nishibata, H.; Odahara, A.; Shimoda, T.

    2016-07-01

    The doubly-odd nucleus 136La is theoretically studied in terms of a large-scale shell model. The energy spectrum and transition rates are calculated and compared with the most updated experimental data. The isomerism is investigated for the first 14+ state, which was found to be an isomer in the previous study [Phys. Rev. C 91, 054305 (2015), 10.1103/PhysRevC.91.054305]. It is found that the 14+ state becomes an isomer due to a band crossing of two bands with completely different configurations. The yrast band with the (ν h11/2 -1⊗π h11 /2 ) configuration is investigated, revealing a staggering nature in M 1 transition rates.

  2. Biomass logistics analysis for large scale biofuel production: case study of loblolly pine and switchgrass.

    PubMed

    Lu, Xiaoming; Withers, Mitch R; Seifkar, Navid; Field, Randall P; Barrett, Steven R H; Herzog, Howard J

    2015-05-01

    The objective of this study was to assess the costs, energy consumption and greenhouse gas (GHG) emissions throughout the biomass supply chain for large scale biofuel production. Two types of energy crop were considered, switchgrass and loblolly pine, as representative of herbaceous and woody biomass. A biomass logistics model has been developed to estimate the feedstock supply system from biomass production through transportation. Biomass in the form of woodchip, bale and pellet was investigated with road, railway and waterway transportation options. Our analysis indicated that the farm or forest gate cost is lowest for loblolly pine whole tree woodchip at $39.7/dry tonne and highest for switchgrass round bale at $72.3/dry tonne. Switchgrass farm gate GHG emissions is approximately 146kgCO2e/dry tonne, about 4 times higher than loblolly pine. The optimum biomass transportation mode and delivered form are determined by the tradeoff between fixed and variable costs for feedstock shipment. PMID:25710677

  3. Parallel computing study for the large-scale generalized eigenvalue problems in modal analysis

    NASA Astrophysics Data System (ADS)

    Fan, XuanHua; Chen, Pu; Wu, RuiAn; Xiao, ShiFu

    2014-03-01

    In this paper we study the algorithms and their parallel implementation for solving large-scale generalized eigenvalue problems in modal analysis. Three predominant subspace algorithms, i.e., Krylov-Schur method, implicitly restarted Arnoldi method and Jacobi-Davidson method, are modified with some complementary techniques to make them suitable for modal analysis. Detailed descriptions of the three algorithms are given. Based on these algorithms, a parallel solution procedure is established via the PANDA framework and its associated eigensolvers. Using the solution procedure on a machine equipped with up to 4800 processors, the parallel performance of the three predominant methods is evaluated via numerical experiments with typical engineering structures, where the maximum testing scale attains twenty million degrees of freedom. The speedup curves for different cases are obtained and compared. The results show that the three methods are good for modal analysis in the scale of ten million degrees of freedom with a favorable parallel scalability.

  4. Large-scale mutagenesis of the mouse to understand the genetic bases of nervous system structure and function

    PubMed Central

    Goldowitz, Dan; Frankel, Wayne N.; Takahashi, Joseph S.; Holtz-Vitaterna, Martha; Bult, Carol; Kibbe, Warren A.; Snoddy, Jay; Li, Yanxia; Pretel, Stephanie; Yates, Jeana; Swanson, Douglas J.

    2013-01-01

    N-ethyl-N-nitrosourea (ENU) mutagenesis is presented as a powerful approach to developing models for human disease. The efforts of three NIH Mutagenesis Centers established for the detection of neuroscience-related phenotypes are described. Each center has developed an extensive panel of phenotype screens that assess nervous system structure and function. In particular, these screens focus on complex behavioral traits from drug and alcohol responses to circadian rhythms to epilepsy. Each of these centers has developed a bioinformatics infrastructure to track the extensive number of transactions that are inherent in these large-scale projects. Over 100 new mouse mutant lines have been defined through the efforts of these three mutagenesis centers and are presented to the research community via the centralized Web presence of the Neuromice.org consortium (http://www.neuromice.org). This community resource provides visitors with the ability to search for specific mutant phenotypes, to view the genetic and phenotypic details of mutant mouse lines, and to order these mice for use in their own research program. PMID:15582151

  5. Anatomically Detailed and Large-Scale Simulations Studying Synapse Loss and Synchrony Using NeuroBox.

    PubMed

    Breit, Markus; Stepniewski, Martin; Grein, Stephan; Gottmann, Pascal; Reinhardt, Lukas; Queisser, Gillian

    2016-01-01

    The morphology of neurons and networks plays an important role in processing electrical and biochemical signals. Based on neuronal reconstructions, which are becoming abundantly available through databases such as NeuroMorpho.org, numerical simulations of Hodgkin-Huxley-type equations, coupled to biochemical models, can be performed in order to systematically investigate the influence of cellular morphology and the connectivity pattern in networks on the underlying function. Development in the area of synthetic neural network generation and morphology reconstruction from microscopy data has brought forth the software tool NeuGen. Coupling this morphology data (either from databases, synthetic, or reconstruction) to the simulation platform UG 4 (which harbors a neuroscientific portfolio) and VRL-Studio, has brought forth the extendible toolbox NeuroBox. NeuroBox allows users to perform numerical simulations on hybrid-dimensional morphology representations. The code basis is designed in a modular way, such that e.g., new channel or synapse types can be added to the library. Workflows can be specified through scripts or through the VRL-Studio graphical workflow representation. Third-party tools, such as ImageJ, can be added to NeuroBox workflows. In this paper, NeuroBox is used to study the electrical and biochemical effects of synapse loss vs. synchrony in neurons, to investigate large morphology data sets within detailed biophysical simulations, and used to demonstrate the capability of utilizing high-performance computing infrastructure for large scale network simulations. Using new synapse distribution methods and Finite Volume based numerical solvers for compartment-type models, our results demonstrate how an increase in synaptic synchronization can compensate synapse loss at the electrical and calcium level, and how detailed neuronal morphology can be integrated in large-scale network simulations. PMID:26903818

  6. Anatomically Detailed and Large-Scale Simulations Studying Synapse Loss and Synchrony Using NeuroBox

    PubMed Central

    Breit, Markus; Stepniewski, Martin; Grein, Stephan; Gottmann, Pascal; Reinhardt, Lukas; Queisser, Gillian

    2016-01-01

    The morphology of neurons and networks plays an important role in processing electrical and biochemical signals. Based on neuronal reconstructions, which are becoming abundantly available through databases such as NeuroMorpho.org, numerical simulations of Hodgkin-Huxley-type equations, coupled to biochemical models, can be performed in order to systematically investigate the influence of cellular morphology and the connectivity pattern in networks on the underlying function. Development in the area of synthetic neural network generation and morphology reconstruction from microscopy data has brought forth the software tool NeuGen. Coupling this morphology data (either from databases, synthetic, or reconstruction) to the simulation platform UG 4 (which harbors a neuroscientific portfolio) and VRL-Studio, has brought forth the extendible toolbox NeuroBox. NeuroBox allows users to perform numerical simulations on hybrid-dimensional morphology representations. The code basis is designed in a modular way, such that e.g., new channel or synapse types can be added to the library. Workflows can be specified through scripts or through the VRL-Studio graphical workflow representation. Third-party tools, such as ImageJ, can be added to NeuroBox workflows. In this paper, NeuroBox is used to study the electrical and biochemical effects of synapse loss vs. synchrony in neurons, to investigate large morphology data sets within detailed biophysical simulations, and used to demonstrate the capability of utilizing high-performance computing infrastructure for large scale network simulations. Using new synapse distribution methods and Finite Volume based numerical solvers for compartment-type models, our results demonstrate how an increase in synaptic synchronization can compensate synapse loss at the electrical and calcium level, and how detailed neuronal morphology can be integrated in large-scale network simulations. PMID:26903818

  7. Large-Scale SNP Discovery and Genotyping for Constructing a High-Density Genetic Map of Tea Plant Using Specific-Locus Amplified Fragment Sequencing (SLAF-seq).

    PubMed

    Ma, Jian-Qiang; Huang, Long; Ma, Chun-Lei; Jin, Ji-Qiang; Li, Chun-Fang; Wang, Rong-Kai; Zheng, Hong-Kun; Yao, Ming-Zhe; Chen, Liang

    2015-01-01

    Genetic maps are important tools in plant genomics and breeding. The present study reports the large-scale discovery of single nucleotide polymorphisms (SNPs) for genetic map construction in tea plant. We developed a total of 6,042 valid SNP markers using specific-locus amplified fragment sequencing (SLAF-seq), and subsequently mapped them into the previous framework map. The final map contained 6,448 molecular markers, distributing on fifteen linkage groups corresponding to the number of tea plant chromosomes. The total map length was 3,965 cM, with an average inter-locus distance of 1.0 cM. This map is the first SNP-based reference map of tea plant, as well as the most saturated one developed to date. The SNP markers and map resources generated in this study provide a wealth of genetic information that can serve as a foundation for downstream genetic analyses, such as the fine mapping of quantitative trait loci (QTL), map-based cloning, marker-assisted selection, and anchoring of scaffolds to facilitate the process of whole genome sequencing projects for tea plant. PMID:26035838

  8. Large scale wildlife monitoring studies: statistical methods for design and analysis

    USGS Publications Warehouse

    Pollock, K.H.; Nichols, J.D.; Simons, T.R.; Farnsworth, G.L.; Bailey, L.L.; Sauer, J.R.

    2002-01-01

    Techniques for estimation of absolute abundance of wildlife populations have received a lot of attention in recent years. The statistical research has been focused on intensive small-scale studies. Recently, however, wildlife biologists have desired to study populations of animals at very large scales for monitoring purposes. Population indices are widely used in these extensive monitoring programs because they are inexpensive compared to estimates of absolute abundance. A crucial underlying assumption is that the population index (C) is directly proportional to the population density (D). The proportionality constant, b, is simply the probability of 'detection' for animals in the survey. As spatial and temporal comparisons of indices are crucial, it is necessary to also assume that the probability of detection is constant over space and time. Biologists intuitively recognize this when they design rigid protocols for the studies where the indices are collected. Unfortunately, however in many field studios the assumption is clearly invalid. We believe that the estimation of detection probability should be built into the monitoring design through a double sampling approach. A large sample of points provides an abundance index, and a smaller sub-sample of the same points is used to estimate detection probability. There is an important need for statistical research on the design and analysis of these complex studies. Some basic concepts based on actual avian, amphibian, and fish monitoring studies are presented in this article.

  9. Influenza epidemic spread simulation for Poland — a large scale, individual based model study

    NASA Astrophysics Data System (ADS)

    Rakowski, Franciszek; Gruziel, Magdalena; Bieniasz-Krzywiec, Łukasz; Radomski, Jan P.

    2010-08-01

    In this work a construction of an agent based model for studying the effects of influenza epidemic in large scale (38 million individuals) stochastic simulations, together with the resulting various scenarios of disease spread in Poland are reported. Simple transportation rules were employed to mimic individuals’ travels in dynamic route-changing schemes, allowing for the infection spread during a journey. Parameter space was checked for stable behaviour, especially towards the effective infection transmission rate variability. Although the model reported here is based on quite simple assumptions, it allowed to observe two different types of epidemic scenarios: characteristic for urban and rural areas. This differentiates it from the results obtained in the analogous studies for the UK or US, where settlement and daily commuting patterns are both substantially different and more diverse. The resulting epidemic scenarios from these ABM simulations were compared with simple, differential equations based, SIR models - both types of the results displaying strong similarities. The pDYN software platform developed here is currently used in the next stage of the project employed to study various epidemic mitigation strategies.

  10. A large-scale proteogenomics study of apicomplexan pathogens—Toxoplasma gondii and Neospora caninum

    PubMed Central

    Krishna, Ritesh; Xia, Dong; Sanderson, Sanya; Shanmugasundram, Achchuthan; Vermont, Sarah; Bernal, Axel; Daniel-Naguib, Gianluca; Ghali, Fawaz; Brunk, Brian P; Roos, David S; Wastling, Jonathan M; Jones, Andrew R

    2015-01-01

    Proteomics data can supplement genome annotation efforts, for example being used to confirm gene models or correct gene annotation errors. Here, we present a large-scale proteogenomics study of two important apicomplexan pathogens: Toxoplasma gondii and Neospora caninum. We queried proteomics data against a panel of official and alternate gene models generated directly from RNASeq data, using several newly generated and some previously published MS datasets for this meta-analysis. We identified a total of 201 996 and 39 953 peptide-spectrum matches for T. gondii and N. caninum, respectively, at a 1% peptide FDR threshold. This equated to the identification of 30 494 distinct peptide sequences and 2921 proteins (matches to official gene models) for T. gondii, and 8911 peptides/1273 proteins for N. caninum following stringent protein-level thresholding. We have also identified 289 and 140 loci for T. gondii and N. caninum, respectively, which mapped to RNA-Seq-derived gene models used in our analysis and apparently absent from the official annotation (release 10 from EuPathDB) of these species. We present several examples in our study where the RNA-Seq evidence can help in correction of the current gene model and can help in discovery of potential new genes. The findings of this study have been integrated into the EuPathDB. The data have been deposited to the ProteomeXchange with identifiers PXD000297and PXD000298. PMID:25867681

  11. Simulating large-scale pedestrian movement using CA and event driven model: Methodology and case study

    NASA Astrophysics Data System (ADS)

    Li, Jun; Fu, Siyao; He, Haibo; Jia, Hongfei; Li, Yanzhong; Guo, Yi

    2015-11-01

    Large-scale regional evacuation is an important part of national security emergency response plan. Large commercial shopping area, as the typical service system, its emergency evacuation is one of the hot research topics. A systematic methodology based on Cellular Automata with the Dynamic Floor Field and event driven model has been proposed, and the methodology has been examined within context of a case study involving the evacuation within a commercial shopping mall. Pedestrians walking is based on Cellular Automata and event driven model. In this paper, the event driven model is adopted to simulate the pedestrian movement patterns, the simulation process is divided into normal situation and emergency evacuation. The model is composed of four layers: environment layer, customer layer, clerk layer and trajectory layer. For the simulation of movement route of pedestrians, the model takes into account purchase intention of customers and density of pedestrians. Based on evacuation model of Cellular Automata with Dynamic Floor Field and event driven model, we can reflect behavior characteristics of customers and clerks at the situations of normal and emergency evacuation. The distribution of individual evacuation time as a function of initial positions and the dynamics of the evacuation process is studied. Our results indicate that the evacuation model using the combination of Cellular Automata with Dynamic Floor Field and event driven scheduling can be used to simulate the evacuation of pedestrian flows in indoor areas with complicated surroundings and to investigate the layout of shopping mall.

  12. A study of the large-scale infrared emission from a selected dark cloud

    NASA Technical Reports Server (NTRS)

    Young, Erick T.

    1990-01-01

    An investigation of the infrared emission energetics and embedded population in the rho Ophiuchi dark cloud is summarized. With a distance of approximately 140 pc, the rho Ophiuchi cloud is one of the closest regions of recent star formation. It is also one of the best studied such regions with numerous observations at all wavelengths. The IRAS data of the cloud provided a new glimpse of the overall structure of the cloud. In particular, the interaction of radiation from the Sco-Oph OB Association on the external heating of the cloud was very evident on Skyflux and Survey Co-Add images produced by IRAS. The infrared survey also revealed a number of new embedded sources in the cloud which have subsequently been observed from the ground. An earlier study explored the overall energetics of the cloud using the IRAS data. The main conclusions of that work were: (1) the overall luminosity of the cloud is well explained by the emission of the known B-stars, HD 147889, SR-3, and S1, along with a 15 percent contribution from the external radiation field; (2) the dust physical temperatures were significantly lower than the observed CO gas temperatures; and (3) dust grains are heated to only 10 percent to 20 percent of the total depth into the cloud. This analysis is extended by drawing on data from large-scale CO maps and from near-infrared surveys of the embedded population.

  13. A study of the large-scale infrared emission from a selected dark cloud

    NASA Technical Reports Server (NTRS)

    Young, Erick T.

    1993-01-01

    An investigation of the infrared emission energetics and embedded population in the rho Ophiuchi dark cloud is summarized. With a distance of approximately 140 pc, the rho Ophiuchi cloud is one of the closest regions of recent star formation. It is also one of the best studied such regions with numerous observations at all wavelengths. The Infrared Astronomy Satellite (IRAS) data of the cloud provided a new glimpse of the overall structure of the cloud. In particular, the interaction of radiation from the Sco-Oph OB Association on the external heating of the cloud was very evident on Skyflux and Survey CO-Add images produced by IRAS. The infrared survey also revealed a number of new embedded sources in the cloud which have subsequently been observed from the ground. In earlier study, the overall energies of the cloud using the IRAS data was explored. The main conclusions of that work were: (1) the overall luminosity of the cloud is well explained by the emission of the known B-stars, HD 147889, SR-3, and S1, along with a 15 percent contribution from the external radiation field; (2) the dust physical temperatures were significantly lower than the observed CO gas temperatures; and (3) dust grains are heated to only 10 percent to 20 percent of the total depth into the cloud. This analysis was extended by drawing on data from large-scale CO maps of Loren (1989) and from near-infrared surveys of the embedded population.

  14. NV Energy Large-Scale Photovoltaic Integration Study: Intra-Hour Dispatch and AGC Simulation

    SciTech Connect

    Lu, Shuai; Etingov, Pavel V.; Meng, Da; Guo, Xinxin; Jin, Chunlian; Samaan, Nader A.

    2013-01-02

    The uncertainty and variability with photovoltaic (PV) generation make it very challenging to balance power system generation and load, especially under high penetration cases. Higher reserve requirements and more cycling of conventional generators are generally anticipated for large-scale PV integration. However, whether the existing generation fleet is flexible enough to handle the variations and how well the system can maintain its control performance are difficult to predict. The goal of this project is to develop a software program that can perform intra-hour dispatch and automatic generation control (AGC) simulation, by which the balancing operations of a system can be simulated to answer the questions posed above. The simulator, named Electric System Intra-Hour Operation Simulator (ESIOS), uses the NV Energy southern system as a study case, and models the system’s generator configurations, AGC functions, and operator actions to balance system generation and load. Actual dispatch of AGC generators and control performance under various PV penetration levels can be predicted by running ESIOS. With data about the load, generation, and generator characteristics, ESIOS can perform similar simulations and assess variable generation integration impacts for other systems as well. This report describes the design of the simulator and presents the study results showing the PV impacts on NV Energy real-time operations.

  15. Analyzing large-scale conservation interventions with Bayesian hierarchical models: a case study of supplementing threatened Pacific salmon

    PubMed Central

    Scheuerell, Mark D; Buhle, Eric R; Semmens, Brice X; Ford, Michael J; Cooney, Tom; Carmichael, Richard W

    2015-01-01

    Myriad human activities increasingly threaten the existence of many species. A variety of conservation interventions such as habitat restoration, protected areas, and captive breeding have been used to prevent extinctions. Evaluating the effectiveness of these interventions requires appropriate statistical methods, given the quantity and quality of available data. Historically, analysis of variance has been used with some form of predetermined before-after control-impact design to estimate the effects of large-scale experiments or conservation interventions. However, ad hoc retrospective study designs or the presence of random effects at multiple scales may preclude the use of these tools. We evaluated the effects of a large-scale supplementation program on the density of adult Chinook salmon Oncorhynchus tshawytscha from the Snake River basin in the northwestern United States currently listed under the U.S. Endangered Species Act. We analyzed 43 years of data from 22 populations, accounting for random effects across time and space using a form of Bayesian hierarchical time-series model common in analyses of financial markets. We found that varying degrees of supplementation over a period of 25 years increased the density of natural-origin adults, on average, by 0–8% relative to nonsupplementation years. Thirty-nine of the 43 year effects were at least two times larger in magnitude than the mean supplementation effect, suggesting common environmental variables play a more important role in driving interannual variability in adult density. Additional residual variation in density varied considerably across the region, but there was no systematic difference between supplemented and reference populations. Our results demonstrate the power of hierarchical Bayesian models to detect the diffuse effects of management interventions and to quantitatively describe the variability of intervention success. Nevertheless, our study could not address whether ecological

  16. Analyzing large-scale conservation interventions with Bayesian hierarchical models: a case study of supplementing threatened Pacific salmon.

    PubMed

    Scheuerell, Mark D; Buhle, Eric R; Semmens, Brice X; Ford, Michael J; Cooney, Tom; Carmichael, Richard W

    2015-05-01

    Myriad human activities increasingly threaten the existence of many species. A variety of conservation interventions such as habitat restoration, protected areas, and captive breeding have been used to prevent extinctions. Evaluating the effectiveness of these interventions requires appropriate statistical methods, given the quantity and quality of available data. Historically, analysis of variance has been used with some form of predetermined before-after control-impact design to estimate the effects of large-scale experiments or conservation interventions. However, ad hoc retrospective study designs or the presence of random effects at multiple scales may preclude the use of these tools. We evaluated the effects of a large-scale supplementation program on the density of adult Chinook salmon Oncorhynchus tshawytscha from the Snake River basin in the northwestern United States currently listed under the U.S. Endangered Species Act. We analyzed 43 years of data from 22 populations, accounting for random effects across time and space using a form of Bayesian hierarchical time-series model common in analyses of financial markets. We found that varying degrees of supplementation over a period of 25 years increased the density of natural-origin adults, on average, by 0-8% relative to nonsupplementation years. Thirty-nine of the 43 year effects were at least two times larger in magnitude than the mean supplementation effect, suggesting common environmental variables play a more important role in driving interannual variability in adult density. Additional residual variation in density varied considerably across the region, but there was no systematic difference between supplemented and reference populations. Our results demonstrate the power of hierarchical Bayesian models to detect the diffuse effects of management interventions and to quantitatively describe the variability of intervention success. Nevertheless, our study could not address whether ecological factors

  17. Large-scale gene-centric meta-analysis across 39 studies identifies type 2 diabetes loci.

    PubMed

    Saxena, Richa; Elbers, Clara C; Guo, Yiran; Peter, Inga; Gaunt, Tom R; Mega, Jessica L; Lanktree, Matthew B; Tare, Archana; Castillo, Berta Almoguera; Li, Yun R; Johnson, Toby; Bruinenberg, Marcel; Gilbert-Diamond, Diane; Rajagopalan, Ramakrishnan; Voight, Benjamin F; Balasubramanyam, Ashok; Barnard, John; Bauer, Florianne; Baumert, Jens; Bhangale, Tushar; Böhm, Bernhard O; Braund, Peter S; Burton, Paul R; Chandrupatla, Hareesh R; Clarke, Robert; Cooper-DeHoff, Rhonda M; Crook, Errol D; Davey-Smith, George; Day, Ian N; de Boer, Anthonius; de Groot, Mark C H; Drenos, Fotios; Ferguson, Jane; Fox, Caroline S; Furlong, Clement E; Gibson, Quince; Gieger, Christian; Gilhuijs-Pederson, Lisa A; Glessner, Joseph T; Goel, Anuj; Gong, Yan; Grant, Struan F A; Grobbee, Diederick E; Hastie, Claire; Humphries, Steve E; Kim, Cecilia E; Kivimaki, Mika; Kleber, Marcus; Meisinger, Christa; Kumari, Meena; Langaee, Taimour Y; Lawlor, Debbie A; Li, Mingyao; Lobmeyer, Maximilian T; Maitland-van der Zee, Anke-Hilse; Meijs, Matthijs F L; Molony, Cliona M; Morrow, David A; Murugesan, Gurunathan; Musani, Solomon K; Nelson, Christopher P; Newhouse, Stephen J; O'Connell, Jeffery R; Padmanabhan, Sandosh; Palmen, Jutta; Patel, Sanjey R; Pepine, Carl J; Pettinger, Mary; Price, Thomas S; Rafelt, Suzanne; Ranchalis, Jane; Rasheed, Asif; Rosenthal, Elisabeth; Ruczinski, Ingo; Shah, Sonia; Shen, Haiqing; Silbernagel, Günther; Smith, Erin N; Spijkerman, Annemieke W M; Stanton, Alice; Steffes, Michael W; Thorand, Barbara; Trip, Mieke; van der Harst, Pim; van der A, Daphne L; van Iperen, Erik P A; van Setten, Jessica; van Vliet-Ostaptchouk, Jana V; Verweij, Niek; Wolffenbuttel, Bruce H R; Young, Taylor; Zafarmand, M Hadi; Zmuda, Joseph M; Boehnke, Michael; Altshuler, David; McCarthy, Mark; Kao, W H Linda; Pankow, James S; Cappola, Thomas P; Sever, Peter; Poulter, Neil; Caulfield, Mark; Dominiczak, Anna; Shields, Denis C; Bhatt, Deepak L; Bhatt, Deepak; Zhang, Li; Curtis, Sean P; Danesh, John; Casas, Juan P; van der Schouw, Yvonne T; Onland-Moret, N Charlotte; Doevendans, Pieter A; Dorn, Gerald W; Farrall, Martin; FitzGerald, Garret A; Hamsten, Anders; Hegele, Robert; Hingorani, Aroon D; Hofker, Marten H; Huggins, Gordon S; Illig, Thomas; Jarvik, Gail P; Johnson, Julie A; Klungel, Olaf H; Knowler, William C; Koenig, Wolfgang; März, Winfried; Meigs, James B; Melander, Olle; Munroe, Patricia B; Mitchell, Braxton D; Bielinski, Susan J; Rader, Daniel J; Reilly, Muredach P; Rich, Stephen S; Rotter, Jerome I; Saleheen, Danish; Samani, Nilesh J; Schadt, Eric E; Shuldiner, Alan R; Silverstein, Roy; Kottke-Marchant, Kandice; Talmud, Philippa J; Watkins, Hugh; Asselbergs, Folkert W; Asselbergs, Folkert; de Bakker, Paul I W; McCaffery, Jeanne; Wijmenga, Cisca; Sabatine, Marc S; Wilson, James G; Reiner, Alex; Bowden, Donald W; Hakonarson, Hakon; Siscovick, David S; Keating, Brendan J

    2012-03-01

    To identify genetic factors contributing to type 2 diabetes (T2D), we performed large-scale meta-analyses by using a custom ∼50,000 SNP genotyping array (the ITMAT-Broad-CARe array) with ∼2000 candidate genes in 39 multiethnic population-based studies, case-control studies, and clinical trials totaling 17,418 cases and 70,298 controls. First, meta-analysis of 25 studies comprising 14,073 cases and 57,489 controls of European descent confirmed eight established T2D loci at genome-wide significance. In silico follow-up analysis of putative association signals found in independent genome-wide association studies (including 8,130 cases and 38,987 controls) performed by the DIAGRAM consortium identified a T2D locus at genome-wide significance (GATAD2A/CILP2/PBX4; p = 5.7 × 10(-9)) and two loci exceeding study-wide significance (SREBF1, and TH/INS; p < 2.4 × 10(-6)). Second, meta-analyses of 1,986 cases and 7,695 controls from eight African-American studies identified study-wide-significant (p = 2.4 × 10(-7)) variants in HMGA2 and replicated variants in TCF7L2 (p = 5.1 × 10(-15)). Third, conditional analysis revealed multiple known and novel independent signals within five T2D-associated genes in samples of European ancestry and within HMGA2 in African-American samples. Fourth, a multiethnic meta-analysis of all 39 studies identified T2D-associated variants in BCL2 (p = 2.1 × 10(-8)). Finally, a composite genetic score of SNPs from new and established T2D signals was significantly associated with increased risk of diabetes in African-American, Hispanic, and Asian populations. In summary, large-scale meta-analysis involving a dense gene-centric approach has uncovered additional loci and variants that contribute to T2D risk and suggests substantial overlap of T2D association signals across multiple ethnic groups. PMID:22325160

  18. An experimental study of heat transfer in a large-scale turbine rotor passage

    SciTech Connect

    Blair, M.F. )

    1994-01-01

    An experimental study of the heat transfer distribution in a turbine rotor passage was conducted in a large-scale, ambient temperature, rotating turbine model. Heat transfer was measured for both the full-span suction and pressure surfaces of the airfoil and for the hub endwall surface. The objective of this program was to document the effects of flow three dimensionality on the heat transfer in a rotating blade row (versus a stationary cascade). Of particular interest were the effects of the hub and tip secondary flows, tip leakage, and the leading-edge horseshoe vortex system. The effect of surface roughness on the passage heat transfer was also investigated. Midspan results are compared with both smooth-wall and rough-wall finite-difference two-dimensional heat transfer predictions. Contour maps of Stanton number for both the rotor airfoil and endwall surfaces revealed numerous regions of high heat transfer produced by the three-dimensional flows within the rotor passage. Of particular importance are regions of local enhancement (as much as 100 percent over midspan values) produced on the airfoil suction surface by the secondary flows and tip-leakage vortices an on the hub endwall by the leading-edge horseshoe vortex system.

  19. Analytical Study on the Cosmological Large-scale Structure in an Accelerating Universe

    NASA Astrophysics Data System (ADS)

    Wang, Xin

    2012-01-01

    Motivated by the roughly log-normal probability density distribution function (PDF) of the small scale density field, we develop cosmological perturbation theory for the power spectrum of a logarithmically transformed density field with the formalism which is developed in the context of the cosmological renormalized perturbation theory. Compared with the standard perturbation theory, our approach help to regulate the convergence behavior of the perturbation series, and of the Taylor series expansion we use for the logarithmic mapping. The perturbation calculation achieved good agreement with simulation results. Then we consider the topology of the iso-density contour of the density field, especially the genus. The genus is relatively insensitive to nonlinear gravitational evolution, clustering bias and redshift distortion, and is approximately conserved over time as structures grow in Einstein's general relativity, hence it can be used as a robust standard ruler for cosmological measurements. However, in modified gravity models where structures grow with different rates on different scales, the genus should change over time, and therefore it can be used to test the gravity models on large scales. We studied the case of the f(R) theory, DGP brane-world theory as well as phenomenological models. We also forecast how the modified gravity models can be constrained with optical/IR or 21cm surveys in the near future.

  20. An experimental study of heat transfer in a large-scale turbine rotor passage

    NASA Technical Reports Server (NTRS)

    Blair, Michael F.

    1992-01-01

    An experimental study of the heat transfer distribution in a turbine rotor passage was conducted in a large-scale, ambient temperature, rotating turbine model. Heat transfer was measured for both the full-span suction and pressure surfaces of the airfoil as well as for the hub endwall surface. The objective of this program was to document the effects of flow three-dimensionality on the heat transfer in a rotating blade row (vs a stationary cascade). Of particular interest were the effects of the hub and tip secondary flows, tip leakage and the leading-edge horseshoe vortex system. The effect of surface roughness on the passage heat transfer was also investigated. Midspan results are compared with both smooth-wall and rough-wall finite-difference two-dimensional heat transfer predictions. Contour maps of Stanton number for both the rotor airfoil and endwall surfaces revealed numerous regions of high heat transfer produced by the three-dimensional flows within the rotor passage. Of particular importance are regions of local enhancement (as much as 100 percent over midspan values) produced on the airfoil suction surface by the secondary flows and tip-leakage vortices and on the hub endwall by the leading-edge horseshoe vortex system.

  1. Large-Scale Recombinant Expression and Purification of Human Tyrosinase Suitable for Structural Studies.

    PubMed

    Lai, Xuelei; Soler-Lopez, Montserrat; Wichers, Harry J; Dijkstra, Bauke W

    2016-01-01

    Human tyrosinase (TYR) is a glycoprotein that initiates the first two reactions in the melanin biosynthesis pathway. Mutations in its encoding gene cause Oculocutaneous Albinism type I (OCA1), the most severe form of albinism, which is a group of autosomal recessive disorders characterized by reduced or absent production of melanin in skin, hair and eyes. Despite extensive structural and characterization studies of its homologues in lower eukaryotic organisms, the catalytic mechanism of human TYR and the molecular basis of OCA1 are largely unknown. In this work, we have carried out a large-scale recombinant expression of TYR that has enabled us to obtain high yields of pure and active protein, required for crystallization trials and screening of skin whitening agents, which is highly demanded in the cosmetic industry. Addition of an N-terminal honeybee melittin signal peptide for secretion of the produced protein into the (protein-free) medium, as well as a cleavable His-tag at the C-terminus, was crucial for increasing the yield of pure protein. We have successfully crystallized two TYR variants, in both glycosylated and deglycosylated forms, showing preliminary X-ray diffraction patterns at 3.5 Å resolution. Hence, we have established an expression and purification protocol suitable for the crystal structure determination of human TYR, which will give unique atomic insight into the nature and conformation of the residues that shape the substrate binding pocket that will ultimately lead to efficient compound design. PMID:27551823

  2. Prospective large-scale field study generates predictive model identifying major contributors to colony losses.

    PubMed

    Kielmanowicz, Merav Gleit; Inberg, Alex; Lerner, Inbar Maayan; Golani, Yael; Brown, Nicholas; Turner, Catherine Louise; Hayes, Gerald J R; Ballam, Joan M

    2015-04-01

    Over the last decade, unusually high losses of colonies have been reported by beekeepers across the USA. Multiple factors such as Varroa destructor, bee viruses, Nosema ceranae, weather, beekeeping practices, nutrition, and pesticides have been shown to contribute to colony losses. Here we describe a large-scale controlled trial, in which different bee pathogens, bee population, and weather conditions across winter were monitored at three locations across the USA. In order to minimize influence of various known contributing factors and their interaction, the hives in the study were not treated with antibiotics or miticides. Additionally, the hives were kept at one location and were not exposed to potential stress factors associated with migration. Our results show that a linear association between load of viruses (DWV or IAPV) in Varroa and bees is present at high Varroa infestation levels (>3 mites per 100 bees). The collection of comprehensive data allowed us to draw a predictive model of colony losses and to show that Varroa destructor, along with bee viruses, mainly DWV replication, contributes to approximately 70% of colony losses. This correlation further supports the claim that insufficient control of the virus-vectoring Varroa mite would result in increased hive loss. The predictive model also indicates that a single factor may not be sufficient to trigger colony losses, whereas a combination of stressors appears to impact hive health. PMID:25875764

  3. Prospective Large-Scale Field Study Generates Predictive Model Identifying Major Contributors to Colony Losses

    PubMed Central

    Kielmanowicz, Merav Gleit; Inberg, Alex; Lerner, Inbar Maayan; Golani, Yael; Brown, Nicholas; Turner, Catherine Louise; Hayes, Gerald J. R.; Ballam, Joan M.

    2015-01-01

    Over the last decade, unusually high losses of colonies have been reported by beekeepers across the USA. Multiple factors such as Varroa destructor, bee viruses, Nosema ceranae, weather, beekeeping practices, nutrition, and pesticides have been shown to contribute to colony losses. Here we describe a large-scale controlled trial, in which different bee pathogens, bee population, and weather conditions across winter were monitored at three locations across the USA. In order to minimize influence of various known contributing factors and their interaction, the hives in the study were not treated with antibiotics or miticides. Additionally, the hives were kept at one location and were not exposed to potential stress factors associated with migration. Our results show that a linear association between load of viruses (DWV or IAPV) in Varroa and bees is present at high Varroa infestation levels (>3 mites per 100 bees). The collection of comprehensive data allowed us to draw a predictive model of colony losses and to show that Varroa destructor, along with bee viruses, mainly DWV replication, contributes to approximately 70% of colony losses. This correlation further supports the claim that insufficient control of the virus-vectoring Varroa mite would result in increased hive loss. The predictive model also indicates that a single factor may not be sufficient to trigger colony losses, whereas a combination of stressors appears to impact hive health. PMID:25875764

  4. Large-scale studies of spontaneous combustion of coal. Rept. of investigations/1991

    SciTech Connect

    Smith, A.C.; Miron, Y.; Lazzara, C.P.

    1991-01-01

    The U.S. Bureau of Mines constructed a large-scale facility to study the self-heating of a large coal mass under conditions that simulate a gob area of a mine. The insulated coal chamber can hold up to 13 short tons (st) of coal and is provided with a forced ventilation system and computer-controlled temperature and gas measurement systems to monitor the heat and mass transfer phenomena that occur in the coalbed. Three experiments were completed with high-volatile C bituminous coals that exhibited high spontaneous combustion potentials in laboratory-scale tests. In the first two tests, a sustained heating was not achieved. In the third test, temperatures throughout the coalbed increased steadily from the start, with thermal runaway occurring near the center of the coalbed after 23 days. The thermal reaction zone then moved toward the front of the coalbed. The results of these tests showed that the self-heating of a large coal mass depends not just on the reactivity of the coal, but also on the particle size of the coal, the freshness of the coal surfaces, the heat-of-wetting effect, and the availability of O2 at optimum ventilation rates.

  5. Large-Scale Recombinant Expression and Purification of Human Tyrosinase Suitable for Structural Studies

    PubMed Central

    Lai, Xuelei; Soler-Lopez, Montserrat; Wichers, Harry J.

    2016-01-01

    Human tyrosinase (TYR) is a glycoprotein that initiates the first two reactions in the melanin biosynthesis pathway. Mutations in its encoding gene cause Oculocutaneous Albinism type I (OCA1), the most severe form of albinism, which is a group of autosomal recessive disorders characterized by reduced or absent production of melanin in skin, hair and eyes. Despite extensive structural and characterization studies of its homologues in lower eukaryotic organisms, the catalytic mechanism of human TYR and the molecular basis of OCA1 are largely unknown. In this work, we have carried out a large-scale recombinant expression of TYR that has enabled us to obtain high yields of pure and active protein, required for crystallization trials and screening of skin whitening agents, which is highly demanded in the cosmetic industry. Addition of an N-terminal honeybee melittin signal peptide for secretion of the produced protein into the (protein-free) medium, as well as a cleavable His-tag at the C-terminus, was crucial for increasing the yield of pure protein. We have successfully crystallized two TYR variants, in both glycosylated and deglycosylated forms, showing preliminary X-ray diffraction patterns at 3.5 Å resolution. Hence, we have established an expression and purification protocol suitable for the crystal structure determination of human TYR, which will give unique atomic insight into the nature and conformation of the residues that shape the substrate binding pocket that will ultimately lead to efficient compound design. PMID:27551823

  6. Large-scale epitaxial growth kinetics of graphene: A kinetic Monte Carlo study

    SciTech Connect

    Jiang, Huijun; Hou, Zhonghuai

    2015-08-28

    Epitaxial growth via chemical vapor deposition is considered to be the most promising way towards synthesizing large area graphene with high quality. However, it remains a big theoretical challenge to reveal growth kinetics with atomically energetic and large-scale spatial information included. Here, we propose a minimal kinetic Monte Carlo model to address such an issue on an active catalyst surface with graphene/substrate lattice mismatch, which facilitates us to perform large scale simulations of the growth kinetics over two dimensional surface with growth fronts of complex shapes. A geometry-determined large-scale growth mechanism is revealed, where the rate-dominating event is found to be C{sub 1}-attachment for concave growth-front segments and C{sub 5}-attachment for others. This growth mechanism leads to an interesting time-resolved growth behavior which is well consistent with that observed in a recent scanning tunneling microscopy experiment.

  7. Large-Scale Genome-Wide Association Studies and Meta-Analyses of Longitudinal Change in Adult Lung Function

    PubMed Central

    Tang, Wenbo; Kowgier, Matthew; Loth, Daan W.; Soler Artigas, María; Joubert, Bonnie R.; Hodge, Emily; Gharib, Sina A.; Smith, Albert V.; Ruczinski, Ingo; Gudnason, Vilmundur; Mathias, Rasika A.; Harris, Tamara B.; Hansel, Nadia N.; Launer, Lenore J.; Barnes, Kathleen C.; Hansen, Joyanna G.; Albrecht, Eva; Aldrich, Melinda C.; Allerhand, Michael; Barr, R. Graham; Brusselle, Guy G.; Couper, David J.; Curjuric, Ivan; Davies, Gail; Deary, Ian J.; Dupuis, Josée; Fall, Tove; Foy, Millennia; Franceschini, Nora; Gao, Wei; Gläser, Sven; Gu, Xiangjun; Hancock, Dana B.; Heinrich, Joachim; Hofman, Albert; Imboden, Medea; Ingelsson, Erik; James, Alan; Karrasch, Stefan; Koch, Beate; Kritchevsky, Stephen B.; Kumar, Ashish; Lahousse, Lies; Li, Guo; Lind, Lars; Lindgren, Cecilia; Liu, Yongmei; Lohman, Kurt; Lumley, Thomas; McArdle, Wendy L.; Meibohm, Bernd; Morris, Andrew P.; Morrison, Alanna C.; Musk, Bill; North, Kari E.; Palmer, Lyle J.; Probst-Hensch, Nicole M.; Psaty, Bruce M.; Rivadeneira, Fernando; Rotter, Jerome I.; Schulz, Holger; Smith, Lewis J.; Sood, Akshay; Starr, John M.; Strachan, David P.; Teumer, Alexander; Uitterlinden, André G.; Völzke, Henry; Voorman, Arend; Wain, Louise V.; Wells, Martin T.; Wilk, Jemma B.; Williams, O. Dale; Heckbert, Susan R.; Stricker, Bruno H.; London, Stephanie J.; Fornage, Myriam; Tobin, Martin D.; O′Connor, George T.; Hall, Ian P.; Cassano, Patricia A.

    2014-01-01

    Background Genome-wide association studies (GWAS) have identified numerous loci influencing cross-sectional lung function, but less is known about genes influencing longitudinal change in lung function. Methods We performed GWAS of the rate of change in forced expiratory volume in the first second (FEV1) in 14 longitudinal, population-based cohort studies comprising 27,249 adults of European ancestry using linear mixed effects model and combined cohort-specific results using fixed effect meta-analysis to identify novel genetic loci associated with longitudinal change in lung function. Gene expression analyses were subsequently performed for identified genetic loci. As a secondary aim, we estimated the mean rate of decline in FEV1 by smoking pattern, irrespective of genotypes, across these 14 studies using meta-analysis. Results The overall meta-analysis produced suggestive evidence for association at the novel IL16/STARD5/TMC3 locus on chromosome 15 (P  =  5.71 × 10-7). In addition, meta-analysis using the five cohorts with ≥3 FEV1 measurements per participant identified the novel ME3 locus on chromosome 11 (P  =  2.18 × 10-8) at genome-wide significance. Neither locus was associated with FEV1 decline in two additional cohort studies. We confirmed gene expression of IL16, STARD5, and ME3 in multiple lung tissues. Publicly available microarray data confirmed differential expression of all three genes in lung samples from COPD patients compared with controls. Irrespective of genotypes, the combined estimate for FEV1 decline was 26.9, 29.2 and 35.7 mL/year in never, former, and persistent smokers, respectively. Conclusions In this large-scale GWAS, we identified two novel genetic loci in association with the rate of change in FEV1 that harbor candidate genes with biologically plausible functional links to lung function. PMID:24983941

  8. A general framework for association tests with multivariate traits in large-scale genomics studies.

    PubMed

    He, Qianchuan; Avery, Christy L; Lin, Dan-Yu

    2013-12-01

    Genetic association studies often collect data on multiple traits that are correlated. Discovery of genetic variants influencing multiple traits can lead to better understanding of the etiology of complex human diseases. Conventional univariate association tests may miss variants that have weak or moderate effects on individual traits. We propose several multivariate test statistics to complement univariate tests. Our framework covers both studies of unrelated individuals and family studies and allows any type/mixture of traits. We relate the marginal distributions of multivariate traits to genetic variants and covariates through generalized linear models without modeling the dependence among the traits or family members. We construct score-type statistics, which are computationally fast and numerically stable even in the presence of covariates and which can be combined efficiently across studies with different designs and arbitrary patterns of missing data. We compare the power of the test statistics both theoretically and empirically. We provide a strategy to determine genome-wide significance that properly accounts for the linkage disequilibrium (LD) of genetic variants. The application of the new methods to the meta-analysis of five major cardiovascular cohort studies identifies a new locus (HSCB) that is pleiotropic for the four traits analyzed. PMID:24227293

  9. RACORO continental boundary layer cloud investigations: 1. Case study development and ensemble large-scale forcings

    NASA Astrophysics Data System (ADS)

    Vogelmann, Andrew M.; Fridlind, Ann M.; Toto, Tami; Endo, Satoshi; Lin, Wuyin; Wang, Jian; Feng, Sha; Zhang, Yunyan; Turner, David D.; Liu, Yangang; Li, Zhijin; Xie, Shaocheng; Ackerman, Andrew S.; Zhang, Minghua; Khairoutdinov, Marat

    2015-06-01

    Observation-based modeling case studies of continental boundary layer clouds have been developed to study cloudy boundary layers, aerosol influences upon them, and their representation in cloud- and global-scale models. Three 60 h case study periods span the temporal evolution of cumulus, stratiform, and drizzling boundary layer cloud systems, representing mixed and transitional states rather than idealized or canonical cases. Based on in situ measurements from the Routine AAF (Atmospheric Radiation Measurement (ARM) Aerial Facility) CLOWD (Clouds with Low Optical Water Depth) Optical Radiative Observations (RACORO) field campaign and remote sensing observations, the cases are designed with a modular configuration to simplify use in large-eddy simulations (LES) and single-column models. Aircraft measurements of aerosol number size distribution are fit to lognormal functions for concise representation in models. Values of the aerosol hygroscopicity parameter, κ, are derived from observations to be ~0.10, which are lower than the 0.3 typical over continents and suggestive of a large aerosol organic fraction. Ensemble large-scale forcing data sets are derived from the ARM variational analysis, European Centre for Medium-Range Weather Forecasts, and a multiscale data assimilation system. The forcings are assessed through comparison of measured bulk atmospheric and cloud properties to those computed in "trial" large-eddy simulations, where more efficient run times are enabled through modest reductions in grid resolution and domain size compared to the full-sized LES grid. Simulations capture many of the general features observed, but the state-of-the-art forcings were limited at representing details of cloud onset, and tight gradients and high-resolution transients of importance. Methods for improving the initial conditions and forcings are discussed. The cases developed are available to the general modeling community for studying continental boundary clouds.

  10. Large-scale structure studies with the unresolved CXB - Challenges from XBOOTES

    NASA Astrophysics Data System (ADS)

    Kolodzig, Alexander; Gilfanov, Marat; Hütsi, Gert; Sunyaev, Rashid

    2015-08-01

    The scientific significance of large-scale structure (LSS) studies with X-ray surveys can be greatly enhanced by analysis of the surface brightness fluctuations of the unresolved cosmic X-ray background (CXB). It enables us to study the clustering properties of source populations, which are otherwise inaccessible with clustering studies of resolved sources of current X-ray surveys due to the lack of deep-wide surveys and selection effects.We have conducted the most accurate measurement to date of the brightness fluctuations of the unresolved CXB in the 0.5-2.0keV band for angular scales of <~17', using XBOOTES, the currently largest continuous Chandra survey (~9 deg2).We find that on small angular scales (<~2') the observed power spectrum of the brightness fluctuations is broadly consistent with the conventional AGN clustering model, although with a ~30% deviation. This deviation demonstrates the current poor knowledge of the clustering properties of AGN within their dark matter halo (DMH). We provide possible explanations for this deviation.For angular scales of >~2' we measure a significant excess with up to an order of magnitude difference in comparison to the standard AGN clustering model. We demonstrate that an instrumental origin can be excluded but also that it can neither be explained with any known X-ray source population based on its clustering strength and the shape of its energy spectrum. We speculate that the excess is caused by more than one type of source and that its dominant source appears to have extragalactic origin.Finally, we make predictions on how the eROSITA all-sky survey (eRASS) will be able to advance the studies of the unresolved CXB.

  11. RACORO Continental Boundary Layer Cloud Investigations: 1. Case Study Development and Ensemble Large-Scale Forcings

    NASA Technical Reports Server (NTRS)

    Vogelmann, Andrew M.; Fridlind, Ann M.; Toto, Tami; Endo, Satoshi; Lin, Wuyin; Wang, Jian; Feng, Sha; Zhang, Yunyan; Turner, David D.; Liu, Yangang; Li, Zhijin; Xie, Shaocheng; Ackerman, Andrew S.; Zhang, Minghua; Khairoutdinov, Marat

    2015-01-01

    Observation-based modeling case studies of continental boundary layer clouds have been developed to study cloudy boundary layers, aerosol influences upon them, and their representation in cloud- and global-scale models. Three 60 h case study periods span the temporal evolution of cumulus, stratiform, and drizzling boundary layer cloud systems, representing mixed and transitional states rather than idealized or canonical cases. Based on in situ measurements from the Routine AAF (Atmospheric Radiation Measurement (ARM) Aerial Facility) CLOWD (Clouds with Low Optical Water Depth) Optical Radiative Observations (RACORO) field campaign and remote sensing observations, the cases are designed with a modular configuration to simplify use in large-eddy simulations (LES) and single-column models. Aircraft measurements of aerosol number size distribution are fit to lognormal functions for concise representation in models. Values of the aerosol hygroscopicity parameter, kappa, are derived from observations to be approximately 0.10, which are lower than the 0.3 typical over continents and suggestive of a large aerosol organic fraction. Ensemble large-scale forcing data sets are derived from the ARM variational analysis, European Centre for Medium-Range Weather Forecasts, and a multiscale data assimilation system. The forcings are assessed through comparison of measured bulk atmospheric and cloud properties to those computed in "trial" large-eddy simulations, where more efficient run times are enabled through modest reductions in grid resolution and domain size compared to the full-sized LES grid. Simulations capture many of the general features observed, but the state-of-the-art forcings were limited at representing details of cloud onset, and tight gradients and high-resolution transients of importance. Methods for improving the initial conditions and forcings are discussed. The cases developed are available to the general modeling community for studying continental boundary

  12. Observational and Model Studies of Large-Scale Mixing Processes in the Stratosphere

    NASA Technical Reports Server (NTRS)

    Bowman, Kenneth P.

    1997-01-01

    The following is the final technical report for grant NAGW-3442, 'Observational and Model Studies of Large-Scale Mixing Processes in the Stratosphere'. Research efforts in the first year concentrated on transport and mixing processes in the polar vortices. Three papers on mixing in the Antarctic were published. The first was a numerical modeling study of wavebreaking and mixing and their relationship to the period of observed stratospheric waves (Bowman). The second paper presented evidence from TOMS for wavebreaking in the Antarctic (Bowman and Mangus 1993). The third paper used Lagrangian trajectory calculations from analyzed winds to show that there is very little transport into the Antarctic polar vortex prior to the vortex breakdown (Bowman). Mixing is significantly greater at lower levels. This research helped to confirm theoretical arguments for vortex isolation and data from the Antarctic field experiments that were interpreted as indicating isolation. A Ph.D. student, Steve Dahlberg, used the trajectory approach to investigate mixing and transport in the Arctic. While the Arctic vortex is much more disturbed than the Antarctic, there still appears to be relatively little transport across the vortex boundary at 450 K prior to the vortex breakdown. The primary reason for the absence of an ozone hole in the Arctic is the earlier warming and breakdown of the vortex compared to the Antarctic, not replenishment of ozone by greater transport. Two papers describing these results have appeared (Dahlberg and Bowman; Dahlberg and Bowman). Steve Dahlberg completed his Ph.D. thesis (Dahlberg and Bowman) and is now teaching in the Physics Department at Concordia College. We also prepared an analysis of the QBO in SBUV ozone data (Hollandsworth et al.). A numerical study in collaboration with Dr. Ping Chen investigated mixing by barotropic instability, which is the probable origin of the 4-day wave in the upper stratosphere (Bowman and Chen). The important result from

  13. [The benefit of large-scale cohort studies for health research: the example of the German National Cohort].

    PubMed

    Ahrens, Wolfgang; Jöckel, K-H

    2015-08-01

    The prospective nature of large-scale epidemiological multi-purpose cohort studies with long observation periods facilitates the search for complex causes of diseases, the analysis of the natural history of diseases and the identification of novel pre-clinical markers of disease. The German National Cohort (GNC) is a population-based, highly standardised and in-depth phenotyped cohort. It shall create the basis for new strategies for risk assessment and identification, early diagnosis and prevention of multifactorial diseases. The GNC is the largest population-based cohort study in Germany to date. In the year 2014 the examination of 200,000 women and men aged 20-69 years started in 18 study centers. The study facilitates the investigation of the etiology of chronic diseases in relation to lifestyle, genetic, socioeconomic, psychosocial and environmental factors. By this the GNC creates the basis for the development of methods for early diagnosis and prevention of these diseases. Cardiovascular and respiratory diseases, cancer, diabetes, neurodegenerative/-psychiatric diseases, musculoskeletal and infectious diseases are in focus of this study. Due to its mere size, the study could be characterized as a Big Data project. We deduce that this is not the case. PMID:26077870

  14. Understanding Participation in E-Learning in Organizations: A Large-Scale Empirical Study of Employees

    ERIC Educational Resources Information Center

    Garavan, Thomas N.; Carbery, Ronan; O'Malley, Grace; O'Donnell, David

    2010-01-01

    Much remains unknown in the increasingly important field of e-learning in organizations. Drawing on a large-scale survey of employees (N = 557) who had opportunities to participate in voluntary e-learning activities, the factors influencing participation in e-learning are explored in this empirical paper. It is hypothesized that key variables…

  15. Numerics-Characteristics-Asymptotics: A Case Study from Large Scale Ocean Circulation

    ERIC Educational Resources Information Center

    Hodnett, P. F.; Courtney, C.

    2007-01-01

    This paper uses a partial differential equation which occurs in a reduced model of large scale circulation in an ocean basin as an educational vehicle through which to demonstrate the usefulness of a set of mathematical techniques in analysing the equation. A parameter occurring in the equation does in reality vary from very small through…

  16. Study of the structure and physical properties of quasicrystals using large scale facilities

    NASA Astrophysics Data System (ADS)

    de Boissieu, Marc

    2012-04-01

    Quasicrystals have been puzzling scientists since their discovery. In this article we review some of the recent advances in this field and show how the use of large scale facilities has brought in decisive information for the understanding of their structure and physical properties.

  17. Image-guided Coring for Large-scale Studies in Molecular Pathology.

    PubMed

    Montaser-Kouhsari, Laleh; Knoblauch, Nicholas W; Oh, Eun-Yeong; Baker, Gabrielle; Christensen, Stephen; Hazra, Aditi; Tamimi, Rulla M; Beck, Andrew H

    2016-07-01

    Sampling of formalin-fixed paraffin-embedded (FFPE) tissue blocks is a critical initial step in molecular pathology. Image-guided coring (IGC) is a new method for using digital pathology images to guide tissue block coring for molecular analyses. The goal of our study is to evaluate the use of IGC for both tissue-based and nucleic acid-based projects in molecular pathology. First, we used IGC to construct a tissue microarray (TMA); second, we used IGC for FFPE block sampling followed by RNA extraction; and third, we assessed the correlation between nuclear counts quantitated from the IGC images and RNA yields. We used IGC to construct a TMA containing 198 normal and breast cancer cores. Histopathologic analysis showed high accuracy for obtaining tumor and normal breast tissue. Next, we used IGC to obtain normal and tumor breast samples before RNA extraction. We selected a random subset of tumor and normal samples to perform computational image analysis to quantify nuclear density, and we built regression models to estimate RNA yields from nuclear count, age of the block, and core diameter. Number of nuclei and core diameter were the strongest predictors of RNA yields in both normal and tumor tissue. IGC is an effective method for sampling FFPE tissue blocks for TMA construction and nucleic acid extraction. We identify significant associations between quantitative nuclear counts obtained from IGC images and RNA yields, suggesting that the integration of computational image analysis with IGC may be an effective approach for tumor sampling in large-scale molecular studies. PMID:26186251

  18. The R3/R5 impoundment study: a large-scale management experiment

    USGS Publications Warehouse

    Lyons, J.E.; Laskowski, H.P.; Runge, M.C.; Lor, S.; Kendall, W.L.; Talbott, S.

    2005-01-01

    Managed wetlands provide a broad spectrum of resources to migratory waterbirds (shorebirds, wading birds, and waterfowl) throughout the annual cycle. Successful conservation and management of waterbirds depends on integrated approaches that (1) incorporate larger spatial and temporal scales than traditional approaches to wetland management, and (2) use experimental designs to reduce uncertainty about the response of the systems to management. In a previous experiment on USFWS National Wildlife Refuges in the Northeast, we explored the effects of water-level management on migratory shorebirds in spring. We documented regional patterns of shorebird use of Refuge wetlands and showed that across the region, a slow drawdown was superior to 2 alternatives. USGS and USFWS have now cooperatively undertaken an expanded study focusing on 3 waterbird guilds in the context of the complete annual cycle and over a larger spatial extent. For this 3-yr study, now in its first year, 2 impoundments were selected at each of 23 NWRs across the Northeast and Upper Midwest Regions. Two experimental treatments (annual water regimes focused on early-season or late-season drawdowns) are being applied each year in a cross-over design. This experimental design will increase our understanding of cross-seasonal interactions which result from specific hydrologic regimes aimed at a particular waterbird guild. Monitoring will allow waterbird responses to be linked with direct effects of water management on plant and invertebrate populations. Results of this large-scale experiment will be used to motivate formal adaptive management of wetlands and waterbirds at refuges following completion of this experiment.

  19. Image-guided Coring for Large-scale Studies in Molecular Pathology

    PubMed Central

    Montaser-Kouhsari, Laleh; Knoblauch, Nicholas W.; Oh, Eun-Yeong; Baker, Gabrielle; Christensen, Stephen; Hazra, Aditi; Tamimi, Rulla M.

    2016-01-01

    Sampling of formalin-fixed paraffin-embedded (FFPE) tissue blocks is a critical initial step in molecular pathology. Image-guided coring (IGC) is a new method for using digital pathology images to guide tissue block coring for molecular analyses. The goal of our study is to evaluate the use of IGC for both tissue-based and nucleic acid–based projects in molecular pathology. First, we used IGC to construct a tissue microarray (TMA); second, we used IGC for FFPE block sampling followed by RNA extraction; and third, we assessed the correlation between nuclear counts quantitated from the IGC images and RNA yields. We used IGC to construct a TMA containing 198 normal and breast cancer cores. Histopathologic analysis showed high accuracy for obtaining tumor and normal breast tissue. Next, we used IGC to obtain normal and tumor breast samples before RNA extraction. We selected a random subset of tumor and normal samples to perform computational image analysis to quantify nuclear density, and we built regression models to estimate RNA yields from nuclear count, age of the block, and core diameter. Number of nuclei and core diameter were the strongest predictors of RNA yields in both normal and tumor tissue. IGC is an effective method for sampling FFPE tissue blocks for TMA construction and nucleic acid extraction. We identify significant associations between quantitative nuclear counts obtained from IGC images and RNA yields, suggesting that the integration of computational image analysis with IGC may be an effective approach for tumor sampling in large-scale molecular studies. PMID:26186251

  20. LUCI: A facility at DUSEL for large-scale experimental study of geologic carbon sequestration

    SciTech Connect

    Peters, C. A.; Dobson, P.F.; Oldenburg, C.M.; Wang, J. S. Y.; Onstott, T.C.; Scherer, G.W.; Freifeld, B.M.; Ramakrishnan, T.S.; Stabinski, E.L.; Liang, K.; Verma, S.

    2010-10-01

    LUCI, the Laboratory for Underground CO{sub 2} Investigations, is an experimental facility being planned for the DUSEL underground laboratory in South Dakota, USA. It is designed to study vertical flow of CO{sub 2} in porous media over length scales representative of leakage scenarios in geologic carbon sequestration. The plan for LUCI is a set of three vertical column pressure vessels, each of which is {approx}500 m long and {approx}1 m in diameter. The vessels will be filled with brine and sand or sedimentary rock. Each vessel will have an inner column to simulate a well for deployment of down-hole logging tools. The experiments are configured to simulate CO{sub 2} leakage by releasing CO{sub 2} into the bottoms of the columns. The scale of the LUCI facility will permit measurements to study CO{sub 2} flow over pressure and temperature variations that span supercritical to subcritical gas conditions. It will enable observation or inference of a variety of relevant processes such as buoyancy-driven flow in porous media, Joule-Thomson cooling, thermal exchange, viscous fingering, residual trapping, and CO{sub 2} dissolution. Experiments are also planned for reactive flow of CO{sub 2} and acidified brines in caprock sediments and well cements, and for CO{sub 2}-enhanced methanogenesis in organic-rich shales. A comprehensive suite of geophysical logging instruments will be deployed to monitor experimental conditions as well as provide data to quantify vertical resolution of sensor technologies. The experimental observations from LUCI will generate fundamental new understanding of the processes governing CO{sub 2} trapping and vertical migration, and will provide valuable data to calibrate and validate large-scale model simulations.

  1. Research guidelines in the era of large-scale collaborations: an analysis of Genome-wide Association Study Consortia.

    PubMed

    Austin, Melissa A; Hair, Marilyn S; Fullerton, Stephanie M

    2012-05-01

    Scientific research has shifted from studies conducted by single investigators to the creation of large consortia. Genetic epidemiologists, for example, now collaborate extensively for genome-wide association studies (GWAS). The effect has been a stream of confirmed disease-gene associations. However, effects on human subjects oversight, data-sharing, publication and authorship practices, research organization and productivity, and intellectual property remain to be examined. The aim of this analysis was to identify all research consortia that had published the results of a GWAS analysis since 2005, characterize them, determine which have publicly accessible guidelines for research practices, and summarize the policies in these guidelines. A review of the National Human Genome Research Institute's Catalog of Published Genome-Wide Association Studies identified 55 GWAS consortia as of April 1, 2011. These consortia were comprised of individual investigators, research centers, studies, or other consortia and studied 48 different diseases or traits. Only 14 (25%) were found to have publicly accessible research guidelines on consortia websites. The available guidelines provide information on organization, governance, and research protocols; half address institutional review board approval. Details of publication, authorship, data-sharing, and intellectual property vary considerably. Wider access to consortia guidelines is needed to establish appropriate research standards with broad applicability to emerging forms of large-scale collaboration. PMID:22491085

  2. Research Guidelines in the Era of Large-scale Collaborations: An Analysis of Genome-wide Association Study Consortia

    PubMed Central

    Austin, Melissa A.; Hair, Marilyn S.; Fullerton, Stephanie M.

    2012-01-01

    Scientific research has shifted from studies conducted by single investigators to the creation of large consortia. Genetic epidemiologists, for example, now collaborate extensively for genome-wide association studies (GWAS). The effect has been a stream of confirmed disease-gene associations. However, effects on human subjects oversight, data-sharing, publication and authorship practices, research organization and productivity, and intellectual property remain to be examined. The aim of this analysis was to identify all research consortia that had published the results of a GWAS analysis since 2005, characterize them, determine which have publicly accessible guidelines for research practices, and summarize the policies in these guidelines. A review of the National Human Genome Research Institute’s Catalog of Published Genome-Wide Association Studies identified 55 GWAS consortia as of April 1, 2011. These consortia were comprised of individual investigators, research centers, studies, or other consortia and studied 48 different diseases or traits. Only 14 (25%) were found to have publicly accessible research guidelines on consortia websites. The available guidelines provide information on organization, governance, and research protocols; half address institutional review board approval. Details of publication, authorship, data-sharing, and intellectual property vary considerably. Wider access to consortia guidelines is needed to establish appropriate research standards with broad applicability to emerging forms of large-scale collaboration. PMID:22491085

  3. Evaluation of Kirkwood-Buff integrals via finite size scaling: a large scale molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Dednam, W.; Botha, A. E.

    2015-01-01

    Solvation of bio-molecules in water is severely affected by the presence of co-solvent within the hydration shell of the solute structure. Furthermore, since solute molecules can range from small molecules, such as methane, to very large protein structures, it is imperative to understand the detailed structure-function relationship on the microscopic level. For example, it is useful know the conformational transitions that occur in protein structures. Although such an understanding can be obtained through large-scale molecular dynamic simulations, it is often the case that such simulations would require excessively large simulation times. In this context, Kirkwood-Buff theory, which connects the microscopic pair-wise molecular distributions to global thermodynamic properties, together with the recently developed technique, called finite size scaling, may provide a better method to reduce system sizes, and hence also the computational times. In this paper, we present molecular dynamics trial simulations of biologically relevant low-concentration solvents, solvated by aqueous co-solvent solutions. In particular we compare two different methods of calculating the relevant Kirkwood-Buff integrals. The first (traditional) method computes running integrals over the radial distribution functions, which must be obtained from large system-size NVT or NpT simulations. The second, newer method, employs finite size scaling to obtain the Kirkwood-Buff integrals directly by counting the particle number fluctuations in small, open sub-volumes embedded within a larger reservoir that can be well approximated by a much smaller simulation cell. In agreement with previous studies, which made a similar comparison for aqueous co-solvent solutions, without the additional solvent, we conclude that the finite size scaling method is also applicable to the present case, since it can produce computationally more efficient results which are equivalent to the more costly radial distribution

  4. Studying large-scale programmes to improve patient safety in whole care systems: challenges for research.

    PubMed

    Benn, Jonathan; Burnett, Susan; Parand, Anam; Pinto, Anna; Iskander, Sandra; Vincent, Charles

    2009-12-01

    Large-scale national and multi-institutional patient safety improvement programmes are being developed in the health care systems of several countries to address problems in the reliability of care delivered to patients. Drawing upon popular collaborative improvement models, these campaigns are ambitious in their aims to improve patient safety in macro-level systems such as whole health care organisations. This article considers the methodological issues involved in conducting research and evaluation of these programmes. Several specific research challenges are outlined, which result from the complexity of longitudinal, multi-level intervention programmes and the variable, highly sociotechnical care systems, with which they interact. Organisational-level improvement programmes are often underspecified due to local variations in context and organisational readiness for improvement work. The result is variable implementation patterns and local adaptations. Programme effects span levels and other boundaries within a system, vary dynamically or are cumulative over time and are problematic to understand in terms of cause and effect, where concurrent external influences exist and the impact upon study endpoints may be mediated by a range of organisational and social factors. We outline the methodological approach to research in the United Kingdom Safer Patients Initiative, to exemplify how some of the challenges for research in this area can be met through a multi-method, longitudinal research design. Specifically, effective research designs must be sensitive to complex variation, through employing multiple qualitative and quantitative measures, collect data over time to understand change and utilise descriptive techniques to capture specific interactions between programme and context for implementation. When considering the long-term, sustained impact of an improvement programme, researchers must consider how to define and measure the capability for continuous safe and

  5. Exploring the feasibility of using copy number variants as genetic markers through large-scale whole genome sequencing experiments

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Copy number variants (CNV) are large scale duplications or deletions of genomic sequence that are caused by a diverse set of molecular phenomena that are distinct from single nucleotide polymorphism (SNP) formation. Due to their different mechanisms of formation, CNVs are often difficult to track us...

  6. Study of Aerodynamic Design Procedure of a Large-Scale Aircraft Noise Suppression Facility

    NASA Astrophysics Data System (ADS)

    Kawai, Masafumi; Nagai, Kiyoyuki; Aso, Shigeru

    The aerodynamic design procedure of a large-scale aircraft noise suppression facility has been developed. Flow quality required for the engine inlet flow has been determined through basic experiment. Aerodynamic design of the facility has been performed by using wind tunnel experiment and CFD. Important relationship between the length of the facility and the inlet flow quality has been found. The operational envelope of the designed facility has been estimated. Then, the aerodynamic characteristics of an actual large-scale aircraft noise suppression facility, constructed based on the new design procedure, have been measured. Obtained flow field showed good agreement with CFD results, and the effectiveness of the design procedure based on CFD and wind tunnel experiment has been confirmed. The engine operations were satisfactory under various wind conditions. Furthermore, the data under commercial operations thereafter have been collected and analyzed. As the result, the aerodynamic design procedure has been validated.

  7. Study of very-large-scale motions in turbulent pipe flow

    NASA Astrophysics Data System (ADS)

    Lee, Jae Hwa; Sung, Hyung Jin

    2012-11-01

    Direct numerical simulation (DNS) of turbulent pipe flow was performed at Reτ=544 to investigate the spatial organization of the very large-scale motions (VLSMs). The streamwise domain length employed here was 30 R, where R is the pipe radius. Inspection of the three-dimensional instantaneous fields showed that adjacent large-scale packet-like structures combine to form the VLSMs, and this formation process was attributed to continuous stretching of the hairpins coupled with lifting-up and backward curling of the vortices. To support our results found in the analysis of the instantaneous flow fields, we applied the spatial filter to decompose the signal into two length scales related to the VLSMs and smaller structures. The resulting streamwise length scale from the streamwise two-point correlations showed that the magnitude of the correlations for the VLSMs is larger than that from the large-scale motions (LSMs) through all directions. In addition, the mean inclination angle to the wall for the smaller scale structures was found to be larger than that of the VLSMs. These findings support the previous conjecture of Kim & Adrian (1999) that the coherent alignment of LSMs creates the VLSMs. This work was supported by KISTI under the Strategic Supercomputing.

  8. Large Scale Numerical Modelling to Study the Dispersion of Persistent Toxic Substances Over Europe

    NASA Astrophysics Data System (ADS)

    Aulinger, A.; Petersen, G.

    2003-12-01

    For the past two decades environmental research at the GKSS Research Centre has been concerned with airborne pollutants with adverse effects on human health. The research was mainly focused on investigating the dispersion and deposition of heavy metals like lead and mercury over Europe by means of numerical modelling frameworks. Lead, in particular, served as a model substance to study the relationship between emissions and human exposition. The major source of airborne lead in Germany was fuel combustion until the 1980ies when its use as gasoline additive declined due to political decisions. Since then, the concentration of lead in ambient air and the deposition rates decreased in the same way as the consumption of leaded fuel. These observations could further be related to the decrease of lead concentrations in human blood measured during medical studies in several German cities. Based on the experience with models for heavy metal transport and deposition we have now started to turn our research focus to organic substances, e.g. PAHs. PAHs have been recognized as significant air borne carcinogens for several decades. However, it is not yet possible to precisely quantify the risk of human exposure to those compounds. Physical and chemical data, known from literature, describing the partitioning of the compounds between particle and gas phase and their degradation in the gas phase are implemented in a tropospheric chemistry module. In this way, the fate of PAHs in the atmosphere due to different particle type and size and different meteorological conditions is tested before carrying out large-scale and long-time studies. First model runs have been carried out for Benzo(a)Pyrene as one of the principal carcinogenic PAHs. Up to now, nearly nothing is known about degradation reactions of particle bound BaP. Thus, they could not be taken into account in the model so far. On the other hand, the proportion of BaP in the gas phase has to be considered at higher ambient

  9. Large-scale screening in sporadic amyotrophic lateral sclerosis identifies genetic modifiers in C9orf72 repeat carriers.

    PubMed

    Dekker, Annelot M; Seelen, Meinie; van Doormaal, Perry T C; van Rheenen, Wouter; Bothof, Reinoud J P; van Riessen, Tim; Brands, William J; van der Kooi, Anneke J; de Visser, Marianne; Voermans, Nicol C; Pasterkamp, R Jeroen; Veldink, Jan H; van den Berg, Leonard H; van Es, Michael A

    2016-03-01

    Sporadic amyotrophic lateral sclerosis (ALS) is considered to be a complex disease with multiple genetic risk factors contributing to the pathogenesis. Identification of genetic risk factors that co-occur frequently could provide relevant insight into underlying mechanisms of motor neuron degeneration. To dissect the genetic architecture of sporadic ALS, we undertook a large sequencing study in 755 apparently sporadic ALS cases and 959 controls, analyzing 10 ALS genes: SOD1, C9orf72, TARDBP, FUS, ANG, CHMP2B, ATXN2, NIPA1, SMN1, and UNC13A. We observed sporadic cases with multiple genetic risk variants in 4.1% compared with 1.3% in controls. The overall difference was not in excess of what is to be expected by chance (binomial test, p = 0.59). We did, however, observe a higher frequency than expected of C9orf72 repeat carriers with co-occurring susceptibility variants (ATXN2, NIPA1, and SMN1; p = 0.001), which is mainly because of the co-occurrence of NIPA1 repeats in 15% of C9orf72 repeat carriers (p = 0.006). PMID:26777436

  10. Development of Large-Scale Forcing Data for GoAmazon2014/5 Cloud Modeling Studies

    NASA Astrophysics Data System (ADS)

    Tang, S.; Xie, S.; Zhang, Y.; Schumacher, C.; Upton, H. M.; Ahlgrimm, M.; Feng, Z.

    2015-12-01

    The Observations and Modeling of the Green Ocean 2014-2015 (GoAmazon2014/5) field campaign is an international collaborated experiment conducted near Manaus, Brazil from January 2014 through December 2015. This experiment is designed to enable the study of aerosols, tropical clouds, convections and their interactions. To support modeling studies of these processes with data collected from the GoAmazon2014/5 campaign, we have developed a large-scale forcing data (e.g., vertical velocities and advective tendencies) during the second intensive operational period (IOP) of GoAmazon2014/5 from 1 Sep to 10 Oct, 2014. The method used in this study is the constrained variational analysis method in which the large-scale state fields are constrained by the surface and top-of-atmosphere observations (e.g. surface precipitation and outgoing longwave radiation) to conserve column-integrated mass, moisture and dry static energy. To address potential uncertainties in the derived forcing data due to uncertainties in surface precipitation, two sets of large-scale forcing data are developed based on the ECMWF analysis constrained by the two precipitation products respectively from SIPAM radar and TRMM 3B42 products. Our initial analysis shows large differences in these two precipitation products, which causes considerable differences in the derived large-scale forcing data. Potential uncertainties in the large-scale forcing data to other surface constraints such as surface latent and sensible fluxes will be explored. The characteristics of the large-scale forcing structures for selected cases will be discussed.

  11. Unraveling Kinase Activation Dynamics Using Kinase-Substrate Relationships from Temporal Large-Scale Phosphoproteomics Studies

    PubMed Central

    Chaudhuri, Rima; Yang, Pengyi; Vafaee, Fatemeh; Fazakerley, Daniel; Humphrey, Sean; James, David; Kuncic, Zdenka

    2016-01-01

    In response to stimuli, biological processes are tightly controlled by dynamic cellular signaling mechanisms. Reversible protein phosphorylation occurs on rapid time-scales (milliseconds to seconds), making it an ideal carrier of these signals. Advances in mass spectrometry-based proteomics have led to the identification of many tens of thousands of phosphorylation sites, yet for the majority of these the kinase is unknown and the underlying network topology of signaling networks therefore remains obscured. Identifying kinase substrate relationships (KSRs) is therefore an important goal in cell signaling research. Existing consensus sequence motif based prediction algorithms do not consider the biological context of KSRs, and are therefore insensitive to many other mechanisms guiding kinase-substrate recognition in cellular contexts. Here, we use temporal information to identify biologically relevant KSRs from Large-scale In Vivo Experiments (KSR-LIVE) in a data-dependent and automated fashion. First, we used available phosphorylation databases to construct a repository of existing experimentally-predicted KSRs. For each kinase in this database, we used time-resolved phosphoproteomics data to examine how its substrates changed in phosphorylation over time. Although substrates for a particular kinase clustered together, they often exhibited a different temporal pattern to the phosphorylation of the kinase. Therefore, although phosphorylation regulates kinase activity, our findings imply that substrate phosphorylation likely serve as a better proxy for kinase activity than kinase phosphorylation. KSR-LIVE can thereby infer which kinases are regulated within a biological context. Moreover, KSR-LIVE can also be used to automatically generate positive training sets for the subsequent prediction of novel KSRs using machine learning approaches. We demonstrate that this approach can distinguish between Akt and Rps6kb1, two kinases that share the same linear consensus motif

  12. Unraveling Kinase Activation Dynamics Using Kinase-Substrate Relationships from Temporal Large-Scale Phosphoproteomics Studies.

    PubMed

    Domanova, Westa; Krycer, James; Chaudhuri, Rima; Yang, Pengyi; Vafaee, Fatemeh; Fazakerley, Daniel; Humphrey, Sean; James, David; Kuncic, Zdenka

    2016-01-01

    In response to stimuli, biological processes are tightly controlled by dynamic cellular signaling mechanisms. Reversible protein phosphorylation occurs on rapid time-scales (milliseconds to seconds), making it an ideal carrier of these signals. Advances in mass spectrometry-based proteomics have led to the identification of many tens of thousands of phosphorylation sites, yet for the majority of these the kinase is unknown and the underlying network topology of signaling networks therefore remains obscured. Identifying kinase substrate relationships (KSRs) is therefore an important goal in cell signaling research. Existing consensus sequence motif based prediction algorithms do not consider the biological context of KSRs, and are therefore insensitive to many other mechanisms guiding kinase-substrate recognition in cellular contexts. Here, we use temporal information to identify biologically relevant KSRs from Large-scale In Vivo Experiments (KSR-LIVE) in a data-dependent and automated fashion. First, we used available phosphorylation databases to construct a repository of existing experimentally-predicted KSRs. For each kinase in this database, we used time-resolved phosphoproteomics data to examine how its substrates changed in phosphorylation over time. Although substrates for a particular kinase clustered together, they often exhibited a different temporal pattern to the phosphorylation of the kinase. Therefore, although phosphorylation regulates kinase activity, our findings imply that substrate phosphorylation likely serve as a better proxy for kinase activity than kinase phosphorylation. KSR-LIVE can thereby infer which kinases are regulated within a biological context. Moreover, KSR-LIVE can also be used to automatically generate positive training sets for the subsequent prediction of novel KSRs using machine learning approaches. We demonstrate that this approach can distinguish between Akt and Rps6kb1, two kinases that share the same linear consensus motif

  13. Consanguinity profile in the Gaza Strip of Palestine: large-scale community-based study.

    PubMed

    Sirdah, Mahmoud M

    2014-02-01

    Consanguineous marriages which have been practiced throughout history continue to be practiced within different ethnic, religious and social groups to varying degrees with highest prevalences in North Africa, Middle East and central and south Asia. In the Gaza Strip of Palestine, little is known about the consanguinity profile, so the present large-scale study aims to explore the consanguinity profile of two generations using data from the β-thalassemia premarital screening program. Sociodemographic data analysis included 156,635 (141,200 males and 15,435 females) persons and their parents, representing 141,200 couples who were referred to the Thalassemia and Hemophilia Center for premarital testing. In addition, the consanguinity characteristics of parents of 217 transfusion-dependent β-thalassemic non-sibling patients were analyzed. Results revealed a significant decrease in the overall prevalence of consanguineous (first- and second-cousin) marriages between the previous (fathers') generation (45.2%) and the current (groom/bride) generation (39.9%). Among the five governorates of the Gaza Strip, records of Gaza Governorate revealed the lowest occurrence (36.9% current generation and 42.1% previous generation) of consanguineous marriages, as compared to all others. Consanguineous marriages are significantly higher in semi-urban areas (41.6%) than in urban areas (39.1%) in the current generation (previous generation, 46.4% vs 44.7%, respectively). Compound consanguinity (two generation) and a single level of consanguinity were seen in 20.7% and 43.7%, respectively, of the cases. The average age of those with first-cousin marriages is significantly lower (22.4±4.4 years) than those with second-cousin marriages (24.3±6.1 years) and the non-consanguineous (26.5±8.2 years). The rate of consanguineous marriages among never married people (42.2%) is significantly much higher than the rate of people with multiple marriages (18.1%). About 74.7% of the non

  14. Prevalence of Psychotropic Drug Use in Adults with Intellectual Disability: Positive and Negative Findings from a Large Scale Study

    ERIC Educational Resources Information Center

    Tsiouris, John A.; Kim, Soh-Yule; Brown, W. Ted; Pettinger, Jill; Cohen, Ira L.

    2013-01-01

    The use of psychotropics by categories and the reason for their prescription was investigated in a large scale study of 4,069 adults with ID, including those with autism spectrum disorder, in New York State. Similar to other studies it was found that 58 % (2,361/4,069) received one or more psychotropics. Six percent received typical, 6 % received…

  15. Large-Scale Field Study of Landfill Covers at Sandia National Laboratories

    SciTech Connect

    Dwyer, S.F.

    1998-09-01

    A large-scale field demonstration comparing final landfill cover designs has been constructed and is currently being monitored at Sandia National Laboratories in Albuquerque, New Mexico. Two conventional designs (a RCRA Subtitle `D' Soil Cover and a RCRA Subtitle `C' Compacted Clay Cover) were constructed side-by-side with four alternative cover test plots designed for dry environments. The demonstration is intended to evaluate the various cover designs based on their respective water balance performance, ease and reliability of construction, and cost. This paper presents an overview of the ongoing demonstration.

  16. Studying Teacher Selection of Resources in an Ultra-Large Scale Interactive System: Does Metadata Guide the Way?

    ERIC Educational Resources Information Center

    Abramovich, Samuel; Schunn, Christian

    2012-01-01

    Ultra-large-scale interactive systems on the Internet have begun to change how teachers prepare for instruction, particularly in regards to resource selection. Consequently, it is important to look at how teachers are currently selecting resources beyond content or keyword search. We conducted a two-part observational study of an existing popular…

  17. A Confirmatory Approach to Examining the Factor Structure of the Strengths and Difficulties Questionnaire (SDQ): A Large Scale Cohort Study

    ERIC Educational Resources Information Center

    Niclasen, Janni; Skovgaard, Anne Mette; Andersen, Anne-Marie Nybo; Somhovd, Mikael Julius; Obel, Carsten

    2013-01-01

    The aim of this study was to examine the factor structure of the Strengths and Difficulties Questionnaire (SDQ) using a Structural Confirmatory Factor Analytic approach. The Danish translation of the SDQ was distributed to 71,840 parents and teachers of 5-7 and 10-12-year-old boys and girls from four large scale cohorts. Three theoretical models…

  18. Use of Large-Scale Data Sets to Study Educational Pathways of American Indian and Alaska Native Students

    ERIC Educational Resources Information Center

    Faircloth, Susan C.; Alcantar, Cynthia M.; Stage, Frances K.

    2014-01-01

    This chapter discusses issues and challenges encountered in using large-scale data sets to study educational experiences and subsequent outcomes for American Indian and Alaska Native (AI/AN) students. In this chapter, we argue that the linguistic and cultural diversity of Native peoples, coupled with the legal and political ways in which education…

  19. Cohort Profile of the Goals Study: A Large-Scale Research of Physical Activity in Dutch Students

    ERIC Educational Resources Information Center

    de Groot, Renate H. M.; van Dijk, Martin L.; Kirschner, Paul A.

    2015-01-01

    The GOALS study (Grootschalig Onderzoek naar Activiteiten van Limburgse Scholieren [Large-scale Research of Activities in Dutch Students]) was set up to investigate possible associations between different forms of physical activity and inactivity with cognitive performance, academic achievement and mental well-being. It was conducted at a…

  20. An Exploratory Study of Student-Paced versus Teacher-Paced Accommodations for Large-Scale Math Tests.

    ERIC Educational Resources Information Center

    Hollenbeck, Keith; Rozek-Tedesco, Marick A.; Tindal, Gerald; Glasgow, Aaron

    2000-01-01

    This study examined whether a teacher-paced video (TPV) accommodation or a student-paced computer (SPC) accommodation provided differential access for student with disabilities versus their general education peers on a large-scale math test. It found that although both pacing accommodations significantly influenced mean scores, the SPC…

  1. Feasibility study of a large-scale tuned mass damper with eddy current damping mechanism

    NASA Astrophysics Data System (ADS)

    Wang, Zhihao; Chen, Zhengqing; Wang, Jianhui

    2012-09-01

    Tuned mass dampers (TMDs) have been widely used in recent years to mitigate structural vibration. However, the damping mechanisms employed in the TMDs are mostly based on viscous dampers, which have several well-known disadvantages, such as oil leakage and difficult adjustment of damping ratio for an operating TMD. Alternatively, eddy current damping (ECD) that does not require any contact with the main structure is a potential solution. This paper discusses the design, analysis, manufacture and testing of a large-scale horizontal TMD based on ECD. First, the theoretical model of ECD is formulated, then one large-scale horizontal TMD using ECD is constructed, and finally performance tests of the TMD are conducted. The test results show that the proposed TMD has a very low intrinsic damping ratio, while the damping ratio due to ECD is the dominant damping source, which can be as large as 15% in a proper configuration. In addition, the damping ratios estimated with the theoretical model are roughly consistent with those identified from the test results, and the source of this error is investigated. Moreover, it is demonstrated that the damping ratio in the proposed TMD can be easily adjusted by varying the air gap between permanent magnets and conductive plates. In view of practical applications, possible improvements and feasibility considerations for the proposed TMD are then discussed. It is confirmed that the proposed TMD with ECD is reliable and feasible for use in structural vibration control.

  2. Bat trait, genetic and pathogen data from large-scale investigations of African fruit bats, Eidolon helvum.

    PubMed

    Peel, Alison J; Baker, Kate S; Hayman, David T S; Suu-Ire, Richard; Breed, Andrew C; Gembu, Guy-Crispin; Lembo, Tiziana; Fernández-Loras, Andrés; Sargan, David R; Fooks, Anthony R; Cunningham, Andrew A; Wood, James L N

    2016-01-01

    Bats, including African straw-coloured fruit bats (Eidolon helvum), have been highlighted as reservoirs of many recently emerged zoonotic viruses. This common, widespread and ecologically important species was the focus of longitudinal and continent-wide studies of the epidemiological and ecology of Lagos bat virus, henipaviruses and Achimota viruses. Here we present a spatial, morphological, demographic, genetic and serological dataset encompassing 2827 bats from nine countries over an 8-year period. Genetic data comprises cytochrome b mitochondrial sequences (n=608) and microsatellite genotypes from 18 loci (n=544). Tooth-cementum analyses (n=316) allowed derivation of rare age-specific serologic data for a lyssavirus, a henipavirus and two rubulaviruses. This dataset contributes a substantial volume of data on the ecology of E. helvum and its viruses and will be valuable for a wide range of studies, including viral transmission dynamic modelling in age-structured populations, investigation of seasonal reproductive asynchrony in wide-ranging species, ecological niche modelling, inference of island colonisation history, exploration of relationships between island and body size, and various spatial analyses of demographic, morphometric or serological data. PMID:27479120

  3. Bat trait, genetic and pathogen data from large-scale investigations of African fruit bats, Eidolon helvum

    PubMed Central

    Peel, Alison J.; Baker, Kate S.; Hayman, David T. S.; Suu-Ire, Richard; Breed, Andrew C.; Gembu, Guy-Crispin; Lembo, Tiziana; Fernández-Loras, Andrés; Sargan, David R.; Fooks, Anthony R.; Cunningham, Andrew A.; Wood, James L. N.

    2016-01-01

    Bats, including African straw-coloured fruit bats (Eidolon helvum), have been highlighted as reservoirs of many recently emerged zoonotic viruses. This common, widespread and ecologically important species was the focus of longitudinal and continent-wide studies of the epidemiological and ecology of Lagos bat virus, henipaviruses and Achimota viruses. Here we present a spatial, morphological, demographic, genetic and serological dataset encompassing 2827 bats from nine countries over an 8-year period. Genetic data comprises cytochrome b mitochondrial sequences (n=608) and microsatellite genotypes from 18 loci (n=544). Tooth-cementum analyses (n=316) allowed derivation of rare age-specific serologic data for a lyssavirus, a henipavirus and two rubulaviruses. This dataset contributes a substantial volume of data on the ecology of E. helvum and its viruses and will be valuable for a wide range of studies, including viral transmission dynamic modelling in age-structured populations, investigation of seasonal reproductive asynchrony in wide-ranging species, ecological niche modelling, inference of island colonisation history, exploration of relationships between island and body size, and various spatial analyses of demographic, morphometric or serological data. PMID:27479120

  4. International Comparative Studies in Education: Descriptions of Selected Large-Scale Assessments and Case Studies.

    ERIC Educational Resources Information Center

    National Academy of Sciences - National Research Council, Washington, DC. Commission on Behavioral and Social Sciences and Education.

    Since its inception in 1988, the Board on International Comparative Studies in Education (BICSE) has monitored U.S. participation in those cross national comparative studies in education that are funded by its sponsors, the National Science Foundation and the National Center for Education Statistics. This set of international study descriptions…

  5. Enhanced ICP for the Registration of Large-Scale 3D Environment Models: An Experimental Study

    PubMed Central

    Han, Jianda; Yin, Peng; He, Yuqing; Gu, Feng

    2016-01-01

    One of the main applications of mobile robots is the large-scale perception of the outdoor environment. One of the main challenges of this application is fusing environmental data obtained by multiple robots, especially heterogeneous robots. This paper proposes an enhanced iterative closest point (ICP) method for the fast and accurate registration of 3D environmental models. First, a hierarchical searching scheme is combined with the octree-based ICP algorithm. Second, an early-warning mechanism is used to perceive the local minimum problem. Third, a heuristic escape scheme based on sampled potential transformation vectors is used to avoid local minima and achieve optimal registration. Experiments involving one unmanned aerial vehicle and one unmanned surface vehicle were conducted to verify the proposed technique. The experimental results were compared with those of normal ICP registration algorithms to demonstrate the superior performance of the proposed method. PMID:26891298

  6. A Chandra Study of the Large-Scale Shock Front in Abell 2219

    NASA Astrophysics Data System (ADS)

    Allen, Steven

    2011-09-01

    Abell 2219 (z=0.225) is the third galaxy cluster in which a clear, large-scale shock front, viewed approximately edge-on and generated by ongoing merging activity, has been discovered. It is highly X-ray luminous and 2.5 times brighter in X-rays than either 1E0657-56 or A520. We propose a 150ks ACIS-I observation to obtain the first precise measurements of the pre- and post-shock gas temperature, enabling improved estimates of the Mach number and shock velocity. The observed gradient of the temperature jump across the shock will constrain the process of post-shock electron-ion equilibration. We will probe the origin of very hot (kT>20 keV) gas observed in the cluster center. High quality radio, optical-dynamical, and ground- and space-based gravitational lensing data are in hand.

  7. Enhanced ICP for the Registration of Large-Scale 3D Environment Models: An Experimental Study.

    PubMed

    Han, Jianda; Yin, Peng; He, Yuqing; Gu, Feng

    2016-01-01

    One of the main applications of mobile robots is the large-scale perception of the outdoor environment. One of the main challenges of this application is fusing environmental data obtained by multiple robots, especially heterogeneous robots. This paper proposes an enhanced iterative closest point (ICP) method for the fast and accurate registration of 3D environmental models. First, a hierarchical searching scheme is combined with the octree-based ICP algorithm. Second, an early-warning mechanism is used to perceive the local minimum problem. Third, a heuristic escape scheme based on sampled potential transformation vectors is used to avoid local minima and achieve optimal registration. Experiments involving one unmanned aerial vehicle and one unmanned surface vehicle were conducted to verify the proposed technique. The experimental results were compared with those of normal ICP registration algorithms to demonstrate the superior performance of the proposed method. PMID:26891298

  8. A modelling case study of a large-scale cirrus in the tropical tropopause layer

    NASA Astrophysics Data System (ADS)

    Podglajen, Aurélien; Plougonven, Riwal; Hertzog, Albert; Legras, Bernard

    2016-03-01

    We use the Weather Research and Forecast (WRF) model to simulate a large-scale tropical tropopause layer (TTL) cirrus in order to understand the formation and life cycle of the cloud. This cirrus event has been previously described through satellite observations by Taylor et al. (2011). Comparisons of the simulated and observed cirrus show a fair agreement and validate the reference simulation regarding cloud extension, location and life time. The validated simulation is used to understand the causes of cloud formation. It is shown that several cirrus clouds successively form in the region due to adiabatic cooling and large-scale uplift rather than from convective anvils. The structure of the uplift is tied to the equatorial response (equatorial wave excitation) to a potential vorticity intrusion from the midlatitudes. Sensitivity tests are then performed to assess the relative importance of the choice of the microphysics parameterization and of the initial and boundary conditions. The initial dynamical conditions (wind and temperature) essentially control the horizontal location and area of the cloud. However, the choice of the microphysics scheme influences the ice water content and the cloud vertical position. Last, the fair agreement with the observations allows to estimate the cloud impact in the TTL in the simulations. The cirrus clouds have a small but not negligible impact on the radiative budget of the local TTL. However, for this particular case, the cloud radiative heating does not significantly influence the simulated dynamics. This result is due to (1) the lifetime of air parcels in the cloud system, which is too short to significantly influence the dynamics, and (2) the fact that induced vertical motions would be comparable to or smaller than the typical mesoscale motions present. Finally, the simulation also provides an estimate of the vertical redistribution of water by the cloud and the results emphasize the importance in our case of both

  9. A modelling case study of a large-scale cirrus in the tropical tropopause layer

    NASA Astrophysics Data System (ADS)

    Podglajen, A.; Plougonven, R.; Hertzog, A.; Legras, B.

    2015-11-01

    We use the Weather Research and Forecast (WRF) model to simulate a large-scale tropical tropopause layer (TTL) cirrus, in order to understand the formation and life cycle of the cloud. This cirrus event has been previously described through satellite observations by Taylor et al. (2011). Comparisons of the simulated and observed cirrus show a fair agreement, and validate the reference simulation regarding cloud extension, location and life time. The validated simulation is used to understand the causes of cloud formation. It is shown that several cirrus clouds successively form in the region due to adiabatic cooling and large-scale uplift rather than from ice lofting from convective anvils. The equatorial response (equatorial wave excitation) to a midlatitude potential vorticity (PV) intrusion structures the uplift. Sensitivity tests are then performed to assess the relative importance of the choice of the microphysics parametrisation and of the initial and boundary conditions. The initial dynamical conditions (wind and temperature) essentially control the horizontal location and area of the cloud. On the other hand, the choice of the microphysics scheme influences the ice water content and the cloud vertical position. Last, the fair agreement with the observations allows to estimate the cloud impact in the TTL in the simulations. The cirrus clouds have a small but not negligible impact on the radiative budget of the local TTL. However, the cloud radiative heating does not significantly influence the simulated dynamics. The simulation also provides an estimate of the vertical redistribution of water by the cloud and the results emphasize the importance in our case of both re and dehydration in the vicinity of the cirrus.

  10. Dealing with missing values in large-scale studies: microarray data imputation and beyond.

    PubMed

    Aittokallio, Tero

    2010-03-01

    High-throughput biotechnologies, such as gene expression microarrays or mass-spectrometry-based proteomic assays, suffer from frequent missing values due to various experimental reasons. Since the missing data points can hinder downstream analyses, there exists a wide variety of ways in which to deal with missing values in large-scale data sets. Nowadays, it has become routine to estimate (or impute) the missing values prior to the actual data analysis. After nearly a decade since the publication of the first missing value imputation methods for gene expression microarray data, new imputation approaches are still being developed at an increasing rate. However, what is lagging behind is a systematic and objective evaluation of the strengths and weaknesses of the different approaches when faced with different types of data sets and experimental questions. In this review, the present strategies for missing value imputation and the measures for evaluating their performance are described. The imputation methods are first reviewed in the context of gene expression microarray data, since most of the methods have been developed for estimating gene expression levels; then, we turn to other large-scale data sets that also suffer from the problems posed by missing values, together with pointers to possible imputation approaches in these settings. Along with a description of the basic principles behind the different imputation approaches, the review tries to provide practical guidance for the users of high-throughput technologies on how to choose the imputation tool for their data and questions, and some additional research directions for the developers of imputation methodologies. PMID:19965979

  11. PlasmoGEM, a database supporting a community resource for large-scale experimental genetics in malaria parasites.

    PubMed

    Schwach, Frank; Bushell, Ellen; Gomes, Ana Rita; Anar, Burcu; Girling, Gareth; Herd, Colin; Rayner, Julian C; Billker, Oliver

    2015-01-01

    The Plasmodium Genetic Modification (PlasmoGEM) database (http://plasmogem.sanger.ac.uk) provides access to a resource of modular, versatile and adaptable vectors for genome modification of Plasmodium spp. parasites. PlasmoGEM currently consists of >2000 plasmids designed to modify the genome of Plasmodium berghei, a malaria parasite of rodents, which can be requested by non-profit research organisations free of charge. PlasmoGEM vectors are designed with long homology arms for efficient genome integration and carry gene specific barcodes to identify individual mutants. They can be used for a wide array of applications, including protein localisation, gene interaction studies and high-throughput genetic screens. The vector production pipeline is supported by a custom software suite that automates both the vector design process and quality control by full-length sequencing of the finished vectors. The PlasmoGEM web interface allows users to search a database of finished knock-out and gene tagging vectors, view details of their designs, download vector sequence in different formats and view available quality control data as well as suggested genotyping strategies. We also make gDNA library clones and intermediate vectors available for researchers to produce vectors for themselves. PMID:25593348

  12. Genetic variation reveals large-scale population expansion and migration during the expansion of Bantu-speaking peoples

    PubMed Central

    Li, Sen; Schlebusch, Carina; Jakobsson, Mattias

    2014-01-01

    The majority of sub-Saharan Africans today speak a number of closely related languages collectively referred to as ‘Bantu’ languages. The current distribution of Bantu-speaking populations has been found to largely be a consequence of the movement of people rather than a diffusion of language alone. Linguistic and single marker genetic studies have generated various hypotheses regarding the timing and the routes of the Bantu expansion, but these hypotheses have not been thoroughly investigated. In this study, we re-analysed microsatellite markers typed for large number of African populations that—owing to their fast mutation rates—capture signatures of recent population history. We confirm the spread of west African people across most of sub-Saharan Africa and estimated the expansion of Bantu-speaking groups, using a Bayesian approach, to around 5600 years ago. We tested four different divergence models for Bantu-speaking populations with a distribution comprising three geographical regions in Africa. We found that the most likely model for the movement of the eastern branch of Bantu-speakers involves migration of Bantu-speaking groups to the east followed by migration to the south. This model, however, is only marginally more likely than other models, which might indicate direct movement from the west and/or significant gene flow with the western Branch of Bantu-speakers. Our study use multi-loci genetic data to explicitly investigate the timing and mode of the Bantu expansion and it demonstrates that west African groups rapidly expanded both in numbers and over a large geographical area, affirming the fact that the Bantu expansion was one of the most dramatic demographic events in human history. PMID:25209939

  13. A 454 multiplex sequencing method for rapid and reliable genotyping of highly polymorphic genes in large-scale studies

    PubMed Central

    2010-01-01

    Background High-throughput sequencing technologies offer new perspectives for biomedical, agronomical and evolutionary research. Promising progresses now concern the application of these technologies to large-scale studies of genetic variation. Such studies require the genotyping of high numbers of samples. This is theoretically possible using 454 pyrosequencing, which generates billions of base pairs of sequence data. However several challenges arise: first in the attribution of each read produced to its original sample, and second, in bioinformatic analyses to distinguish true from artifactual sequence variation. This pilot study proposes a new application for the 454 GS FLX platform, allowing the individual genotyping of thousands of samples in one run. A probabilistic model has been developed to demonstrate the reliability of this method. Results DNA amplicons from 1,710 rodent samples were individually barcoded using a combination of tags located in forward and reverse primers. Amplicons consisted in 222 bp fragments corresponding to DRB exon 2, a highly polymorphic gene in mammals. A total of 221,789 reads were obtained, of which 153,349 were finally assigned to original samples. Rules based on a probabilistic model and a four-step procedure, were developed to validate sequences and provide a confidence level for each genotype. The method gave promising results, with the genotyping of DRB exon 2 sequences for 1,407 samples from 24 different rodent species and the sequencing of 392 variants in one half of a 454 run. Using replicates, we estimated that the reproducibility of genotyping reached 95%. Conclusions This new approach is a promising alternative to classical methods involving electrophoresis-based techniques for variant separation and cloning-sequencing for sequence determination. The 454 system is less costly and time consuming and may enhance the reliability of genotypes obtained when high numbers of samples are studied. It opens up new perspectives

  14. Large-scale gene expression profiling of discrete brain regions: potential, limitations, and application in genetics of aggressive behavior.

    PubMed

    Feldker, Dorine E M; de Kloet, E Ronald; Kruk, Menno R; Datson, Nicole A

    2003-09-01

    Many behavioral geneticists are interested in unraveling the molecular mechanisms underlying aggressive behavior. So far, most scientists have based their search for aggression-related genes on a preliminary functional hypothesis. Large-scale gene expression profiling techniques, such as serial analysis of gene expression (SAGE) and DNA microarrays, now enable the screening of expression levels of thousands of genes simultaneously, allowing the identification of new candidate aggression-related genes expressed in brain and thus the generation of new hypotheses. However, expression profiling in the brain is challenging, as brain is a complex heterogeneous tissue where large numbers of genes are expressed and relatively small changes in gene expression occur. In this special issue, we focus on the principles of SAGE and DNA microarrays, as well as their advantages and disadvantages and application to analysis in brain tissue in order to identify aggression-related genes. PMID:14574131

  15. A large-scale mutant panel in wheat developed using heavy-ion beam mutagenesis and its application to genetic research

    NASA Astrophysics Data System (ADS)

    Murai, Koji; Nishiura, Aiko; Kazama, Yusuke; Abe, Tomoko

    2013-11-01

    Mutation analysis is a powerful tool for studying gene function. Heavy-ion beam mutagenesis is a comparatively new approach to inducing mutations in plants and is particularly efficient because of its high linear energy transfer (LET). High LET radiation induces a higher rate of DNA double-strand breaks than other mutagenic methods. Over the last 12 years, we have constructed a large-scale mutant panel in diploid einkorn wheat (Triticum monococcum) using heavy-ion beam mutagenesis. Einkorn wheat seeds were exposed to a heavy-ion beam and then sown in the field. Selfed seeds from each spike of M1 plants were used to generate M2 lines. Every year, we obtained approximately 1000 M2 lines and eventually developed a mutant panel with 10,000 M2 lines in total. This mutant panel is being systematically screened for mutations affecting reproductive growth, and especially for flowering-time mutants. To date, we have identified several flowering-time mutants of great interest: non-flowering mutants (mvp: maintained vegetative phase), late-flowering mutants, and early-flowering mutants. These novel mutations will be of value for investigations of the genetic mechanism of flowering in wheat.

  16. Small-Scale Screening to Large-Scale Over-Expression of Human Membrane Proteins for Structural Studies.

    PubMed

    Chaudhary, Sarika; Saha, Sukanya; Thamminana, Sobrahani; Stroud, Robert M

    2016-01-01

    Membrane protein structural studies are frequently hampered by poor expression. The low natural abundance of these proteins implies a need for utilizing different heterologous expression systems. E. coli and yeast are commonly used expression systems due to rapid cell growth at high cell density, economical production, and ease of manipulation. Here we report a simplified, systematically developed robust strategy from small-scale screening to large-scale over-expression of human integral membrane proteins in the mammalian expression system for structural studies. This methodology streamlines small-scale screening of several different constructs utilizing fluorescence size-exclusion chromatography (FSEC) towards optimization of buffer, additives, and detergents for achieving stability and homogeneity. This is followed by the generation of stable clonal cell lines expressing desired constructs, and lastly large-scale expression for crystallization. These techniques are designed to rapidly advance the structural studies of eukaryotic integral membrane proteins including that of human membrane proteins. PMID:27485338

  17. Indexed PCR Primers Induce Template-Specific Bias in Large-Scale DNA Sequencing Studies

    PubMed Central

    O’Donnell, James L.; Kelly, Ryan P.; Lowell, Natalie C.; Port, Jesse A.

    2016-01-01

    Massively parallel sequencing is rapidly emerging as an efficient way to quantify biodiversity at all levels, from genetic variation and expression to ecological community assemblage. However, the number of reads produced per sequencing run far exceeds the number required per sample for many applications, compelling researchers to sequence multiple samples per run in order to maximize efficiency. For studies that include a PCR step, this can be accomplished using primers that include an index sequence allowing sample origin to be determined after sequencing. The use of indexed primers assumes they behave no differently than standard primers; however, we found that indexed primers cause substantial template sequence-specific bias, resulting in radically different profiles of the same environmental sample. Likely the outcome of differential amplification efficiency due to primer-template mismatch, two indexed primer sets spuriously change the inferred sequence abundance from the same DNA extraction by up to 77.1%. We demonstrate that a double PCR approach alleviates these effects in applications where indexed primers are necessary. PMID:26950069

  18. An Infrared Study of the Large-Scale Jet in Quasar PKS 1136-135

    SciTech Connect

    Uchiyama, Yasunobu; Urry, C.Megan; Coppi, Paolo; Van Duyne, Jeffrey; Cheung, C.C.; Sambruna, Rita M.; Takahashi, Tadayuki; Tavecchio, Fabrizio; Maraschi, Laura; /Brera Observ.

    2007-03-16

    We present Spitzer IRAC imaging of the large-scale jet in the quasar PKS 1136-135 at wavelengths of 3.6 and 5.8 {micro}m, combined with previous VLA, HST, and Chandra observations. We clearly detect infrared emission from the jet, resulting in the most detailed multifrequency data among the jets in lobe-dominated quasars. The spectral energy distributions of the jet knots have significant variations along the jet, like the archetypal jet in 3C 273. The infrared measurements with IRAC are consistent with the previous idea that the jet has two spectral components, namely (1) the low-energy synchrotron spectrum extending from radio to infrared, and (2) the high-energy component responsible for the X-ray flux. The optical fluxes may be a mixture of the two components. We consider three radiation models for the high-energy component: inverse Compton scattering of cosmic microwave background (CMB) photons by radio-emitting electrons in a highly relativistic jet, synchrotron radiation by a second distinct electron population, and synchrotron radiation by ultra high energy protons. Each hypothesis leads to important insights into and constraints on particle acceleration in the jet, as well as the basic physical properties of the jet such as bulk velocity, transporting power, and particle contents.

  19. Infrared study of large scale h-BN film and graphene/h-BN heterostructure

    NASA Astrophysics Data System (ADS)

    Yu, Kwangnam; Kim, Jiho; Lee, Chul; Jang, A.-Rang; Shin, Hyeon Suk; Kim, Keun Soo; Yu, Young-Jun; Choi, E. J.

    2016-06-01

    We synthesize a series of CVD h-BN films and perform critical infrared spectroscopic characterization. For high-temperature (HT, Temp = 1400 °C) grown h-BN thin film, only E1 u -mode infrared phonon is activated demonstrating highly aligned 2D h-BN planes over large area, whereas low-temperature (LT, Temp = 1000 °C) grown film shows two phonon peaks, E1 u and A2 u , due to stacking of h-BN plane at tilted angle. For CVD graphene transferred on HT h-BN/SiO2/Si substrate, interband transition spectrum σ1 shifts strongly to lower energy compared with that on LT h-BN/SiO2/Si and on bare SiO2/Si substrates, revealing that the residual carrier density n in graphene is suppressed by the use of HT h-BN layer. Also, the interband transition width of σ1 defined by effective temperature is reduced from 400 K for G/SiO2/Si to 300 K for HT h-BN/SiO2/Si. The behaviors of n and effective temperature show that the HT h-BN film can decouple CVD graphene from the impurity and defect of SiO2 leading to a large scale free-standing like graphene.

  20. Study of wavelength-shifting chemicals for use in large-scale water Cherenkov detectors

    SciTech Connect

    Sweany, M; Bernstein, A; Dazeley, S; Dunmore, J; Felde, J; Svoboda, R; Tripathi, S M

    2011-09-21

    Cherenkov detectors employ various methods to maximize light collection at the photomultiplier tubes (PMTs). These generally involve the use of highly reflective materials lining the interior of the detector, reflective materials around the PMTs, or wavelength-shifting sheets around the PMTs. Recently, the use of water-soluble wavelength-shifters has been explored to increase the measurable light yield of Cherenkov radiation in water. These wave-shifting chemicals are capable of absorbing light in the ultravoilet and re-emitting the light in a range detectable by PMTs. Using a 250 L water Cherenkov detector, we have characterized the increase in light yield from three compounds in water: 4-Methylumbelliferone, Carbostyril-124, and Amino-G Salt. We report the gain in PMT response at a concentration of 1 ppm as: 1.88 {+-} 0.02 for 4-Methylumbelliferone, stable to within 0.5% over 50 days, 1.37 {+-} 0.03 for Carbostyril-124, and 1.20 {+-} 0.02 for Amino-G Salt. The response of 4-Methylumbelliferone was modeled, resulting in a simulated gain within 9% of the experimental gain at 1 ppm concentration. Finally, we report an increase in neutron detection performance of a large-scale (3.5 kL) gadolinium-doped water Cherenkov detector at a 4-Methylumbelliferone concentration of 1 ppm.

  1. The Nature of Global Large-scale Sea Level Variability in Relation to Atmospheric Forcing: A Modeling Study

    NASA Technical Reports Server (NTRS)

    Fukumori, I.; Raghunath, R.; Fu, L. L.

    1996-01-01

    The relation between large-scale sea level variability and ocean circulation is studied using a numerical model. A global primitive equaiton model of the ocean is forced by daily winds and climatological heat fluxes corresponding to the period from January 1992 to February 1996. The physical nature of the temporal variability from periods of days to a year, are examined based on spectral analyses of model results and comparisons with satellite altimetry and tide gauge measurements.

  2. QSAR Modeling Using Large-Scale Databases: Case Study for HIV-1 Reverse Transcriptase Inhibitors.

    PubMed

    Tarasova, Olga A; Urusova, Aleksandra F; Filimonov, Dmitry A; Nicklaus, Marc C; Zakharov, Alexey V; Poroikov, Vladimir V

    2015-07-27

    Large-scale databases are important sources of training sets for various QSAR modeling approaches. Generally, these databases contain information extracted from different sources. This variety of sources can produce inconsistency in the data, defined as sometimes widely diverging activity results for the same compound against the same target. Because such inconsistency can reduce the accuracy of predictive models built from these data, we are addressing the question of how best to use data from publicly and commercially accessible databases to create accurate and predictive QSAR models. We investigate the suitability of commercially and publicly available databases to QSAR modeling of antiviral activity (HIV-1 reverse transcriptase (RT) inhibition). We present several methods for the creation of modeling (i.e., training and test) sets from two, either commercially or freely available, databases: Thomson Reuters Integrity and ChEMBL. We found that the typical predictivities of QSAR models obtained using these different modeling set compilation methods differ significantly from each other. The best results were obtained using training sets compiled for compounds tested using only one method and material (i.e., a specific type of biological assay). Compound sets aggregated by target only typically yielded poorly predictive models. We discuss the possibility of "mix-and-matching" assay data across aggregating databases such as ChEMBL and Integrity and their current severe limitations for this purpose. One of them is the general lack of complete and semantic/computer-parsable descriptions of assay methodology carried by these databases that would allow one to determine mix-and-matchability of result sets at the assay level. PMID:26046311

  3. Open-path Fourier transform infrared studies of large-scale laboratory biomass fires

    NASA Astrophysics Data System (ADS)

    Yokelson, Robert J.; Griffith, David W. T.; Ward, Darold E.

    1996-09-01

    A series of nine large-scale, open fires was conducted in the Intermountain Fire Sciences Laboratory (IFSL) controlled-environment combustion facility. The fuels were pure pine needles or sagebrush or mixed fuels simulating forest-floor, ground fires; crown fires; broadcast burns; and slash pile burns. Mid-infrared spectra of the smoke were recorded throughout each fire by open path Fourier transform infrared (FTIR) spectroscopy at 0.12 cm-1 resolution over a 3 m cross-stack pathlength and analyzed to provide pseudocontinuous, simultaneous concentrations of up to 16 compounds. Simultaneous measurements were made of fuel mass loss, stack gas temperature, and total mass flow up the stack. The products detected are classified by the type of process that dominates in producing them. Carbon dioxide is the dominant emission of (and primarily produced by) flaming combustion, from which we also measure nitric oxide, nitrogen dioxide, sulfur dioxide, and most of the water vapor from combustion and fuel moisture. Carbon monoxide is the dominant emission formed primarily by smoldering combustion from which we also measure carbon dioxide, methane, ammonia, and ethane. A significant fraction of the total emissions is unoxidized pyrolysis products; examples are methanol, formaldehyde, acetic and formic acid, ethene (ethylene), ethyne (acetylene), and hydrogen cyanide. Relatively few previous data exist for many of these compounds and they are likely to have an important but as yet poorly understood role in plume chemistry. Large differences in emissions occur from different fire and fuel types, and the observed temporal behavior of the emissions is found to depend strongly on the fuel bed and product type.

  4. Large-scale gene-centric meta-analysis across 32 studies identifies multiple lipid loci.

    PubMed

    Asselbergs, Folkert W; Guo, Yiran; van Iperen, Erik P A; Sivapalaratnam, Suthesh; Tragante, Vinicius; Lanktree, Matthew B; Lange, Leslie A; Almoguera, Berta; Appelman, Yolande E; Barnard, John; Baumert, Jens; Beitelshees, Amber L; Bhangale, Tushar R; Chen, Yii-Der Ida; Gaunt, Tom R; Gong, Yan; Hopewell, Jemma C; Johnson, Toby; Kleber, Marcus E; Langaee, Taimour Y; Li, Mingyao; Li, Yun R; Liu, Kiang; McDonough, Caitrin W; Meijs, Matthijs F L; Middelberg, Rita P S; Musunuru, Kiran; Nelson, Christopher P; O'Connell, Jeffery R; Padmanabhan, Sandosh; Pankow, James S; Pankratz, Nathan; Rafelt, Suzanne; Rajagopalan, Ramakrishnan; Romaine, Simon P R; Schork, Nicholas J; Shaffer, Jonathan; Shen, Haiqing; Smith, Erin N; Tischfield, Sam E; van der Most, Peter J; van Vliet-Ostaptchouk, Jana V; Verweij, Niek; Volcik, Kelly A; Zhang, Li; Bailey, Kent R; Bailey, Kristian M; Bauer, Florianne; Boer, Jolanda M A; Braund, Peter S; Burt, Amber; Burton, Paul R; Buxbaum, Sarah G; Chen, Wei; Cooper-Dehoff, Rhonda M; Cupples, L Adrienne; deJong, Jonas S; Delles, Christian; Duggan, David; Fornage, Myriam; Furlong, Clement E; Glazer, Nicole; Gums, John G; Hastie, Claire; Holmes, Michael V; Illig, Thomas; Kirkland, Susan A; Kivimaki, Mika; Klein, Ronald; Klein, Barbara E; Kooperberg, Charles; Kottke-Marchant, Kandice; Kumari, Meena; LaCroix, Andrea Z; Mallela, Laya; Murugesan, Gurunathan; Ordovas, Jose; Ouwehand, Willem H; Post, Wendy S; Saxena, Richa; Scharnagl, Hubert; Schreiner, Pamela J; Shah, Tina; Shields, Denis C; Shimbo, Daichi; Srinivasan, Sathanur R; Stolk, Ronald P; Swerdlow, Daniel I; Taylor, Herman A; Topol, Eric J; Toskala, Elina; van Pelt, Joost L; van Setten, Jessica; Yusuf, Salim; Whittaker, John C; Zwinderman, A H; Anand, Sonia S; Balmforth, Anthony J; Berenson, Gerald S; Bezzina, Connie R; Boehm, Bernhard O; Boerwinkle, Eric; Casas, Juan P; Caulfield, Mark J; Clarke, Robert; Connell, John M; Cruickshanks, Karen J; Davidson, Karina W; Day, Ian N M; de Bakker, Paul I W; Doevendans, Pieter A; Dominiczak, Anna F; Hall, Alistair S; Hartman, Catharina A; Hengstenberg, Christian; Hillege, Hans L; Hofker, Marten H; Humphries, Steve E; Jarvik, Gail P; Johnson, Julie A; Kaess, Bernhard M; Kathiresan, Sekar; Koenig, Wolfgang; Lawlor, Debbie A; März, Winfried; Melander, Olle; Mitchell, Braxton D; Montgomery, Grant W; Munroe, Patricia B; Murray, Sarah S; Newhouse, Stephen J; Onland-Moret, N Charlotte; Poulter, Neil; Psaty, Bruce; Redline, Susan; Rich, Stephen S; Rotter, Jerome I; Schunkert, Heribert; Sever, Peter; Shuldiner, Alan R; Silverstein, Roy L; Stanton, Alice; Thorand, Barbara; Trip, Mieke D; Tsai, Michael Y; van der Harst, Pim; van der Schoot, Ellen; van der Schouw, Yvonne T; Verschuren, W M Monique; Watkins, Hugh; Wilde, Arthur A M; Wolffenbuttel, Bruce H R; Whitfield, John B; Hovingh, G Kees; Ballantyne, Christie M; Wijmenga, Cisca; Reilly, Muredach P; Martin, Nicholas G; Wilson, James G; Rader, Daniel J; Samani, Nilesh J; Reiner, Alex P; Hegele, Robert A; Kastelein, John J P; Hingorani, Aroon D; Talmud, Philippa J; Hakonarson, Hakon; Elbers, Clara C; Keating, Brendan J; Drenos, Fotios

    2012-11-01

    Genome-wide association studies (GWASs) have identified many SNPs underlying variations in plasma-lipid levels. We explore whether additional loci associated with plasma-lipid phenotypes, such as high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), total cholesterol (TC), and triglycerides (TGs), can be identified by a dense gene-centric approach. Our meta-analysis of 32 studies in 66,240 individuals of European ancestry was based on the custom ∼50,000 SNP genotyping array (the ITMAT-Broad-CARe array) covering ∼2,000 candidate genes. SNP-lipid associations were replicated either in a cohort comprising an additional 24,736 samples or within the Global Lipid Genetic Consortium. We identified four, six, ten, and four unreported SNPs in established lipid genes for HDL-C, LDL-C, TC, and TGs, respectively. We also identified several lipid-related SNPs in previously unreported genes: DGAT2, HCAR2, GPIHBP1, PPARG, and FTO for HDL-C; SOCS3, APOH, SPTY2D1, BRCA2, and VLDLR for LDL-C; SOCS3, UGT1A1, BRCA2, UBE3B, FCGR2A, CHUK, and INSIG2 for TC; and SERPINF2, C4B, GCK, GATA4, INSR, and LPAL2 for TGs. The proportion of explained phenotypic variance in the subset of studies providing individual-level data was 9.9% for HDL-C, 9.5% for LDL-C, 10.3% for TC, and 8.0% for TGs. This large meta-analysis of lipid phenotypes with the use of a dense gene-centric approach identified multiple SNPs not previously described in established lipid genes and several previously unknown loci. The explained phenotypic variance from this approach was comparable to that from a meta-analysis of GWAS data, suggesting that a focused genotyping approach can further increase the understanding of heritability of plasma lipids. PMID:23063622

  5. Large-Scale Gene-Centric Meta-analysis across 32 Studies Identifies Multiple Lipid Loci

    PubMed Central

    Asselbergs, Folkert W.; Guo, Yiran; van Iperen, Erik P.A.; Sivapalaratnam, Suthesh; Tragante, Vinicius; Lanktree, Matthew B.; Lange, Leslie A.; Almoguera, Berta; Appelman, Yolande E.; Barnard, John; Baumert, Jens; Beitelshees, Amber L.; Bhangale, Tushar R.; Chen, Yii-Der Ida; Gaunt, Tom R.; Gong, Yan; Hopewell, Jemma C.; Johnson, Toby; Kleber, Marcus E.; Langaee, Taimour Y.; Li, Mingyao; Li, Yun R.; Liu, Kiang; McDonough, Caitrin W.; Meijs, Matthijs F.L.; Middelberg, Rita P.S.; Musunuru, Kiran; Nelson, Christopher P.; O’Connell, Jeffery R.; Padmanabhan, Sandosh; Pankow, James S.; Pankratz, Nathan; Rafelt, Suzanne; Rajagopalan, Ramakrishnan; Romaine, Simon P.R.; Schork, Nicholas J.; Shaffer, Jonathan; Shen, Haiqing; Smith, Erin N.; Tischfield, Sam E.; van der Most, Peter J.; van Vliet-Ostaptchouk, Jana V.; Verweij, Niek; Volcik, Kelly A.; Zhang, Li; Bailey, Kent R.; Bailey, Kristian M.; Bauer, Florianne; Boer, Jolanda M.A.; Braund, Peter S.; Burt, Amber; Burton, Paul R.; Buxbaum, Sarah G.; Chen, Wei; Cooper-DeHoff, Rhonda M.; Cupples, L. Adrienne; deJong, Jonas S.; Delles, Christian; Duggan, David; Fornage, Myriam; Furlong, Clement E.; Glazer, Nicole; Gums, John G.; Hastie, Claire; Holmes, Michael V.; Illig, Thomas; Kirkland, Susan A.; Kivimaki, Mika; Klein, Ronald; Klein, Barbara E.; Kooperberg, Charles; Kottke-Marchant, Kandice; Kumari, Meena; LaCroix, Andrea Z.; Mallela, Laya; Murugesan, Gurunathan; Ordovas, Jose; Ouwehand, Willem H.; Post, Wendy S.; Saxena, Richa; Scharnagl, Hubert; Schreiner, Pamela J.; Shah, Tina; Shields, Denis C.; Shimbo, Daichi; Srinivasan, Sathanur R.; Stolk, Ronald P.; Swerdlow, Daniel I.; Taylor, Herman A.; Topol, Eric J.; Toskala, Elina; van Pelt, Joost L.; van Setten, Jessica; Yusuf, Salim; Whittaker, John C.; Zwinderman, A.H.; Anand, Sonia S.; Balmforth, Anthony J.; Berenson, Gerald S.; Bezzina, Connie R.; Boehm, Bernhard O.; Boerwinkle, Eric; Casas, Juan P.; Caulfield, Mark J.; Clarke, Robert; Connell, John M.; Cruickshanks, Karen J.; Davidson, Karina W.; Day, Ian N.M.; de Bakker, Paul I.W.; Doevendans, Pieter A.; Dominiczak, Anna F.; Hall, Alistair S.; Hartman, Catharina A.; Hengstenberg, Christian; Hillege, Hans L.; Hofker, Marten H.; Humphries, Steve E.; Jarvik, Gail P.; Johnson, Julie A.; Kaess, Bernhard M.; Kathiresan, Sekar; Koenig, Wolfgang; Lawlor, Debbie A.; März, Winfried; Melander, Olle; Mitchell, Braxton D.; Montgomery, Grant W.; Munroe, Patricia B.; Murray, Sarah S.; Newhouse, Stephen J.; Onland-Moret, N. Charlotte; Poulter, Neil; Psaty, Bruce; Redline, Susan; Rich, Stephen S.; Rotter, Jerome I.; Schunkert, Heribert; Sever, Peter; Shuldiner, Alan R.; Silverstein, Roy L.; Stanton, Alice; Thorand, Barbara; Trip, Mieke D.; Tsai, Michael Y.; van der Harst, Pim; van der Schoot, Ellen; van der Schouw, Yvonne T.; Verschuren, W.M. Monique; Watkins, Hugh; Wilde, Arthur A.M.; Wolffenbuttel, Bruce H.R.; Whitfield, John B.; Hovingh, G. Kees; Ballantyne, Christie M.; Wijmenga, Cisca; Reilly, Muredach P.; Martin, Nicholas G.; Wilson, James G.; Rader, Daniel J.; Samani, Nilesh J.; Reiner, Alex P.; Hegele, Robert A.; Kastelein, John J.P.; Hingorani, Aroon D.; Talmud, Philippa J.; Hakonarson, Hakon; Elbers, Clara C.; Keating, Brendan J.; Drenos, Fotios

    2012-01-01

    Genome-wide association studies (GWASs) have identified many SNPs underlying variations in plasma-lipid levels. We explore whether additional loci associated with plasma-lipid phenotypes, such as high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), total cholesterol (TC), and triglycerides (TGs), can be identified by a dense gene-centric approach. Our meta-analysis of 32 studies in 66,240 individuals of European ancestry was based on the custom ∼50,000 SNP genotyping array (the ITMAT-Broad-CARe array) covering ∼2,000 candidate genes. SNP-lipid associations were replicated either in a cohort comprising an additional 24,736 samples or within the Global Lipid Genetic Consortium. We identified four, six, ten, and four unreported SNPs in established lipid genes for HDL-C, LDL-C, TC, and TGs, respectively. We also identified several lipid-related SNPs in previously unreported genes: DGAT2, HCAR2, GPIHBP1, PPARG, and FTO for HDL-C; SOCS3, APOH, SPTY2D1, BRCA2, and VLDLR for LDL-C; SOCS3, UGT1A1, BRCA2, UBE3B, FCGR2A, CHUK, and INSIG2 for TC; and SERPINF2, C4B, GCK, GATA4, INSR, and LPAL2 for TGs. The proportion of explained phenotypic variance in the subset of studies providing individual-level data was 9.9% for HDL-C, 9.5% for LDL-C, 10.3% for TC, and 8.0% for TGs. This large meta-analysis of lipid phenotypes with the use of a dense gene-centric approach identified multiple SNPs not previously described in established lipid genes and several previously unknown loci. The explained phenotypic variance from this approach was comparable to that from a meta-analysis of GWAS data, suggesting that a focused genotyping approach can further increase the understanding of heritability of plasma lipids. PMID:23063622

  6. Issues and Methodologies in Large-Scale Assessments. Special Issue 2: Measuring Students' Family Background in Large-Scale International Education Studies. IERI Monograph Series

    ERIC Educational Resources Information Center

    Brese, Falk; Mirazchiyski, Plamen

    2013-01-01

    The relationship between students' family background and achievement is often seen as an important topic in regard to equality and equity of educational provision. The results of various education studies show that the family background of students correlates with students' academic achievement at school. This paper focuses on the measurement of…

  7. Crowdsourcing the General Public for Large Scale Molecular Pathology Studies in Cancer

    PubMed Central

    Candido dos Reis, Francisco J.; Lynn, Stuart; Ali, H. Raza; Eccles, Diana; Hanby, Andrew; Provenzano, Elena; Caldas, Carlos; Howat, William J.; McDuffus, Leigh-Anne; Liu, Bin; Daley, Frances; Coulson, Penny; Vyas, Rupesh J.; Harris, Leslie M.; Owens, Joanna M.; Carton, Amy F.M.; McQuillan, Janette P.; Paterson, Andy M.; Hirji, Zohra; Christie, Sarah K.; Holmes, Amber R.; Schmidt, Marjanka K.; Garcia-Closas, Montserrat; Easton, Douglas F.; Bolla, Manjeet K.; Wang, Qin; Benitez, Javier; Milne, Roger L.; Mannermaa, Arto; Couch, Fergus; Devilee, Peter; Tollenaar, Robert A.E.M.; Seynaeve, Caroline; Cox, Angela; Cross, Simon S.; Blows, Fiona M.; Sanders, Joyce; de Groot, Renate; Figueroa, Jonine; Sherman, Mark; Hooning, Maartje; Brenner, Hermann; Holleczek, Bernd; Stegmaier, Christa; Lintott, Chris; Pharoah, Paul D.P.

    2015-01-01

    Background Citizen science, scientific research conducted by non-specialists, has the potential to facilitate biomedical research using available large-scale data, however validating the results is challenging. The Cell Slider is a citizen science project that intends to share images from tumors with the general public, enabling them to score tumor markers independently through an internet-based interface. Methods From October 2012 to June 2014, 98,293 Citizen Scientists accessed the Cell Slider web page and scored 180,172 sub-images derived from images of 12,326 tissue microarray cores labeled for estrogen receptor (ER). We evaluated the accuracy of Citizen Scientist's ER classification, and the association between ER status and prognosis by comparing their test performance against trained pathologists. Findings The area under ROC curve was 0.95 (95% CI 0.94 to 0.96) for cancer cell identification and 0.97 (95% CI 0.96 to 0.97) for ER status. ER positive tumors scored by Citizen Scientists were associated with survival in a similar way to that scored by trained pathologists. Survival probability at 15 years were 0.78 (95% CI 0.76 to 0.80) for ER-positive and 0.72 (95% CI 0.68 to 0.77) for ER-negative tumors based on Citizen Scientists classification. Based on pathologist classification, survival probability was 0.79 (95% CI 0.77 to 0.81) for ER-positive and 0.71 (95% CI 0.67 to 0.74) for ER-negative tumors. The hazard ratio for death was 0.26 (95% CI 0.18 to 0.37) at diagnosis and became greater than one after 6.5 years of follow-up for ER scored by Citizen Scientists, and 0.24 (95% CI 0.18 to 0.33) at diagnosis increasing thereafter to one after 6.7 (95% CI 4.1 to 10.9) years of follow-up for ER scored by pathologists. Interpretation Crowdsourcing of the general public to classify cancer pathology data for research is viable, engages the public and provides accurate ER data. Crowdsourced classification of research data may offer a valid solution to problems of

  8. Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes.

    PubMed

    Morris, Andrew P; Voight, Benjamin F; Teslovich, Tanya M; Ferreira, Teresa; Segrè, Ayellet V; Steinthorsdottir, Valgerdur; Strawbridge, Rona J; Khan, Hassan; Grallert, Harald; Mahajan, Anubha; Prokopenko, Inga; Kang, Hyun Min; Dina, Christian; Esko, Tonu; Fraser, Ross M; Kanoni, Stavroula; Kumar, Ashish; Lagou, Vasiliki; Langenberg, Claudia; Luan, Jian'an; Lindgren, Cecilia M; Müller-Nurasyid, Martina; Pechlivanis, Sonali; Rayner, N William; Scott, Laura J; Wiltshire, Steven; Yengo, Loic; Kinnunen, Leena; Rossin, Elizabeth J; Raychaudhuri, Soumya; Johnson, Andrew D; Dimas, Antigone S; Loos, Ruth J F; Vedantam, Sailaja; Chen, Han; Florez, Jose C; Fox, Caroline; Liu, Ching-Ti; Rybin, Denis; Couper, David J; Kao, Wen Hong L; Li, Man; Cornelis, Marilyn C; Kraft, Peter; Sun, Qi; van Dam, Rob M; Stringham, Heather M; Chines, Peter S; Fischer, Krista; Fontanillas, Pierre; Holmen, Oddgeir L; Hunt, Sarah E; Jackson, Anne U; Kong, Augustine; Lawrence, Robert; Meyer, Julia; Perry, John R B; Platou, Carl G P; Potter, Simon; Rehnberg, Emil; Robertson, Neil; Sivapalaratnam, Suthesh; Stančáková, Alena; Stirrups, Kathleen; Thorleifsson, Gudmar; Tikkanen, Emmi; Wood, Andrew R; Almgren, Peter; Atalay, Mustafa; Benediktsson, Rafn; Bonnycastle, Lori L; Burtt, Noël; Carey, Jason; Charpentier, Guillaume; Crenshaw, Andrew T; Doney, Alex S F; Dorkhan, Mozhgan; Edkins, Sarah; Emilsson, Valur; Eury, Elodie; Forsen, Tom; Gertow, Karl; Gigante, Bruna; Grant, George B; Groves, Christopher J; Guiducci, Candace; Herder, Christian; Hreidarsson, Astradur B; Hui, Jennie; James, Alan; Jonsson, Anna; Rathmann, Wolfgang; Klopp, Norman; Kravic, Jasmina; Krjutškov, Kaarel; Langford, Cordelia; Leander, Karin; Lindholm, Eero; Lobbens, Stéphane; Männistö, Satu; Mirza, Ghazala; Mühleisen, Thomas W; Musk, Bill; Parkin, Melissa; Rallidis, Loukianos; Saramies, Jouko; Sennblad, Bengt; Shah, Sonia; Sigurðsson, Gunnar; Silveira, Angela; Steinbach, Gerald; Thorand, Barbara; Trakalo, Joseph; Veglia, Fabrizio; Wennauer, Roman; Winckler, Wendy; Zabaneh, Delilah; Campbell, Harry; van Duijn, Cornelia; Uitterlinden, Andre G; Hofman, Albert; Sijbrands, Eric; Abecasis, Goncalo R; Owen, Katharine R; Zeggini, Eleftheria; Trip, Mieke D; Forouhi, Nita G; Syvänen, Ann-Christine; Eriksson, Johan G; Peltonen, Leena; Nöthen, Markus M; Balkau, Beverley; Palmer, Colin N A; Lyssenko, Valeriya; Tuomi, Tiinamaija; Isomaa, Bo; Hunter, David J; Qi, Lu; Shuldiner, Alan R; Roden, Michael; Barroso, Ines; Wilsgaard, Tom; Beilby, John; Hovingh, Kees; Price, Jackie F; Wilson, James F; Rauramaa, Rainer; Lakka, Timo A; Lind, Lars; Dedoussis, George; Njølstad, Inger; Pedersen, Nancy L; Khaw, Kay-Tee; Wareham, Nicholas J; Keinanen-Kiukaanniemi, Sirkka M; Saaristo, Timo E; Korpi-Hyövälti, Eeva; Saltevo, Juha; Laakso, Markku; Kuusisto, Johanna; Metspalu, Andres; Collins, Francis S; Mohlke, Karen L; Bergman, Richard N; Tuomilehto, Jaakko; Boehm, Bernhard O; Gieger, Christian; Hveem, Kristian; Cauchi, Stephane; Froguel, Philippe; Baldassarre, Damiano; Tremoli, Elena; Humphries, Steve E; Saleheen, Danish; Danesh, John; Ingelsson, Erik; Ripatti, Samuli; Salomaa, Veikko; Erbel, Raimund; Jöckel, Karl-Heinz; Moebus, Susanne; Peters, Annette; Illig, Thomas; de Faire, Ulf; Hamsten, Anders; Morris, Andrew D; Donnelly, Peter J; Frayling, Timothy M; Hattersley, Andrew T; Boerwinkle, Eric; Melander, Olle; Kathiresan, Sekar; Nilsson, Peter M; Deloukas, Panos; Thorsteinsdottir, Unnur; Groop, Leif C; Stefansson, Kari; Hu, Frank; Pankow, James S; Dupuis, Josée; Meigs, James B; Altshuler, David; Boehnke, Michael; McCarthy, Mark I

    2012-09-01

    To extend understanding of the genetic architecture and molecular basis of type 2 diabetes (T2D), we conducted a meta-analysis of genetic variants on the Metabochip, including 34,840 cases and 114,981 controls, overwhelmingly of European descent. We identified ten previously unreported T2D susceptibility loci, including two showing sex-differentiated association. Genome-wide analyses of these data are consistent with a long tail of additional common variant loci explaining much of the variation in susceptibility to T2D. Exploration of the enlarged set of susceptibility loci implicates several processes, including CREBBP-related transcription, adipocytokine signaling and cell cycle regulation, in diabetes pathogenesis. PMID:22885922

  9. Large-Scale Development of Gene-Associated Single-Nucleotide Polymorphism Markers for Molluscan Population Genomic, Comparative Genomic, and Genome-Wide Association Studies

    PubMed Central

    Jiao, Wenqian; Fu, Xiaoteng; Li, Jinqin; Li, Ling; Feng, Liying; Lv, Jia; Zhang, Lu; Wang, Xiaojian; Li, Yangping; Hou, Rui; Zhang, Lingling; Hu, Xiaoli; Wang, Shi; Bao, Zhenmin

    2014-01-01

    Mollusca is the second most diverse group of animals in the world. Despite their perceived importance, omics-level studies have seldom been applied to this group of animals largely due to a paucity of genomic resources. Here, we report the first large-scale gene-associated marker development and evaluation for a bivalve mollusc, Chlamys farreri. More than 21,000 putative single-nucleotide polymorphisms (SNPs) were identified from the C. farreri transcriptome. Primers and probes were designed and synthesized for 4500 SNPs, and 1492 polymorphic markers were successfully developed using a high-resolution melting genotyping platform. These markers are particularly suitable for population genomic analysis due to high polymorphism within and across populations, a low frequency of null alleles, and conformation to neutral expectations. Unexpectedly, high cross-species transferability was observed, suggesting that the transferable SNPs may largely represent ancestral genetic variations that have been preserved differentially among subfamilies of Pectinidae. Gene annotations were available for 73% of the markers, and 65% could be anchored to the recently released Pacific oyster genome. Large-scale association analysis revealed key candidate genes responsible for scallop growth regulation, and provided markers for further genetic improvement of C. farreri in breeding programmes. PMID:24277739

  10. Identification of Genes Important for Cutaneous Function Revealed by a Large Scale Reverse Genetic Screen in the Mouse

    PubMed Central

    DiTommaso, Tia; Jones, Lynelle K.; Cottle, Denny L.; Gerdin, Anna-Karin; Vancollie, Valerie E.; Watt, Fiona M.; Ramirez-Solis, Ramiro; Bradley, Allan; Steel, Karen P.; Sundberg, John P.; White, Jacqueline K.; Smyth, Ian M.

    2014-01-01

    The skin is a highly regenerative organ which plays critical roles in protecting the body and sensing its environment. Consequently, morbidity and mortality associated with skin defects represent a significant health issue. To identify genes important in skin development and homeostasis, we have applied a high throughput, multi-parameter phenotype screen to the conditional targeted mutant mice generated by the Wellcome Trust Sanger Institute's Mouse Genetics Project (Sanger-MGP). A total of 562 different mouse lines were subjected to a variety of tests assessing cutaneous expression, macroscopic clinical disease, histological change, hair follicle cycling, and aberrant marker expression. Cutaneous lesions were associated with mutations in 23 different genes. Many of these were not previously associated with skin disease in the organ (Mysm1, Vangl1, Trpc4ap, Nom1, Sparc, Farp2, and Prkab1), while others were ascribed new cutaneous functions on the basis of the screening approach (Krt76, Lrig1, Myo5a, Nsun2, and Nf1). The integration of these skin specific screening protocols into the Sanger-MGP primary phenotyping pipelines marks the largest reported reverse genetic screen undertaken in any organ and defines approaches to maximise the productivity of future projects of this nature, while flagging genes for further characterisation. PMID:25340873

  11. A rat genetic map constructed by representational difference analysis markers with suitability for large-scale typing.

    PubMed Central

    Toyota, M; Canzian, F; Ushijima, T; Hosoya, Y; Kuramoto, T; Serikawa, T; Imai, K; Sugimura, T; Nagao, M

    1996-01-01

    Representational difference analysis (RDA) was applied to isolate chromosomal markers in the rat. Four series of RDA [restriction enzymes, BamHI and HindIII; subtraction of ACI/N (ACI) amplicon from BUF/Nac (BUF) amplicon and vice versa] yielded 131 polymorphic markers; 125 of these markers were mapped to all chromosomes except for chromosome X. This was done by using a mapping panel of 105 ACI x BUF F2 rats. To complement the relative paucity of chromosomal markers in the rat, genetically directed RDA, which allows isolation of polymorphic markers in the specific chromosomal region, was performed. By changing the F2 driver-DNA allele frequency around the region, four markers were isolated from the D1Ncc1 locus. Twenty-five of 27 RDA markers were informative regarding the dot blot analysis of amplicons, hybridizing only with tester amplicons. Dot blot analysis at a high density per unit of area made it possible to process a large number of samples. Quantitative trait loci can now be mapped in the rat genome by processing a large number of samples with RDA markers and then by isolating markers close to the loci of interest by genetically directed RDA. Images Fig. 1 Fig. 3 Fig. 4 PMID:8632989

  12. Constraints on neutrino masses from the study of the nearby large-scale structure and galaxy cluster counts

    NASA Astrophysics Data System (ADS)

    Böhringer, Hans; Chon, Gayoung

    2016-07-01

    The high precision measurements of the cosmic microwave background by the Planck survey yielded tight constraints on cosmological parameters and the statistics of the density fluctuations at the time of recombination. This provides the means for a critical study of structure formation in the Universe by comparing the microwave background results with present epoch measurements of the cosmic large-scale structure. It can reveal subtle effects such as how different forms of Dark Matter may modify structure growth. Currently most interesting is the damping effect of structure growth by massive neutrinos. Different observations of low redshift matter density fluctuations provided evidence for a signature of massive neutrinos. Here we discuss the study of the cosmic large-scale structure with a complete sample of nearby, X-ray luminous clusters from our REFLEX cluster survey. From the observed X-ray luminosity function and its reproduction for different cosmological models, we obtain tight constraints on the cosmological parameters describing the matter density, Ωm, and the density fluctuation amplitude, σ8. A comparison of these constraints with the Planck results shows a discrepancy in the framework of a pure ΛCDM model, but the results can be reconciled, if we allow for a neutrino mass in the range of 0.17 eV to 0.7 eV. Also some others, but not all of the observations of the nearby large-scale structure provide evidence or trends for signatures of massive neutrinos. With further improvement in the systematics and future survey projects, these indications will develop into a definitive measurement of neutrino masses.

  13. Multi-stage sampling for large scale natural resources surveys: A case study of rice and waterfowl

    USGS Publications Warehouse

    Stafford, J.D.; Reinecke, K.J.; Kaminski, R.M.; Gerard, P.D.

    2005-01-01

    Large-scale sample surveys to estimate abundance and distribution of organisms and their habitats are increasingly important in ecological studies. Multi-stage sampling (MSS) is especially suited to large-scale surveys because of the natural clustering of resources. To illustrate an application, we: (1) designed a stratified MSS to estimate late autumn abundance (kg/ha) of rice seeds in harvested fields as food for waterfowl wintering in the Mississippi Alluvial Valley (MAV); (2) investigated options for improving the MSS design; and (3) compared statistical and cost efficiency of MSS to simulated simple random sampling (SRS). During 2000?2002, we sampled 25?35 landowners per year, 1 or 2 fields per landowner per year, and measured seed mass in 10 soil cores collected within each field. Analysis of variance components and costs for each stage of the survey design indicated that collecting 10 soil cores per field was near the optimum of 11?15, whereas sampling >1 field per landowner provided few benefits because data from fields within landowners were highly correlated. Coefficients of variation (CV) of annual estimates of rice abundance ranged from 0.23 to 0.31 and were limited by variation among landowners and the number of landowners sampled. Design effects representing the statistical efficiency of MSS relative to SRS ranged from 3.2 to 9.0, and simulations indicated SRS would cost, on average, 1.4 times more than MSS because clustering of sample units in MSS decreased travel costs. We recommend MSS as a potential sampling strategy for large-scale natural resource surveys and specifically for future surveys of the availability of rice as food for waterfowl in the MAV and similar areas.

  14. Genetic Diversity and Ecological Niche Modelling of Wild Barley: Refugia, Large-Scale Post-LGM Range Expansion and Limited Mid-Future Climate Threats?

    PubMed Central

    Russell, Joanne; van Zonneveld, Maarten; Dawson, Ian K.; Booth, Allan; Waugh, Robbie; Steffenson, Brian

    2014-01-01

    Describing genetic diversity in wild barley (Hordeum vulgare ssp. spontaneum) in geographic and environmental space in the context of current, past and potential future climates is important for conservation and for breeding the domesticated crop (Hordeum vulgare ssp. vulgare). Spatial genetic diversity in wild barley was revealed by both nuclear- (2,505 SNP, 24 nSSR) and chloroplast-derived (5 cpSSR) markers in 256 widely-sampled geo-referenced accessions. Results were compared with MaxEnt-modelled geographic distributions under current, past (Last Glacial Maximum, LGM) and mid-term future (anthropogenic scenario A2, the 2080s) climates. Comparisons suggest large-scale post-LGM range expansion in Central Asia and relatively small, but statistically significant, reductions in range-wide genetic diversity under future climate. Our analyses support the utility of ecological niche modelling for locating genetic diversity hotspots and determine priority geographic areas for wild barley conservation under anthropogenic climate change. Similar research on other cereal crop progenitors could play an important role in tailoring conservation and crop improvement strategies to support future human food security. PMID:24505252

  15. Utilisation of ISA Reverse Genetics and Large-Scale Random Codon Re-Encoding to Produce Attenuated Strains of Tick-Borne Encephalitis Virus within Days

    PubMed Central

    Aubry, Fabien; Gould, Ernest A.; de Lamballerie, Xavier

    2016-01-01

    Large-scale codon re-encoding is a new method of attenuating RNA viruses. However, the use of infectious clones to generate attenuated viruses has inherent technical problems. We previously developed a bacterium-free reverse genetics protocol, designated ISA, and now combined it with large-scale random codon-re-encoding method to produce attenuated tick-borne encephalitis virus (TBEV), a pathogenic flavivirus which causes febrile illness and encephalitis in humans. We produced wild-type (WT) and two re-encoded TBEVs, containing 273 or 273+284 synonymous mutations in the NS5 and NS5+NS3 coding regions respectively. Both re-encoded viruses were attenuated when compared with WT virus using a laboratory mouse model and the relative level of attenuation increased with the degree of re-encoding. Moreover, all infected animals produced neutralizing antibodies. This novel, rapid and efficient approach to engineering attenuated viruses could potentially expedite the development of safe and effective new-generation live attenuated vaccines. PMID:27548676

  16. Pre- and Postnatal Influences on Preschool Mental Health: A Large-Scale Cohort Study

    ERIC Educational Resources Information Center

    Robinson, Monique; Oddy, Wendy H.; Li, Jianghong; Kendall, Garth E.; de Klerk, Nicholas H.; Silburn, Sven R.; Zubrick, Stephen R.; Newnham, John P.; Stanley, Fiona J.; Mattes, Eugen

    2008-01-01

    Background: Methodological challenges such as confounding have made the study of the early determinants of mental health morbidity problematic. This study aims to address these challenges in investigating antenatal, perinatal and postnatal risk factors for the development of mental health problems in pre-school children in a cohort of Western…

  17. Large-scale optimization-based non-negative computational framework for diffusion equations: Parallel implementation and performance studies

    DOE PAGESBeta

    Chang, Justin; Karra, Satish; Nakshatrala, Kalyana B.

    2016-07-26

    It is well-known that the standard Galerkin formulation, which is often the formulation of choice under the finite element method for solving self-adjoint diffusion equations, does not meet maximum principles and the non-negative constraint for anisotropic diffusion equations. Recently, optimization-based methodologies that satisfy maximum principles and the non-negative constraint for steady-state and transient diffusion-type equations have been proposed. To date, these methodologies have been tested only on small-scale academic problems. The purpose of this paper is to systematically study the performance of the non-negative methodology in the context of high performance computing (HPC). PETSc and TAO libraries are, respectively, usedmore » for the parallel environment and optimization solvers. For large-scale problems, it is important for computational scientists to understand the computational performance of current algorithms available in these scientific libraries. The numerical experiments are conducted on the state-of-the-art HPC systems, and a single-core performance model is used to better characterize the efficiency of the solvers. Furthermore, our studies indicate that the proposed non-negative computational framework for diffusion-type equations exhibits excellent strong scaling for real-world large-scale problems.« less

  18. Submarine ridges do not prevent large-scale dispersal of abyssal fauna: A case study of Mesocletodes (Crustacea, Copepoda, Harpacticoida)

    NASA Astrophysics Data System (ADS)

    Menzel, Lena; George, Kai Horst; Arbizu, Pedro Martínez

    2011-08-01

    We examined the large-scale distribution of deep-sea harpacticoid copepods at the species level, in order to clarify the underlying processes of copepod dispersal. The study was based on samples collected from 12 regions and a total of 113 stations: 57 stations at depths between 1107 and 5655 m on abyssal plains in the South and North Atlantic, Southern Ocean, southern Indian Ocean, and the Pacific Ocean, and 56 stations above 900 m in the North Atlantic and eastern Mediterranean Sea. We chose the genus Mesocletodes Sars, 1909 as an ideal group to study the large-scale distribution of harpacticoid copepods in the deep oceans. Clear apomorphies and a comparatively large body size of about 1 mm allow rapid recognition of allied species in meiofauna samples. In addition, Mesocletodes represents more than 50% of the family Argestidae Por, 1986, one of the most abundant harpacticoid families in the deep sea. The geographical distributions of 793 adult females of Mesocletodes belonging to 61 species throughout the South and North Atlantic, Southern Ocean, southern Indian Ocean, Pacific Ocean, and eastern Mediterranean Sea indicated that most species are cosmopolitan. Neither the topography of the sea bottom nor long distances seem to prevent species from dispersing. Passive transport by bottom currents after resuspension is likely the propulsive factor for the dispersal of Harpacticoida, while plate tectonics and movement of individuals in the sediment may play relatively minor roles.

  19. Development of Residential Prototype Building Models and Analysis System for Large-Scale Energy Efficiency Studies Using EnergyPlus

    SciTech Connect

    Mendon, Vrushali V.; Taylor, Zachary T.

    2014-09-10

    ABSTRACT: Recent advances in residential building energy efficiency and codes have resulted in increased interest in detailed residential building energy models using the latest energy simulation software. One of the challenges of developing residential building models to characterize new residential building stock is to allow for flexibility to address variability in house features like geometry, configuration, HVAC systems etc. Researchers solved this problem in a novel way by creating a simulation structure capable of creating fully-functional EnergyPlus batch runs using a completely scalable residential EnergyPlus template system. This system was used to create a set of thirty-two residential prototype building models covering single- and multifamily buildings, four common foundation types and four common heating system types found in the United States (US). A weighting scheme with detailed state-wise and national weighting factors was designed to supplement the residential prototype models. The complete set is designed to represent a majority of new residential construction stock. The entire structure consists of a system of utility programs developed around the core EnergyPlus simulation engine to automate the creation and management of large-scale simulation studies with minimal human effort. The simulation structure and the residential prototype building models have been used for numerous large-scale studies, one of which is briefly discussed in this paper.

  20. Stormbow: A Cloud-Based Tool for Reads Mapping and Expression Quantification in Large-Scale RNA-Seq Studies

    PubMed Central

    Zhao, Shanrong; Prenger, Kurt; Smith, Lance

    2013-01-01

    RNA-Seq is becoming a promising replacement to microarrays in transcriptome profiling and differential gene expression study. Technical improvements have decreased sequencing costs and, as a result, the size and number of RNA-Seq datasets have increased rapidly. However, the increasing volume of data from large-scale RNA-Seq studies poses a practical challenge for data analysis in a local environment. To meet this challenge, we developed Stormbow, a cloud-based software package, to process large volumes of RNA-Seq data in parallel. The performance of Stormbow has been tested by practically applying it to analyse 178 RNA-Seq samples in the cloud. In our test, it took 6 to 8 hours to process an RNA-Seq sample with 100 million reads, and the average cost was $3.50 per sample. Utilizing Amazon Web Services as the infrastructure for Stormbow allows us to easily scale up to handle large datasets with on-demand computational resources. Stormbow is a scalable, cost effective, and open-source based tool for large-scale RNA-Seq data analysis. Stormbow can be freely downloaded and can be used out of box to process Illumina RNA-Seq datasets. PMID:25937948

  1. The first large scale molecular study of Cryptosporidium and Giardia in horses

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The prevalence of species and genotypes of Giardia and Cryptosporidium in horses is poorly known. The present study examined feces from 195 horses, 1 month to 17 years of age, in 4 locations in Colombia. Prevalence and age distribution of Giardia and Cryptosporidium were determined by PCR. All PCR p...

  2. Comparing Achievement between K-8 and Middle Schools: A Large-Scale Empirical Study

    ERIC Educational Resources Information Center

    Byrnes, Vaughan; Ruby, Allen

    2007-01-01

    This study compares middle schools to K-8 schools, as well as to newly formed K-8 schools that are part of a K-8 conversion policy. The outcome is student achievement, and our sample includes 40,883 eighth-grade students from 95 schools across five cohorts. The analysis uses multilevel modeling to account for student, cohort, and school-level…

  3. Emotional Competencies in Geriatric Nursing: Empirical Evidence from a Computer Based Large Scale Assessment Calibration Study

    ERIC Educational Resources Information Center

    Kaspar, Roman; Hartig, Johannes

    2016-01-01

    The care of older people was described as involving substantial emotion-related affordances. Scholars in vocational training and nursing disagree whether emotion-related skills could be conceptualized and assessed as a professional competence. Studies on emotion work and empathy regularly neglect the multidimensionality of these phenomena and…

  4. A large scale molecular study of Giardia duodenalis in horses in Colombia

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The prevalence of Giardia duodenalis genotypes in horses is poorly known. The present study examined feces from 195 horses, 1 month to 17 years of age, in 4 locations in Colombia. Prevalence of infection was determined by PCR and all positives were sequenced to determine the genotypes. Thirty four (...

  5. Segmentation of Object Outlines into Parts: A Large-Scale Integrative Study

    ERIC Educational Resources Information Center

    De Winter, Joeri; Wagemans, Johan

    2006-01-01

    In this study, a large number of observers (N=201) were asked to segment a collection of outlines derived from line drawings of everyday objects (N=88). This data set was then used as a benchmark to evaluate current models of object segmentation. All of the previously proposed rules of segmentation were found supported in our results. For example,…

  6. Uncovering Implicit Assumptions: A Large-Scale Study on Students' Mental Models of Diffusion

    ERIC Educational Resources Information Center

    Stains, Marilyne; Sevian, Hannah

    2015-01-01

    Students' mental models of diffusion in a gas phase solution were studied through the use of the Structure and Motion of Matter (SAMM) survey. This survey permits identification of categories of ways students think about the structure of the gaseous solute and solvent, the origin of motion of gas particles, and trajectories of solute particles in…

  7. Large-scale gene-centric meta-analysis across 32 studies identifies multiple lipid loci

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genome-wide association studies (GWASs) have identified many SNPs underlying variations in plasma-lipid levels. We explore whether additional loci associated with plasma-lipid phenotypes, such as high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), total cholest...

  8. Study of the high energy Cosmic Rays large scale anisotropies with the ANTARES neutrino telescope

    NASA Astrophysics Data System (ADS)

    Illuminati, Giulia

    2016-02-01

    We present the analysis method used to search for an anisotropy in the high energy Cosmic Rays arrival distribution using data collected by the ANTARES telescope. ANTARES is a neutrino detector, where the collected data are dominated by a large background of cosmic ray muons. Therefore, the background data are suitable for high-statistics studies of cosmic rays in the Northern sky. The main challenge for this analysis is accounting for those effects which can mimic an apparent anisotropy in the muon arrival direction: the detector exposure asymmetries, non-uniform time coverage, diurnal and seasonal variation of the atmospheric temperature. Once all these effects have been corrected, a study of the anisotropy profiles along the right ascension can be performed.

  9. Large scale dynamic systems

    NASA Technical Reports Server (NTRS)

    Doolin, B. F.

    1975-01-01

    Classes of large scale dynamic systems were discussed in the context of modern control theory. Specific examples discussed were in the technical fields of aeronautics, water resources and electric power.

  10. Study of an engine flow diverter system for a large scale ejector powered aircraft model

    NASA Technical Reports Server (NTRS)

    Springer, R. J.; Langley, B.; Plant, T.; Hunter, L.; Brock, O.

    1981-01-01

    Requirements were established for a conceptual design study to analyze and design an engine flow diverter system and to include accommodations for an ejector system in an existing 3/4 scale fighter model equipped with YJ-79 engines. Model constraints were identified and cost-effective limited modification was proposed to accept the ejectors, ducting and flow diverter valves. Complete system performance was calculated and a versatile computer program capable of analyzing any ejector system was developed.

  11. Weather and headache onset: a large-scale study of headache medicine purchases

    NASA Astrophysics Data System (ADS)

    Ozeki, Kayoko; Noda, Tatsuya; Nakamura, Mieko; Ojima, Toshiyuki

    2015-04-01

    It is widely recognized that weather changes can trigger headache onset. Most people who develop headaches choose to self-medicate rather than visit a hospital or clinic. We investigated the association between weather and headache onset using large-sample sales of the headache medicine, loxoprofen. We collected daily sales figures of loxoprofen and over-the-counter drugs over a 1-year period from a drugstore chain in western Shizuoka prefecture, Japan. To adjust for changes in daily sales of loxoprofen due to social environmental factors, we calculated a proportion of loxoprofen daily sales to over-the-counter drug daily sales. At the same time, we obtained weather data for the study region from the website of the Japan Meteorological Agency. We performed linear regression analysis to ascertain the association between weather conditions and the loxoprofen daily sales proportion. We also conducted a separate questionnaire survey at the same drugstores to determine the reason why people purchased loxoprofen. Over the study period, we surveyed the sale of hundreds of thousands of loxoprofen tablets. Most people purchased loxoprofen because they had a headache. We found that the sales proportion of loxoprofen increased when average barometric pressure decreased, and that precipitation, average humidity, and minimum humidity increased on loxoprofen purchase days compared to the previous day of purchases. This study, performed using a large dataset that was easy-to-collect and representative of the general population, revealed that sales of loxoprofen, which can represent the onset and aggravation of headache, significantly increased with worsening weather conditions.

  12. User Friendly Open GIS Tool for Large Scale Data Assimilation - a Case Study of Hydrological Modelling

    NASA Astrophysics Data System (ADS)

    Gupta, P. K.

    2012-08-01

    Open source software (OSS) coding has tremendous advantages over proprietary software. These are primarily fuelled by high level programming languages (JAVA, C++, Python etc...) and open source geospatial libraries (GDAL/OGR, GEOS, GeoTools etc.). Quantum GIS (QGIS) is a popular open source GIS package, which is licensed under GNU GPL and is written in C++. It allows users to perform specialised tasks by creating plugins in C++ and Python. This research article emphasises on exploiting this capability of QGIS to build and implement plugins across multiple platforms using the easy to learn - Python programming language. In the present study, a tool has been developed to assimilate large spatio-temporal datasets such as national level gridded rainfall, temperature, topographic (digital elevation model, slope, aspect), landuse/landcover and multi-layer soil data for input into hydrological models. At present this tool has been developed for Indian sub-continent. An attempt is also made to use popular scientific and numerical libraries to create custom applications for digital inclusion. In the hydrological modelling calibration and validation are important steps which are repetitively carried out for the same study region. As such the developed tool will be user friendly and used efficiently for these repetitive processes by reducing the time required for data management and handling. Moreover, it was found that the developed tool can easily assimilate large dataset in an organised manner.

  13. Infrared and Raman screening of seized novel psychoactive substances: a large scale study of >200 samples.

    PubMed

    Jones, L E; Stewart, A; Peters, K L; McNaul, M; Speers, S J; Fletcher, N C; Bell, S E J

    2016-02-01

    The potential of IR absorption and Raman spectroscopy for rapid identification of novel psychoactive substances (NPS) has been tested using a set of 221 unsorted seized samples suspected of containing NPS. Both IR and Raman spectra showed large variation between the different sub-classifications of NPS and smaller, but still distinguishable, differences between closely related compounds within the same class. In initial tests, screening the samples using spectral searching against a limited reference library allowed only 41% of the samples to be fully identified. The limiting factor in the identification was the large number of active compounds in the seized samples for which no reference vibrational data were available in the libraries rather than poor spectral quality. Therefore, when 33 of these compounds were independently identified by NMR and mass spectrometry and their spectra used to extend the libraries, the percentage of samples identified by IR and Raman screening alone increased to 76%, with only 7% of samples having no identifiable constituents. This study, which is the largest of its type ever carried out, therefore demonstrates that this approach of detecting non-matching samples and then identifying them using standard analytical methods has considerable potential in NPS screening since it allows rapid identification of the constituents of the majority of street quality samples. Only one complete feedback cycle was carried out in this study but there is clearly the potential to carry out continuous identification/updating when this system is used in operational settings. PMID:26779571

  14. Uncovering Implicit Assumptions: a Large-Scale Study on Students' Mental Models of Diffusion

    NASA Astrophysics Data System (ADS)

    Stains, Marilyne; Sevian, Hannah

    2015-12-01

    Students' mental models of diffusion in a gas phase solution were studied through the use of the Structure and Motion of Matter (SAMM) survey. This survey permits identification of categories of ways students think about the structure of the gaseous solute and solvent, the origin of motion of gas particles, and trajectories of solute particles in the gaseous medium. A large sample of data ( N = 423) from students across grade 8 (age 13) through upper-level undergraduate was subjected to a cluster analysis to determine the main mental models present. The cluster analysis resulted in a reduced data set ( N = 308), and then, mental models were ascertained from robust clusters. The mental models that emerged from analysis were triangulated through interview data and characterised according to underlying implicit assumptions that guide and constrain thinking about diffusion of a solute in a gaseous medium. Impacts of students' level of preparation in science and relationships of mental models to science disciplines studied by students were examined. Implications are discussed for the value of this approach to identify typical mental models and the sets of implicit assumptions that constrain them.

  15. Study on the sensing performance of OFBG under large-scale negative strain

    NASA Astrophysics Data System (ADS)

    Wang, Chuan; Hu, Qingli; Ou, Jinping

    2010-03-01

    As a new and sensitive sensing element, OFBG(Optical Fiber Bragg Grating) has been widely used in aerospace engineering and civil engineering. The sensing mechanism and properties have been widely studied by lots of researchers, but the sensing properties of OFBG under large negative strain are still destitute. In this paper, with the aids of large shrinkage performance of PP(polypropylene) during its curing, we gained about -13000 μɛ's strain changes by embeding bare OFBG inside the PP bar to study the sensing properties of OFBG in this strain level. The results show that OFBG can remain its sensing properties well---- linearity, repeatability and the shape of centre wavelength are both reasonably. And the strain sensitivity coefficient of PP-OFBG is about 0.85 pm/μɛ, this is very near with that of calculating results considering strain transmission between PP and OFBG. Which are all helpful and useful for further use of OFBG in other applications.

  16. Large scale prop-fan structural design study. Volume 1: Initial concepts

    NASA Technical Reports Server (NTRS)

    Billman, L. C.; Gruska, C. J.; Ladden, R. M.; Leishman, D. K.; Turnberg, J. E.

    1988-01-01

    In recent years, considerable attention has been directed toward improving aircraft fuel consumption. Studies have shown that the inherent efficiency advantage that turboprop propulsion systems have demonstrated at lower cruise speeds may now be extended to the higher speeds of today's turbofan and turbojet-powered aircraft. To achieve this goal, new propeller designs will require features such as thin, high speed airfoils and aerodynamic sweep, features currently found only in wing designs for high speed aircraft. This is Volume 1 of a 2 volume study to establish structural concepts for such advanced propeller blades, to define their structural properties, to identify any new design, analysis, or fabrication techniques which were required, and to determine the structural tradeoffs involved with several blade shapes selected primarily on the basis of aero/acoustic design considerations. The feasibility of fabricating and testing dynamically scaled models of these blades for aeroelastic testing was also established. The preliminary design of a blade suitable for flight use in a testbed advanced turboprop was conducted and is described in Volume 2.

  17. Large scale prop-fan structural design study. Volume 2: Preliminary design of SR-7

    NASA Technical Reports Server (NTRS)

    Billman, L. C.; Gruska, C. J.; Ladden, R. M.; Leishman, D. K.; Turnberg, J. E.

    1988-01-01

    In recent years, considerable attention has been directed toward improving aircraft fuel consumption. Studies have shown that the inherent efficiency advantage that turboprop propulsion systems have demonstrated at lower cruise speeds may now be extended to the higher speeds of today's turbofan and turbojet-powered aircraft. To achieve this goal, new propeller designs will require features such as thin, high speed airfoils and aerodynamic sweep, features currently found only in wing designs for high speed aircraft. This is Volume 2 of a 2 volume study to establish structural concepts for such advanced propeller blades, to define their structural properties, to identify any new design, analysis, or fabrication techniques which were required, and to determine the structural tradeoffs involved with several blade shapes selected primarily on the basis of aero/acoustic design considerations. The feasibility of fabricating and testing dynamically scaled models of these blades for aeroelastic testing was also established. The preliminary design of a blade suitable for flight use in a testbed advanced turboprop was conducted and is described.

  18. A comparative study of all-vanadium and iron-chromium redox flow batteries for large-scale energy storage

    NASA Astrophysics Data System (ADS)

    Zeng, Y. K.; Zhao, T. S.; An, L.; Zhou, X. L.; Wei, L.

    2015-12-01

    The promise of redox flow batteries (RFBs) utilizing soluble redox couples, such as all vanadium ions as well as iron and chromium ions, is becoming increasingly recognized for large-scale energy storage of renewables such as wind and solar, owing to their unique advantages including scalability, intrinsic safety, and long cycle life. An ongoing question associated with these two RFBs is determining whether the vanadium redox flow battery (VRFB) or iron-chromium redox flow battery (ICRFB) is more suitable and competitive for large-scale energy storage. To address this concern, a comparative study has been conducted for the two types of battery based on their charge-discharge performance, cycle performance, and capital cost. It is found that: i) the two batteries have similar energy efficiencies at high current densities; ii) the ICRFB exhibits a higher capacity decay rate than does the VRFB; and iii) the ICRFB is much less expensive in capital costs when operated at high power densities or at large capacities.

  19. Efficient and large scale synthesis of graphene from coal and its film electrical properties studies.

    PubMed

    Wu, Yingpeng; Ma, Yanfeng; Wang, Yan; Huang, Lu; Li, Na; Zhang, Tengfei; Zhang, Yi; Wan, Xiangjian; Huang, Yi; Chen, Yongsheng

    2013-02-01

    Coal, which is abundant and has an incompact structure, is a good candidate to replace graphite as the raw material for the production of graphene. Here, a new solution phase technique for the preparation of graphene from coal has been developed. The precursor: graphene oxide got from coal was examined by atomic force microscopy, dynamic light scattering and X-ray diffraction, the results showed the GO was a small and single layer sheet. The graphene was examined by X-ray photoelectron spectroscopy, and Raman spectroscopy. Furthermore, graphene films have been prepared using direct solution process and the electrical conductivity and Hall effect have been studied. The results showed the conductivity of the films could reach as high as 2.5 x 10(5) Sm(-1) and exhibited an n-type behavior. PMID:23646544

  20. Atmospheric pressure photoionization as a powerful tool for large-scale lipidomic studies.

    PubMed

    Gaudin, Mathieu; Imbert, Laurent; Libong, Danielle; Chaminade, Pierre; Brunelle, Alain; Touboul, David; Laprévote, Olivier

    2012-05-01

    Lipidomic studies often use liquid chromatography/electrospray ionization mass spectrometry (LC/ESI-MS) for separation, identification, and quantification. However, due to the wide structural diversity of lipids, the most apolar part of the lipidome is often detected with low sensitivity in ESI. Atmospheric pressure (APPI) can be an alternative ionization source since normal-phase solvents are known to enhance photoionization of these classes. In this paper, we intend to show the efficiency of APPI to identify different lipid classes, with a special interest on sphingolipids. In-source APPI fragmentation appears to be an added value for the structural analysis of lipids. It provides a detailed characterization of both the polar head and the non polar moiety of most lipid classes, and it makes possible the detection of all lipids in both polarities, which is not always possible with ESI. PMID:22359092

  1. The relationship between religiosity and cardiovascular risk factors in Japan: a large-scale cohort study.

    PubMed

    Kobayashi, Daiki; Shimbo, Takuro; Takahashi, Osamu; Davis, Roger B; Wee, Christina C

    2015-07-01

    The goal of this study was to examine the relationship between religiosity and cardiovascular risk factors in a Japanese population. A retrospective cohort study was conducted involving individuals who underwent annual health check-ups at St. Luke's International Hospital from 2005 to 2010. Data collected included self-reported demographics, clinical information, and health habits, as well as religiosity, baseline examination, and laboratory measures. We conducted multivariable regression analyses to examine the associations between religiosity and cardiovascular risk factors at baseline and longitudinally. The analyses were performed in 2012. A total of 36,965 participants were enrolled, and 13,846 (37.8%) reported being at least somewhat religious. Compared with those who were not religious at baseline, religious participants (n = 3685) were less likely to be current smokers (odds ratio [OR], 0.59; 95% confidence interval [CI], 0.53-0.67) and to report excessive alcohol consumption (OR, 0.74; 95% CI, 0.67-0.82), and more likely to exercise at least three times a week (OR, 1.27; 95% CI,1.16-1.39) and to be obese (OR, 1.32; 95% CI, 1.19-1.47). There were no significant differences in the rate of hypertension, diabetes mellitus, or dyslipidemia prevalence. In longitudinal data analyses, religiosity was associated with a lower likelihood of smoking and excessive alcohol consumption, and a higher likelihood of regular exercise and a lower incidence of diabetes over time. Individuals who were more religious were significantly more likely to have favorable health habits and fewer cardiovascular risk factors, except for a higher prevalence of overweight/obesity at baseline. Religiosity was also associated with better health habits over time and less likely to be associated with future diabetes but not with blood pressure or lipid levels. PMID:26188400

  2. A large-scale study of CAPE-based mass-flux closures and precipitation

    NASA Astrophysics Data System (ADS)

    Jeevanjee, N.; Romps, D. M.; Sugioka, K.

    2013-12-01

    A popular way to close mass-flux-based deep-convective parameterizations is to assume that convective available potential energy (CAPE) is consumed by convection on some fixed time-scale. Such schemes predict that cloud-base mass fluxes, and hence precipitation rates, are tightly correlated with CAPE values. Previous studies, which have found this prediction unrealistic, have typically tested it by running global circulation models in single-column mode, forced by data from highly localized observational campaigns. Here, we extend these studies by using data from 50 radiosonde stations across the continental US, along with comprehensive radar/rain gauge US precipitation data. We compare correlations between CAPE and precipitation in these observations to that produced by the Community Atmosphere Model (CAM) 5.1, which uses a CAPE-based mass-flux closure. Our results strongly reinforce the finding that such closures predict unrealistically tight temporal correlations between CAPE and precipitation, at least on hourly time scales. If we perform a seasonal average, however, we find that the spatial correlation between seasonal-mean CAPE and precipitation predicted by CAM's convection scheme is reasonably well borne-out by observations. This may help account for the longevity of these otherwise problematic parameterizations. R-values between observed CAPE and precipitation time series for JJA 2011 for 48 radiosonde sites around CONUS. No discernible correlation is evident at any location R-values between model ouput CAPE and precipitation time series for JJA 2011 for 48 locations around CONUS. Note high correlation in most locations.

  3. Treatability studies and large-scale treatment of aqueous mixed waste containing heavy metals

    SciTech Connect

    Haefner, D.R.

    1995-12-01

    Wastes have accumulated at the Idaho National Engineering Laboratory through routine laboratory practices, experimental engineering operations, and decommissioning and decontamination of nuclear reactor facilities. A storage tank at the Test Area North held approximately 129,000 L of acidic wastewater and contained prohibited levels of lead and mercury. Radioactive constituents were also present; the most predominant being radiocesium Cs-137 and radiocobalt Co-60. Bench-scale studio were undertaken to evaluate ion exchange as a means of removing the contaminants. A set of breakthrough curves was obtained and identified capacity constraints, selectivities, and operating requirements of candidate resins. Treatment studies indicated that Purolite S-920 resin could effectively remove mercury, while Rohm and Haas` Amberlite 200-CH was used for lead and radionuclide removal. Based on these laboratory tests a full-scale facility, using multiple ion exchange columns, was designed and operated in the spring of 1994. The liquid effluents were discharged to an onsite evaporation pond and met RCRA disposal limits for hazardous metals and self-imposed radionuclide limits. All secondary wastes and residues were sampled and subjected to the to)dc characteristic leaching procedure. The resulting leachate concentrations were below RCRA discharge limits and, therefore, these will be disposed of at the onsite low-level disposal facility. After concluding the tank wastewater operations, enough reserve resin capacity was available to treat three additional mixed wastes residing onsite. These totaled about 1,900 L (500 gal) and contained prohibited levels of chromium, cadmium, and barium. Laboratory studies demonstrated that these heavy metals could also be removed by the existing resins. Treatment was performed at the full-scale facility with the effluents discharged to the evaporation pond.

  4. Determinants of brominated flame retardants in breast milk from a large scale Norwegian study.

    PubMed

    Thomsen, Cathrine; Stigum, Hein; Frøshaug, May; Broadwell, Sharon L; Becher, Georg; Eggesbø, Merete

    2010-01-01

    Brominated flame retardants (BFRs), particularly polybrominated diphenyl ethers (PBDEs), are widely present in human populations. In order to investigate human exposure pathways and associations with socioeconomic and lifestyle factors, 393 breast milk samples from mothers living in various regions throughout Norway were analyzed. Up to ten PBDE congeners were measured in all the samples, hexabromocyclododecane (HBCD) and BDE-209 in subsets of 310 and 46, respectively. The median concentrations of the sum of the seven most prominent PBDEs (BDE-28, 47, 99, 100, 153, 154 and 183), BDE-209 and HBCD were 2.1, 0.32 and 0.86ng/g lipids, respectively. These concentrations are comparable to the levels generally observed in human populations in Europe. The frequency distributions were quite skewed with long tails towards higher concentrations. Maternal age, parity, education, having a cohabitant employed as electrician, and ventilation were factors significantly associated with some of the BFRs, although these factors only explained a small amount of the variability (R(2) 0.04-0.16). The mothers' diet was not found to influence the breast milk PBDE and HBCD levels. Our results show that sources other than the diet are important for the variability seen in breast milk BFR concentrations and that exposure from the indoor atmosphere should be emphasized in future studies. PMID:19889457

  5. Study of fog in Bulgaria by using the GNSS tropospheric products and large scale dynamic analysis

    NASA Astrophysics Data System (ADS)

    Stoycheva, A.; Guerova, G.

    2015-10-01

    The fog formation, development, and dissipation are studied by employing the synergy between surface observations and vertically Integrated Water Vapor (IWV) from Global Navigation Satellite Systems (GNSS). Selected are three fog cases in February and November 2012 and the fog development in 4 locations in north Bulgaria is analysed. It is found that the IWV tends to decrease during fog formation, and densification. Increase of IWV leads to fog dispersion and can be a result of evaporation or advection of new humid air mass. The mixing ratio also decreases during the fog formation and increases during dissipation but has a distinct diurnal variability, which limits its short range forecasting potential. IWV is found to have a very high sensitivity to both air mass transformation and/or advection at altitude. In one case it is found that the arrival time of a new air mass at altitude is of key importance for further fog development or suppression. The change of the air mass leads to change of the diurnal cycle of surface parameters like temperature thus controlling the fog life cycle. Further complication of fog diagnosis is introduced by a dynamic component, reflecting the orography difference in west and east part of Bulgaria. The behaviour of the IWV and mixing ratio can be a valuable additional tool in decision making processes for very short range fog diagnosis and prognosis. For monitoring fog life cycle hourly or sub-hourly data-sets will be an advantage.

  6. Emotional competencies in geriatric nursing: empirical evidence from a computer based large scale assessment calibration study.

    PubMed

    Kaspar, Roman; Hartig, Johannes

    2016-03-01

    The care of older people was described as involving substantial emotion-related affordances. Scholars in vocational training and nursing disagree whether emotion-related skills could be conceptualized and assessed as a professional competence. Studies on emotion work and empathy regularly neglect the multidimensionality of these phenomena and their relation to the care process, and are rarely conclusive with respect to nursing behavior in practice. To test the status of emotion-related skills as a facet of client-directed geriatric nursing competence, 402 final-year nursing students from 24 German schools responded to a 62-item computer-based test. 14 items were developed to represent emotion-related affordances. Multi-dimensional IRT modeling was employed to assess a potential subdomain structure. Emotion-related test items did not form a separate subdomain, and were found to be discriminating across the whole competence continuum. Tasks concerning emotion work and empathy are reliable indicators for various levels of client-directed nursing competence. Claims for a distinct emotion-related competence in geriatric nursing, however, appear excessive with a process-oriented perspective. PMID:26108300

  7. Large-Scale Overexpression and Purification of ADARs from Saccharomyces cerevisiae for Biophysical and Biochemical Studies

    PubMed Central

    Macbeth, Mark R.; Bass, Brenda L.

    2008-01-01

    Many biochemical and biophysical analyses of enzymes require quantities of protein that are difficult to obtain from expression in an endogenous system. To further complicate matters, native adenosine deaminases that act on RNA (ADARs) are expressed at very low levels, and overexpression of active protein has been unsuccessful in common bacterial systems. Here we describe the plasmid construction, expression, and purification procedures for ADARs overexpressed in the yeast Saccharomyces cerevisiae. ADAR expression is controlled by the Gal promoter, which allows for rapid induction of transcription when the yeast are grown in media containing galactose. The ADAR is translated with an N-terminal histidine tag that is cleaved by the tobacco etch virus protease, generating one nonnative glycine residue at the N-terminus of the ADAR protein. ADARs expressed using this system can be purified to homogeneity, are highly active in deaminating RNA, and are produced in quantities (from 3 to 10 mg of pure protein per liter of yeast culture) that are sufficient for most biophysical studies. PMID:17662848

  8. An HST Proper-motion Study of the Large-scale Jet of 3C273

    NASA Astrophysics Data System (ADS)

    Meyer, Eileen T.; Sparks, William B.; Georganopoulos, Markos; Anderson, Jay; van der Marel, Roeland; Biretta, John; Sohn, Sangmo Tony; Chiaberge, Marco; Perlman, Eric; Norman, Colin

    2016-02-01

    The radio galaxy 3C 273 hosts one of the nearest and best-studied powerful quasar jets. Having been imaged repeatedly by the Hubble Space Telescope (HST) over the past twenty years, it was chosen for an HST program to measure proper motions in the kiloparsec-scale resolved jets of nearby radio-loud active galaxies. The jet in 3C 273 is highly relativistic on sub-parsec scales, with apparent proper motions up to 15c observed by very long baseline interferometry. In contrast, we find that the kiloparsec-scale knots are compatible with being stationary, with a mean speed of -0.2 ± 0.5c over the whole jet. Assuming the knots are packets of moving plasma, an upper limit of 1c implies a bulk Lorentz factor Γ < 2.9. This suggests that the jet has either decelerated significantly by the time it reaches the kiloparsec scale, or that the knots in the jet are standing shock features. The second scenario is incompatible with the inverse Compton off the Cosmic Microwave Background (IC/CMB) model for the X-ray emission of these knots, which requires the knots to be in motion, but IC/CMB is also disfavored in the first scenario due to energetic considerations, in agreement with the recent finding of Meyer & Georganopoulos which ruled out the IC/CMB model for the X-ray emission of 3C 273 via gamma-ray upper limits.

  9. A large-scale validation study of the Medication Adherence Rating Scale (MARS).

    PubMed

    Fialko, Laura; Garety, Philippa A; Kuipers, Elizabeth; Dunn, Graham; Bebbington, Paul E; Fowler, David; Freeman, Daniel

    2008-03-01

    Adherence to medication is an important predictor of illness course and outcome in psychosis. The Medication Adherence Rating Scale (MARS) is a ten-item self-report measure of medication adherence in psychosis [Thompson, K., Kulkarni, J., Sergejew, A.A., 2000. Reliability and validity of a new Medication Adherence Rating Scale (MARS) for the psychoses. Schizophrenia Research. 42. 241-247]. Although initial results suggested that the scale has good reliability and validity, the development sample was small. The current study aimed to establish the psychometric properties of the MARS in a sample over four times larger. The scale was administered to 277 individuals with psychosis, along with measures of insight and psychopathology. Medication adherence was independently rated by each individual's keyworker. Results showed the internal consistency of the MARS to be lower than in the original sample, though adequate. MARS total score correlated weakly with keyworker-rated adherence, hence concurrent validity of the scale appeared only moderate to weak. The three factor structure of the MARS was replicated. Examination of the factor scores suggested that the factor 1 total score, which corresponds to the Medication Adherence Questionnaire [Morisky,D.E., Green,L.W. and Levine,D.M., 1986. Concurrent and predictive validity of a self-reported measure of medication adherence. Medical Care. 24, 67-74] may be a preferable measure of medication adherence behaviour to the total scale score. PMID:18083007

  10. Clinical prediction from structural brain MRI scans: a large-scale empirical study.

    PubMed

    Sabuncu, Mert R; Konukoglu, Ender

    2015-01-01

    Multivariate pattern analysis (MVPA) methods have become an important tool in neuroimaging, revealing complex associations and yielding powerful prediction models. Despite methodological developments and novel application domains, there has been little effort to compile benchmark results that researchers can reference and compare against. This study takes a significant step in this direction. We employed three classes of state-of-the-art MVPA algorithms and common types of structural measurements from brain Magnetic Resonance Imaging (MRI) scans to predict an array of clinically relevant variables (diagnosis of Alzheimer's, schizophrenia, autism, and attention deficit and hyperactivity disorder; age, cerebrospinal fluid derived amyloid-β levels and mini-mental state exam score). We analyzed data from over 2,800 subjects, compiled from six publicly available datasets. The employed data and computational tools are freely distributed ( https://www.nmr.mgh.harvard.edu/lab/mripredict), making this the largest, most comprehensive, reproducible benchmark image-based prediction experiment to date in structural neuroimaging. Finally, we make several observations regarding the factors that influence prediction performance and point to future research directions. Unsurprisingly, our results suggest that the biological footprint (effect size) has a dramatic influence on prediction performance. Though the choice of image measurement and MVPA algorithm can impact the result, there was no universally optimal selection. Intriguingly, the choice of algorithm seemed to be less critical than the choice of measurement type. Finally, our results showed that cross-validation estimates of performance, while generally optimistic, correlate well with generalization accuracy on a new dataset. PMID:25048627

  11. Quantifying Uncertainties in Large Scale Water Budget: Case Study in Siberia

    NASA Astrophysics Data System (ADS)

    Joe, S.; Brubaker, K. L.

    2004-12-01

    Assessment and prediction of Arctic River flows' effects on ocean circulation and climate are hindered by lack of knowledge about the terrestial water balance in remote regions. In this study, we quantify the components of the annual water budget for a large Siberian river basin and -- most importantly -- the uncertainty in the components. The water budget for a watershed can be simplified to basic inputs and outputs: Precipitation (P), Streamflow (Q), and Evapotranspiration (E). Over the long term, assuming negligible change in storage, inputs and outputs should balance, P = Q + E. However, errors in measuring and estimating the components lead to a nonzero closure error, CE = P - Q - E. The uncertainty in the water balance can be quantified by the variance of CE, which is equal to the sum of the component variances (assumed independent). The closure error and its variance were estimated for the 57000 km2 Tom River basin (a subbasin of the Ob River) for five water years, 1981- 1985. We hypothesized that (a) the CE would be negative due to underestimation of P by the sparse, low-elevation precipitation network, and (b) statistical hypothesis testing would show that the CE is not significantly different from 0, due to uncertainty in the components. The basin mean and variance of P were estimated by kriging station observations. The annual mean Q was obtained from discharge measurements at Tomsk, Russia; the uncertainty in Q was based on published estimates of rating curve error bars. The basin mean and variance of E were computed from a derived distribution based on Monte Carlo simulation of the Penman Monteith model, driven by measured meteorological data at Tomsk, and accounting for variation in elevation and vegetation. Annual CEs were negative, ranging from -160 to -325 mm, and the standard deviations ranged from 50 to 60 mm. The CE was significantly different from 0 for all five water years, supporting the belief that annual P is underestimated by the gage

  12. A New Model for Conducting Large-Scale Aerogeophysical Studies in Antarctica Through International Collaboration

    NASA Astrophysics Data System (ADS)

    Holt, J. W.; Blankenship, D. D.; Peters, M. E.; Vaughan, D. G.; Corr, H. F.

    2006-12-01

    The aerogeophysical surveys of the 1970's conducted by the Scott Polar Research Institute (SPRI), the National Science Foundation (NSF), and the Technical University of Denmark (TUD) were the successful result of an international collaboration to implement geophysical capabilities, primarily ice penetrating radar, onto a long-range aircraft and operate that system in Antarctica for multiple field seasons in a reconnaissance mode. This produced the first continental-scale insights into the Antarctic ice sheet and subglacial geomorphology, and this context made it possible to plan more detailed studies with new geophysical systems. The University of Texas Institute for Geophysics (UTIG) led such an effort through the successful implementation of a multi-instrumented Twin Otter aerogeophysical platform. UTIG, in collaboration with others, modified the 60 MHz TUD radar used in the SPRI/NSF/TUD survey and integrated it with a gravity meter, towed magnetometer, and laser altimeter. First used in 1991, this system later became the basis for the Support Office for Aerogeophysical Research (SOAR), an NSF facility operated by UTIG from 1994 2001. SOAR acquired over 200,000 line-km of data in both East and West Antarctica during seven field seasons. Subsequent to this, UTIG further modified the system, combining components of a coherent, chirped radar built by NASA's Jet Propulsion Laboratory with the TUD high power transmitter. Meanwhile, the British Antarctic Survey (BAS) designed and built a 150 MHz coherent radar system and integrated it into their Twin Otter aerogeophysical platform with gravity meter and wingtip magnetometers. In 2004-05, UTIG and BAS joined forces to conduct the largest single aerogeophysical survey undertaken in Antarctica to date. The target was the Amundsen Sea Embayment, a largely unexplored and scientifically critical area located far from the logistical centers of the US and UK. Both aerogeophysical systems were deployed using two temporary field

  13. A Large-Scale Genetic Analysis Reveals a Strong Contribution of the HLA Class II Region to Giant Cell Arteritis Susceptibility

    PubMed Central

    Carmona, F. David; Mackie, Sarah L.; Martín, Jose-Ezequiel; Taylor, John C.; Vaglio, Augusto; Eyre, Stephen; Bossini-Castillo, Lara; Castañeda, Santos; Cid, Maria C.; Hernández-Rodríguez, José; Prieto-González, Sergio; Solans, Roser; Ramentol-Sintas, Marc; González-Escribano, M. Francisca; Ortiz-Fernández, Lourdes; Morado, Inmaculada C.; Narváez, Javier; Miranda-Filloy, José A.; Martínez-Berriochoa, Agustín; Unzurrunzaga, Ainhoa; Hidalgo-Conde, Ana; Madroñero-Vuelta, Ana B.; Fernández-Nebro, Antonio; Ordóñez-Cañizares, M. Carmen; Escalante, Begoña; Marí-Alfonso, Begoña; Sopeña, Bernardo; Magro, César; Raya, Enrique; Grau, Elena; Román, José A.; de Miguel, Eugenio; López-Longo, F. Javier; Martínez, Lina; Gómez-Vaquero, Carmen; Fernández-Gutiérrez, Benjamín; Rodríguez-Rodríguez, Luis; Díaz-López, J. Bernardino; Caminal-Montero, Luis; Martínez-Zapico, Aleida; Monfort, Jordi; Tío, Laura; Sánchez-Martín, Julio; Alegre-Sancho, Juan J.; Sáez-Comet, Luis; Pérez-Conesa, Mercedes; Corbera-Bellalta, Marc; García-Villanueva, M. Jesús; Fernández-Contreras, M. Encarnación; Sanchez-Pernaute, Olga; Blanco, Ricardo; Ortego-Centeno, Norberto; Ríos-Fernández, Raquel; Callejas, José L.; Fanlo-Mateo, Patricia; Martínez-Taboada, Víctor M.; Beretta, Lorenzo; Lunardi, Claudio; Cimmino, Marco A.; Gianfreda, Davide; Santilli, Daniele; Ramirez, Giuseppe A.; Soriano, Alessandra; Muratore, Francesco; Pazzola, Giulia; Addimanda, Olga; Wijmenga, Cisca; Witte, Torsten; Schirmer, Jan H.; Moosig, Frank; Schönau, Verena; Franke, Andre; Palm, Øyvind; Molberg, Øyvind; Diamantopoulos, Andreas P.; Carette, Simon; Cuthbertson, David; Forbess, Lindsy J.; Hoffman, Gary S.; Khalidi, Nader A.; Koening, Curry L.; Langford, Carol A.; McAlear, Carol A.; Moreland, Larry; Monach, Paul A.; Pagnoux, Christian; Seo, Philip; Spiera, Robert; Sreih, Antoine G.; Warrington, Kenneth J.; Ytterberg, Steven R.; Gregersen, Peter K.; Pease, Colin T.; Gough, Andrew; Green, Michael; Hordon, Lesley; Jarrett, Stephen; Watts, Richard; Levy, Sarah; Patel, Yusuf; Kamath, Sanjeet; Dasgupta, Bhaskar; Worthington, Jane; Koeleman, Bobby P.C.; de Bakker, Paul I.W.; Barrett, Jennifer H.; Salvarani, Carlo; Merkel, Peter A.; González-Gay, Miguel A.; Morgan, Ann W.; Martín, Javier

    2015-01-01

    We conducted a large-scale genetic analysis on giant cell arteritis (GCA), a polygenic immune-mediated vasculitis. A case-control cohort, comprising 1,651 case subjects with GCA and 15,306 unrelated control subjects from six different countries of European ancestry, was genotyped by the Immunochip array. We also imputed HLA data with a previously validated imputation method to perform a more comprehensive analysis of this genomic region. The strongest association signals were observed in the HLA region, with rs477515 representing the highest peak (p = 4.05 × 10−40, OR = 1.73). A multivariate model including class II amino acids of HLA-DRβ1 and HLA-DQα1 and one class I amino acid of HLA-B explained most of the HLA association with GCA, consistent with previously reported associations of classical HLA alleles like HLA-DRB1∗04. An omnibus test on polymorphic amino acid positions highlighted DRβ1 13 (p = 4.08 × 10−43) and HLA-DQα1 47 (p = 4.02 × 10−46), 56, and 76 (both p = 1.84 × 10−45) as relevant positions for disease susceptibility. Outside the HLA region, the most significant loci included PTPN22 (rs2476601, p = 1.73 × 10−6, OR = 1.38), LRRC32 (rs10160518, p = 4.39 × 10−6, OR = 1.20), and REL (rs115674477, p = 1.10 × 10−5, OR = 1.63). Our study provides evidence of a strong contribution of HLA class I and II molecules to susceptibility to GCA. In the non-HLA region, we confirmed a key role for the functional PTPN22 rs2476601 variant and proposed other putative risk loci for GCA involved in Th1, Th17, and Treg cell function. PMID:25817017

  14. A large-scale genetic analysis reveals a strong contribution of the HLA class II region to giant cell arteritis susceptibility.

    PubMed

    Carmona, F David; Mackie, Sarah L; Martín, Jose-Ezequiel; Taylor, John C; Vaglio, Augusto; Eyre, Stephen; Bossini-Castillo, Lara; Castañeda, Santos; Cid, Maria C; Hernández-Rodríguez, José; Prieto-González, Sergio; Solans, Roser; Ramentol-Sintas, Marc; González-Escribano, M Francisca; Ortiz-Fernández, Lourdes; Morado, Inmaculada C; Narváez, Javier; Miranda-Filloy, José A; Beretta, Lorenzo; Lunardi, Claudio; Cimmino, Marco A; Gianfreda, Davide; Santilli, Daniele; Ramirez, Giuseppe A; Soriano, Alessandra; Muratore, Francesco; Pazzola, Giulia; Addimanda, Olga; Wijmenga, Cisca; Witte, Torsten; Schirmer, Jan H; Moosig, Frank; Schönau, Verena; Franke, Andre; Palm, Øyvind; Molberg, Øyvind; Diamantopoulos, Andreas P; Carette, Simon; Cuthbertson, David; Forbess, Lindsy J; Hoffman, Gary S; Khalidi, Nader A; Koening, Curry L; Langford, Carol A; McAlear, Carol A; Moreland, Larry; Monach, Paul A; Pagnoux, Christian; Seo, Philip; Spiera, Robert; Sreih, Antoine G; Warrington, Kenneth J; Ytterberg, Steven R; Gregersen, Peter K; Pease, Colin T; Gough, Andrew; Green, Michael; Hordon, Lesley; Jarrett, Stephen; Watts, Richard; Levy, Sarah; Patel, Yusuf; Kamath, Sanjeet; Dasgupta, Bhaskar; Worthington, Jane; Koeleman, Bobby P C; de Bakker, Paul I W; Barrett, Jennifer H; Salvarani, Carlo; Merkel, Peter A; González-Gay, Miguel A; Morgan, Ann W; Martín, Javier

    2015-04-01

    We conducted a large-scale genetic analysis on giant cell arteritis (GCA), a polygenic immune-mediated vasculitis. A case-control cohort, comprising 1,651 case subjects with GCA and 15,306 unrelated control subjects from six different countries of European ancestry, was genotyped by the Immunochip array. We also imputed HLA data with a previously validated imputation method to perform a more comprehensive analysis of this genomic region. The strongest association signals were observed in the HLA region, with rs477515 representing the highest peak (p = 4.05 × 10(-40), OR = 1.73). A multivariate model including class II amino acids of HLA-DRβ1 and HLA-DQα1 and one class I amino acid of HLA-B explained most of the HLA association with GCA, consistent with previously reported associations of classical HLA alleles like HLA-DRB1(∗)04. An omnibus test on polymorphic amino acid positions highlighted DRβ1 13 (p = 4.08 × 10(-43)) and HLA-DQα1 47 (p = 4.02 × 10(-46)), 56, and 76 (both p = 1.84 × 10(-45)) as relevant positions for disease susceptibility. Outside the HLA region, the most significant loci included PTPN22 (rs2476601, p = 1.73 × 10(-6), OR = 1.38), LRRC32 (rs10160518, p = 4.39 × 10(-6), OR = 1.20), and REL (rs115674477, p = 1.10 × 10(-5), OR = 1.63). Our study provides evidence of a strong contribution of HLA class I and II molecules to susceptibility to GCA. In the non-HLA region, we confirmed a key role for the functional PTPN22 rs2476601 variant and proposed other putative risk loci for GCA involved in Th1, Th17, and Treg cell function. PMID:25817017

  15. High-throughput genotyping assay for the large-scale genetic characterization of Cryptosporidium parasites from human and bovine samples.

    PubMed

    Abal-Fabeiro, J L; Maside, X; Llovo, J; Bello, X; Torres, M; Treviño, M; Moldes, L; Muñoz, A; Carracedo, A; Bartolomé, C

    2014-04-01

    The epidemiological study of human cryptosporidiosis requires the characterization of species and subtypes involved in human disease in large sample collections. Molecular genotyping is costly and time-consuming, making the implementation of low-cost, highly efficient technologies increasingly necessary. Here, we designed a protocol based on MALDI-TOF mass spectrometry for the high-throughput genotyping of a panel of 55 single nucleotide variants (SNVs) selected as markers for the identification of common gp60 subtypes of four Cryptosporidium species that infect humans. The method was applied to a panel of 608 human and 63 bovine isolates and the results were compared with control samples typed by Sanger sequencing. The method allowed the identification of species in 610 specimens (90·9%) and gp60 subtype in 605 (90·2%). It displayed excellent performance, with sensitivity and specificity values of 87·3 and 98·0%, respectively. Up to nine genotypes from four different Cryptosporidium species (C. hominis, C. parvum, C. meleagridis and C. felis) were detected in humans; the most common ones were C. hominis subtype Ib, and C. parvum IIa (61·3 and 28·3%, respectively). 96·5% of the bovine samples were typed as IIa. The method performs as well as the widely used Sanger sequencing and is more cost-effective and less time consuming. PMID:24238396

  16. Large-scale Clinical Endodontic Research in The National Dental Practice-Based Research Network: Study Overview and Methods

    PubMed Central

    Nixdorf, Donald R.; Law, Alan S.; Look, John O.; Rindal, D. Brad; Durand, Emily U.; Kang, Wenjun; Agee, Bonita S.; Fellows, Jeffrey L.; Gordan, Valeria V.; Gilbert, Gregg H.

    2013-01-01

    Introduction This paper reports on the feasibility of conducting a large-scale endodontic prospective cohort study in The National Dental Practice-Based Research Network. This study was designed to measure pain and burden associated with initial orthograde root canal therapy (RCT) and to explore potential prognostic factors for pain outcomes. The main objectives of this first report in a series are to describe the project’s feasibility and methods and the demographics of the sample obtained. Methods Sixty-two dentist practitioner-investigators (46 generalists, 16 endodontists) in five geographical areas were certified within the network and trained regarding the standardized study protocol. Enrollment and baseline data collection occurred over 6 months, with post-obturation follow-up for another 6 months. Patients and dentists completed questionnaires before and immediately after treatment visits. Patients also completed questionnaires at 1 week, 3 months, and 6 months after obturation. Results Enrollment exceeded target expectations, with 708 eligible patient-participants. Questionnaire return rates were good, ranging between 90% to 100%. Patient demographics were typical of persons who receive RCT in the United States: mean age 48 years (SD 13 years), with most being female (59%), college-educated (81%), white non-Hispanic (86%), and having dental insurance (81%). The tooth types being treated were also typical: 61% molars, 28% premolars, and 11% anteriors, with maxillary teeth being predominant (59%). Conclusions This study demonstrates the feasibility of conducting large-scale endodontic prospective cohort studies in the network. Patients were rapidly recruited, with high levels of compliance in data collection. PMID:23063220

  17. The tensorial nature of effective porosity and large-scale dispersion coefficients: Application to the Creston study area, Eastern Washington

    SciTech Connect

    McKee, C.R.; Way, S.C.

    1988-12-01

    To describe flow in a complex system of fractures requires an understanding of the effects of direction or orientation on several hydrologic characteristics, such as hydraulic conductivity, porosity, and dispersion coefficient. The theory for hydraulic conductivity is well understood; this report deals with the effects of fracture orientation on porosity and dispersion coefficient. The tensorial nature of effective porosity was examined and was found to be a second-rank tensor in fractured rock units. Porosity varies at a fixed point, depending on its orientation. A method to calculate a dispersion coefficient from field tracer tests is described. The components of the dispersion coefficient can be calculated from the concentration profiles observed in downgradient observation wells. The method provides a procedure for studying the dispersion effect in large-scale field testing. The application of this method was successfully demonstrated in a tracer test performed in the research wellfield at the Creston study area, Lincoln County, Washington.

  18. Self-sampling for analysis of respiratory viruses in a large-scale epidemiological study in Sweden.

    PubMed

    Plymoth, A; Rotzen-Ostlund, M; Zweygberg-Wirgart, B; Sundin, C G; Ploner, A; Nyren, O; Linde, A

    2015-01-01

    Viral diagnosis of respiratory tract infections has so far required sampling by health professionals,hampering large-scale epidemiological studies of virus-specific disease outcomes. As part of a population-based, prospective study of work-related risk factors for transmission of viral infections (SWEDE-I), we developed a scheme for self-sampling with nasal swabs. Random selection from the gainfully employed population of a medium-sized town in central Sweden resulted in a study cohort of 2,237 men and women aged 25 to 63 years. From September 2011 through May 2012, the cohort reported all instances of respiratory tract infection or gastroenteritis and participants concomitantly sent self-sampled nasal swabs for analysis using regular mail. Diagnosis of 14 viruses was performed. A total of 1,843 samples were received. The week-wise average delay between disease on set and arrival of the specimens at the laboratory varied between four and six days, and the corresponding median delay was between 3.5 and six days. In line with previous community-based studies, picorna- and coronaviruses dominated in specimens obtained from the self-sampling scheme. The results of self-sampling were contrasted to those from contemporaneous routine clinical sampling, on the same age group, in the adjacent Stockholm county. Although higher proportions of positive samples for respiratory syncytial virus and influenza were observed in the clinical sampling scheme, estimations of seasonality for influenza A and picornaviruses derived from both schemes were similar. Our findings show that nasal self-sampling is feasible in large-scale surveillance of respiratory infections and opens new prospects for population based,virologically verified research on virus spread,burden of disease, and effects of environmental factors or interventions. PMID:25811646

  19. A topological analysis of large-scale structure, studied using the CMASS sample of SDSS-III

    SciTech Connect

    Parihar, Prachi; Gott, J. Richard III; Vogeley, Michael S.; Choi, Yun-Young; Kim, Juhan; Kim, Sungsoo S.; Speare, Robert; Brownstein, Joel R.; Brinkmann, J. E-mail: yy.choi@khu.ac.kr

    2014-12-01

    We study the three-dimensional genus topology of large-scale structure using the northern region of the CMASS Data Release 10 (DR10) sample of the SDSS-III Baryon Oscillation Spectroscopic Survey. We select galaxies with redshift 0.452 < z < 0.625 and with a stellar mass M {sub stellar} > 10{sup 11.56} M {sub ☉}. We study the topology at two smoothing lengths: R {sub G} = 21 h {sup –1} Mpc and R {sub G} = 34 h {sup –1} Mpc. The genus topology studied at the R {sub G} = 21 h {sup –1} Mpc scale results in the highest genus amplitude observed to date. The CMASS sample yields a genus curve that is characteristic of one produced by Gaussian random phase initial conditions. The data thus support the standard model of inflation where random quantum fluctuations in the early universe produced Gaussian random phase initial conditions. Modest deviations in the observed genus from random phase are as expected from shot noise effects and the nonlinear evolution of structure. We suggest the use of a fitting formula motivated by perturbation theory to characterize the shift and asymmetries in the observed genus curve with a single parameter. We construct 54 mock SDSS CMASS surveys along the past light cone from the Horizon Run 3 (HR3) N-body simulations, where gravitationally bound dark matter subhalos are identified as the sites of galaxy formation. We study the genus topology of the HR3 mock surveys with the same geometry and sampling density as the observational sample and find the observed genus topology to be consistent with ΛCDM as simulated by the HR3 mock samples. We conclude that the topology of the large-scale structure in the SDSS CMASS sample is consistent with cosmological models having primordial Gaussian density fluctuations growing in accordance with general relativity to form galaxies in massive dark matter halos.

  20. Parents' perceived vulnerability and perceived control in preventing Meningococcal C infection: a large-scale interview study about vaccination

    PubMed Central

    Timmermans, Danielle RM; Henneman, Lidewij; Hirasing, Remy A; van der Wal, Gerrit

    2008-01-01

    Background Parents' reported ambivalence toward large-scale vaccination programs for childhood diseases may be related to their perception of the risks of side-effects or safety of vaccination and the risk of contracting the disease. The aim of this study is to evaluate parents' perceptions of their child's risk contracting a Meningococcal C infection and parents' perceived control in preventing infection in relation to their evaluation of the safety, effectiveness and usefulness of vaccination. Methods In a large-scale interview study, a random sample of parents was interviewed after their children had received vaccination against Meningococcal C in a catch-up campaign. Questions were asked about the perceived relative vulnerability of their child contracting an infection, perceived control in preventing an infection, and parents' evaluation of the safety, usefulness and effectiveness of vaccination. Results 61% of 2910 (N = 1763) parents who were approached participated. A higher perceived relative vulnerability of their own child contracting the disease was related to a more positive evaluation of the vaccination campaign, while a lower perceived vulnerability did not result in a more negative evaluation. A higher perceived control in being able to prevent an infection was, however, related to a more critical attitude toward the safety, usefulness and effectiveness of vaccination. Conclusion Perceived relative vulnerability contracting an infection and parents' perceived control in preventing an infection seem to influence parents' evaluation of the vaccination programme. Future studies should determine if, and under which circumstances, these perceptions also affect parents' vaccination behaviour and would be relevant to be taken into account when educating parents about vaccination. PMID:18241345

  1. Experimental study on seismic responses of piping systems with friction. Part 1: Large-scale shaking table vibration test

    SciTech Connect

    Suzuki, K.; Watanabe, T.; Mitsumori, T.; Shimizu, N.; Kobayashi, H.; Ogawa, N.

    1995-08-01

    This report deals with the experimental study of seismic response behavior of piping systems in industrial facilities such as petrochemical, oil refinery, and nuclear plants. Special attention is focused on the nonlinear dynamic response of piping systems due to frictional vibration appearing in piping and supporting devices. A three-dimensional mock-up piping and supporting structure model wherein piping is of 30-m length and 200-mm diameter is excited by a large-scale (15 m x 15 m) shaking table belong to the National Research Institute for Earth Science and Disaster Prevention in Tsukuba, Ibaraki. Power spectra of the response vibration and the loading-response relationship in the form of a hysteresis loop under several loading conditions are obtained. The response reduction effect caused by frictional vibration is evaluated and demonstrated in terms of response reduction factor.

  2. Large-Scale Urban Riots and Residential Segregation: A Case Study of the 1960s U.S. Riots.

    PubMed

    Brazil, Noli

    2016-04-01

    Despite a well-established literature investigating race-related predictors of riot incidence, the racial aftermath of riots remains unexamined. In this study, I use the 1960s U.S. race riots to investigate trends in black residential segregation levels following large-scale riot activity in seven major U.S. cities. I use a novel approach--namely, synthetic control matching--to select a group of cities against which segregation trends can be compared. I find that levels of black segregation rose in 1970 for four of the seven cities, but these increases disappeared in 1980 and 1990 except in Detroit. These results mask differential trends at lower geographic levels: suburban neighborhoods in affected areas experienced larger and longer-term increases in segregation, particularly in traditionally hypersegregated cities in the Midwest and Northeast. PMID:26940025

  3. Large Scale Computing

    NASA Astrophysics Data System (ADS)

    Capiluppi, Paolo

    2005-04-01

    Large Scale Computing is acquiring an important role in the field of data analysis and treatment for many Sciences and also for some Social activities. The present paper discusses the characteristics of Computing when it becomes "Large Scale" and the current state of the art for some particular application needing such a large distributed resources and organization. High Energy Particle Physics (HEP) Experiments are discussed in this respect; in particular the Large Hadron Collider (LHC) Experiments are analyzed. The Computing Models of LHC Experiments represent the current prototype implementation of Large Scale Computing and describe the level of maturity of the possible deployment solutions. Some of the most recent results on the measurements of the performances and functionalities of the LHC Experiments' testing are discussed.

  4. Assessment of climate change impacts on rainfall using large scale climate variables and downscaling models - A case study

    NASA Astrophysics Data System (ADS)

    Ahmadi, Azadeh; Moridi, Ali; Lafdani, Elham Kakaei; Kianpisheh, Ghasem

    2014-10-01

    Many of the applied techniques in water resources management can be directly or indirectly influenced by hydro-climatology predictions. In recent decades, utilizing the large scale climate variables as predictors of hydrological phenomena and downscaling numerical weather ensemble forecasts has revolutionized the long-lead predictions. In this study, two types of rainfall prediction models are developed to predict the rainfall of the Zayandehrood dam basin located in the central part of Iran. The first seasonal model is based on large scale climate signals data around the world. In order to determine the inputs of the seasonal rainfall prediction model, the correlation coefficient analysis and the new Gamma Test (GT) method are utilized. Comparison of modelling results shows that the Gamma test method improves the Nash-Sutcliffe efficiency coefficient of modelling performance as 8% and 10% for dry and wet seasons, respectively. In this study, Support Vector Machine (SVM) model for predicting rainfall in the region has been used and its results are compared with the benchmark models such as K-nearest neighbours (KNN) and Artificial Neural Network (ANN). The results show better performance of the SVM model at testing stage. In the second model, statistical downscaling model (SDSM) as a popular downscaling tool has been used. In this model, using the outputs from GCM, the rainfall of Zayandehrood dam is projected under two climate change scenarios. Most effective variables have been identified among 26 predictor variables. Comparison of the results of the two models shows that the developed SVM model has lesser errors in monthly rainfall estimation. The results show that the rainfall in the future wet periods are more than historical values and it is lower than historical values in the dry periods. The highest monthly uncertainty of future rainfall occurs in March and the lowest in July.

  5. Multiresolution analysis of precipitation teleconnections with large-scale climate signals: A case study in South Australia

    NASA Astrophysics Data System (ADS)

    He, Xinguang; Guan, Huade

    2013-10-01

    Climatic teleconnections are often used to interpret and sometimes to predict precipitation temporal variability at various time scales. However, the teleconnections are intertwined between the effects of multiple large-scale climate signals which are often interdependent. Each climate signal is composed of multitemporal components, which may result in different teleconnection patterns. The time lags of precipitation response may vary with climate signals and their multitemporal components. In order to effectively address these problems, a multiresolution analysis (MRA) with a discrete wavelet transform is utilized, and a stepwise linear regression model based on MRA and cross correlation analysis is developed in this study. The method is applied to examine monthly precipitation teleconnections in South Australia (SA) with five large-scale climate signals. The MRA first decomposes each of original monthly precipitation anomaly and climate signals into several component series at different temporal scales. Then the hierarchical lag relationships between them are determined for regression modeling using cross-correlation analysis. The results indicate that the MRA-based method is able to reveal at which time scale(s) and with what time lag(s) the teleconnections occur, and their spatial patterns. The method is also useful to examine the time-scale patterns of the interdependence between climate signals. These altogether make the MRA-based method a promising tool to address the difficulties in the climate teleconnection studies. The multiple linear regression based on MRA-decomposed climate signals is expected to better interpret monthly precipitation temporal variability than that based on the original climate signals.

  6. Assimilation of satellite data to optimize large-scale hydrological model parameters: a case study for the SWOT mission

    NASA Astrophysics Data System (ADS)

    Pedinotti, V.; Boone, A.; Ricci, S.; Biancamaria, S.; Mognard, N.

    2014-11-01

    During the last few decades, satellite measurements have been widely used to study the continental water cycle, especially in regions where in situ measurements are not readily available. The future Surface Water and Ocean Topography (SWOT) satellite mission will deliver maps of water surface elevation (WSE) with an unprecedented resolution and provide observation of rivers wider than 100 m and water surface areas greater than approximately 250 x 250 m over continental surfaces between 78° S and 78° N. This study aims to investigate the potential of SWOT data for parameter optimization for large-scale river routing models. The method consists in applying a data assimilation approach, the extended Kalman filter (EKF) algorithm, to correct the Manning roughness coefficients of the ISBA (Interactions between Soil, Biosphere, and Atmosphere)-TRIP (Total Runoff Integrating Pathways) continental hydrologic system. Parameters such as the Manning coefficient, used within such models to describe water basin characteristics, are generally derived from geomorphological relationships, which leads to significant errors at reach and large scales. The current study focuses on the Niger Basin, a transboundary river. Since the SWOT observations are not available yet and also to assess the proposed assimilation method, the study is carried out under the framework of an observing system simulation experiment (OSSE). It is assumed that modeling errors are only due to uncertainties in the Manning coefficient. The true Manning coefficients are then supposed to be known and are used to generate synthetic SWOT observations over the period 2002-2003. The impact of the assimilation system on the Niger Basin hydrological cycle is then quantified. The optimization of the Manning coefficient using the EKF (extended Kalman filter) algorithm over an 18-month period led to a significant improvement of the river water levels. The relative bias of the water level is globally improved (a 30

  7. Organizational aspects and implementation of data systems in large-scale epidemiological studies in less developed countries

    PubMed Central

    Ali, Mohammad; Park, Jin-Kyung; von Seidlein, Lorenz; Acosta, Camilo J; Deen, Jacqueline L; Clemens, John D

    2006-01-01

    Background In the conduct of epidemiological studies in less developed countries, while great emphasis is placed on study design, data collection, and analysis, often little attention is paid to data management. As a consequence, investigators working in these countries frequently face challenges in cleaning, analyzing and interpreting data. In most research settings, the data management team is formed with temporary and unskilled persons. A proper working environment and training or guidance in constructing a reliable database is rarely available. There is little information available that describes data management problems and solutions to those problems. Usually a line or two can be obtained in the methods section of research papers stating that the data are doubly-entered and that outliers and inconsistencies were removed from the data. Such information provides little assurance that the data are reliable. There are several issues in data management that if not properly practiced may create an unreliable database, and outcomes of this database will be spurious. Results We have outlined the data management practices for epidemiological studies that we have modeled for our research sites in seven Asian countries and one African country. Conclusion Information from this model data management structure may help others construct reliable databases for large-scale epidemiological studies in less developed countries. PMID:16584571

  8. A large-scale study of the world wide web: network correlation functions with scale-invariant boundaries

    NASA Astrophysics Data System (ADS)

    Ludueña, Guillermo A.; Meixner, Harald; Kaczor, Gregor; Gros, Claudius

    2013-08-01

    We performed a large-scale crawl of the world wide web, covering 6.9 million domains and 57 million subdomains, including all high-traffic sites of the internet. We present a study of the correlations found between quantities measuring the structural relevance of each node in the network (the in- and out-degree, the local clustering coefficient, the first-neighbor in-degree and the Alexa rank). We find that some of these properties show strong correlation effects and that the dependencies occurring out of these correlations follow power laws not only for the averages, but also for the boundaries of the respective density distributions. In addition, these scale-free limits do not follow the same exponents as the corresponding averages. In our study we retain the directionality of the hyperlinks and develop a statistical estimate for the clustering coefficient of directed graphs. We include in our study the correlations between the in-degree and the Alexa traffic rank, a popular index for the traffic volume, finding non-trivial power-law correlations. We find that sites with more/less than about 103 links from different domains have remarkably different statistical properties, for all correlation functions studied, indicating towards an underlying hierarchical structure of the world wide web.

  9. An experimentally verified finite element study of the stress-strain response of crack geometries experiencing large-scale yielding

    SciTech Connect

    Panontin, T.L.; Sheppard, S.D.

    1997-12-01

    Large-strain, 3-D finite element analyses with incremental plasticity were performed for a variety of crack geometries to study local crack-tip stress-strain fields and associated global fracture parameters under conditions of large-scale yielding. The geometries analyzed include thin, single-edge crack tension, single-edge crack bending, and center-crack tension fracture specimens with varying crack depth (a/W) ratios. Two materials were investigated: a high-hardening, low-strength steel and a moderate-hardening, high-strength steel. Mesh refinement studies were performed to ensure convergence of the finite element predictions. The studies examine the effects of in-plane crack-tip element size, initial crack-tip radius size, and number of through-thickness layers on predicted distributions of crack-tip stress and plastic strain and predicted values of the J-integral and CTOD. In addition, the finite element predictions of specimen behavior were verified experimentally by direct measurements, namely load displacement, load longitudinal strain, and load CTOS, made during and following testing of the fracture specimens. Representative results of the finite element analyses are presented and compared to previously published data where pertinent. Results from the mesh refinement studies and the verification testing are shown. Predicted trends among the specimens and materials in local distributions of crack-tip plastic strain, triaxiality, and opening stress as well as in global parameters, J-integral and m-factor, are discussed.

  10. Large-scale, prospective, observational studies in patients with psoriasis and psoriatic arthritis: A systematic and critical review

    PubMed Central

    2011-01-01

    Background Observational studies, if conducted appropriately, play an important role in the decision-making process providing invaluable information on effectiveness, patient-reported outcomes and costs in a real-world environment. We conducted a systematic review of large-scale, prospective, cohort studies with the aim of (a) summarising design characteristics, the interventions or aspects of the disease studied and the outcomes measured and (b) investigating methodological quality. Methods We included prospective, cohort studies which included at least 100 adults with psoriasis or psoriatic arthritis. Studies were identified through searches in electronic databases (Pubmed, Medline, Cochrane library, Centre for Reviews and Dissemination). Information on study characteristics were extracted and tabulated and quality assessment, using a checklist of 18 questions, was conducted. Results Thirty five papers covering 16 cohorts met the inclusion criteria. There were ten treatment-related studies, only two of which provided a comparison between treatments, and six non-treatment studies which examined a number of characteristics of the disease including mortality, morbidity, cost of illness and health-related quality of life. All studies included a clinical outcome measure and 11 included patient-reported outcomes, however only two studies reported information on patient utilities and two on costs. The quality of the assessed studies varied widely. Studies did well on a number of quality assessment questions including having clear objectives, documenting selection criteria, providing a representative sample, defining interventions/characteristics under study, defining and using appropriate outcomes, describing results clearly and using appropriate statistical tests. The quality assessment criteria least adhered to involved questions regarding sample size calculations, describing potential selection bias, defining and adjusting for confounders and losses to follow-up, and

  11. Large-Scale Disasters

    NASA Astrophysics Data System (ADS)

    Gad-El-Hak, Mohamed

    "Extreme" events - including climatic events, such as hurricanes, tornadoes, and drought - can cause massive disruption to society, including large death tolls and property damage in the billions of dollars. Events in recent years have shown the importance of being prepared and that countries need to work together to help alleviate the resulting pain and suffering. This volume presents a review of the broad research field of large-scale disasters. It establishes a common framework for predicting, controlling and managing both manmade and natural disasters. There is a particular focus on events caused by weather and climate change. Other topics include air pollution, tsunamis, disaster modeling, the use of remote sensing and the logistics of disaster management. It will appeal to scientists, engineers, first responders and health-care professionals, in addition to graduate students and researchers who have an interest in the prediction, prevention or mitigation of large-scale disasters.

  12. Study of materials and machines for 3D printed large-scale, flexible electronic structures using fused deposition modeling

    NASA Astrophysics Data System (ADS)

    Hwang, Seyeon

    The 3 dimensional printing (3DP), called to additive manufacturing (AM) or rapid prototyping (RP), is emerged to revolutionize manufacturing and completely transform how products are designed and fabricated. A great deal of research activities have been carried out to apply this new technology to a variety of fields. In spite of many endeavors, much more research is still required to perfect the processes of the 3D printing techniques especially in the area of the large-scale additive manufacturing and flexible printed electronics. The principles of various 3D printing processes are briefly outlined in the Introduction Section. New types of thermoplastic polymer composites aiming to specified functional applications are also introduced in this section. Chapter 2 shows studies about the metal/polymer composite filaments for fused deposition modeling (FDM) process. Various metal particles, copper and iron particles, are added into thermoplastics polymer matrices as the reinforcement filler. The thermo-mechanical properties, such as thermal conductivity, hardness, tensile strength, and fracture mechanism, of composites are tested to figure out the effects of metal fillers on 3D printed composite structures for the large-scale printing process. In Chapter 3, carbon/polymer composite filaments are developed by a simple mechanical blending process with an aim of fabricating the flexible 3D printed electronics as a single structure. Various types of carbon particles consisting of multi-wall carbon nanotube (MWCNT), conductive carbon black (CCB), and graphite are used as the conductive fillers to provide the thermoplastic polyurethane (TPU) with improved electrical conductivity. The mechanical behavior and conduction mechanisms of the developed composite materials are observed in terms of the loading amount of carbon fillers in this section. Finally, the prototype flexible electronics are modeled and manufactured by the FDM process using Carbon/TPU composite filaments and

  13. Characterizing Coherent Wind Structures using Large-Scale Particle Tracking Velocimetry: A Proof-of-Principle Study

    NASA Astrophysics Data System (ADS)

    Rosi, G. A.; la Bastide, B.; Gaebler, J.; Kinzel, M.; Rival, D. E.

    2014-12-01

    The following study proposes a two-dimensional large-scale particle tracking velocimetry (LS-PTV) system to characterize coherent wind structures. Seven minutes of LS-PTV data is collected via an apparatus that seeds fog-filled soap bubbles into the wind at a height of 6m from the ground. The LS-PTV data is compared to 20 minutes of data collected concurrently from a wind mast at the same site. The LS-PTV system recorded a mean streamwise velocity of 1.35m/s with a standard deviation of 0.23m/s at a mean height of 2.50m with a standard deviation of 0.7m, which agrees well with the velocity profile measured by the wind mast. Furthermore, the Reynolds stresses measured by the LS-PTV system are found to compare to those measured by the wind mast and by Klebanoff [1] for a canonical turbulent boundary layer. The current study assumes that the centre-of-curvature trajectories of the particle pathlines are representative of the trajectories followed by the spanwise vortices. As a proof-of-principle study, this work has been successful in accurately describing the vortex distribution very near to the ground. However, the trajectories followed by the centres-of- curvat.ure belonging to pathlines concurrently passing through the field-of-view were sporadic and uncorrelated.

  14. Sensitivity study of a large-scale air pollution model by using high-performance computations and Monte Carlo algorithms

    NASA Astrophysics Data System (ADS)

    Ostromsky, Tz.; Dimov, I.; Georgieva, R.; Marinov, P.; Zlatev, Z.

    2013-10-01

    In this paper we present some new results of our work on sensitivity analysis of a large-scale air pollution model, more specificly the Danish Eulerian Model (DEM). The main purpose of this study is to analyse the sensitivity of ozone concentrations with respect to the rates of some chemical reactions. The current sensitivity study considers the rates of six important chemical reactions and is done for the areas of several European cities with different geographical locations, climate, industrialization and population density. One of the most widely used variance-based techniques for sensitivity analysis, such as Sobol estimates and their modifications, have been used in this study. A vast number of numerical experiments with a specially adapted for the purpose version of the Danish Eulerian Model (SA-DEM) were carried out to compute global Sobol sensitivity measures. SA-DEM was implemented and run on two powerful cluster supercomputers: IBM Blue Gene/P, the most powerful parallel supercomputer in Bulgaria and IBM MareNostrum III, the most powerful parallel supercomputer in Spain. The refined (480 × 480) mesh version of the model was used in the experiments on MareNostrum III, which is a challenging computational problem even on such a powerful machine. Some optimizations of the code with respect to the parallel efficiency and the memory use were performed. Tables with performance results of a number of numerical experiments on IBM BlueGene/P and on IBM MareNostrum III are presented and analysed.

  15. Programmed Nanomaterial Assemblies in Large Scales: Applications of Synthetic and Genetically- Engineered Peptides to Bridge Nano-Assemblies and Macro-Assemblies

    SciTech Connect

    Matsui, Hiroshi

    2014-09-09

    Work is reported in these areas: Large-scale & reconfigurable 3D structures of precise nanoparticle assemblies in self-assembled collagen peptide grids; Binary QD-Au NP 3D superlattices assembled with collagen-like peptides and energy transfer between QD and Au NP in 3D peptide frameworks; Catalytic peptides discovered by new hydrogel-based combinatorial phage display approach and their enzyme-mimicking 2D assembly; New autonomous motors of metal-organic frameworks (MOFs) powered by reorganization of self-assembled peptides at interfaces; Biomimetic assembly of proteins into microcapsules on oil-in-water droplets with structural reinforcement via biomolecular recognition-based cross-linking of surface peptides; and Biomimetic fabrication of strong freestanding genetically-engineered collagen peptide films reinforced by quantum dot joints. We gained the broad knowledge about biomimetic material assembly from nanoscale to microscale ranges by coassembling peptides and NPs via biomolecular recognition. We discovered: Genetically-engineered collagen-like peptides can be self-assembled with Au NPs to generate 3D superlattices in large volumes (> μm{sup 3}); The assembly of the 3D peptide-Au NP superstructures is dynamic and the interparticle distance changes with assembly time as the reconfiguration of structure is triggered by pH change; QDs/NPs can be assembled with the peptide frameworks to generate 3D superlattices and these QDs/NPs can be electronically coupled for the efficient energy transfer; The controlled assembly of catalytic peptides mimicking the catalytic pocket of enzymes can catalyze chemical reactions with high selectivity; and, For the bacteria-mimicking swimmer fabrication, peptide-MOF superlattices can power translational and propellant motions by the reconfiguration of peptide assembly at the MOF-liquid interface.

  16. Large-scale introduction of the Indo-Pacific damselfish Abudefduf vaigiensis into Hawai'i promotes genetic swamping of the endemic congener A. abdominalis.

    PubMed

    Coleman, Richard R; Gaither, Michelle R; Kimokeo, Bethany; Stanton, Frank G; Bowen, Brian W; Toonen, Robert J

    2014-11-01

    Hybridization in the ocean was once considered rare, a process prohibited by the rapid evolution of intrinsic reproductive barriers in a high-dispersal medium. However, recent genetic surveys have prompted a reappraisal of marine hybridization as an important demographic and evolutionary process. The Hawaiian Archipelago offers an unusual case history in this arena, due to the recent arrival of the widely distributed Indo-Pacific sergeant (Abudefduf vaigiensis), which is hybridizing with the endemic congener, A. abdominalis. Surveys of mtDNA and three nuclear loci across Hawai'i (N = 396, Abudefduf abdominalis and N = 314, A. vaigiensis) reveal that hybridization is significantly higher in the human-perturbed southeast archipelago (19.8%), tapering off to 5.9% in the pristine northwest archipelago. While densities of the two species varied throughout Hawai'i, hybridization was highest in regions with similar species densities, contradicting the generalization that the rarity of one species promotes interspecific mating. Our finding of later generation hybrids throughout the archipelago invokes the possibility of genetic swamping of the endemic species. Exaptation, an adaptation with unintended consequences, may explain these findings: the endemic species has transient yellow coloration during reproduction, whereas the introduced species has yellow coloration continuously as adults, in effect a permanent signal of reproductive receptivity. Haplotype diversity is higher in Hawaiian A. vaigiensis than in our samples from the native range, indicating large-scale colonization almost certainly facilitated by the historically recent surge of marine debris. In this chain of events, marine debris promotes colonization, exaptation promotes hybridization, and introgression invokes the possible collapse of an endemic species. PMID:25283736

  17. Development of the first marmoset-specific DNA microarray (EUMAMA): a new genetic tool for large-scale expression profiling in a non-human primate

    PubMed Central

    Datson, Nicole A; Morsink, Maarten C; Atanasova, Srebrena; Armstrong, Victor W; Zischler, Hans; Schlumbohm, Christina; Dutilh, Bas E; Huynen, Martijn A; Waegele, Brigitte; Ruepp, Andreas; de Kloet, E Ronald; Fuchs, Eberhard

    2007-01-01

    Background The common marmoset monkey (Callithrix jacchus), a small non-endangered New World primate native to eastern Brazil, is becoming increasingly used as a non-human primate model in biomedical research, drug development and safety assessment. In contrast to the growing interest for the marmoset as an animal model, the molecular tools for genetic analysis are extremely limited. Results Here we report the development of the first marmoset-specific oligonucleotide microarray (EUMAMA) containing probe sets targeting 1541 different marmoset transcripts expressed in hippocampus. These 1541 transcripts represent a wide variety of different functional gene classes. Hybridisation of the marmoset microarray with labelled RNA from hippocampus, cortex and a panel of 7 different peripheral tissues resulted in high detection rates of 85% in the neuronal tissues and on average 70% in the non-neuronal tissues. The expression profiles of the 2 neuronal tissues, hippocampus and cortex, were highly similar, as indicated by a correlation coefficient of 0.96. Several transcripts with a tissue-specific pattern of expression were identified. Besides the marmoset microarray we have generated 3215 ESTs derived from marmoset hippocampus, which have been annotated and submitted to GenBank [GenBank: EF214838 – EF215447, EH380242 – EH382846]. Conclusion We have generated the first marmoset-specific DNA microarray and demonstrated its use to characterise large-scale gene expression profiles of hippocampus but also of other neuronal and non-neuronal tissues. In addition, we have generated a large collection of ESTs of marmoset origin, which are now available in the public domain. These new tools will facilitate molecular genetic research into this non-human primate animal model. PMID:17592630

  18. Stick-slip behavior of Indian gabbro as studied using a NIED large-scale biaxial friction apparatus

    NASA Astrophysics Data System (ADS)

    Togo, Tetsuhiro; Shimamoto, Toshihiko; Yamashita, Futoshi; Fukuyama, Eiichi; Mizoguchi, Kazuo; Urata, Yumi

    2015-04-01

    This paper reports stick-slip behaviors of Indian gabbro as studied using a new large-scale biaxial friction apparatus, built in the National Research Institute for Earth Science and Disaster Prevention (NIED), Tsukuba, Japan. The apparatus consists of the existing shaking table as the shear-loading device up to 3,600 kN, the main frame for holding two large rectangular prismatic specimens with a sliding area of 0.75 m2 and for applying normal stresses σ n up to 1.33 MPa, and a reaction force unit holding the stationary specimen to the ground. The shaking table can produce loading rates v up to 1.0 m/s, accelerations up to 9.4 m/s2, and displacements d up to 0.44 m, using four servocontrolled actuators. We report results from eight preliminary experiments conducted with room humidity on the same gabbro specimens at v = 0.1-100 mm/s and σ n = 0.66-1.33 MPa, and with d of about 0.39 m. The peak and steady-state friction coefficients were about 0.8 and 0.6, respectively, consistent with the Byerlee friction. The axial force drop or shear stress drop during an abrupt slip is linearly proportional to the amount of displacement, and the slope of this relationship determines the stiffness of the apparatus as 1.15 × 108 N/m or 153 MPa/m for the specimens we used. This low stiffness makes fault motion very unstable and the overshooting of shear stress to a negative value was recognized in some violent stick-slip events. An abrupt slip occurred in a constant rise time of 16-18 ms despite wide variation of the stress drop, and an average velocity during an abrupt slip is linearly proportional to the stress drop. The use of a large-scale shaking table has a great potential in increasing the slip rate and total displacement in biaxial friction experiments with large specimens.

  19. Concurrent Validity and Feasibility of Short Tests Currently Used to Measure Early Childhood Development in Large Scale Studies.

    PubMed

    Rubio-Codina, Marta; Araujo, M Caridad; Attanasio, Orazio; Muñoz, Pablo; Grantham-McGregor, Sally

    2016-01-01

    months, and language above. Predictive validity investigation is needed to further guide the choice of instruments for large scale studies. PMID:27548634

  20. Concurrent Validity and Feasibility of Short Tests Currently Used to Measure Early Childhood Development in Large Scale Studies

    PubMed Central

    Rubio-Codina, Marta; Araujo, M. Caridad; Attanasio, Orazio; Muñoz, Pablo; Grantham-McGregor, Sally

    2016-01-01

    below 19 months, and language above. Predictive validity investigation is needed to further guide the choice of instruments for large scale studies. PMID:27548634

  1. Calibration of a large-scale groundwater flow model using GRACE data: a case study in the Qaidam Basin, China

    NASA Astrophysics Data System (ADS)

    Hu, Litang; Jiao, Jiu Jimmy

    2015-11-01

    Traditional numerical models usually use extensive observed hydraulic-head data as calibration targets. However, this calibration process is not applicable in remote areas with limited or no monitoring data. This study presents an approach to calibrate a large-scale groundwater flow model using the monthly Gravity Recovery and Climate Experiment (GRACE) satellite data, which have been available globally on a spatial grid of 1° in the geographic coordinate system since 2002. A groundwater storage anomaly isolated from the terrestrial water storage (TWS) anomaly is converted into hydraulic head at the center of the grid, which is then used as observed data to calibrate a numerical model to estimate aquifer hydraulic conductivity. The aquifer system in the remote and hyperarid Qaidam Basin, China, is used as a case study to demonstrate the applicability of this approach. A groundwater model using FEFLOW is constructed for the Qaidam Basin and the GRACE-derived groundwater storage anomaly over the period 2003-2012 is included to calibrate the model, which is done using an automatic estimation method (PEST). The calibrated model is then run to output hydraulic heads at three sites where long-term hydraulic head data are available. The reasonably good fit between the calculated and observed hydraulic heads, together with the very similar groundwater storage anomalies from the numerical model and GRACE data, demonstrate that this approach is generally applicable in regions of groundwater data scarcity.

  2. High Intake of Manganese During Second Trimester, Increases the Risk of Preterm Delivery: A Large Scale Cohort Study

    PubMed Central

    Bakouei, Sare; Reisian, Fatemeh; Lamyian, Minoor; Zadeh, Ebrahim Haji; Zamanian, Hadi; Kharameh, Zahra Taheri

    2015-01-01

    Evidence indicates that nutrients and minerals might play an important role in preterm delivery (PTD). The aim of this study was to determine maternal nutritional status during second trimester of pregnancy and its association with preterm delivery (< 34 weeks gestation) in Iranian women. In a large scale longitudinal study, 1033 pregnant women were recruited from prenatal clinics since December 2012 to June 2013. Dietary intake was assessed by Food Frequency Questionnaire (FFQ) in pregnant women of 14 to 20 weeks gestational age. The participants were followed up until delivery. Dietary intake of women with preterm delivery was compared with women who had term delivery. The results show that 61.2% of women were primiparous and that the incidence of preterm delivery was 7%. Manganese dietary intake was significantly higher in mothers with preterm delivery than those with term delivery (P = .03). Manganese was the only micronutrient correlated with preterm delivery after adjustment for maternal characteristics during second trimesters of pregnancy (OR = 1.12; P = .01). These results suggest that high maternal manganese dietary intake during the second trimester of pregnancy may be associated with the risk of preterm delivery in Iranian pregnant women. PMID:26156900

  3. A large-scale study of the random variability of a coding sequence: a study on the CFTR gene.

    PubMed

    Modiano, Guido; Bombieri, Cristina; Ciminelli, Bianca Maria; Belpinati, Francesca; Giorgi, Silvia; Georges, Marie des; Scotet, Virginie; Pompei, Fiorenza; Ciccacci, Cinzia; Guittard, Caroline; Audrézet, Marie Pierre; Begnini, Angela; Toepfer, Michael; Macek, Milan; Ferec, Claude; Claustres, Mireille; Pignatti, Pier Franco

    2005-02-01

    Coding single nucleotide substitutions (cSNSs) have been studied on hundreds of genes using small samples (n(g) approximately 100-150 genes). In the present investigation, a large random European population sample (average n(g) approximately 1500) was studied for a single gene, the CFTR (Cystic Fibrosis Transmembrane conductance Regulator). The nonsynonymous (NS) substitutions exhibited, in accordance with previous reports, a mean probability of being polymorphic (q > 0.005), much lower than that of the synonymous (S) substitutions, but they showed a similar rate of subpolymorphic (q < 0.005) variability. This indicates that, in autosomal genes that may have harmful recessive alleles (nonduplicated genes with important functions), genetic drift overwhelms selection in the subpolymorphic range of variability, making disadvantageous alleles behave as neutral. These results imply that the majority of the subpolymorphic nonsynonymous alleles of these genes are selectively negative or even pathogenic. PMID:15536480

  4. Absolute pitch among students at the Shanghai Conservatory of Music: a large-scale direct-test study.

    PubMed

    Deutsch, Diana; Li, Xiaonuo; Shen, Jing

    2013-11-01

    This paper reports a large-scale direct-test study of absolute pitch (AP) in students at the Shanghai Conservatory of Music. Overall note-naming scores were very high, with high scores correlating positively with early onset of musical training. Students who had begun training at age ≤5 yr scored 83% correct not allowing for semitone errors and 90% correct allowing for semitone errors. Performance levels were higher for white key pitches than for black key pitches. This effect was greater for orchestral performers than for pianists, indicating that it cannot be attributed to early training on the piano. Rather, accuracy in identifying notes of different names (C, C#, D, etc.) correlated with their frequency of occurrence in a large sample of music taken from the Western tonal repertoire. There was also an effect of pitch range, so that performance on tones in the two-octave range beginning on Middle C was higher than on tones in the octave below Middle C. In addition, semitone errors tended to be on the sharp side. The evidence also ran counter to the hypothesis, previously advanced by others, that the note A plays a special role in pitch identification judgments. PMID:24180794

  5. Comparative climatological study of large-scale traveling ionospheric disturbances over North America and China in 2011-2012

    NASA Astrophysics Data System (ADS)

    Ding, Feng; Wan, Weixing; Li, Qiang; Zhang, Rui; Song, Qian; Ning, Baiqi; Liu, Libo; Zhao, Biqiang; Xiong, Bo

    2014-01-01

    This paper describes a comparative study of the climatology of large-scale traveling ionospheric disturbances (LSTIDs) over North America and China based on observations obtained in 2011-2012 using two GPS networks characterized by dense regional coverage. We identified a total of 390 LSTIDs in China and 363 events in North America. These can be categorized into three types, namely south, north, and westward propagating LSTIDs. The southward LSTIDs over North America show similar diurnal and seasonal variations to those of geomagnetic disturbances, but the southward LSTIDs over China do not show such variations. The occurrence of southward LSTIDs over China increases at ~1-2 h after the time of geomagnetic activity maximum; this increase lasts several hours until the geomagnetic minimum, which happens during the local evening. The southward LSTIDs over North America show a semiannual variation with two peaks in March and October, while the southward LSTIDs over China show a major peak in January. Northward LSTIDs occur much less frequently than their southward counterparts, and they are mainly observed in China. They mostly occur during geomagnetic activity maximum, indicating a possible relation with the degree of geomagnetic activity. Westward LSTIDs are seen in both regions during local sunrise and may be excited by the moving solar terminator. No relationship was found between these latter LSTIDs and the geomagnetic disturbances. The propagation direction of westward events changed from northwestward during winter solstice to southwestward at summer solstice. This is consistent with the seasonal orientation of the solar terminator.

  6. The importance of large scale flood over the regular sedimentation in delta development: A case study involving Wax lake delta

    NASA Astrophysics Data System (ADS)

    Ullah, M. S.; Kolker, A.; Li, C.

    2011-12-01

    It has been widely hypothesized that catastrophic floods can play an important role in the development of a young and growing delta. This study examines the nature and rate of sediment deposition in the Wax lake delta in the Atchafalaya Basin of Louisiana during the Mississippi River flood of from April, 2011 to June, 2011. We hypothesize that the deposition rate that results from large scales floods in the Mississippi/Atchafalaya river outlets have a greater impact in the Wax lake delta development than the deposition rates that result from typical yearly sedimentation. Preliminary results from the cosmogenic 7Be counts from sediment collected from the delta show distinct regional and local sediment deposition patterns during the flood, and rates that are significantly higher when compared to the sedimentation rate of the last few decades. This application of cosmogenic 7Be to distinguish the sediment deposition rate provides a first-order understanding of the deltaic evolution and stratigraphic sequence development in a high-discharge setting.

  7. The importance of combining MRI and large-scale digital histology in neuroimaging studies of brain connectivity and disease

    PubMed Central

    Annese, Jacopo

    2012-01-01

    One of the major issues hindering a comprehensive connectivity model for the human brain is the difficulty in linking Magnetic Resonance Imaging (MRI) measurements to anatomical evidence produced by histological methods. In vivo and postmortem neuroimaging methodologies are still largely incompatible in terms of sample size, scale, and resolution. To help bridge the hiatus between different approaches we have established a program that characterizes the brain of individual subjects, combining MRI with postmortem neuroanatomy. The direct correlation of MRI and histological features is possible, because registered images from different modalities represent the same regions in the same brain. Comparisons are also facilitated by large-scale, digital microscopy techniques that afford images of the whole-brain sections at cellular resolution. The goal is to create a neuroimaging catalog representative of discrete age groups and specific neurological conditions. Individually, the datasets allow for investigating the relationship between different modalities; combined, they provide sufficient predictive power to inform analyses and interpretations made in the context of non-invasive studies of brain connectivity and disease. PMID:22536182

  8. Large scale dynamics of the Michaelis complex in Bacillus stearothermophilus lactate dehydrogenase revealed by a single-tryptophan mutant study.

    PubMed

    Nie, Beining; Deng, Hua; Desamero, Ruel; Callender, Robert

    2013-03-19

    Large scale dynamics within the Michaelis complex mimic of Bacillus stearothermophilus thermophilic lactate dehydrogenase, bsLDH·NADH·oxamate, were studied with site specific resolution by laser-induced temperature jump relaxation spectroscopy with a time resolution of 20 ns. NADH emission and Trp emission from the wild type and a series of single-tryptophan bsLDH mutants, with the tryptophan positions different distances from the active site, were used as reporters of evolving structure in response to the rapid change in temperature. Several distinct dynamical events were observed on the millisecond to microsecond time scale involving motion of atoms spread over the protein, some occurring concomitantly or nearly concomitantly with structural changes at the active site. This suggests that a large portion of the protein-substrate complex moves in a rather concerted fashion to bring about catalysis. The catalytically important surface loop undergoes two distinct movements, both needed for a competent enzyme. Our results also suggest that what is called "loop motion" is not just localized to the loop and active site residues. Rather, it involves the motion of atoms spread over the protein, even some quite distal from the active site. How these results bear on the catalytic mechanism of bsLDH is discussed. PMID:23428201

  9. Large-scale traveling ionospheric disturbances using ionospheric imaging at storm time: A case study on 17 march 2013

    NASA Astrophysics Data System (ADS)

    Tang, Jun; Yao, Yibin; Kong, Jian; Zhang, Liang

    2016-07-01

    A moderate geomagnetic storm occurred on March 17, 2013, during which large-scale traveling ionospheric disturbances (LSTIDs) are observed over China by ionosondes and GPS from Crustal Movement Observation Network of China (CMONOC) and the International GNSS Service (IGS). Ionosonde data and computerized ionospheric tomography (CIT) technique are employed to analyze the disturbances in our study. The maximum entropy cross spectral analysis (MECSA) method is used to obtain the propagation parameters of the LSTIDs. Spatio-temporal variations of ionospheric electron density (IED) and total electron content (TEC) during this geomagnetic storm over China are investigated. Disturbance images of IED and TEC are also presented in the paper. The results show two LSTID events at about 12:00 UT and 15:00 UT during the main phase of the storm. Besides, the LSTIDs with a duration of 40 min are detected over China. It is confirmed that the LSTIDs travel from north to south with a horizontal velocity of 400-500 m/s, and moved southwestwards with a horizontal velocity of 250-300 m/s, respectively.

  10. A field study of large-scale oscillation ripples in a very coarse-grained, high-energy marine environment

    USGS Publications Warehouse

    Hirschaut, D.W.; Dingler, J.R.

    1982-01-01

    Monastery Beach, Carmel, California is a pocket beach that sits within 200 m of the head of Carmel Submarine Canyon. Coarse to very coarse sand covers both the beach and adjacent shelf; in the latter area incoming waves have shaped the sand into large oscillation ripples. The accessibility of this area and a variable wave climate produce a unique opportunity to study large-scale coarse-grained ripples in a high-energy environment. These ripples, which only occur in very coarse sand, form under the intense, wave-generated currents that exist during storm conditions. Once formed, these ripples do not significantly change under lower energy waves. On three separate occasions scuba divers measured ripples and collected sand samples from ripple crests near fixed reference stakes along three transects. Ripple wavelength and grain size decreased with an increase in water depth. Sediment sorting was best closest to the surf zone and poorest at the rim of Carmel Canyon. Cobbles and gravel observed in ripple troughs represent lag deposits. Carmel Canyon refracts waves approaching Monastery Beach such that wave energy is focused towards the northern and southern portions of the beach, leaving the central part of the beach lower in energy. This energy distribution causes spatial variations in the ripples and grain sizes with the shortest wavelengths and smallest grain sizes being in the central part of the shelf.

  11. A numerical study of large-scale ionospheric modulation due to the thermal process by powerful wave heating

    NASA Astrophysics Data System (ADS)

    Zhou, Chen; Ni, Binbin; Wang, Xiang; Liu, Moran; Xu, Xiang; Wang, Chen; Shi, Run; Gu, Xudong; Zhang, Yuannong; Zhao, Zhengyu

    2016-03-01

    We present a three-dimensional numerical model of large-scale ionospheric electron density and temperature modulation by powerful electromagnetic waves by incorporating the transport equations and the three-dimensional ray-tracing algorithm. Based on this numerical model, the changes of ionospheric electron density and temperature at nighttime are investigated. The simulation results present (1) the ionospheric electron temperature enhancement due to the energy absorption; (2) the ionospheric electron density depletion at the reflection region and enhancement at the upper/lower region along the field line due to the thermal pressure; and (3) large-scale field-aligned irregularities (FAIs) due to the thermal self-focusing instability with transverse scale of ~10 km. The results are quantitatively consistent with the previous theoretical predictions and experimental observations, which indicate that the thermal processes play an important role in the ionospheric electron density/temperature modulation and large-scale FAI generation.

  12. Galaxy clustering on large scales.

    PubMed

    Efstathiou, G

    1993-06-01

    I describe some recent observations of large-scale structure in the galaxy distribution. The best constraints come from two-dimensional galaxy surveys and studies of angular correlation functions. Results from galaxy redshift surveys are much less precise but are consistent with the angular correlations, provided the distortions in mapping between real-space and redshift-space are relatively weak. The galaxy two-point correlation function, rich-cluster two-point correlation function, and galaxy-cluster cross-correlation function are all well described on large scales ( greater, similar 20h-1 Mpc, where the Hubble constant, H0 = 100h km.s-1.Mpc; 1 pc = 3.09 x 10(16) m) by the power spectrum of an initially scale-invariant, adiabatic, cold-dark-matter Universe with Gamma = Omegah approximately 0.2. I discuss how this fits in with the Cosmic Background Explorer (COBE) satellite detection of large-scale anisotropies in the microwave background radiation and other measures of large-scale structure in the Universe. PMID:11607400

  13. The Relationships between Workaholism and Symptoms of Psychiatric Disorders: A Large-Scale Cross-Sectional Study.

    PubMed

    Andreassen, Cecilie Schou; Griffiths, Mark D; Sinha, Rajita; Hetland, Jørn; Pallesen, Ståle

    2016-01-01

    Despite the many number of studies examining workaholism, large-scale studies have been lacking. The present study utilized an open web-based cross-sectional survey assessing symptoms of psychiatric disorders and workaholism among 16,426 workers (Mage = 37.3 years, SD = 11.4, range = 16-75 years). Participants were administered the Adult ADHD Self-Report Scale, the Obsession-Compulsive Inventory-Revised, the Hospital Anxiety and Depression Scale, and the Bergen Work Addiction Scale, along with additional questions examining demographic and work-related variables. Correlations between workaholism and all psychiatric disorder symptoms were positive and significant. Workaholism comprised the dependent variable in a three-step linear multiple hierarchical regression analysis. Basic demographics (age, gender, relationship status, and education) explained 1.2% of the variance in workaholism, whereas work demographics (work status, position, sector, and annual income) explained an additional 5.4% of the variance. Age (inversely) and managerial positions (positively) were of most importance. The psychiatric symptoms (ADHD, OCD, anxiety, and depression) explained 17.0% of the variance. ADHD and anxiety contributed considerably. The prevalence rate of workaholism status was 7.8% of the present sample. In an adjusted logistic regression analysis, all psychiatric symptoms were positively associated with being a workaholic. The independent variables explained between 6.1% and 14.4% in total of the variance in workaholism cases. Although most effect sizes were relatively small, the study's findings expand our understanding of possible psychiatric predictors of workaholism, and particularly shed new insight into the reality of adult ADHD in work life. The study's implications, strengths, and shortcomings are also discussed. PMID:27192149

  14. Kicking Triturus arntzeni when it's down: large-scale nuclear genetic data confirm that newts from the type locality are genetically admixed.

    PubMed

    Wielstra, B; Arntzen, J W

    2014-01-01

    We collected nuclear DNA data (52 markers) with next-generation sequencing for nine Triturus newt specimens, including the holotype and two of the paratypes of T. arntzeni, from the type locality at Vrtovać in eastern Serbia. We compare these data to a reference set composed of the four crested newt species distributed in eastern Serbia namely T. cristatus, T. dobrogicus, T. ivanbureschi and T. macedonicus to determine to which of these species the newts from the type locality of T. arntzeni should be attributed. The majority of alleles in individuals from Vrtovać is derived from T. macedonicus, but a considerable number of T. ivanbureschi alleles is also present; alleles typical for T. cristatus and T. dobrogicus are found at low frequency. Accordingly, we interpret Vrtovać as a T. macedonicus - T. ivanbureschi hybrid population, albeit not composed of F1 hybrids but of genetically admixed individuals derived through multiple generations of backcrossing. The data support the notion that the name T. arntzeni should not be applied to a species newly distinguished in T. karelinii sensu lato (to which the name T. ivanbureschi has been given). We conclude that because of the hybrid nature of the individuals from Vrtovać, the name T. arntzeni should be placed not only in the synonymy of T. macedonicus but also in the synonymy of T. ivanbureschi. In this study we demonstrate that next-generation sequencing can provide high quality data for type material with degraded DNA and therefore can play an important role in taxonomy. PMID:24871018

  15. RACORO continental boundary layer cloud investigations. Part I: Case study development and ensemble large-scale forcings

    SciTech Connect

    Vogelmann, Andrew M.; Fridlind, Ann M.; Toto, Tami; Endo, Satoshi; Lin, Wuyin; Wang, Jian; Feng, Sha; Zhang, Yunyan; Turner, David D.; Liu, Yangang; Li, Zhijin; Xie, Shaocheng; Ackerman, Andrew S.; Zhang, Minghua; Khairoutdinov, Marat

    2015-06-19

    Observation-based modeling case studies of continental boundary layer clouds have been developed to study cloudy boundary layers, aerosol influences upon them, and their representation in cloud- and global-scale models. Three 60-hour case study periods span the temporal evolution of cumulus, stratiform, and drizzling boundary layer cloud systems, representing mixed and transitional states rather than idealized or canonical cases. Based on in-situ measurements from the RACORO field campaign and remote-sensing observations, the cases are designed with a modular configuration to simplify use in large-eddy simulations (LES) and single-column models. Aircraft measurements of aerosol number size distribution are fit to lognormal functions for concise representation in models. Values of the aerosol hygroscopicity parameter, κ, are derived from observations to be ~0.10, which are lower than the 0.3 typical over continents and suggestive of a large aerosol organic fraction. Ensemble large-scale forcing datasets are derived from the ARM variational analysis, ECMWF forecasts, and a multi-scale data assimilation system. The forcings are assessed through comparison of measured bulk atmospheric and cloud properties to those computed in 'trial' large-eddy simulations, where more efficient run times are enabled through modest reductions in grid resolution and domain size compared to the full-sized LES grid. Simulations capture many of the general features observed, but the state-of-the-art forcings were limited at representing details of cloud onset, and tight gradients and high-resolution transients of importance. Methods for improving the initial conditions and forcings are discussed. The cases developed are available to the general modeling community for studying continental boundary clouds.

  16. RACORO continental boundary layer cloud investigations. Part I: Case study development and ensemble large-scale forcings

    DOE PAGESBeta

    Vogelmann, Andrew M.; Fridlind, Ann M.; Toto, Tami; Endo, Satoshi; Lin, Wuyin; Wang, Jian; Feng, Sha; Zhang, Yunyan; Turner, David D.; Liu, Yangang; et al

    2015-06-19

    Observation-based modeling case studies of continental boundary layer clouds have been developed to study cloudy boundary layers, aerosol influences upon them, and their representation in cloud- and global-scale models. Three 60-hour case study periods span the temporal evolution of cumulus, stratiform, and drizzling boundary layer cloud systems, representing mixed and transitional states rather than idealized or canonical cases. Based on in-situ measurements from the RACORO field campaign and remote-sensing observations, the cases are designed with a modular configuration to simplify use in large-eddy simulations (LES) and single-column models. Aircraft measurements of aerosol number size distribution are fit to lognormal functionsmore » for concise representation in models. Values of the aerosol hygroscopicity parameter, κ, are derived from observations to be ~0.10, which are lower than the 0.3 typical over continents and suggestive of a large aerosol organic fraction. Ensemble large-scale forcing datasets are derived from the ARM variational analysis, ECMWF forecasts, and a multi-scale data assimilation system. The forcings are assessed through comparison of measured bulk atmospheric and cloud properties to those computed in 'trial' large-eddy simulations, where more efficient run times are enabled through modest reductions in grid resolution and domain size compared to the full-sized LES grid. Simulations capture many of the general features observed, but the state-of-the-art forcings were limited at representing details of cloud onset, and tight gradients and high-resolution transients of importance. Methods for improving the initial conditions and forcings are discussed. The cases developed are available to the general modeling community for studying continental boundary clouds.« less

  17. The Relationships between Workaholism and Symptoms of Psychiatric Disorders: A Large-Scale Cross-Sectional Study

    PubMed Central

    Griffiths, Mark D.; Sinha, Rajita; Hetland, Jørn

    2016-01-01

    Despite the many number of studies examining workaholism, large-scale studies have been lacking. The present study utilized an open web-based cross-sectional survey assessing symptoms of psychiatric disorders and workaholism among 16,426 workers (Mage = 37.3 years, SD = 11.4, range = 16–75 years). Participants were administered the Adult ADHD Self-Report Scale, the Obsession-Compulsive Inventory-Revised, the Hospital Anxiety and Depression Scale, and the Bergen Work Addiction Scale, along with additional questions examining demographic and work-related variables. Correlations between workaholism and all psychiatric disorder symptoms were positive and significant. Workaholism comprised the dependent variable in a three-step linear multiple hierarchical regression analysis. Basic demographics (age, gender, relationship status, and education) explained 1.2% of the variance in workaholism, whereas work demographics (work status, position, sector, and annual income) explained an additional 5.4% of the variance. Age (inversely) and managerial positions (positively) were of most importance. The psychiatric symptoms (ADHD, OCD, anxiety, and depression) explained 17.0% of the variance. ADHD and anxiety contributed considerably. The prevalence rate of workaholism status was 7.8% of the present sample. In an adjusted logistic regression analysis, all psychiatric symptoms were positively associated with being a workaholic. The independent variables explained between 6.1% and 14.4% in total of the variance in workaholism cases. Although most effect sizes were relatively small, the study’s findings expand our understanding of possible psychiatric predictors of workaholism, and particularly shed new insight into the reality of adult ADHD in work life. The study’s implications, strengths, and shortcomings are also discussed. PMID:27192149

  18. NAEP Validity Studies: Improving the Information Value of Performance Items in Large Scale Assessments. Working Paper No. 2003-08

    ERIC Educational Resources Information Center

    Pearson, P. David; Garavaglia, Diane R.

    2003-01-01

    The purpose of this essay is to explore both what is known and what needs to be learned about the information value of performance items "when they are used in large scale assessments." Within the context of the National Assessment of Educational Progress (NAEP), there is substantial motivation for answering these questions. Over the…

  19. Linking Errors in Trend Estimation in Large-Scale Surveys: A Case Study. Research Report. ETS RR-10-10

    ERIC Educational Resources Information Center

    Xu, Xueli; von Davier, Matthias

    2010-01-01

    One of the major objectives of large-scale educational surveys is reporting trends in academic achievement. For this purpose, a substantial number of items are carried from one assessment cycle to the next. The linking process that places academic abilities measured in different assessments on a common scale is usually based on a concurrent…

  20. Effectiveness of Large-Scale Community-Based Intensive Behavioral Intervention: A Waitlist Comparison Study Exploring Outcomes and Predictors

    ERIC Educational Resources Information Center

    Flanagan, Helen E.; Perry, Adrienne; Freeman, Nancy L.

    2012-01-01

    File review data were used to explore the impact of a large-scale publicly funded Intensive Behavioral Intervention (IBI) program for young children with autism. Outcomes were compared for 61 children who received IBI and 61 individually matched children from a waitlist comparison group. In addition, predictors of better cognitive outcomes were…

  1. Self-Beliefs Mediate Math Performance between Primary and Lower Secondary School: A Large-Scale Longitudinal Cohort Study

    ERIC Educational Resources Information Center

    Reed, Helen C.; Kirschner, Paul A.; Jolles, Jelle

    2015-01-01

    It is often argued that enhancement of self-beliefs should be one of the key goals of education. However, very little is known about the relation between self-beliefs and performance when students move from primary to secondary school in highly differentiated educational systems with early tracking. This large-scale longitudinal cohort study…

  2. Association between toothbrushing and risk factors for cardiovascular disease: a large-scale, cross-sectional Japanese study

    PubMed Central

    Kuwabara, Masanari; Motoki, Yoko; Ichiura, Kayoko; Fujii, Mizue; Inomata, Chisato; Sato, Hiroki; Morisawa, Taichiro; Morita, Yoshinori; Kuwabara, Kazumichi; Nakamura, Yosikazu

    2016-01-01

    Objectives To clarify the association between toothbrushing and risk factors for cardiovascular disease—namely, hypertension (HT), diabetes mellitus (DM), dyslipidaemia (DL), hyperuricaemia (HUA) and chronic kidney disease (CKD). Design A large-scale, single-centre, cross-sectional study. Setting St Luke's International Hospital, Center for Preventive Medicine, Tokyo, Japan, between January 2004 and June 2010. Participants This study examined the toothbrushing practices of 85 866 individuals according to the 3-category frequency criterion: ‘after every meal’, ‘at least once a day’ and ‘less than once a day’. The ORs by frequency were calculated for the prevalences of HT, DM, DL, HUA and CKD according to binominal logistic regression analyses adjusted for age, gender, body mass index and lifestyle habits—smoking, drinking, walk time and sleep time. Results The prevalences of the risk factors were as follows: HT (‘after every meal’: 13.3%, ‘at least once a day’: 17.9% and ‘less than once a day’: 31.0%), DM (3.1%, 5.3% and 17.4%, respectively), DL (29.0%, 42.1% and 60.3%, respectively), HUA (8.6%, 17.5% and 27.2%, respectively) and CKD (3.8%, 3.1% and 8.3%, respectively). The prevalences were significantly higher in the ‘less than once a day’ group than in the ‘after every meal’ group for DM (OR=2.03; 95% CI 1.29 to 3.21) and DL (OR=1.50; 95% CI 1.06 to 2.14), but not for HT, HUA and CKD. Conclusions Even taking into account lifestyle habits, a lower frequency of toothbrushing was associated with high prevalences of DM and DL. Toothbrushing practices may be beneficial for oral health improvement and also for prevention of certain systemic diseases. PMID:26769787

  3. The SRG/eROSITA All-Sky Survey: A new era of large-scale structure studies with AGN

    NASA Astrophysics Data System (ADS)

    Kolodzig, Alexander; Gilfanov, Marat; Hütsi, Gert; Sunyaev, Rashid

    2015-08-01

    The four-year X-ray All-Sky Survey (eRASS) of the eROSITA telescope aboard the Spektrum-Roentgen-Gamma (SRG) satellite will detect about 3 million active galactic nuclei (AGN) with a median redshift of z~1 and typical luminosity of L0.5-2.0keV ~ 1044 erg/s. We demonstrate that this unprecedented AGN sample, complemented with redshift information, will supply us with outstanding opportunities for large-scale structure (LSS) studies.We show that with this sample of X-ray selected AGN, it will become possible for the first time to perform detailed redshift- and luminosity-resolved studies of the AGN clustering. This enable us to put strong constraints on different AGN triggering/fueling models as a function of AGN environment, which will dramatically improve our understanding of super-massive black hole growth and its correlation with the co-evolving LSS.Further, the eRASS AGN sample will become a powerful cosmological probe. We demonstrate for the first time that, given the breadth and depth of eRASS, it will become possible to convincingly detect baryonic acoustic oscillations (BAOs) with ~8σ confidence in the 0.8 < z < 2.0 range, currently uncovered by any existing BAO survey.Finally, we discuss the requirements for follow-up missions and demonstrate that in order to fully exploit the potential of the eRASS AGN sample, photometric and spectroscopic surveys of large areas and a sufficient depth will be needed.

  4. The invasive bighead goby Ponticola kessleri displays large-scale genetic similarities and small-scale genetic differentiation in relation to shipping patterns.

    PubMed

    Adrian-Kalchhauser, I; Hirsch, P E; Behrmann-Godel, J; N'Guyen, A; Watzlawczyk, S; Gertzen, S; Borcherding, J; Burkhardt-Holm, P

    2016-05-01

    Colonization events, range expansions and species invasions leave genetic signatures in the genomes of invasive organisms and produce intricate special patterns. Predictions have been made as to how those patterns arise, but only very rarely, genetic processes can be monitored in real time during range expansions. In an attempt to change that, we track a very recently established invasive population of a fish species, the bighead goby Ponticola kessleri, with high temporal and spatial resolution through 2 years to identify patterns over time. We then compare Swiss and German samples of bighead goby along the river Rhine using microsatellites, mitochondrial D-loop sequences and geometric morphometrics to investigate geographic patterns. We detect weak temporal and strong geographic patterns in the data, which are inconsistent with isolation by distance and indicate long range transport. In search of an explanation for our observations, we analyse the vector properties and travel patterns of commercial vessels on the river Rhine. We present evidence that freshwater cargo ships and tankers are plausible vectors for larvae of invasive goby species. We also present indications that cargo ships and tankers act as differential vectors for this species. In summary, we present genetic data at unique temporal resolution from a vertebrate invasion front and substantiate the paramount role of commercial shipping in freshwater fish translocations. PMID:26928748

  5. Water Research within the SPRUCE Experiment, a Large-Scale Study of Climate Change Effects on a Northern Peatland

    NASA Astrophysics Data System (ADS)

    Mulholland, P. J.; Sebestyen, S. D.; Hanson, P. J.; Warren, J.; Kolka, R. K.

    2010-12-01

    Scientists at the Oak Ridge National Laboratory and the USDA Forest Service along with cooperating research institutions are developing a large-scale ecosystem study in which temperature and carbon dioxide will be experimentally increased to quantify effects of climatic forcing on ecological, hydrological, and biogeochemical processes in a northern peatland. In this poster, we provide an overview of the water science research directions within the Spruce and Peatland Responses Under Climate and Environmental change Experiment (SPRUCE) that will occur at the Marcell Experiment Forest in northern Minnesota, USA. Design and prototyping is now occurring with full operation for 10 years starting in 2013. Air and soil temperatures inside replicated 12-m diameter, open-topped chambers will be maintained at ambient, +3, +6, and +9 degrees Celsius with enhanced carbon dioxide (+900 ppm in the ambient and +6 degree treatments). We will quantify changes in the timing and magnitude of runoff due to earlier snowmelt and longer growing seasons as well as associated changes in runoff chemistry. Measurements of plant-water, physiological, and vapor flux responses from the chambers will advance our understanding of hydrological responses and thresholds of climate tipping points. This experiment will provide quantitative evidence of the effects of climatic forcing by temperature and elevated carbon dioxide on northern peatland ecosystems and the vast stores of carbon that are associated with the hydrology and biogeochemistry of these globally widespread landscape features. The data are also crucial to predicting feedbacks on global climate as well as water availability, solute yields, and biogeochemical transformations in these ecosystems.

  6. Embarking on large-scale qualitative research: reaping the benefits of mixed methods in studying youth, clubs and drugs

    PubMed Central

    Hunt, Geoffrey; Moloney, Molly; Fazio, Adam

    2012-01-01

    Qualitative research is often conceptualized as inherently small-scale research, primarily conducted by a lone researcher enmeshed in extensive and long-term fieldwork or involving in-depth interviews with a small sample of 20 to 30 participants. In the study of illicit drugs, traditionally this has often been in the form of ethnographies of drug-using subcultures. Such small-scale projects have produced important interpretive scholarship that focuses on the culture and meaning of drug use in situated, embodied contexts. Larger-scale projects are often assumed to be solely the domain of quantitative researchers, using formalistic survey methods and descriptive or explanatory models. In this paper, however, we will discuss qualitative research done on a comparatively larger scale—with in-depth qualitative interviews with hundreds of young drug users. Although this work incorporates some quantitative elements into the design, data collection, and analysis, the qualitative dimension and approach has nevertheless remained central. Larger-scale qualitative research shares some of the challenges and promises of smaller-scale qualitative work including understanding drug consumption from an emic perspective, locating hard-to-reach populations, developing rapport with respondents, generating thick descriptions and a rich analysis, and examining the wider socio-cultural context as a central feature. However, there are additional challenges specific to the scale of qualitative research, which include data management, data overload and problems of handling large-scale data sets, time constraints in coding and analyzing data, and personnel issues including training, organizing and mentoring large research teams. Yet large samples can prove to be essential for enabling researchers to conduct comparative research, whether that be cross-national research within a wider European perspective undertaken by different teams or cross-cultural research looking at internal divisions

  7. Comparative climatological study of large-scale traveling ionospheric disturbances over North America and China in 2011-2012

    NASA Astrophysics Data System (ADS)

    Ding, Feng; Ning, Baiqi; Wan, Weixing; Zhao, Biqiang; Xiong, Bo

    This paper describes a comparative study of the climatology of large-scale traveling ionospheric disturbances (LSTIDs) over North America and China based on observations obtained in 2011-2012 using two GPS networks characterized by dense regional coverage. We identified a total of 390 LSTIDs in China and 363 events in North America. These can be categorized into three types, namely south-, north-, and westward-propagating LSTIDs. The southward-moving LSTIDs over North America show similar diurnal and seasonal variations to those of geomagnetic disturbances, but the southward LSTIDs over China do not show such variations. The occurrence of southward-propagating LSTIDs over China increases at ~1-2 hours after the time of geomagnetic activity maximum; this increase lasts several hours until the geomagnetic activity minimum, which happens during the local evening. The southward-moving LSTIDs over North America show a weak semiannual variation, with two major peaks in March and October, while the southward-propagating LSTIDs over China show a major peak in January. Northward-propagating LSTIDs occur much less frequently than their southward-moving counterparts, and they are mainly observed in China. They mostly occur during geomagnetic activity maximum, indicating a possible relation with the degree of geomagnetic activity. Westward-traveling LSTIDs are seen in both regions during local sunrise and may be excited by the moving solar terminator. No relationship was found between these latter LSTIDs and the geomagnetic disturbances. The propagation direction of westward-moving events changed from northwestward during winter solstice to southwestward at summer solstice. This is consistent with the seasonal orientation of the solar terminator.

  8. Comparative study of large scale simulation of underground explosions inalluvium and in fractured granite using stochastic characterization

    NASA Astrophysics Data System (ADS)

    Vorobiev, O.; Ezzedine, S. M.; Antoun, T.; Glenn, L.

    2014-12-01

    This work describes a methodology used for large scale modeling of wave propagation fromunderground explosions conducted at the Nevada Test Site (NTS) in two different geological settings:fractured granitic rock mass and in alluvium deposition. We show that the discrete nature of rockmasses as well as the spatial variability of the fabric of alluvium is very important to understand groundmotions induced by underground explosions. In order to build a credible conceptual model of thesubsurface we integrated the geological, geomechanical and geophysical characterizations conductedduring recent test at the NTS as well as historical data from the characterization during the undergroundnuclear test conducted at the NTS. Because detailed site characterization is limited, expensive and, insome instances, impossible we have numerically investigated the effects of the characterization gaps onthe overall response of the system. We performed several computational studies to identify the keyimportant geologic features specific to fractured media mainly the joints; and those specific foralluvium porous media mainly the spatial variability of geological alluvium facies characterized bytheir variances and their integral scales. We have also explored common key features to both geologicalenvironments such as saturation and topography and assess which characteristics affect the most theground motion in the near-field and in the far-field. Stochastic representation of these features based onthe field characterizations have been implemented in Geodyn and GeodynL hydrocodes. Both codeswere used to guide site characterization efforts in order to provide the essential data to the modelingcommunity. We validate our computational results by comparing the measured and computed groundmotion at various ranges. This work performed under the auspices of the U.S. Department of Energy by Lawrence LivermoreNational Laboratory under Contract DE-AC52-07NA27344.

  9. Using electronic medical records to enable large-scale studies in psychiatry: treatment resistant depression as a model

    PubMed Central

    Perlis, R. H.; Iosifescu, D. V.; Castro, V. M.; Murphy, S. N.; Gainer, V. S.; Minnier, J.; Cai, T.; Goryachev, S.; Zeng, Q.; Gallagher, P. J.; Fava, M.; Weilburg, J. B.; Churchill, S. E.; Kohane, I. S.; Smoller, J. W.

    2013-01-01

    Background Electronic medical records (EMR) provide a unique opportunity for efficient, large-scale clinical investigation in psychiatry. However, such studies will require development of tools to define treatment outcome. Method Natural language processing (NLP) was applied to classify notes from 127 504 patients with a billing diagnosis of major depressive disorder, drawn from out-patient psychiatry practices affiliated with multiple, large New England hospitals. Classifications were compared with results using billing data (ICD-9 codes) alone and to a clinical gold standard based on chart review by a panel of senior clinicians. These cross-sectional classifications were then used to define longitudinal treatment outcomes, which were compared with a clinician-rated gold standard. Results Models incorporating NLP were superior to those relying on billing data alone for classifying current mood state (area under receiver operating characteristic curve of 0.85–0.88 v. 0.54–0.55). When these cross-sectional visits were integrated to define longitudinal outcomes and incorporate treatment data, 15% of the cohort remitted with a single antidepressant treatment, while 13% were identified as failing to remit despite at least two antidepressant trials. Non-remitting patients were more likely to be non-Caucasian (p<0.001). Conclusions The application of bioinformatics tools such as NLP should enable accurate and efficient determination of longitudinal outcomes, enabling existing EMR data to be applied to clinical research, including biomarker investigations. Continued development will be required to better address moderators of outcome such as adherence and co-morbidity. PMID:21682950

  10. Large-scale adeno-associated viral vector production using a herpesvirus-based system enables manufacturing for clinical studies.

    PubMed

    Clément, Nathalie; Knop, David R; Byrne, Barry J

    2009-08-01

    The ability of recombinant adeno-associated viral (rAAV) vectors to exhibit minimal immunogenicity and little to no toxicity or inflammation while eliciting robust, multiyear gene expression in vivo are only a few of the salient features that make them ideally suited for many gene therapy applications. A major hurdle for the use of rAAV in sizeable research and clinical applications is the lack of efficient and versatile large-scale production systems. Continued progression toward flexible, scalable production techniques is a prerequisite to support human clinical evaluation of these novel biotherapeutics. This review examines the current state of large-scale production methods that employ the herpes simplex virus type 1 (HSV) platform to produce rAAV vectors for gene delivery. Improvements have substantially advanced the HSV/AAV hybrid method for large-scale rAAV manufacture, facilitating the generation of highly potent, clinical-grade purity rAAV vector stocks. At least one human clinical trial employing rAAV generated via rHSV helper-assisted replication is poised to commence, highlighting the advances and relevance of this production method. PMID:19569968

  11. A study of large scaled landslide susceptibility by using Weight-of-Evidence method: A case study from the Laonung River Watershed, Southern Taiwan

    NASA Astrophysics Data System (ADS)

    Chen, Chih-Hao; Lin, Ching-Weei; Tseng, Chih-Ming

    2013-04-01

    The Laonung River watershed which covered an area 1367 km2 is selected as the study area to construct large scaled landslides susceptibility model by using Weight-of-Evidence method. Within the study area, 950 landslides with an area more than 10 ha are identified from FORMOSAT 2 images, aerial photos, and LiDAR derived 1 m high resolution Digital-Elevation-Model (DEM) taken after typhoon Moratko in 2009. Among these, 271 landslides occurred recently and they show bare ground in aerial photos and satellite images. 318 landslides are vegetation recovery, and they are inferred from their topographic characteristics by using aerial photos with topographic map. Additionally, 361 landslides with topographic features of deep seated landslide such as crown main escarpment, down slop scarp, up slop scarp, and transverse cracks are identified from 1m resolution LiDAR derived DEM. Weight-of-Evidence method is a bivariate statistical approach which uses the concept of Bayes' theorem and odds ratio to calculate the weighting of each evaluation parameter. In this study, ten parameters including slope gradient, slope aspect, landform, elevation, lithology, dip-slope, undercut slope, normalized difference vegetation index (NDVI), the distance from geological structure and the distance from stream are selected as evaluation factors. For each parameter, the weighting for landslide susceptibility is calculated, and the weighting of all parameters are then summed to generate the landslide susceptibility map. The study results show the area under the success rate curves reaching 80%, and 70% of large scaled landslides falls within top 30% susceptibility index. It implies that the susceptibility model constructed by this study can effectively predict the location of large scaled landslides in the study area. The results can benefit to the management of mitigation plan of the large scaled landslides in southern Taiwan.

  12. Large-Scale Fluorescence Calcium-Imaging Methods for Studies of Long-Term Memory in Behaving Mammals.

    PubMed

    Jercog, Pablo; Rogerson, Thomas; Schnitzer, Mark J

    2016-01-01

    During long-term memory formation, cellular and molecular processes reshape how individual neurons respond to specific patterns of synaptic input. It remains poorly understood how such changes impact information processing across networks of mammalian neurons. To observe how networks encode, store, and retrieve information, neuroscientists must track the dynamics of large ensembles of individual cells in behaving animals, over timescales commensurate with long-term memory. Fluorescence Ca(2+)-imaging techniques can monitor hundreds of neurons in behaving mice, opening exciting avenues for studies of learning and memory at the network level. Genetically encoded Ca(2+) indicators allow neurons to be targeted by genetic type or connectivity. Chronic animal preparations permit repeated imaging of neural Ca(2+) dynamics over multiple weeks. Together, these capabilities should enable unprecedented analyses of how ensemble neural codes evolve throughout memory processing and provide new insights into how memories are organized in the brain. PMID:27048190

  13. Low-calorie sweetener use and energy balance: Results from experimental studies in animals, and large-scale prospective studies in humans.

    PubMed

    Fowler, Sharon P G

    2016-10-01

    For more than a decade, pioneering animal studies conducted by investigators at Purdue University have provided evidence to support a central thesis: that the uncoupling of sweet taste and caloric intake by low-calorie sweeteners (LCS) can disrupt an animal's ability to predict the metabolic consequences of sweet taste, and thereby impair the animal's ability to respond appropriately to sweet-tasting foods. These investigators' work has been replicated and extended internationally. There now exists a body of evidence, from a number of investigators, that animals chronically exposed to any of a range of LCSs - including saccharin, sucralose, acesulfame potassium, aspartame, or the combination of erythritol+aspartame - have exhibited one or more of the following conditions: increased food consumption, lower post-prandial thermogenesis, increased weight gain, greater percent body fat, decreased GLP-1 release during glucose tolerance testing, and significantly greater fasting glucose, glucose area under the curve during glucose tolerance testing, and hyperinsulinemia, compared with animals exposed to plain water or - in many cases - even to calorically-sweetened foods or liquids. Adverse impacts of LCS have appeared diminished in animals on dietary restriction, but were pronounced among males, animals genetically predisposed to obesity, and animals with diet-induced obesity. Impacts have been especially striking in animals on high-energy diets: diets high in fats and sugars, and diets which resemble a highly-processed 'Western' diet, including trans-fatty acids and monosodium glutamate. These studies have offered both support for, and biologically plausible mechanisms to explain, the results from a series of large-scale, long-term prospective observational studies conducted in humans, in which longitudinal increases in weight, abdominal adiposity, and incidence of overweight and obesity have been observed among study participants who reported using diet sodas and other

  14. Genetic manipulation of sex ratio for the large-scale breeding of YY super-male and XY all-male yellow catfish (Pelteobagrus fulvidraco (Richardson)).

    PubMed

    Liu, Hanqin; Guan, Bo; Xu, Jiang; Hou, Changchun; Tian, Hua; Chen, Hongxi

    2013-06-01

    Yellow catfish has become one of the most important freshwater aquaculture species in China. The mono-sex male yellow catfish has important application value in aquaculture because the male grows generally faster than the sibling females under the same conditions. This study has screened YY super-male and YY physiological female yellow catfish by sex reversal, gynogenesis, and progeny testing, which can help to achieve the large-scale production of YY super-male and XY all-male. From 2008 to 2010, about 123,000 YY super-male were produced, and about 81 million XY all-male fry were produced with 100% male rate by random sampling. Therefore, these results indicate that YY super-male and YY physiological female yellow catfish can be viable and fertile. We conclude that the mono-sex breeding technique by YY super-male yellow catfish is stable and reliable, which has great potential for application in yellow catfish aquaculture. PMID:23053056

  15. A large-scale study of the Trichinella genus in the golden jackal (Canis aureus) population in Serbia.

    PubMed

    Ćirović, Duško; Teodorović, Vlado; Vasilev, Dragan; Marković, Marija; Ćosić, Nada; Dimitrijević, Mirjana; Klun, Ivana; Djurković-Djaković, Olgica

    2015-09-15

    Over the last decades the golden jackal (Canis aureus) has significantly expanded its range throughout Southeast and Central Europe, and the Balkan Peninsula is considered to be a core area of the species distribution in this part of the range. Due to its increasing number, ability of long distance movement through a wide range of landscapes and opportunistic feeding habits, the golden jackal may represent an important reservoir and transmitter of a variety of zoonotic agents, including parasites. The Balkans, Serbia included, remain an endemic area for various zoonotic parasites including Trichinella spp. Trichinella has recently been recorded in jackals in Serbia, which prompted us to carry out a large-scale survey of its prevalence, distribution and species identification in this host. In cooperation with local hunters, carcasses of a total of 738 legally hunted golden jackals were collected at 24 localities over an 11-year period (2003-2013). Analysis of tongue base tissue revealed Trichinella larvae in 122, indicating a prevalence of infection of 16.5%. No difference in the prevalence of infection was found between genders [16.2% in males and 16.9% in females (χ(2)=0.05, p=0.821)], or among the study years (G=7.22, p=0.705). Trichinella larvae were found in 13 out of the 24 examined localities. Molecular identification was performed for 90 isolates, and 64 (71.1%) larvae were identified as Trichinella spiralis and 25 (27.9%) as Trichinella britovi. Mixed infection (T. spiralis and T. britovi) was recorded in a single case. Although T. spiralis was more prevalent, T. britovi had a wider distribution, and was the only recorded species in jackal populations from the mountainous region of eastern Serbia. On the other hand, T. spiralis was dominant in jackals in the lowlands of central and northern Serbia, where domestic pigs are mostly reared. These results show that the golden jackal is involved in both the domestic and sylvatic cycle, and that it has emerged as

  16. Large scale tracking algorithms.

    SciTech Connect

    Hansen, Ross L.; Love, Joshua Alan; Melgaard, David Kennett; Karelitz, David B.; Pitts, Todd Alan; Zollweg, Joshua David; Anderson, Dylan Z.; Nandy, Prabal; Whitlow, Gary L.; Bender, Daniel A.; Byrne, Raymond Harry

    2015-01-01

    Low signal-to-noise data processing algorithms for improved detection, tracking, discrimination and situational threat assessment are a key research challenge. As sensor technologies progress, the number of pixels will increase signi cantly. This will result in increased resolution, which could improve object discrimination, but unfortunately, will also result in a significant increase in the number of potential targets to track. Many tracking techniques, like multi-hypothesis trackers, suffer from a combinatorial explosion as the number of potential targets increase. As the resolution increases, the phenomenology applied towards detection algorithms also changes. For low resolution sensors, "blob" tracking is the norm. For higher resolution data, additional information may be employed in the detection and classfication steps. The most challenging scenarios are those where the targets cannot be fully resolved, yet must be tracked and distinguished for neighboring closely spaced objects. Tracking vehicles in an urban environment is an example of such a challenging scenario. This report evaluates several potential tracking algorithms for large-scale tracking in an urban environment.

  17. Large scale traffic simulations

    SciTech Connect

    Nagel, K.; Barrett, C.L.; Rickert, M.

    1997-04-01

    Large scale microscopic (i.e. vehicle-based) traffic simulations pose high demands on computational speed in at least two application areas: (i) real-time traffic forecasting, and (ii) long-term planning applications (where repeated {open_quotes}looping{close_quotes} between the microsimulation and the simulated planning of individual person`s behavior is necessary). As a rough number, a real-time simulation of an area such as Los Angeles (ca. 1 million travellers) will need a computational speed of much higher than 1 million {open_quotes}particle{close_quotes} (= vehicle) updates per second. This paper reviews how this problem is approached in different projects and how these approaches are dependent both on the specific questions and on the prospective user community. The approaches reach from highly parallel and vectorizable, single-bit implementations on parallel supercomputers for Statistical Physics questions, via more realistic implementations on coupled workstations, to more complicated driving dynamics implemented again on parallel supercomputers. 45 refs., 9 figs., 1 tab.

  18. Validation of a two-step quality control approach for a large-scale human urine metabolomic study conducted in seven experimental batches with LC/QTOF-MS.

    PubMed

    Demetrowitsch, Tobias J; Petersen, Beate; Keppler, Julia K; Koch, Andreas; Schreiber, Stefan; Laudes, Matthias; Schwarz, Karin

    2015-01-01

    After his study of food science at the Rheinische Friedrich-Wilhelms University of Bonn, Tobias J Demetrowitsch obtained his doctoral degree in the research field of metabolomics at the Christian-Albrechts-University of Kiel. The present paper is part of his doctoral thesis and describes an extended strategy to evaluate and verify complex or large-scale experiments and data sets. Large-scale studies result in high sample numbers, requiring the analysis of samples in different batches. So far, the verification of such LC-MS-based metabolomics studies is difficult. Common approaches have not provided a reliable validation procedure to date. This article shows a novel verification process for a large-scale human urine study (analyzed by a LC/QToF-MS system) using a two-step validation procedure. The first step comprises a targeted approach that aims to examine and exclude statistical outliers. The second step consists of a principle component analysis, with the aim of a tight cluster of all quality controls and a second for all volunteer samples. The applied study design provides a reliable two-step validation procedure for large-scale studies and additionally contains an inhouse verification procedure. PMID:25558939

  19. Assimilation of satellite data to optimize large scale hydrological model parameters: a case study for the SWOT mission

    NASA Astrophysics Data System (ADS)

    Pedinotti, V.; Boone, A.; Ricci, S.; Biancamaria, S.; Mognard, N.

    2014-04-01

    During the last few decades, satellite measurements have been widely used to study the continental water cycle, especially in regions where in situ measurements are not readily available. The future Surface Water and Ocean Topography (SWOT) satellite mission will deliver maps of water surface elevation (WSE) with an unprecedented resolution and provide observation of rivers wider than 100 m and water surface areas greater than approximately 250 m × 250 m over continental surfaces between 78° S and 78° N. This study aims to investigate the potential of SWOT data for parameter optimization for large scale river routing models which are typically employed in Land Surface Models (LSM) for global scale applications. The method consists in applying a data assimilation approach, the Extended Kalman Filter (EKF) algorithm, to correct the Manning roughness coefficients of the ISBA-TRIP Continental Hydrologic System. Indeed, parameters such as the Manning coefficient, used within such models to describe water basin characteristics, are generally derived from geomorphological relationships, which might have locally significant errors. The current study focuses on the Niger basin, a trans-boundary river, which is the main source of fresh water for all the riparian countries. In addition, geopolitical issues in this region can restrict the exchange of hydrological data, so that SWOT should help improve this situation by making hydrological data freely available. In a previous study, the model was first evaluated against in-situ and satellite derived data sets within the framework of the international African Monsoon Multi-disciplinary Analysis (AMMA) project. Since the SWOT observations are not available yet and also to assess the proposed assimilation method, the study is carried out under the framework of an Observing System Simulation Experiment (OSSE). It is assumed that modeling errors are only due to uncertainties in the Manning coefficient. The true Manning

  20. Gender Differences in Reading Impairment and in the Identification of Impaired Readers: Results from a Large-Scale Study of At-Risk Readers

    ERIC Educational Resources Information Center

    Quinn, Jamie M.; Wagner, Richard K.

    2015-01-01

    Reading impairment is more common in males, but the magnitude and origin of this gender difference are debated. In a large-scale study of reading impairment among 491,103 beginning second-graders, gender differences increased with greater severity of reading impairment, peaking at a ratio of 2.4:1 for a broad measure of fluency and a ratio of…

  1. Large-Scale Patterns of Genetic Variation in a Female-Biased Dispersing Passerine: The Importance of Sex-Based Analyses

    PubMed Central

    Guerrini, Monica; Gennai, Clizia; Panayides, Panicos; Crabtree, Alan; Zuberogoitia, Iñigo; Copland, Alex S.; Babushkina, Olga; Politi, Paolo M.; Giunchi, Dimitri; Barbanera, Filippo

    2014-01-01

    Dispersal affects the distribution, dynamics and genetic structure of natural populations, and can be significantly different between sexes. However, literature records dealing with the dispersal of migratory birds are scarce, as migratory behaviour can notably complicate the study of dispersal. We used the barn swallow Hirundo rustica as model taxon to investigate patterns of genetic variability in males and in females of a migratory species showing sex-biased dispersal. We collected blood samples (n = 186) over the period 2006 to 2011 from adults (H. r. rustica subspecies) nesting in the same breeding site at either high (Ireland, Germany and Russia) or low (Spain, Italy and Cyprus) latitude across Europe. We amplified the Chromo Helicase DNA gene in all birds in order to warrant a sex-balanced sample size (92 males, 94 females). We investigated both uniparental (mitochondrial ND2 gene) and biparental (microsatellite DNA: 10 loci) genetic systems. The mtDNA provided evidence for demographic expansion yet no significant partition of the genetic variability was disclosed. Nevertheless, a comparatively distant Russian population investigated in another study, whose sequences were included in the present dataset, significantly diverged from all other ones. Different to previous studies, microsatellites highlighted remarkable genetic structure among the studied populations, and pointed to the occurrence of differences between male and female barn swallows. We produced evidence for non-random patterns of gene flow among barn swallow populations probably mediated by female natal dispersal, and we found significant variability in the philopatry of males of different populations. Our data emphasize the importance of taking into account the sex of sampled individuals in order to obtain reliable inferences on species characterized by different patterns of dispersal between males and females. PMID:24886720

  2. Large-scale patterns of genetic variation in a female-biased dispersing passerine: the importance of sex-based analyses.

    PubMed

    Guerrini, Monica; Gennai, Clizia; Panayides, Panicos; Crabtree, Alan; Zuberogoitia, Iñigo; Copland, Alex S; Babushkina, Olga; Politi, Paolo M; Giunchi, Dimitri; Barbanera, Filippo

    2014-01-01

    Dispersal affects the distribution, dynamics and genetic structure of natural populations, and can be significantly different between sexes. However, literature records dealing with the dispersal of migratory birds are scarce, as migratory behaviour can notably complicate the study of dispersal. We used the barn swallow Hirundo rustica as model taxon to investigate patterns of genetic variability in males and in females of a migratory species showing sex-biased dispersal. We collected blood samples (n = 186) over the period 2006 to 2011 from adults (H. r. rustica subspecies) nesting in the same breeding site at either high (Ireland, Germany and Russia) or low (Spain, Italy and Cyprus) latitude across Europe. We amplified the Chromo Helicase DNA gene in all birds in order to warrant a sex-balanced sample size (92 males, 94 females). We investigated both uniparental (mitochondrial ND2 gene) and biparental (microsatellite DNA: 10 loci) genetic systems. The mtDNA provided evidence for demographic expansion yet no significant partition of the genetic variability was disclosed. Nevertheless, a comparatively distant Russian population investigated in another study, whose sequences were included in the present dataset, significantly diverged from all other ones. Different to previous studies, microsatellites highlighted remarkable genetic structure among the studied populations, and pointed to the occurrence of differences between male and female barn swallows. We produced evidence for non-random patterns of gene flow among barn swallow populations probably mediated by female natal dispersal, and we found significant variability in the philopatry of males of different populations. Our data emphasize the importance of taking into account the sex of sampled individuals in order to obtain reliable inferences on species characterized by different patterns of dispersal between males and females. PMID:24886720

  3. Designing Topology-Aware Collective Communication Algorithms for Large Scale InfiniBand Clusters: Case Studies with Scatter and Gather

    SciTech Connect

    Kandalla, Krishna; Subramoni, Hari; Vishnu, Abhinav; Panda, Dhabaleswar K.

    2010-04-01

    Modern high performance computing systems are being increasingly deployed in a hierarchical fashion with multi-core computing platforms forming the base of the hierarchy. These systems are usually comprised of multiple racks, with each rack consisting of a finite number of chassis, with each chassis having multiple compute nodes or blades, based on multi-core architectures. The networks are also hierarchical with multiple levels of switches. Message exchange operations between processes that belong to different racks involve multiple hops across different switches and this directly affects the performance of collective operations. In this paper, we take on the challenges involved in detecting the topology of large scale InfiniBand clusters and leveraging this knowledge to design efficient topology-aware algorithms for collective operations. We also propose a communication model to analyze the communication costs involved in collective operations on large scale supercomputing systems. We have analyzed the performance characteristics of two collectives, MPI_Gather and MPI_Scatter on such systems and we have proposed topology-aware algorithms for these operations. Our experimental results have shown that the proposed algorithms can improve the performance of these collective operations by almost 54% at the micro-benchmark level.

  4. A large-scale candidate-gene association study of age at menarche and age at natural menopause

    PubMed Central

    Kraft, Peter; Chasman, Daniel I.; Buring, Julie E.; Chen, Constance; Hankinson, Susan E.; Paré, Guillaume; Chanock, Stephen; Ridker, Paul M.; Hunter, David J.

    2010-01-01

    Recent genome-wide association (GWA) studies have identified several novel genetic loci associated with age at menarche and age at natural menopause. However, the stringent significance threshold used in GWA studies potentially lead to false negatives and true associations may have been overlooked. Incorporating biologically relevant information, we examined whether common genetic polymorphisms in candidate genes of 9 groups of biologically plausible pathways and related phenotypes are associated with age at menarche and age at natural menopause. A total of 18,862 genotyped and imputed single nucleotide polymorphisms (SNPs) in 278 genes were assessed for their associations with these two traits among a total of 24,341 women from the Nurses’ Health Study (NHS, N=2,287) and the Women’s Genome Health Study (WGHS, N=22,054). Linear regression was used to assess the marginal association of each SNP with each phenotype. We adjusted for multiple testing within each gene to identify statistically significant SNP associations at the gene level. To evaluate the overall evidence for an excess of statistically significant gene associations over the proportion expected by chance, we applied a one-sample test of proportion to each group of candidate genes. The steroid-hormone metabolism and biosynthesis pathway was found significantly associated with both age at menarche and age at natural menopause (p=0.040 and 0.011, respectively). Additionally, the group of genes associated with precocious or delayed puberty was found significantly associated with age at menarche (p=0.013), and the group of genes involved in premature ovarian failure with age at menopause (p=0.025). PMID:20734064

  5. Parallel Visualization of Large-Scale Aerodynamics Calculations: A Case Study on the Cray T3E

    NASA Technical Reports Server (NTRS)

    Ma, Kwan-Liu; Crockett, Thomas W.

    1999-01-01

    This paper reports the performance of a parallel volume rendering algorithm for visualizing a large-scale, unstructured-grid dataset produced by a three-dimensional aerodynamics simulation. This dataset, containing over 18 million tetrahedra, allows us to extend our performance results to a problem which is more than 30 times larger than the one we examined previously. This high resolution dataset also allows us to see fine, three-dimensional features in the flow field. All our tests were performed on the Silicon Graphics Inc. (SGI)/Cray T3E operated by NASA's Goddard Space Flight Center. Using 511 processors, a rendering rate of almost 9 million tetrahedra/second was achieved with a parallel overhead of 26%.

  6. Application of cooperative and non-cooperative games in large-scale water quantity and quality management: a case study.

    PubMed

    Mahjouri, Najmeh; Ardestani, Mojtaba

    2011-01-01

    In this paper, two cooperative and non-cooperative methodologies are developed for a large-scale water allocation problem in Southern Iran. The water shares of the water users and their net benefits are determined using optimization models having economic objectives with respect to the physical and environmental constraints of the system. The results of the two methodologies are compared based on the total obtained economic benefit, and the role of cooperation in utilizing a shared water resource is demonstrated. In both cases, the water quality in rivers satisfies the standards. Comparing the results of the two mentioned approaches shows the importance of acting cooperatively to achieve maximum revenue in utilizing a surface water resource while the river water quantity and quality issues are addressed. PMID:20135217

  7. A case study of the intraseasonal oscillation traversing the TOGA-COARE LSD. [large-scale domain

    NASA Technical Reports Server (NTRS)

    Vincent, Dayton G.; Schrage, Jon M.; Sliwinski, L. D.

    1993-01-01

    The paper presents examination of tree intraseasonal (30-60 day) oscillations (ISOs) that occurred during the southern summer season (December 1, 1985 - February 28, 1986) traversing the Large-Scale Domain (LSD) TOGA-COARE, the region which also plays an important role in ENSO, Australian monsoon, and extratropical circulations. Data presented include Hovmoeller diagrams of 5-day running means of 250-mb velocity potential anomalies and OLR anomalies; graphs of five-day running means of OLR in precipitable water (W) per sq m, averaged over 10 x 10 deg boxes centered on 5 S and (1) 145 E, (2) 155 E, (3) 165 E, and (4) 165 D, indicating the midpoint of each ISO; and vertical profiles of zonal wind in m/s averaged over the time period that each ISO spends in the 10 x 10 deg box centered at 5 S, and 175 E and 145 E.

  8. A Preliminary Model Study of the Large-Scale Seasonal Cycle in Bottom Pressure Over the Global Ocean

    NASA Technical Reports Server (NTRS)

    Ponte, Rui M.

    1998-01-01

    Output from the primitive equation model of Semtner and Chervin is used to examine the seasonal cycle in bottom pressure (Pb) over the global ocean. Effects of the volume-conserving formulation of the model on the calculation Of Pb are considered. The estimated seasonal, large-scale Pb signals have amplitudes ranging from less than 1 cm over most of the deep ocean to several centimeters over shallow, boundary regions. Variability generally increases toward the western sides of the basins, and is also larger in some Southern Ocean regions. An oscillation between subtropical and higher latitudes in the North Pacific is clear. Comparison with barotropic simulations indicates that, on basin scales, seasonal Pb variability is related to barotropic dynamics and the seasonal cycle in Ekman pumping, and results from a small, net residual in mass divergence from the balance between Ekman and Sverdrup flows.

  9. CASE STUDY OF FOUR HOMOLOGOUS LARGE-SCALE CORONAL WAVES OBSERVED ON 2010 APRIL 28 AND 29

    SciTech Connect

    Kienreich, I. W.; Veronig, A. M.; Muhr, N.; Temmer, M.; Vrsnak, B.; Nitta, N.

    2011-02-01

    On 2010 April 28 and 29, the Solar TErrestrial Relations Observatory B/Extreme Ultraviolet Imager observed four homologous large-scale coronal waves, the so-called EIT-waves, within 8 hr. All waves emerged from the same source active region, were accompanied by weak flares and faint coronal mass ejections, and propagated into the same direction at constant velocities in the range of {approx}220-340 km s{sup -1}. The last of these four coronal wave events was the strongest and fastest, with a velocity of 337 {+-} 31 km s{sup -1} and a peak perturbation amplitude of {approx}1.24, corresponding to a magnetosonic Mach number of M{sub ms} {approx} 1.09. The magnetosonic Mach numbers and velocities of the four waves are distinctly correlated, suggestive of the nonlinear fast-mode magnetosonic wave nature of the events. We also found a correlation between the magnetic energy buildup times and the velocity and magnetosonic Mach number.

  10. HAPEX-Sahel: A large-scale study of land-atmosphere interactions in the semi-arid tropics

    NASA Technical Reports Server (NTRS)

    Gutorbe, J-P.; Lebel, T.; Tinga, A.; Bessemoulin, P.; Brouwer, J.; Dolman, A.J.; Engman, E. T.; Gash, J. H. C.; Hoepffner, M.; Kabat, P.

    1994-01-01

    The Hydrologic Atmospheric Pilot EXperiment in the Sahel (HAPEX-Sahel) was carried out in Niger, West Africa, during 1991-1992, with an intensive observation period (IOP) in August-October 1992. It aims at improving the parameteriztion of land surface atmospheric interactions at the Global Circulation Model (GCM) gridbox scale. The experiment combines remote sensing and ground based measurements with hydrological and meteorological modeling to develop aggregation techniques for use in large scale estimates of the hydrological and meteorological behavior of large areas in the Sahel. The experimental strategy consisted of a period of intensive measurements during the transition period of the rainy to the dry season, backed up by a series of long term measurements in a 1 by 1 deg square in Niger. Three 'supersites' were instrumented with a variety of hydrological and (micro) meteorological equipment to provide detailed information on the surface energy exchange at the local scale. Boundary layer measurements and aircraft measurements were used to provide information at scales of 100-500 sq km. All relevant remote sensing images were obtained for this period. This program of measurements is now being analyzed and an extensive modelling program is under way to aggregate the information at all scales up to the GCM grid box scale. The experimental strategy and some preliminary results of the IOP are described.

  11. Structure of Wall-Eddies at Very Large Reynolds Number--A Large-Scale PIV Study

    NASA Astrophysics Data System (ADS)

    Hommema, S. E.; Adrian, R. J.

    2000-11-01

    The results of an experiment performed in the first 5 m of the neutral atmospheric boundary layer are presented. Large-scale PIV measurements (up to 2 m × 2 m field-of-view) were obtained in the streamwise / wall-normal plane of a very-large Reynolds number (Re_θ > 10^6, based on momentum thickness and freestream velocity), flat-plate, zero-pressure-gradient boundary layer. Measurements were obtained at the SLTEST facility in the U.S. Army's Dugway Proving Grounds. Coherent packets of ramp-like structures with downstream inclination are observed and show a remarkable resemblance to those observed in typical laboratory-scale experiments at far lower Reynolds number. The results are interpreted in terms of a vortex packet paradigm(Adrian, R.J., C.D. Meinhart, and C.D. Tomkins, Vortex organization in the outer region of the turbulent boundary layer, to appear in J. Fluid Mech., 2000.) and begin to extend the model to high Reynolds numbers of technological importance. Additional results obtained during periods of non-neutral atmospheric stability are contrasted with those of the canonical neutral boundary layer. Sample smoke visualization images (3 m × 15 m field-of-view) are available online from the author.

  12. The Landscape Evolution Observatory: A large-scale controllable infrastructure to study coupled Earth-surface processes

    NASA Astrophysics Data System (ADS)

    Pangle, Luke A.; DeLong, Stephen B.; Abramson, Nate; Adams, John; Barron-Gafford, Greg A.; Breshears, David D.; Brooks, Paul D.; Chorover, Jon; Dietrich, William E.; Dontsova, Katerina; Durcik, Matej; Espeleta, Javier; Ferre, T. P. A.; Ferriere, Regis; Henderson, Whitney; Hunt, Edward A.; Huxman, Travis E.; Millar, David; Murphy, Brendan; Niu, Guo-Yue; Pavao-Zuckerman, Mitch; Pelletier, Jon D.; Rasmussen, Craig; Ruiz, Joaquin; Saleska, Scott; Schaap, Marcel; Sibayan, Michael; Troch, Peter A.; Tuller, Markus; van Haren, Joost; Zeng, Xubin

    2015-09-01

    Zero-order drainage basins, and their constituent hillslopes, are the fundamental geomorphic unit comprising much of Earth's uplands. The convergent topography of these landscapes generates spatially variable substrate and moisture content, facilitating biological diversity and influencing how the landscape filters precipitation and sequesters atmospheric carbon dioxide. In light of these significant ecosystem services, refining our understanding of how these functions are affected by landscape evolution, weather variability, and long-term climate change is imperative. In this paper we introduce the Landscape Evolution Observatory (LEO): a large-scale controllable infrastructure consisting of three replicated artificial landscapes (each 330 m2 surface area) within the climate-controlled Biosphere 2 facility in Arizona, USA. At LEO, experimental manipulation of rainfall, air temperature, relative humidity, and wind speed are possible at unprecedented scale. The Landscape Evolution Observatory was designed as a community resource to advance understanding of how topography, physical and chemical properties of soil, and biological communities coevolve, and how this coevolution affects water, carbon, and energy cycles at multiple spatial scales. With well-defined boundary conditions and an extensive network of sensors and samplers, LEO enables an iterative scientific approach that includes numerical model development and virtual experimentation, physical experimentation, data analysis, and model refinement. We plan to engage the broader scientific community through public dissemination of data from LEO, collaborative experimental design, and community-based model development.

  13. The Landscape Evolution Observatory: a large-scale controllable infrastructure to study coupled Earth-surface processes

    USGS Publications Warehouse

    Pangle, Luke A.; DeLong, Stephen B.; Abramson, Nate; Adams, John; Barron-Gafford, Greg A.; Breshears, David D.; Brooks, Paul D.; Chorover, Jon; Dietrich, William E.; Dontsova, Katerina; Durcik, Matej; Espeleta, Javier; Ferre, T. P. A.; Ferriere, Regis; Henderson, Whitney; Hunt, Edward A.; Huxman, Travis E.; Millar, David; Murphy, Brendan; Niu, Guo-Yue; Pavao-Zuckerman, Mitch; Pelletier, Jon D.; Rasmussen, Craig; Ruiz, Joaquin; Saleska, Scott; Schaap, Marcel; Sibayan, Michael; Troch, Peter A.; Tuller, Markus; van Haren, Joost; Zeng, Xubin

    2015-01-01

    Zero-order drainage basins, and their constituent hillslopes, are the fundamental geomorphic unit comprising much of Earth's uplands. The convergent topography of these landscapes generates spatially variable substrate and moisture content, facilitating biological diversity and influencing how the landscape filters precipitation and sequesters atmospheric carbon dioxide. In light of these significant ecosystem services, refining our understanding of how these functions are affected by landscape evolution, weather variability, and long-term climate change is imperative. In this paper we introduce the Landscape Evolution Observatory (LEO): a large-scale controllable infrastructure consisting of three replicated artificial landscapes (each 330 m2 surface area) within the climate-controlled Biosphere 2 facility in Arizona, USA. At LEO, experimental manipulation of rainfall, air temperature, relative humidity, and wind speed are possible at unprecedented scale. The Landscape Evolution Observatory was designed as a community resource to advance understanding of how topography, physical and chemical properties of soil, and biological communities coevolve, and how this coevolution affects water, carbon, and energy cycles at multiple spatial scales. With well-defined boundary conditions and an extensive network of sensors and samplers, LEO enables an iterative scientific approach that includes numerical model development and virtual experimentation, physical experimentation, data analysis, and model refinement. We plan to engage the broader scientific community through public dissemination of data from LEO, collaborative experimental design, and community-based model development.

  14. Large-scale exploration of gene-gene interactions in prostate cancer using a multistage genome-wide association study.

    PubMed

    Ciampa, Julia; Yeager, Meredith; Amundadottir, Laufey; Jacobs, Kevin; Kraft, Peter; Chung, Charles; Wacholder, Sholom; Yu, Kai; Wheeler, William; Thun, Michael J; Divers, W Ryan; Gapstur, Susan; Albanes, Demetrius; Virtamo, Jarmo; Weinstein, Stephanie; Giovannucci, Edward; Willett, Walter C; Cancel-Tassin, Geraldine; Cussenot, Olivier; Valeri, Antoine; Hunter, David; Hoover, Robert; Thomas, Gilles; Chanock, Stephen; Chatterjee, Nilanjan

    2011-05-01

    Recent genome-wide association studies have identified independent susceptibility loci for prostate cancer that could influence risk through interaction with other, possibly undetected, susceptibility loci. We explored evidence of interaction between pairs of 13 known susceptibility loci and single nucleotide polymorphisms (SNP) across the genome to generate hypotheses about the functionality of prostate cancer susceptibility regions. We used data from Cancer Genetic Markers of Susceptibility: Stage I included 523,841 SNPs in 1,175 cases and 1,100 controls; Stage II included 27,383 SNPs in an additional 3,941 cases and 3,964 controls. Power calculations assessed the magnitude of interactions our study is likely to detect. Logistic regression was used with alternative methods that exploit constraints of gene-gene independence between unlinked loci to increase power. Our empirical evaluation demonstrated that an empirical Bayes (EB) technique is powerful and robust to possible violation of the independence assumption. Our EB analysis identified several noteworthy interacting SNP pairs, although none reached genome-wide significance. We highlight a Stage II interaction between the major prostate cancer susceptibility locus in the subregion of 8q24 that contains POU5F1B and an intronic SNP in the transcription factor EPAS1, which has potentially important functional implications for 8q24. Another noteworthy result involves interaction of a known prostate cancer susceptibility marker near the prostate protease genes KLK2 and KLK3 with an intronic SNP in PRXX2. Overall, the interactions we have identified merit follow-up study, particularly the EPAS1 interaction, which has implications not only in prostate cancer but also in other epithelial cancers that are associated with the 8q24 locus. PMID:21372204

  15. Dietary habits and risk of urothelial cancer death in a large-scale cohort study (JACC Study) in Japan.

    PubMed

    Sakauchi, Fumio; Mori, Mitsuru; Washio, Masakazu; Watanabe, Yoshiyuki; Ozasa, Kotaro; Hayashi, Kyohei; Miki, Tsuneharu; Nakao, Masahiro; Mikami, Kazuya; Ito, Yoshinori; Wakai, Kenji; Tamakoshi, Akiko

    2004-01-01

    In the present study, the associations of dietary habits with the risk of urothelial cancer death were evaluated taking into consideration sex, age, and smoking habits. The Japan Collaborative Cohort Study was established in 1988-1990 and consisted of 47,997 men and 66,520 women observed until the end of 1999. A self-administered food-frequency questionnaire was used as a baseline survey. Hazard ratios for dietary factors were calculated by Cox's proportional hazards model. During the observation period, 63 men and 25 women died of urothelial cancer. Increasing age, male gender, and history of smoking were all significantly associated with increased risk of urothelial cancer death. A high intake of milk and fruits other than oranges reduced the risk significantly and dose dependently, in particular among subjects with smoking history. However, consumption of butter and yogurt had no associations with the risk. Intakes of cabbage, lettuce, green leafy vegetables, carrots, squash, tomatoes, and oranges were not significantly associated with the risk. It was suggested that urothelial cancer death could be potentially preventable by smoking cessation and regular intake of milk and fruit. PMID:15572295

  16. Evaluation of Multiplex-Based Antibody Testing for Use in Large-Scale Surveillance for Yaws: a Comparative Study.

    PubMed

    Cooley, Gretchen M; Mitja, Oriol; Goodhew, Brook; Pillay, Allan; Lammie, Patrick J; Castro, Arnold; Moses, Penias; Chen, Cheng; Ye, Tun; Ballard, Ronald; Martin, Diana L

    2016-05-01

    WHO has targeted yaws for global eradication by 2020. The program goals are to interrupt the transmission in countries where yaws is endemic and to certify countries as yaws free where yaws was endemic in the past. No new rapid plasmin reagin (RPR) seroreactivity in young children is required for certification of elimination at a country level. We sought to evaluate whether antibody responses to specific treponemal antigens measured in a high-throughput multiplex bead array (MBA) assay differentiate past versus current infection and whether a nontreponemal lipoidal antigen test can be incorporated into the MBA. Serum and dried blood spot specimens collected for yaws surveillance projects in Ghana, Vanuatu, and Papua New Guinea (PNG) were run on MBA to measure antibodies against recombinant p17 (rp17) and treponemal membrane protein A (TmpA) treponemal antigens. Results were compared to standard treponemal laboratory (TPPA or TPHA [TPP(H)A]) and quantitative RPR test data. Of 589 specimens, 241 were TPP(H)A(+)/RPR(+), 88 were TPP(H)A(+)/RPR(-), 6 were TPP(H)A(-)/RPR(+), and 254 were negative for both tests. Compared to TPP(H)A, reactive concordance of rp17 was 93.7%, while reactive concordance of TmpA was only 81.9%. TmpA-specific reactivity showed good correlation with RPR titers (R(2) = 0.41; P < 0.0001). IgG responses to the lipoidal antigen used in RPR testing (cardiolipin) were not detected in the MBA. Our results suggest that TmpA can be used as a treponemal antigen marker for recent or active infection and potentially replace RPR in a high-throughput multiplex tool for large-scale yaws surveillance. PMID:26962086

  17. Zolpidem Reduces Hippocampal Neuronal Activity in Freely Behaving Mice: A Large Scale Calcium Imaging Study with Miniaturized Fluorescence Microscope

    PubMed Central

    Berdyyeva, Tamara; Otte, Stephani; Aluisio, Leah; Ziv, Yaniv; Burns, Laurie D.; Dugovic, Christine; Yun, Sujin; Ghosh, Kunal K.; Schnitzer, Mark J.; Lovenberg, Timothy; Bonaventure, Pascal

    2014-01-01

    Therapeutic drugs for cognitive and psychiatric disorders are often characterized by their molecular mechanism of action. Here we demonstrate a new approach to elucidate drug action on large-scale neuronal activity by tracking somatic calcium dynamics in hundreds of CA1 hippocampal neurons of pharmacologically manipulated behaving mice. We used an adeno-associated viral vector to express the calcium sensor GCaMP3 in CA1 pyramidal cells under control of the CaMKII promoter and a miniaturized microscope to observe cellular dynamics. We visualized these dynamics with and without a systemic administration of Zolpidem, a GABAA agonist that is the most commonly prescribed drug for the treatment of insomnia in the United States. Despite growing concerns about the potential adverse effects of Zolpidem on memory and cognition, it remained unclear whether Zolpidem alters neuronal activity in the hippocampus, a brain area critical for cognition and memory. Zolpidem, when delivered at a dose known to induce and prolong sleep, strongly suppressed CA1 calcium signaling. The rate of calcium transients after Zolpidem administration was significantly lower compared to vehicle treatment. To factor out the contribution of changes in locomotor or physiological conditions following Zolpidem treatment, we compared the cellular activity across comparable epochs matched by locomotor and physiological assessments. This analysis revealed significantly depressive effects of Zolpidem regardless of the animal’s state. Individual hippocampal CA1 pyramidal cells differed in their responses to Zolpidem with the majority (∼65%) significantly decreasing the rate of calcium transients, and a small subset (3%) showing an unexpected and significant increase. By linking molecular mechanisms with the dynamics of neural circuitry and behavioral states, this approach has the potential to contribute substantially to the development of new therapeutics for the treatment of CNS disorders. PMID:25372144

  18. Evaluation of Multiplex-Based Antibody Testing for Use in Large-Scale Surveillance for Yaws: a Comparative Study

    PubMed Central

    Cooley, Gretchen M.; Mitja, Oriol; Goodhew, Brook; Pillay, Allan; Lammie, Patrick J.; Castro, Arnold; Moses, Penias; Chen, Cheng; Ye, Tun; Ballard, Ronald

    2016-01-01

    WHO has targeted yaws for global eradication by 2020. The program goals are to interrupt the transmission in countries where yaws is endemic and to certify countries as yaws free where yaws was endemic in the past. No new rapid plasmin reagin (RPR) seroreactivity in young children is required for certification of elimination at a country level. We sought to evaluate whether antibody responses to specific treponemal antigens measured in a high-throughput multiplex bead array (MBA) assay differentiate past versus current infection and whether a nontreponemal lipoidal antigen test can be incorporated into the MBA. Serum and dried blood spot specimens collected for yaws surveillance projects in Ghana, Vanuatu, and Papua New Guinea (PNG) were run on MBA to measure antibodies against recombinant p17 (rp17) and treponemal membrane protein A (TmpA) treponemal antigens. Results were compared to standard treponemal laboratory (TPPA or TPHA [TPP(H)A]) and quantitative RPR test data. Of 589 specimens, 241 were TPP(H)A+/RPR+, 88 were TPP(H)A+/RPR−, 6 were TPP(H)A−/RPR+, and 254 were negative for both tests. Compared to TPP(H)A, reactive concordance of rp17 was 93.7%, while reactive concordance of TmpA was only 81.9%. TmpA-specific reactivity showed good correlation with RPR titers (R2 = 0.41; P < 0.0001). IgG responses to the lipoidal antigen used in RPR testing (cardiolipin) were not detected in the MBA. Our results suggest that TmpA can be used as a treponemal antigen marker for recent or active infection and potentially replace RPR in a high-throughput multiplex tool for large-scale yaws surveillance. PMID:26962086

  19. Construction of a High-Density Genetic Map Based on Large-Scale Marker Development in Mango Using Specific-Locus Amplified Fragment Sequencing (SLAF-seq)

    PubMed Central

    Luo, Chun; Shu, Bo; Yao, Quangsheng; Wu, Hongxia; Xu, Wentian; Wang, Songbiao

    2016-01-01

    Genetic maps are particularly important and valuable tools for quantitative trait locus (QTL) mapping and marker assisted selection (MAS) of plant with desirable traits. In this study, 173 F1 plants from a cross between Mangifera indica L. “Jin-Hwang” and M. indica L. “Irwin” and their parent plants were subjected to high-throughput sequencing and specific-locus amplified fragment (SLAF) library construction. After preprocessing, 66.02 Gb of raw data containing 330.64 M reads were obtained. A total of 318,414 SLAFs were detected, of which 156,368 were polymorphic. Finally, 6594 SLAFs were organized into a linkage map consisting of 20 linkage groups (LGs). The total length of the map was 3148.28 cM and the average distance between adjacent markers was 0.48 cM. This map could be considered, to our knowledge, the first high-density genetic map of mango, and might form the basis for fine QTL mapping and MAS of mango. PMID:27625670

  20. Construction of a High-Density Genetic Map Based on Large-Scale Marker Development in Mango Using Specific-Locus Amplified Fragment Sequencing (SLAF-seq).

    PubMed

    Luo, Chun; Shu, Bo; Yao, Quangsheng; Wu, Hongxia; Xu, Wentian; Wang, Songbiao

    2016-01-01

    Genetic maps are particularly important and valuable tools for quantitative trait locus (QTL) mapping and marker assisted selection (MAS) of plant with desirable traits. In this study, 173 F1 plants from a cross between Mangifera indica L. "Jin-Hwang" and M. indica L. "Irwin" and their parent plants were subjected to high-throughput sequencing and specific-locus amplified fragment (SLAF) library construction. After preprocessing, 66.02 Gb of raw data containing 330.64 M reads were obtained. A total of 318,414 SLAFs were detected, of which 156,368 were polymorphic. Finally, 6594 SLAFs were organized into a linkage map consisting of 20 linkage groups (LGs). The total length of the map was 3148.28 cM and the average distance between adjacent markers was 0.48 cM. This map could be considered, to our knowledge, the first high-density genetic map of mango, and might form the basis for fine QTL mapping and MAS of mango. PMID:27625670

  1. Lessons learned from 25+ years of piggybacking environmental isotope studies onto large-scale federal and state water quality monitoring programs (Invited)

    NASA Astrophysics Data System (ADS)

    Kendall, C.; Silva, S. R.; Young, M. B.

    2010-12-01

    Isotopes are a potentially powerful component of monitoring and assessment programs aimed at quantifying and mitigating alterations to environments from human activities. Locations exhibiting unusually high rates of biogeochemical cycling or elevated pollution levels usually have distinctive isotopic compositions that are suggestive or diagnostic of the reactions and pollution sources. Isotopes can be more effective at identifying hot spots and hot moments than concentrations alone because isotopic ratios may change even when concentrations do not. Hence, isotopes facilitate the identification of hot spots and moments that otherwise would not be apparent, thereby providing a valuable addition to standard chemical and hydrological mass balance methods. In addition, isotopic techniques have proved useful for tracing sources and sinks of various pollutants in large river basins, wetlands, and airsheds. Many of these studies have been conducted at the regional to national scale by building on existing large-scale water, air, and ecological monitoring programs managed by federal and state agencies, and demonstrate the usefulness of isotopes as a complement to standard chemical and hydrological mass balance methods. This presentation presents an overview of how a multi-isotope approach can be used to interpret spatial patterns and temporal changes in pollution sources, biogeochemical processes, and ecosystem function in large watersheds, at the regional to national scale. Examples from several of our recent and ongoing studies in the San Joaquin, Sacramento, and Mississippi Rivers are presented. From the insights developed using (1) a multi-isotope approach (emphasizing nitrate, seston, and water isotopes) used in conjunction with detailed hydrologic and chemical data collected from both mainstem and tributary sites as part of annual or multi-year studies; (2) varied sampling strategies including fixed site, synoptic, Lagrangian, and diel approaches; (3) different types

  2. Large scale topography of Io

    NASA Technical Reports Server (NTRS)

    Gaskell, R. W.; Synnott, S. P.

    1987-01-01

    To investigate the large scale topography of the Jovian satellite Io, both limb observations and stereographic techniques applied to landmarks are used. The raw data for this study consists of Voyager 1 images of Io, 800x800 arrays of picture elements each of which can take on 256 possible brightness values. In analyzing this data it was necessary to identify and locate landmarks and limb points on the raw images, remove the image distortions caused by the camera electronics and translate the corrected locations into positions relative to a reference geoid. Minimizing the uncertainty in the corrected locations is crucial to the success of this project. In the highest resolution frames, an error of a tenth of a pixel in image space location can lead to a 300 m error in true location. In the lowest resolution frames, the same error can lead to an uncertainty of several km.

  3. Laparoendoscopic single-site cholecystectomy vs three-port laparoscopic cholecystectomy: A large-scale retrospective study

    PubMed Central

    Cheng, Yuan; Jiang, Ze-Sheng; Xu, Xiao-Ping; Zhang, Zhi; Xu, Ting-Cheng; Zhou, Chen-Jie; Qin, Jia-Sheng; He, Guo-Lin; Gao, Yi; Pan, Ming-Xin

    2013-01-01

    AIM: To perform a large-scale retrospective comparison of laparoendoscopic single-site cholecystectomy (LESSC) and three-port laparoscopic cholecystectomy (TPLC) in a single institution. METHODS: Data were collected from 366 patients undergoing LESSC between January 2005 and July 2008 and were compared with the data from 355 patients undergoing TPLC between August 2008 and November 2011 in our department. Patients with body mass index greater than 35 kg/m2, a history of major upper abdominal surgery, signs of acute cholecystitis, such as fever, right upper quadrant tenderness with or without Murphy’s sign, elevated white blood cell count, imaging findings suggestive of pericholecystic fluid, gallbladder wall thickening > 4 mm, and gallstones > 3 cm, were excluded to avoid bias. RESULTS: Altogether, 298 LESSC and 315 TPLC patients met the inclusion criteria. The groups were well matched with regard to demographic data. There were no significant differences in terms of postoperative complications (contusion: 19 vs 25 and hematoma at incision: 11 vs 19), hospital stay (mean ± SD, 1.4 ± 0.2 d vs 1.4 ± 0.7 d) and visual analogue pain score (mean ± SD, 8 h after surgery: 2.3 ± 1.4 vs 2.3 ± 1.3 and at day 1: 1.2 ± 0.4 vs 1.3 ± 1.2) between the LESSC and TPLC patients. Four patients required the addition of extra ports and 2 patients were converted to open surgery in the LESSC group, which was not significantly different when compared with TPLC patients converted to laparotomy (2 vs 2). LESSC resulted in a longer operating time (mean ± SD, 54.8 ± 11.0 min vs 33.5 ± 9.0 min), a higher incidence of intraoperative gallbladder perforation (56 vs 6) and higher operating cost (mean ± SD, 1933.7 ± 64.4 USD vs 1874.7 ± 46.2 USD) than TPLC. No significant differences in operating time (mean ± SD, 34.3 ± 6.0 min vs 32.7 ± 8.7 min) and total cost (mean ± SD, 1881.3 ± 32.8 USD vs 1876.2 ± 33.4 USD) were found when the last 100 cases in the two groups were

  4. Will investments in large-scale prospective cohorts and biobanks limit our ability to discover weaker, less common genetic and environmental contributors to complex diseases?

    PubMed

    Foster, Morris W; Sharp, Richard R

    2005-02-01

    Increasing the size of prospective cohorts and biobanks is one approach to discovering previously unknown contributors to complex diseases, but it may come at the price of concealing contributors that are less common across all the participants in those larger studies and of limiting hypothesis generation. Prospective cohorts and biobanks constitute significant, long-term investments in research infrastructure that will have ongoing consequences for opportunities in biomedical research for the foreseeable future. Thus, it is important to think about how these major additions to research infrastructure can be designed to be more productive in generating hypotheses for novel environmental contributors to complex diseases and to help identify genetic and environmental contributors that may not be common across the larger samples but are more frequent within local or ancestral subsets. Incorporating open-ended inquiries and qualitative information about local communal and ecologic contexts and the political, economic, and other social structures that affect health status and outcome will enable qualitative hypothesis generation in those localized contexts, as well as the collection of more detailed genealogic and family health history information that may be useful in designing future studies. Using communities as building blocks for larger cohorts and biobanks presents some practical and ethical challenges but also enhances opportunities for interdisciplinary, multilevel investigations of the multifactorial contributors to complex diseases. PMID:15687047

  5. Inference of potential genetic risks associated with large-scale releases of red sea bream in Kanagawa prefecture, Japan based on nuclear and mitochondrial DNA analysis.

    PubMed

    Blanco Gonzalez, Enrique; Aritaki, Masato; Sakurai, Shigeru; Taniguchi, Nobuhiko

    2013-04-01

    Since 1978, millions of hatchery-reared red sea bream (Pagrus major) juveniles have been released in Sagami Bay and Tokyo Bay in Kanagawa Prefecture, Japan. The stock enhancement program has contributed to total catch; however, no information regarding the genetic interactions with wild counterparts is available. Here, we combined 15 microsatellite loci and mitochondrial D-loop sequencing to characterize the genetic resources of red sea bream in Sagami Bay and Tokyo Bay and to elucidate the potential harmful genetic effects associated with fish releases. Both types of markers evidenced higher levels of genetic diversity in wild samples (SB and TB) compared with offspring before stocking (H07 and H08) as well as a hatchery-released sample recaptured in Sagami Bay (HR). Microsatellite F (ST) estimates and Bayesian clustering analysis found significant genetic differences among samples (F (ST) = 0.013-0.054), except for the two wild samples (F (ST) = 0.002) and HR vs. H07 (F (ST) = 0.007). On the other hand, mitochondrial-based Ф (ST) suggested haplotypic similarity between SB, H07, and HR. The low effective number of females contributing to the offspring over multiple generations may be responsible for the lack of haplotypic differentiation. Moreover, the putative hatchery origin to three fish (8 %) without deformity in the inter-nostril epidermis was inferred for the first time. Our results showed the usefulness of combining nuclear and mitochondrial markers to elucidate genetic interactions between hatchery-released and wild red sea bream and warned about potential harmful genetic effects should interbreeding takes place. PMID:22855399

  6. A Large-Scale Genetic Screen in Arabidopsis to Identify Genes Involved in Pollen Exine Production1[C][W][OA

    PubMed Central

    Dobritsa, Anna A.; Geanconteri, Aliza; Shrestha, Jay; Carlson, Ann; Kooyers, Nicholas; Coerper, Daniel; Urbanczyk-Wochniak, Ewa; Bench, Bennie J.; Sumner, Lloyd W.; Swanson, Robert; Preuss, Daphne

    2011-01-01

    Exine, the outer plant pollen wall, has elaborate species-specific patterns, provides a protective barrier for male gametophytes, and serves as a mediator of strong and species-specific pollen-stigma adhesion. Exine is made of sporopollenin, a material remarkable for its strength, elasticity, and chemical durability. The chemical nature of sporopollenin, as well as the developmental mechanisms that govern its assembly into diverse patterns in different species, are poorly understood. Here, we describe a simple yet effective genetic screen in Arabidopsis (Arabidopsis thaliana) that was undertaken to advance our understanding of sporopollenin synthesis and exine assembly. This screen led to the recovery of mutants with a variety of defects in exine structure, including multiple mutants with novel phenotypes. Fifty-six mutants were selected for further characterization and are reported here. In 14 cases, we have mapped defects to specific genes, including four with previously demonstrated or suggested roles in exine development (MALE STERILITY2, CYP703A2, ANTHER-SPECIFIC PROTEIN6, TETRAKETIDE α-PYRONE REDUCTASE/DIHYDROFLAVONOL-4-REDUCTASE-LIKE1), and a number of genes that have not been implicated in exine production prior to this screen (among them, fatty acid ω-hydroxylase CYP704B1, putative glycosyl transferases At1g27600 and At1g33430, 4-coumarate-coenzyme A ligase 4CL3, polygalacturonase QUARTET3, novel gene At5g58100, and nucleotide-sugar transporter At5g65000). Our study illustrates that morphological screens of pollen can be extremely fruitful in identifying previously unknown exine genes and lays the foundation for biochemical, developmental, and evolutionary studies of exine production. PMID:21849515

  7. Mining the genome for susceptibility to diabetic nephropathy: the role of large-scale studies and consortia.

    PubMed

    Iyengar, Sudha K; Freedman, Barry I; Sedor, John R

    2007-03-01

    Approximately 30% of individuals with type 1 and type 2 diabetes develop persistent albuminuria, lose renal function, and are at increased risk for cardiovascular and other microvascular complications. Diabetes and kidney diseases rank within the top 10 causes of death in Westernized countries and cause significant morbidity. Given these observations, genetic, genomic, and proteomic investigations have been initiated to better define basic mechanisms for disease initiation and progression, to identify individuals at risk for diabetic complications, and to develop more efficacious therapies. In this review we have focused on linkage analyses of candidate genes or chromosomal regions, or coarse genome-wide scans, which have mapped either categorical (chronic kidney disease or end-stage renal disease) or quantitative kidney traits (albuminuria/proteinuria or glomerular filtration rate). Most loci identified to date have not been replicated, however, several linked chromosomal regions are concordant between independent samples, suggesting the presence of a diabetic nephropathy gene. Two genes, carnosinase (CNDP1) on 18q, and engulfment and cell motility 1 (ELMO1) on 7p14, have been identified as diabetic nephropathy susceptibility genes, but these results require authentication. The availability of patient data sets with large sample sizes, improvements in informatics, genotyping technology, and statistical methodologies should accelerate the discovery of valid diabetic nephropathy susceptibility genes. PMID:17418689

  8. The innovative use of a large-scale industry biomedical consortium to research the genetic basis of drug induced serious adverse events.

    PubMed

    Holden, Arthur L

    2007-01-01

    The International Serious Adverse Event Consortium (SAEC) is a pharmaceutical industry and FDA led international (501 c3 non-profit) consortium, focused on identifying and validating DNA-variants useful in predicting the risk of drug induced, rare serious adverse events (SAEs). As such, it functions with the explicit purpose of enhancing the 'public good'. Its members are (i) organizations engaged principally in the business of discovering, developing and marketing pharmaceutical products, or (ii) a charitable, governmental, or other non-profit organization with an interest in researching the molecular basis of drug response.Drug-induced, rare SAEs present significant health issues for patients; and pose challenges for the safe use of approved drugs and the development of new drugs. Examples of drug-induced, rare SAEs include hepatotoxicity, QT prolongation, rhabdomyolosis, serious skin rashes (e.g. SJS), edema, acute renal failure, acute hypersensitivity, anemias/neutropenias, excessive weigh gain, retinopathy, vasculitis, among others. The rarity of such drug induced SAEs and the absence of effective government surveillance/research networks, makes it extremely difficult for any one company or research entity to accrue enough SAE cases and controls to conduct effective whole genome studies. Central to the notion of the SAEC is industry, government and health care providers can join forces to make use of a variety of sample and data resources in researching the genetic basis of these events.The purpose of the SAEC is threefold:•To carry out research directed toward the discovery of DNA-variants clinically useful in understanding and predicting the risk of drug induced serious adverse events and similar scientific research.•To ensure the widespread availability of the results of such research to the scientific research community and the public at large for no charge through publication and web-based methods; and•To educate the scientific research and medical

  9. Development of a superconductor magnetic suspension and balance prototype facility for studying the feasibility of applying this technique to large scale aerodynamic testing

    NASA Technical Reports Server (NTRS)

    Zapata, R. N.; Humphris, R. R.; Henderson, K. C.

    1975-01-01

    The basic research and development work towards proving the feasibility of operating an all-superconductor magnetic suspension and balance device for aerodynamic testing is presented. The feasibility of applying a quasi-six-degree-of freedom free support technique to dynamic stability research was studied along with the design concepts and parameters for applying magnetic suspension techniques to large-scale aerodynamic facilities. A prototype aerodynamic test facility was implemented. Relevant aspects of the development of the prototype facility are described in three sections: (1) design characteristics; (2) operational characteristics; and (3) scaling to larger facilities.

  10. Large-Scale Phenotyping of an Accurate Genetic Mouse Model of JNCL Identifies Novel Early Pathology Outside the Central Nervous System

    PubMed Central

    Staropoli, John F.; Haliw, Larissa; Biswas, Sunita; Garrett, Lillian; Hölter, Sabine M.; Becker, Lore; Skosyrski, Sergej; Da Silva-Buttkus, Patricia; Calzada-Wack, Julia; Neff, Frauke; Rathkolb, Birgit; Rozman, Jan; Schrewe, Anja; Adler, Thure; Puk, Oliver; Sun, Minxuan; Favor, Jack; Racz, Ildikó; Bekeredjian, Raffi; Busch, Dirk H.; Graw, Jochen; Klingenspor, Martin; Klopstock, Thomas; Wolf, Eckhard; Wurst, Wolfgang; Zimmer, Andreas; Lopez, Edith; Harati, Hayat; Hill, Eric; Krause, Daniela S.; Guide, Jolene; Dragileva, Ella; Gale, Evan; Wheeler, Vanessa C.; Boustany, Rose-Mary; Brown, Diane E.; Breton, Sylvie; Ruether, Klaus; Gailus-Durner, Valérie; Fuchs, Helmut; de Angelis, Martin Hrabě; Cotman, Susan L.

    2012-01-01

    Cln3Δex7/8 mice harbor the most common genetic defect causing juvenile neuronal ceroid lipofuscinosis (JNCL), an autosomal recessive disease involving seizures, visual, motor and cognitive decline, and premature death. Here, to more thoroughly investigate the manifestations of the common JNCL mutation, we performed a broad phenotyping study of Cln3Δex7/8 mice. Homozygous Cln3Δex7/8 mice, congenic on a C57BL/6N background, displayed subtle deficits in sensory and motor tasks at 10–14 weeks of age. Homozygous Cln3Δex7/8 mice also displayed electroretinographic changes reflecting cone function deficits past 5 months of age and a progressive decline of retinal post-receptoral function. Metabolic analysis revealed increases in rectal body temperature and minimum oxygen consumption in 12–13 week old homozygous Cln3Δex7/8mice, which were also seen to a lesser extent in heterozygous Cln3Δex7/8 mice. Heart weight was slightly increased at 20 weeks of age, but no significant differences were observed in cardiac function in young adults. In a comprehensive blood analysis at 15–16 weeks of age, serum ferritin concentrations, mean corpuscular volume of red blood cells (MCV), and reticulocyte counts were reproducibly increased in homozygous Cln3Δex7/8 mice, and male homozygotes had a relative T-cell deficiency, suggesting alterations in hematopoiesis. Finally, consistent with findings in JNCL patients, vacuolated peripheral blood lymphocytes were observed in homozygous Cln3Δex7/8 neonates, and to a greater extent in older animals. Early onset, severe vacuolation in clear cells of the epididymis of male homozygous Cln3Δex7/8 mice was also observed. These data highlight additional organ systems in which to study CLN3 function, and early phenotypes have been established in homozygous Cln3Δex7/8 mice that merit further study for JNCL biomarker development. PMID:22701626

  11. Extrinsic Motivation for Large-Scale Assessments: A Case Study of a Student Achievement Program at One Urban High School

    ERIC Educational Resources Information Center

    Emmett, Joshua; McGee, Dean

    2013-01-01

    The purpose of this case study was to discover the critical attributes of a student achievement program, known as "Think Gold," implemented at one urban comprehensive high school as part of the improvement process. Student achievement on state assessments improved during the period under study. The study draws upon perspectives on motivation as a…

  12. Large-scale development of cost-effective SNP marker assays for diversity assessment and genetic mapping in chickpea and comparative mapping in legumes

    PubMed Central

    Hiremath, Pavana J; Kumar, Ashish; Penmetsa, Ramachandra Varma; Farmer, Andrew; Schlueter, Jessica A; Chamarthi, Siva K; Whaley, Adam M; Carrasquilla-Garcia, Noelia; Gaur, Pooran M; Upadhyaya, Hari D; Kavi Kishor, Polavarapu B; Shah, Trushar M; Cook, Douglas R; Varshney, Rajeev K

    2012-01-01

    A set of 2486 single nucleotide polymorphisms (SNPs) were compiled in chickpea using four approaches, namely (i) Solexa/Illumina sequencing (1409), (ii) amplicon sequencing of tentative orthologous genes (TOGs) (604), (iii) mining of expressed sequence tags (ESTs) (286) and (iv) sequencing of candidate genes (187). Conversion of these SNPs to the cost-effective and flexible throughput Competitive Allele Specific PCR (KASPar) assays generated successful assays for 2005 SNPs. These marker assays have been designated as Chickpea KASPar Assay Markers (CKAMs). Screening of 70 genotypes including 58 diverse chickpea accessions and 12 BC3F2 lines showed 1341 CKAMs as being polymorphic. Genetic analysis of these data clustered chickpea accessions based on geographical origin. Genotyping data generated for 671 CKAMs on the reference mapping population (Cicer arietinum ICC 4958 × Cicer reticulatum PI 489777) were compiled with 317 unpublished TOG-SNPs and 396 published markers for developing the genetic map. As a result, a second-generation genetic map comprising 1328 marker loci including novel 625 CKAMs, 314 TOG-SNPs and 389 published marker loci with an average inter-marker distance of 0.59 cM was constructed. Detailed analyses of 1064 mapped loci of this second-generation chickpea genetic map showed a higher degree of synteny with genome of Medicago truncatula, followed by Glycine max, Lotus japonicus and least with Vigna unguiculata. Development of these cost-effective CKAMs for SNP genotyping will be useful not only for genetics research and breeding applications in chickpea, but also for utilizing genome information from other sequenced or model legumes. PMID:22703242

  13. Large scale and synoptic features associated with extreme precipitation over South America: A review and case studies for the first decade of the 21st century

    NASA Astrophysics Data System (ADS)

    Cavalcanti, Iracema Fonseca Albuquerque

    2012-11-01

    Flooding or droughts over South America affect the population and several sectors of the economy such as agriculture, energy and transport. Floods occur due to extreme precipitation from mesoscale precipitating systems, which can often be embedded in synoptic systems that are influenced by large scale conditions that are in turn influenced by climate variability. Droughts are associated with lack of or reduced influence of these synoptic systems, and also affected by persistent large scale conditions. El Niño-Southern Oscillation episodes have been related to droughts in Amazonia and northeastern Brazil and flooding in southeastern South America. Other extreme cases have been associated with Atlantic sea surface temperature (SST) anomalies. Extreme cases also occur in association with tropical-extratropical interactions, through atmospheric circulation anomalies in both tropics and extratropics. In the present review, studies of precipitation extremes in South America and some examples of extreme precipitation in several regions of South America in the 21st century are shown, and a discussion of the associated mechanisms is included. The influences of tropical and extratropical large scale climate variability - such as the Pacific and Atlantic SST, the Pacific South America pattern, the Southern Hemisphere annular mode and features of the North Atlantic Oscillation - on extremes over South America are mentioned. Daily precipitation extremes over South America are often related to convective development within synoptic systems, such as frontal systems and the South Atlantic Convergence Zone, in the Southeastern Brazil. Intertropical Convergence Zone and easterly disturbances are the main systems in which convective development can occur related to precipitation extremes in Northeastern region. In La Plata basin, extremes are associated with highly organized convective systems originating in the lee of the Andes that propagate eastward.

  14. Integration of Technology, Curriculum, and Professional Development for Advancing Middle School Mathematics: Three Large-Scale Studies

    ERIC Educational Resources Information Center

    Roschelle, Jeremy; Shechtman, Nicole; Tatar, Deborah; Hegedus, Stephen; Hopkins, Bill; Empson, Susan; Knudsen, Jennifer; Gallagher, Lawrence P.

    2010-01-01

    The authors present three studies (two randomized controlled experiments and one embedded quasi-experiment) designed to evaluate the impact of replacement units targeting student learning of advanced middle school mathematics. The studies evaluated the SimCalc approach, which integrates an interactive representational technology, paper curriculum,…

  15. Implementing telemetry on new species in remote areas: Recommendations from a large-scale satellite tracking study of African waterfowl

    USGS Publications Warehouse

    Cappelle, J.; Iverson, S.A.; Takekawa, J.Y.; Newman, S.H.; Dodman, T.; Gaidet, N.

    2011-01-01

    We provide recommendations for implementing telemetry studies on waterfowl on the basis of our experience in a tracking study conducted in three countries of sub-Saharan Africa. The aim of the study was to document movements by duck species identified as priority candidates for the potential spread of avian influenza. Our study design included both captive and field test components on four wild duck species (Garganey, Comb Duck, White-faced Duck and Fulvous Duck). We used our location data to evaluate marking success and determine when signal loss occurred. The captive study of eight ducks marked with non-working transmitters in a zoo in Montpellier, France, prior to fieldwork showed no evidence of adverse effects, and the harness design appeared to work well. The field study in Malawi, Nigeria and Mali started in 2007 on 2 February, 6 February and 14 February, and ended on 22 November 2007 (288 d), 20 January 2010 (1 079 d), and 3 November 2008 (628 d), respectively. The field study indicated that 38 of 47 (81%) of the platform transmitter terminals (PTTs) kept transmitting after initial deployment, and the transmitters provided 15 576 locations. Signal loss during the field study was attributed to three main causes: PTT loss, PTT failure and mortality (natural, human-caused and PTT-related). The PTT signal quality varied by geographic region, and interference caused signal loss in the Mediterranean Sea region. We recommend careful attention at the beginning of the study to determine the optimum timing of transmitter deployment and the number of transmitters to be deployed per species. These sample sizes should be calculated by taking into account region-specific causes of signal loss to ensure research objectives are met. These recommendations should be useful for researchers undertaking a satellite tracking program, especially when working in remote areas of Africa where logistics are difficult or with poorly-known species. ?? NISC (Pty) Ltd.

  16. Large-scale development of cost-effective single-nucleotide polymorphism marker assays for genetic mapping in pigeonpea and comparative mapping in legumes.

    PubMed

    Saxena, Rachit K; Penmetsa, R Varma; Upadhyaya, Hari D; Kumar, Ashish; Carrasquilla-Garcia, Noelia; Schlueter, Jessica A; Farmer, Andrew; Whaley, Adam M; Sarma, Birinchi K; May, Gregory D; Cook, Douglas R; Varshney, Rajeev K

    2012-12-01

    Single-nucleotide polymorphisms (SNPs, >2000) were discovered by using RNA-seq and allele-specific sequencing approaches in pigeonpea (Cajanus cajan). For making the SNP genotyping cost-effective, successful competitive allele-specific polymerase chain reaction (KASPar) assays were developed for 1616 SNPs and referred to as PKAMs (pigeonpea KASPar assay markers). Screening of PKAMs on 24 genotypes [23 from cultivated species and 1 wild species (Cajanus scarabaeoides)] defined a set of 1154 polymorphic markers (77.4%) with a polymorphism information content (PIC) value from 0.04 to 0.38. One thousand and ninety-four PKAMs showed polymorphisms between parental lines of the reference mapping population (C. cajan ICP 28 × C. scarabaeoides ICPW 94). By using high-quality marker genotyping data on 167 F(2) lines from the population, a comprehensive genetic map comprising 875 PKAMs with an average inter-marker distance of 1.11 cM was developed. Previously mapped 35 simple sequence repeat markers were integrated into the PKAM map and an integrated genetic map of 996.21 cM was constructed. Mapped PKAMs showed a higher degree of synteny with the genome of Glycine max followed by Medicago truncatula and Lotus japonicus and least with Vigna unguiculata. These PKAMs will be useful for genetics research and breeding applications in pigeonpea and for utilizing genome information from other legume species. PMID:23103470

  17. Predicting Reading Difficulty in First Grade Using Dynamic Assessment of Decoding in Early Kindergarten: A Large-Scale Longitudinal Study

    ERIC Educational Resources Information Center

    Petersen, Douglas B.; Allen, Melissa M.; Spencer, Trina D.

    2016-01-01

    The purpose of this study was to examine and compare the classification accuracy of early static prereading measures and early dynamic assessment reading measures administered to 600 kindergarten students. At the beginning of kindergarten, all of the participants were administered two commonly used static prereading measures. The participants were…

  18. A large-scale, higher-level, molecular phylogenetic study of the insect order Lepidoptera (moths and butterflies)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Higher-level relationships within the Lepidoptera, and particularly within the species-rich subclade Ditrysia, are generally not well understood, although recent studies have yielded progress. 483 taxa spanning 115 of 124 families were sampled for 19 protein-coding nuclear genes. Their aligned nucle...

  19. Large-Scale Studies on the Transferability of General Problem-Solving Skills and the Pedagogic Potential of Physics

    ERIC Educational Resources Information Center

    Mashood, K. K.; Singh, Vijay A.

    2013-01-01

    Research suggests that problem-solving skills are transferable across domains. This claim, however, needs further empirical substantiation. We suggest correlation studies as a methodology for making preliminary inferences about transfer. The correlation of the physics performance of students with their performance in chemistry and mathematics in…

  20. A Systematic, Large-Scale Study of Synaesthesia: Implications for the Role of Early Experience in Lexical-Colour Associations

    ERIC Educational Resources Information Center

    Rich, A. N.; Bradshaw, J. L.; Mattingley, J. B.

    2005-01-01

    For individuals with synaesthesia, stimuli in one sensory modality elicit anomalous experiences in another modality. For example, the sound of a particular piano note may be "seen" as a unique colour, or the taste of a familiar food may be "felt" as a distinct bodily sensation. We report a study of 192 adult synaesthetes, in which we administered…

  1. Sparse conditional logistic regression for analyzing large-scale matched data from epidemiological studies: a simple algorithm

    PubMed Central

    2015-01-01

    This paper considers the problem of estimation and variable selection for large high-dimensional data (high number of predictors p and large sample size N, without excluding the possibility that N < p) resulting from an individually matched case-control study. We develop a simple algorithm for the adaptation of the Lasso and related methods to the conditional logistic regression model. Our proposal relies on the simplification of the calculations involved in the likelihood function. Then, the proposed algorithm iteratively solves reweighted Lasso problems using cyclical coordinate descent, computed along a regularization path. This method can handle large problems and deal with sparse features efficiently. We discuss benefits and drawbacks with respect to the existing available implementations. We also illustrate the interest and use of these techniques on a pharmacoepidemiological study of medication use and traffic safety. PMID:25916593

  2. Study of the Large-Scale Distribution of Gamma-Ray Burst Sources by the Method of Pairwise Distances

    NASA Astrophysics Data System (ADS)

    Gerasim, R. V.; Orlov, V. V.; Raikov, A. A.

    2015-06-01

    The method of pairwise distances developed earlier by the authors is used to study the spatial distribution of 352 sources of gamma-ray bursts with measured redshifts. Three cosmological models are considered: a model with a Euclidean metric, the "tired light" model, and the standard ΛCDM model. It is found that this set has fractal features and may be multifractal. The fractal dimensionalities are estimated.

  3. Study and enhancement of large-scale exact-diagonalization for strongly correlated systems on emerging hybrid architectures

    NASA Astrophysics Data System (ADS)

    Thakur, Bhupender; Tam, Ka-Ming; Ragavan, Kaushik; Jarrell, Mark; Moreno, Juana

    2012-02-01

    Exact diagonalization(ED) provides a powerful machinery for the study of many strongly correlated systems, in which other methods fail to provide unbiased results. In addition, the ED method has also been employed as a cluster solver for dynamical mean field approaches. The two main obstacles for the ED are the storage of the basis vector and the computationally intensive matrix-vector multiplication. With the Graphics Processing Unit (GPU) platform becoming more widely accessible, the challenge now is to effectively scale the ED method to use hybrid CPU-GPU node topology, which is fast becoming the default route to exascale computing. The goal of this study is to develop a highly scalable and efficient implementation of the ED method on this next generation infrastructure, via GPU accelerated modules. We compare the performance of our implementation with that of the conventional CPU implementation via the study of the Hubbard-Anderson model, where Quantum Monte Carlo method suffers from severe minus sign problem.

  4. An evaluation of two large scale demand side financing programs for maternal health in India: the MATIND study protocol

    PubMed Central

    2012-01-01

    Background High maternal mortality in India is a serious public health challenge. Demand side financing interventions have emerged as a strategy to promote access to emergency obstetric care. Two such state run programs, Janani Suraksha Yojana (JSY)and Chiranjeevi Yojana (CY), were designed and implemented to reduce financial access barriers that preclude women from obtaining emergency obstetric care. JSY, a conditional cash transfer, awards money directly to a woman who delivers in a public health facility. This will be studied in Madhya Pradesh province. CY, a voucher based program, empanels private obstetricians in Gujarat province, who are reimbursed by the government to perform deliveries of socioeconomically disadvantaged women. The programs have been in operation for the last seven years. Methods/designs The study outlined in this protocol will assess and compare the influence of the two programs on various aspects of maternal health care including trends in program uptake, institutional delivery rates, maternal and neonatal outcomes, quality of care, experiences of service providers and users, and cost effectiveness. The study will collect primary data using a combination of qualitative and quantitative methods, including facility level questionnaires, observations, a population based survey, in-depth interviews, and focus group discussions. Primary data will be collected in three districts of each province. The research will take place at three levels: the state health departments, obstetric facilities in the districts and among recently delivered mothers in the community. Discussion The protocol is a comprehensive assessment of the performance and impact of the programs and an economic analysis. It will fill existing evidence gaps in the scientific literature including access and quality to services, utilization, coverage and impact. The implementation of the protocol will also generate evidence to facilitate decision making among policy makers and

  5. Distinct severity stages of obstructive sleep apnoea are correlated with unique dyslipidaemia: large-scale observational study

    PubMed Central

    Guan, Jian; Yi, Hongliang; Zou, Jianyin; Meng, Lili; Tang, Xulan; Zhu, Huaming; Yu, Dongzhen; Zhou, Huiqun; Su, Kaiming; Yang, Mingpo; Chen, Haoyan; Shi, Yongyong; Wang, Yue; Wang, Jian; Yin, Shankai

    2016-01-01

    Background Dyslipidaemia is an intermediary exacerbation factor for various diseases but the impact of obstructive sleep apnoea (OSA) on dyslipidaemia remains unclear. Methods A total of 3582 subjects with suspected OSA consecutively admitted to our hospital sleep centre were screened and 2983 (2422 with OSA) were included in the Shanghai Sleep Health Study. OSA severity was quantified using the apnoea–hypopnea index (AHI), the oxygen desaturation index and the arousal index. Biochemical indicators and anthropometric data were also collected. The relationship between OSA severity and the risk of dyslipidaemia was evaluated via ordinal logistic regression, restricted cubic spline (RCS) analysis and multivariate linear regressions. Results The RCS mapped a nonlinear dose–effect relationship between the risk of dyslipidaemia and OSA severity, and yielded knots of the AHI (9.4, 28.2, 54.4 and 80.2). After integrating the clinical definition and RCS-selected knots, all subjects were regrouped into four AHI severity stages. Following segmented multivariate linear modelling of each stage, distinguishable sets of OSA risk factors were quantified: low-density lipoprotein cholesterol (LDL-C), apolipoprotein E and high-density lipoprotein cholesterol (HDL-C); body mass index and/or waist to hip ratio; and HDL-C, LDL-C and triglycerides were specifically associated with stage I, stages II and III, and stages II–IV with different OSA indices. Conclusions Our study revealed the multistage and non-monotonic relationships between OSA and dyslipidaemia and quantified the relationships between OSA severity indexes and distinct risk factors for specific OSA severity stages. Our study suggests that a new interpretive and predictive strategy for dynamic assessment of the risk progression over the clinical course of OSA should be adopted. PMID:26883674

  6. The project De Caldas International Project: An example of a large-scale radwaste isolation natural analogue study

    SciTech Connect

    Shea, M.

    1995-09-01

    The proper isolation of radioactive waste is one of today`s most pressing environmental issues. Research is being carried out by many countries around the world in order to answer critical and perplexing questions regarding the safe disposal of radioactive waste. Natural analogue studies are an increasingly important facet of this international research effort. The Pocos de Caldas Project represents a major effort of the international technical and scientific community towards addressing one of modern civilization`s most critical environmental issues - radioactive waste isolation.

  7. On the consistency of personality types across adulthood: latent profile analyses in two large-scale panel studies.

    PubMed

    Specht, Jule; Luhmann, Maike; Geiser, Christian

    2014-09-01

    Consistency and change in personality were analyzed by examining personality types across adulthood and old age using data from 2 nationally representative panel studies from Germany (N = 14,718; 16-82 years) and Australia (N = 8,315; 15-79 years). In both samples, the Big Five personality traits were measured twice across a period of 4 years. Latent profile analyses and latent profile transition analyses revealed 4 main findings: First, solutions with 3 (in the German sample) or 4 (in the Australian sample) personality types were found to be most interpretable. Second, measurement invariance tests revealed that these personality types were consistent across all age groups but differed slightly between men and women. Third, age was related to the number of individuals classified within each personality type. Namely, there were more resilients and fewer undercontrollers in older compared with younger age groups. Fourth, there was strong consistency of personality type membership across a period of 4 years in both genders and most age cohorts. Comparatively less consistency across time was found for undercontrollers and individuals in old age. Taken together, these findings show that in the 2 nations studied here, personality types were highly consistent across gender, age, and time. PMID:25133730

  8. Study of mean- and turbulent-velocity fields in a large-scale turbine-vane passage

    NASA Technical Reports Server (NTRS)

    Bailey, D. A.

    1979-01-01

    Laser-Doppler velocimetry, and to a lesser extent hot-wire anemometry, were employed to measure three components of the mean velocity and the six turbulent stresses at four planes within the turbine inlet-guide-vane passage. One variation in the turbulent inlet boundary layer thickness and one variation in the blade aspect ratio (span/axial chord) were studied. A longitudinal vortex (passage vortex) was clearly identified in the exit plane of the passage for the three test cases. The maximum turbulence intensities within the longitudinal vortex were found to be on the order of 2 to 4 percent, with large regions appearing nonturbulent. Because a turbulent wall boundary layer was the source of vorticity that produced the passage vortex, these low turbulence levels were not anticipated. For the three test cases studied, the lateral velocity field extended significantly beyond the region of the longitudinal velocity defect. Changing the inlet boundary layer thickness produced a difference in the location, the strength, and the extent of the passage vortex. Changing the aspect ratio of the blade passage had a measurable but less significant effect. The experiment was performed in a 210 mm pitch, 272 mm axial chord model in low speed wind tunnel at an inlet Mach number of 0.07.

  9. Applications of MALDI-TOF MS to large-scale human mtDNA population-based studies.

    PubMed

    Cerezo, María; Cerný, Viktor; Carracedo, Angel; Salas, Antonio

    2009-11-01

    Analysis of the mitochondrial DNA variation in populations is commonly carried out in many fields of biomedical research. We propose the analysis of mitochondrial DNA coding region SNP (mtSNP) variation to a high level of phylogenetic resolution based on MALDI-TOF MS. The African phylogeny has been chosen to test the applicability of the technique but any other part of the worldwide phylogeny (or any other mtSNP panel) could be equally suitable for MALDI-TOF MS genotyping. SNP selection thus aimed to fully cover all the mtSNPs defining major and minor branches of the known African tree, including, macro-haplogroup L, and haplogroups M1, and U6. A total of 230 mtSNPs were finally selected. We used tests samples collected from two different African locations, namely, Mozambique and Chad Basin. Different internal genotyping controls and other indirect approaches (e.g. phylogenetic checking coupled with automatic sequencing) were used in order to evaluate the reproducibility of the technique, which resulted to be 100% using samples previously subjected to whole genome amplification. The advantages of the MALDI-TOF MS are also discussed in comparison with other popular methods such as minisequencing, highlighting its high-throughput nature, which is particularly suitable for case-control medical studies, forensic databasing or population and anthropological studies. PMID:19862743

  10. A Study of Parameters of the Counterpropagating Leader and its Influence on the Lightning Protection of Objects Using Large-Scale Laboratory Modeling

    NASA Astrophysics Data System (ADS)

    Syssoev, V. S.; Kostinskiy, A. Yu.; Makalskiy, L. M.; Rakov, A. V.; Andreev, M. G.; Bulatov, M. U.; Sukharevsky, D. I.; Naumova, M. U.

    2014-04-01

    In this work, the results of experiments on initiating the upward and descending leaders during the development of a long spark when studying lightning protection of objects with the help of large-scale models are shown. The influence of the counterpropagating leaders on the process of the lightning strike of ground-based and insulated objects is discussed. In the first case, the upward negative leader is initiated by the positive downward leader, which propagates from the high-voltage electrode of the "rod-rod"-type Marx generator (the rod is located on the plane and is 3-m high) in the gap with a length of 9-12 m. The positive-voltage pulse with a duration of 7500 μs had an amplitude of up to 3 MV. In the second case, initiation of the positive upward leader was performed in the electric field created by a cloud of negatively charged aerosol, which simulates the charged thunderstorm cell. In this case, all the phases characteristic of the ascending lightnings initiated by the tall ground-based objects and the triggered lightnings during the experiments with an actual thunderstorm cloud were observed in the forming spark discharge with a length of 1.5-2.0 m. The main parameters of the counterpropagating leader, which is initiated by the objects during the large-scale model experiments with a long spark, are shown.

  11. A comparative study of the growth of Tetraselmis sp. in large scale fixed depth and decreasing depth raceway ponds.

    PubMed

    Das, Probir; Thaher, Mahmoud Ibrahim; Hakim, Mohammed Abdul Quadir Mohd Abdul; Al-Jabri, Hareb Mohammed S J; Alghasal, Ghamza Saed H S

    2016-09-01

    In this study, an alternative approach was proposed where excess seawater would be added only during inoculation (DD) rather than daily addition (FD). Growth and metabolite contents of Tetraselmis sp. weren't affected for daily increase of 2% NaCl salinity. Tetraselmis sp. was then cultured in DD and FD pond. In DD pond, initial culture depth was 23.5cm and its depth reduced as no water was added; for FD pond, everyday sterilized seawater was added to maintain 20cm depth. DD pond had higher biomass productivity compared to FD pond, until DD pond was deeper than FD pond; metabolite content and FAME profile of Tetraselmis sp. were also similar in both cultures. Therefore, considering the simplicity in operation, halo tolerant microalgae can be grown in DD pond method. PMID:27235973

  12. Managing and analysing data from a large-scale study on Framingham Offspring relating brain structure to cognitive function.

    PubMed

    Massaro, Joseph M; D'Agostino, Ralph B; Sullivan, Lisa M; Beiser, Alexa; DeCarli, Charles; Au, Rhoda; Elias, Merrill F; Wolf, Philip A

    2004-01-30

    At the Framingham Heart Study under separate research grant funding from the National Institute of Aging, NIH, we are gathering brain structure and cognitive information on the Framingham Offspring, creating one of the largest known data sets to assess changes in brain structure associated with normative ageing and cognitive decline. Subject recruitment, data collection, data management and statistical analysis require a collaborative integrated effort on the part of the Framingham project team. Here we describe this effort, as well as the various brain structure and cognitive function parameters we are now collecting. We are currently performing analyses of data collected through 2002, and we discuss the statistical issues arising relating brain structure parameters to cognitive function. PMID:14716734

  13. An Integrated Approach for the Large-Scale Simulation of Sedimentary Basins to Study Seismic Wave Amplification

    NASA Astrophysics Data System (ADS)

    Poursartip, B.

    2015-12-01

    Seismic hazard assessment to predict the behavior of infrastructures subjected to earthquake relies on ground motion numerical simulation because the analytical solution of seismic waves is limited to only a few simple geometries. Recent advances in numerical methods and computer architectures make it ever more practical to reliably and quickly obtain the near-surface response to seismic events. The key motivation stems from the need to access the performance of sensitive components of the civil infrastructure (nuclear power plants, bridges, lifelines, etc), when subjected to realistic scenarios of seismic events. We discuss an integrated approach that deploys best-practice tools for simulating seismic events in arbitrarily heterogeneous formations, while also accounting for topography. Specifically, we describe an explicit forward wave solver based on a hybrid formulation that couples a single-field formulation for the computational domain with an unsplit mixed-field formulation for Perfectly-Matched-Layers (PMLs and/or M-PMLs) used to limit the computational domain. Due to the material heterogeneity and the contrasting discretization needs it imposes, an adaptive time solver is adopted. We use a Runge-Kutta-Fehlberg time-marching scheme that adjusts optimally the time step such that the local truncation error rests below a predefined tolerance. We use spectral elements for spatial discretization, and the Domain Reduction Method in accordance with double couple method to allow for the efficient prescription of the input seismic motion. Of particular interest to this development is the study of the effects idealized topographic features have on the surface motion when compared against motion results that are based on a flat-surface assumption. We discuss the components of the integrated approach we followed, and report the results of parametric studies in two and three dimensions, for various idealized topographic features, which show motion amplification that

  14. Risk of Retinal Artery Occlusion in Patients With End-Stage Renal Disease: A Retrospective Large-Scale Cohort Study.

    PubMed

    Chang, Yuh-Shin; Weng, Shih-Feng; Chang, Chun; Wang, Jhi-Joung; Tseng, Sung-Huei; Ko, Shun-Yao; Su, Shih-Bin; Huang, Chien-Cheng; Wang, Jiu-Yao; Jan, Ren-Long

    2016-04-01

    There is globally increasing prevalence and incidence in end-stage renal disease (ESRD). These patients are frequently reported to have retinal abnormalities and both diseases share some systemic risk factors. Hence, it is clinically relevant to determine whether ESRD is a predictor of retinal artery occlusion (RAO).To investigate the risk of RAO in ESRD patients.A retrospective, nationwide, matched cohort study. The study included 93,766 ESRD patients recruited between 2000 and 2009 from the Taiwan National Health Insurance Research Database. The same number control group included age- and sex-matched patients without ESRD selected from the Taiwan Longitudinal Health Insurance Database, 2000. Data for each patient were collected from the index date until December 2011.The incidence and risk of RAO were compared between the 2 groups. The hazard ratio (HR) for RAO after adjustment for potential confounders was calculated using Cox proportional hazards regression. Kaplan-Meier analysis was used to calculate the cumulative RAO incidence rate.In total, 237 ESRD patients and 73 controls exhibited RAO during follow-up; thus, the RAO incidence rate in ESRD patients was 4.49 times (95% confidence interval (CI), 3.45-5.83) that in the control patients. After adjustment for potential confounders, including diabetes mellitus, hypertension, hyperlipidemia, congestive heart failure, and coronary artery disease, ESRD patients were 2.78 times (95% CI, 2.02-3.84) more likely to develop RAO in cohort for the total sample. Among patients with hypertension, the RAO incidence rate was significantly higher in the ESRD group, and hypertension significantly increased RAO risk even after adjustment for other confounders in the cohort.ESRD increases the risk of RAO, particularly in ESRD patients with hypertension. Therefore, clinicians should educate ESRD patients about RAO and ensure appropriate blood pressure control. PMID:27057891

  15. Associations between sleep disturbance and alcohol drinking: A large-scale epidemiological study of adolescents in Japan.

    PubMed

    Morioka, Hisayoshi; Itani, Osamu; Kaneita, Yoshitaka; Ikeda, Maki; Kondo, Shuji; Yamamoto, Ryuichiro; Osaki, Yoneatsu; Kanda, Hideyuki; Higuchi, Susumu; Ohida, Takashi

    2013-12-01

    In this study, we attempted to clarify the associations between various sleep disturbance symptoms and the frequency and amount of alcohol use among Japanese adolescents. This study was designed as a cross-sectional sampling survey. A self-administered questionnaire survey was administered to students enrolled in randomly selected junior and senior high schools throughout Japan. A total of 99,416 adolescents responded, and 98,867 questionnaires were subjected to analysis. The prevalence rates of sleep disturbance in the 30 days preceding the day of the survey were as follows: subjectively insufficient sleep (SIS) (boys: 37.6%, girls: 38.7%); short sleep duration (SSD) with less than 6 h of sleep (boys: 28.0%, girls: 33.0%); difficulty initiating sleep (DIS) (boys: 12.5%, girls: 14.1%); difficulty maintaining sleep (DMS) (boys: 10.1%, girls: 10.9%); and early morning awakening (EMA) (boys: 5.1%, girls: 5.0%). Adolescents reporting one or more symptoms of DIS, DMS, and EMA were classified as having insomnia, and its prevalence was 21.5%. The prevalence of each symptom of sleep disturbance increased significantly with the number of days on which alcohol was consumed in the previous 30 days and the amount of alcohol consumed per drinking session (p < 0.01). Multiple logistic regression analyses showed that the adjusted odds ratio (AOR) for each symptom of sleep disturbance, except SIS and EMA, tended to increase with the number of days on which alcohol was consumed and the amount of alcohol consumed per drinking session. The prevalence of sleep disturbance is particularly high among adolescents drinking alcohol. The risk of having each symptom of sleep disturbance, except SIS and EMA, increases with the number of days on which alcohol was consumed and the amount of alcohol consumed per drinking session. These findings reconfirm the need to eliminate underage drinking to ensure good sleep among adolescents. PMID:24188738

  16. A Large-Scale, Higher-Level, Molecular Phylogenetic Study of the Insect Order Lepidoptera (Moths and Butterflies)

    PubMed Central

    Regier, Jerome C.; Mitter, Charles; Zwick, Andreas; Bazinet, Adam L.; Cummings, Michael P.; Kawahara, Akito Y.; Sohn, Jae-Cheon; Zwickl, Derrick J.; Cho, Soowon; Davis, Donald R.; Baixeras, Joaquin; Brown, John; Parr, Cynthia; Weller, Susan; Lees, David C.; Mitter, Kim T.

    2013-01-01

    Background Higher-level relationships within the Lepidoptera, and particularly within the species-rich subclade Ditrysia, are generally not well understood, although recent studies have yielded progress. We present the most comprehensive molecular analysis of lepidopteran phylogeny to date, focusing on relationships among superfamilies. Methodology / Principal Findings 483 taxa spanning 115 of 124 families were sampled for 19 protein-coding nuclear genes, from which maximum likelihood tree estimates and bootstrap percentages were obtained using GARLI. Assessment of heuristic search effectiveness showed that better trees and higher bootstrap percentages probably remain to be discovered even after 1000 or more search replicates, but further search proved impractical even with grid computing. Other analyses explored the effects of sampling nonsynonymous change only versus partitioned and unpartitioned total nucleotide change; deletion of rogue taxa; and compositional heterogeneity. Relationships among the non-ditrysian lineages previously inferred from morphology were largely confirmed, plus some new ones, with strong support. Robust support was also found for divergences among non-apoditrysian lineages of Ditrysia, but only rarely so within Apoditrysia. Paraphyly for Tineoidea is strongly supported by analysis of nonsynonymous-only signal; conflicting, strong support for tineoid monophyly when synonymous signal was added back is shown to result from compositional heterogeneity. Conclusions / Significance Support for among-superfamily relationships outside the Apoditrysia is now generally strong. Comparable support is mostly lacking within Apoditrysia, but dramatically increased bootstrap percentages for some nodes after rogue taxon removal, and concordance with other evidence, strongly suggest that our picture of apoditrysian phylogeny is approximately correct. This study highlights the challenge of finding optimal topologies when analyzing hundreds of taxa. It also

  17. Multiserotype Enzyme-Linked Immunosorbent Assay as a Diagnostic Aid for Periodontitis in Large-Scale Studies

    PubMed Central

    Pussinen, P. J.; Vilkuna-Rautiainen, T.; Alfthan, G.; Mattila, K.; Asikainen, S.

    2002-01-01

    Periodontitis is a common chronic oral infection caused by gram-negative bacteria, including Actinobacillus actinomycetemcomitans and Porphyromonas gingivalis. Periodontitis evokes inflammatory host response locally in the periodontium but also systemically. The systemic humoral antibody response against oral pathogens can conveniently be measured by an immunoassay. The aim of the study was to measure serum immunoglobulin G class antibodies against A. actinomycetemcomitans and P. gingivalis by an enzyme-linked immunosorbent assay (ELISA) in which mixtures of several serotypes of the pathogens were used as antigens to avoid biasing of the results in favor of a particular strain. For A. actinomycetemcomitans the antigen consisted of six strains representing serotypes a, b, c, d, and e and one nonserotypeable strain. In the P. gingivalis ELISA, antigens representing serotypes a, b, and c were used. Serum samples from 90 subjects, including 35 samples from patients with diagnosed periodontitis, 10 samples from periodontally healthy controls, and 45 samples from randomly selected apparently healthy volunteers (referred to as “healthy subjects”), were tested. For both pathogens the antibody levels (means ± standard deviations) of the patients—expressed as area under the dilution curve—were significantly higher than those for healthy controls or healthy subjects, with values for A. actinomycetemcomitans and P. gingivalis, respectively, as follows: patients, 22.60 ± 9.94 mm2 and 26.72 ± 11.13 mm2; healthy controls, 9.99 ± 3.92 mm2 and 6.90 ± 3.38 mm2; and healthy subjects, 16.85 ± 6.67 mm2 and 8.51 ± 4.23 mm2. The serotype mixture ELISA is suitable for measuring antibodies against periodontal pathogens in large epidemiological studies in order to evaluate the role of periodontitis as a risk factor for other diseases. PMID:11825965

  18. In vitro large-scale experimental and theoretical studies for the realization of bi-directional brain-prostheses

    PubMed Central

    Bonifazi, Paolo; Difato, Francesco; Massobrio, Paolo; Breschi, Gian L.; Pasquale, Valentina; Levi, Timothée; Goldin, Miri; Bornat, Yannick; Tedesco, Mariateresa; Bisio, Marta; Kanner, Sivan; Galron, Ronit; Tessadori, Jacopo; Taverna, Stefano; Chiappalone, Michela

    2013-01-01

    Brain-machine interfaces (BMI) were born to control “actions from thoughts” in order to recover motor capability of patients with impaired functional connectivity between the central and peripheral nervous system. The final goal of our studies is the development of a new proof-of-concept BMI—a neuromorphic chip for brain repair—to reproduce the functional organization of a damaged part of the central nervous system. To reach this ambitious goal, we implemented a multidisciplinary “bottom-up” approach in which in vitro networks are the paradigm for the development of an in silico model to be incorporated into a neuromorphic device. In this paper we present the overall strategy and focus on the different building blocks of our studies: (i) the experimental characterization and modeling of “finite size networks” which represent the smallest and most general self-organized circuits capable of generating spontaneous collective dynamics; (ii) the induction of lesions in neuronal networks and the whole brain preparation with special attention on the impact on the functional organization of the circuits; (iii) the first production of a neuromorphic chip able to implement a real-time model of neuronal networks. A dynamical characterization of the finite size circuits with single cell resolution is provided. A neural network model based on Izhikevich neurons was able to replicate the experimental observations. Changes in the dynamics of the neuronal circuits induced by optical and ischemic lesions are presented respectively for in vitro neuronal networks and for a whole brain preparation. Finally the implementation of a neuromorphic chip reproducing the network dynamics in quasi-real time (10 ns precision) is presented. PMID:23503997

  19. MOBE-ChIP: a large-scale chromatin immunoprecipitation assay for cell type-specific studies.

    PubMed

    Lau, On Sun; Bergmann, Dominique C

    2015-10-01

    Cell type-specific transcriptional regulators play critical roles in the generation and maintenance of multicellularity. As they are often expressed at low levels, in vivo DNA-binding studies of these regulators by standard chromatin immunoprecipitation (ChIP) assays are technically challenging. We describe here an optimized ChIP protocol termed Maximized Objects for Better Enrichment (MOBE)-ChIP, which enhances the sensitivity of ChIP assays for detecting cell type-specific signals. The protocol, which is based on the disproportional increase of target signals over background at higher scales, uses substantially greater volume of starting materials than conventional ChIPs to achieve high signal enrichment. This technique can capture weak binding events that are ambiguous in standard ChIP assays, and is useful both in gene-specific and whole-genome analysis. This protocol has been optimized for Arabidopsis, but should be applicable to other model systems with minor modifications. The full procedure can be completed within 3 days. PMID:26332947

  20. Compact Wireless Microscope for In-Situ Time Course Study of Large Scale Cell Dynamics within an Incubator

    PubMed Central

    Jin, Di; Wong, Dennis; Li, Junxiang; Luo, Zhang; Guo, Yiran; Liu, Bifeng; Wu, Qiong; Ho, Chih-Ming; Fei, Peng

    2015-01-01

    Imaging of live cells in a region of interest is essential to life science research. Unlike the traditional way that mounts CO2 incubator onto a bulky microscope for observation, here we propose a wireless microscope (termed w-SCOPE) that is based on the “microscope-in-incubator” concept and can be easily housed into a standard CO2 incubator for prolonged on-site observation of the cells. The w-SCOPE is capable of tunable magnification, remote control and wireless image transmission. At the same time, it is compact, measuring only ~10 cm in each dimension, and cost-effective. With the enhancement of compressive sensing computation, the acquired images can achieve a wide field of view (FOV) of ~113 mm2 as well as a cellular resolution of ~3 μm, which enables various forms of follow-up image-based cell analysis. We performed 12 hours time-lapse study on paclitaxel-treated MCF-7 and HEK293T cell lines using w-SCOPE. The analytic results, such as the calculated viability and therapeutic window, from our device were validated by standard cell detection assays and imaging-based cytometer. In addition to those end-point detection methods, w-SCOPE further uncovered the time course of the cell’s response to the drug treatment over the whole period of drug exposure. PMID:26681552

  1. Development of design and simulation model and safety study of large-scale hydrogen production using nuclear power.

    SciTech Connect

    Gelbard, Fred; Oh, Seungmin; Rodriguez, Salvador B.; Revankar, Shripad T.; Gauntt, Randall O.; Cole, Randall K., Jr.; Espinosa, Flor; Drennen, Thomas E.; Tournier, Jean-Michel; Hogan, Kevin; Archuleta, Louis; Malczynski, Leonard A.; Vierow, Karen; McFadden, Katherine Letizia; Martin, William Joseph; El-Genk, Mohamed S.; Louie, David L. Y.

    2007-10-01

    Before this LDRD research, no single tool could simulate a very high temperature reactor (VHTR) that is coupled to a secondary system and the sulfur iodine (SI) thermochemistry. Furthermore, the SI chemistry could only be modeled in steady state, typically via flow sheets. Additionally, the MELCOR nuclear reactor analysis code was suitable only for the modeling of light water reactors, not gas-cooled reactors. We extended MELCOR in order to address the above deficiencies. In particular, we developed three VHTR input models, added generalized, modular secondary system components, developed reactor point kinetics, included transient thermochemistry for the most important cycles [SI and the Westinghouse hybrid sulfur], and developed an interactive graphical user interface for full plant visualization. The new tool is called MELCOR-H2, and it allows users to maximize hydrogen and electrical production, as well as enhance overall plant safety. We conducted validation and verification studies on the key models, and showed that the MELCOR-H2 results typically compared to within less than 5% from experimental data, code-to-code comparisons, and/or analytical solutions.

  2. Compact Wireless Microscope for In-Situ Time Course Study of Large Scale Cell Dynamics within an Incubator.

    PubMed

    Jin, Di; Wong, Dennis; Li, Junxiang; Luo, Zhang; Guo, Yiran; Liu, Bifeng; Wu, Qiong; Ho, Chih-Ming; Fei, Peng

    2015-01-01

    Imaging of live cells in a region of interest is essential to life science research. Unlike the traditional way that mounts CO2 incubator onto a bulky microscope for observation, here we propose a wireless microscope (termed w-SCOPE) that is based on the "microscope-in-incubator" concept and can be easily housed into a standard CO2 incubator for prolonged on-site observation of the cells. The w-SCOPE is capable of tunable magnification, remote control and wireless image transmission. At the same time, it is compact, measuring only ~10 cm in each dimension, and cost-effective. With the enhancement of compressive sensing computation, the acquired images can achieve a wide field of view (FOV) of ~113 mm(2) as well as a cellular resolution of ~3 μm, which enables various forms of follow-up image-based cell analysis. We performed 12 hours time-lapse study on paclitaxel-treated MCF-7 and HEK293T cell lines using w-SCOPE. The analytic results, such as the calculated viability and therapeutic window, from our device were validated by standard cell detection assays and imaging-based cytometer. In addition to those end-point detection methods, w-SCOPE further uncovered the time course of the cell's response to the drug treatment over the whole period of drug exposure. PMID:26681552

  3. Coding task performance in early adolescence: a large-scale controlled study into boy-girl differences

    PubMed Central

    Dekker, Sanne; Krabbendam, Lydia; Aben, Aukje; de Groot, Renate; Jolles, Jelle

    2013-01-01

    This study examined differences between boys and girls regarding efficiency of information processing in early adolescence. Three hundred and six healthy adolescents (50.3% boys) in grade 7 and 9 (aged 13 and 15, respectively) performed a coding task based on over-learned symbols. An age effect was revealed as subjects in grade 9 performed better than subjects in grade 7. Main effects for sex were found in the advantage of girls. The 25% best-performing students comprised twice as many girls as boys. The opposite pattern was found for the worst performing 25%. In addition, a main effect was found for educational track in favor of the highest track. No interaction effects were found. School grades did not explain additional variance in LDST performance. This indicates that cognitive performance is relatively independent from school performance. Student characteristics like age, sex, and education level were more important for efficiency of information processing than school performance. The findings imply that after age 13, efficiency of information processing is still developing and that girls outperform boys in this respect. The findings provide new information on the mechanisms underlying boy-girl differences in scholastic performance. PMID:23986733

  4. Compact Wireless Microscope for In-Situ Time Course Study of Large Scale Cell Dynamics within an Incubator

    NASA Astrophysics Data System (ADS)

    Jin, Di; Wong, Dennis; Li, Junxiang; Luo, Zhang; Guo, Yiran; Liu, Bifeng; Wu, Qiong; Ho, Chih-Ming; Fei, Peng

    2015-12-01

    Imaging of live cells in a region of interest is essential to life science research. Unlike the traditional way that mounts CO2 incubator onto a bulky microscope for observation, here we propose a wireless microscope (termed w-SCOPE) that is based on the “microscope-in-incubator” concept and can be easily housed into a standard CO2 incubator for prolonged on-site observation of the cells. The w-SCOPE is capable of tunable magnification, remote control and wireless image transmission. At the same time, it is compact, measuring only ~10 cm in each dimension, and cost-effective. With the enhancement of compressive sensing computation, the acquired images can achieve a wide field of view (FOV) of ~113 mm2 as well as a cellular resolution of ~3 μm, which enables various forms of follow-up image-based cell analysis. We performed 12 hours time-lapse study on paclitaxel-treated MCF-7 and HEK293T cell lines using w-SCOPE. The analytic results, such as the calculated viability and therapeutic window, from our device were validated by standard cell detection assays and imaging-based cytometer. In addition to those end-point detection methods, w-SCOPE further uncovered the time course of the cell’s response to the drug treatment over the whole period of drug exposure.

  5. A study of large scale gust generation in a small scale atmospheric wind tunnel with applications to Micro Aerial Vehicles

    NASA Astrophysics Data System (ADS)

    Roadman, Jason Markos

    Modern technology operating in the atmospheric boundary layer can always benefit from more accurate wind tunnel testing. While scaled atmospheric boundary layer tunnels have been well developed, tunnels replicating portions of the atmospheric boundary layer turbulence at full scale are a comparatively new concept. Testing at full-scale Reynolds numbers with full-scale turbulence in an "atmospheric wind tunnel" is sought. Many programs could utilize such a tool including Micro Aerial Vehicle(MAV) development, the wind energy industry, fuel efficient vehicle design, and the study of bird and insect flight, to name just a few. The small scale of MAVs provide the somewhat unique capability of full scale Reynolds number testing in a wind tunnel. However, that same small scale creates interactions under real world flight conditions, atmospheric gusts for example, that lead to a need for testing under more complex flows than the standard uniform flow found in most wind tunnels. It is for these reasons that MAVs are used as the initial testing application for the atmospheric gust tunnel. An analytical model for both discrete gusts and a continuous spectrum of gusts is examined. Then, methods for generating gusts in agreement with that model are investigated. Previously used methods are reviewed and a gust generation apparatus is designed. Expected turbulence and gust characteristics of this apparatus are compared with atmospheric data. The construction of an active "gust generator" for a new atmospheric tunnel is reviewed and the turbulence it generates is measured utilizing single and cross hot wires. Results from this grid are compared to atmospheric turbulence and it is shown that various gust strengths can be produced corresponding to weather ranging from calm to quite gusty. An initial test is performed in the atmospheric wind tunnel whereby the effects of various turbulence conditions on transition and separation on the upper surface of a MAV wing is investigated

  6. Thermal-hydrological analysis of large-scale thermal tests in the exploratory studies facility at Yucca Mountain

    SciTech Connect

    Buscheck, T.A.; Nitao, J.J.

    1996-02-20

    In situ thermal tests, which are to be conducted in the Exploratory Studies Facility (ESF) at Yucca Mountain, will provide a major portion of the experimental basis supporting the validation of coupled thermal-hydrological-geomechanical-geochemicaI (T-H-M-C) process models required to assess the total system performance at the site. With respect to advective rock dryout, we have identified three major T-H flow regimes: (1) throttled, nonbuoyant, advective rock dryout; (2) unthrottled, nonbuoyant, advective rock dryout; and (3) unthrottled, buoyant, advective rock dryout. With the V-TOUGH code, we modeled a range of heater test sizes, heating rates, and heating durations under a range of plausible hydrological conditions to help optimize an in situ thermal test design that provides sufficient information for determining (a) the dominant mode(s) of heat flow, (b) the major T-H regime(s) and processes (such as vapor diffusion) that govern the magnitude and direction of vapor and condensate flow, and (c) the influence of heterogeneous properties and conditions on the flow of heat, vapor, and condensate. For the plate thermal test, which uniformly heats a disk-shaped area, we evaluated a wide range of test areas, ranging from 50 to 5077 m{sup 2}. We evaluated the single-drift thermal test, which consists of a row of large-waste-package-sized heaters sitting on the floor of the heater drift, and then developed an optimized thermal test configuration, called the single-drift, winged thermal test, in which the heater drift is flanked by wing heater arrays. For this configuration, we considered three heating schedules (with 1-, 2-, and 4-yr full-power heating periods) and three heating rates (122, 177, and 236 W/m{sup 2}). For determining the dominant T-H regime(s) and dominant heat-flow mode(s), the most important diagnostic measurements are vertical temperature and gas-phase pressure profiles and gas-phase pressure and relative humidity RH histories in the drift.

  7. Synchronization of coupled large-scale Boolean networks

    SciTech Connect

    Li, Fangfei

    2014-03-15

    This paper investigates the complete synchronization and partial synchronization of two large-scale Boolean networks. First, the aggregation algorithm towards large-scale Boolean network is reviewed. Second, the aggregation algorithm is applied to study the complete synchronization and partial synchronization of large-scale Boolean networks. Finally, an illustrative example is presented to show the efficiency of the proposed results.

  8. Generating Large-Scale Longitudinal Data Resources for Aging Research

    PubMed Central

    Hofer, Scott M.

    2011-01-01

    Objectives. The need for large studies and the types of large-scale data resources (LSDRs) are discussed along with their general scientific utility, role in aging research, and affordability. The diversification of approaches to large-scale data resourcing is described in order to facilitate their use in aging research. Methods. The need for LSDRs is discussed in terms of (a) large sample size; (b) longitudinal design; (c) as platforms for additional investigator-initiated research projects; and (d) broad-based access to core genetic, biological, and phenotypic data. Discussion. It is concluded that a “lite-touch, lo-tech, lo-cost” approach to LSDRs is a viable strategy for the development of LSDRs and would enhance the likelihood of LSDRs being established which are dedicated to the wide range of important aging-related issues. PMID:21743049

  9. Large-scale objective phenotyping of 3D facial morphology

    PubMed Central

    Hammond, Peter; Suttie, Michael

    2012-01-01

    Abnormal phenotypes have played significant roles in the discovery of gene function, but organized collection of phenotype data has been overshadowed by developments in sequencing technology. In order to study phenotypes systematically, large-scale projects with standardized objective assessment across populations are considered necessary. The report of the 2006 Human Variome Project meeting recommended documentation of phenotypes through electronic means by collaborative groups of computational scientists and clinicians using standard, structured descriptions of disease-specific phenotypes. In this report, we describe progress over the past decade in 3D digital imaging and shape analysis of the face, and future prospects for large-scale facial phenotyping. Illustrative examples are given throughout using a collection of 1107 3D face images of healthy controls and individuals with a range of genetic conditions involving facial dysmorphism. PMID:22434506

  10. Very Large Scale Integration (VLSI).

    ERIC Educational Resources Information Center

    Yeaman, Andrew R. J.

    Very Large Scale Integration (VLSI), the state-of-the-art production techniques for computer chips, promises such powerful, inexpensive computing that, in the future, people will be able to communicate with computer devices in natural language or even speech. However, before full-scale VLSI implementation can occur, certain salient factors must be…

  11. A Numeric Scorecard Assessing the Mental Health Preparedness for Large-Scale Crises at College and University Campuses: A Delphi Study

    ERIC Educational Resources Information Center

    Burgin, Rick A.

    2012-01-01

    Large-scale crises continue to surprise, overwhelm, and shatter college and university campuses. While the devastation to physical plants and persons is often evident and is addressed with crisis management plans, the number of emotional casualties left in the wake of these large-scale crises may not be apparent and are often not addressed with…

  12. Improved Large-Scale Inundation Modelling by 1D-2D Coupling and Consideration of Hydrologic and Hydrodynamic Processes - a Case Study in the Amazon

    NASA Astrophysics Data System (ADS)

    Hoch, J. M.; Bierkens, M. F.; Van Beek, R.; Winsemius, H.; Haag, A.

    2015-12-01

    Understanding the dynamics of fluvial floods is paramount to accurate flood hazard and risk modeling. Currently, economic losses due to flooding constitute about one third of all damage resulting from natural hazards. Given future projections of climate change, the anticipated increase in the World's population and the associated implications, sound knowledge of flood hazard and related risk is crucial. Fluvial floods are cross-border phenomena that need to be addressed accordingly. Yet, only few studies model floods at the large-scale which is preferable to tiling the output of small-scale models. Most models cannot realistically model flood wave propagation due to a lack of either detailed channel and floodplain geometry or the absence of hydrologic processes. This study aims to develop a large-scale modeling tool that accounts for both hydrologic and hydrodynamic processes, to find and understand possible sources of errors and improvements and to assess how the added hydrodynamics affect flood wave propagation. Flood wave propagation is simulated by DELFT3D-FM (FM), a hydrodynamic model using a flexible mesh to schematize the study area. It is coupled to PCR-GLOBWB (PCR), a macro-scale hydrological model, that has its own simpler 1D routing scheme (DynRout) which has already been used for global inundation modeling and flood risk assessments (GLOFRIS; Winsemius et al., 2013). A number of model set-ups are compared and benchmarked for the simulation period 1986-1996: (0) PCR with DynRout; (1) using a FM 2D flexible mesh forced with PCR output and (2) as in (1) but discriminating between 1D channels and 2D floodplains, and, for comparison, (3) and (4) the same set-ups as (1) and (2) but forced with observed GRDC discharge values. Outputs are subsequently validated against observed GRDC data at Óbidos and flood extent maps from the Dartmouth Flood Observatory. The present research constitutes a first step into a globally applicable approach to fully couple

  13. Survey on large scale system control methods

    NASA Technical Reports Server (NTRS)

    Mercadal, Mathieu

    1987-01-01

    The problem inherent to large scale systems such as power network, communication network and economic or ecological systems were studied. The increase in size and flexibility of future spacecraft has put those dynamical systems into the category of large scale systems, and tools specific to the class of large systems are being sought to design control systems that can guarantee more stability and better performance. Among several survey papers, reference was found to a thorough investigation on decentralized control methods. Especially helpful was the classification made of the different existing approaches to deal with large scale systems. A very similar classification is used, even though the papers surveyed are somehow different from the ones reviewed in other papers. Special attention is brought to the applicability of the existing methods to controlling large mechanical systems like large space structures. Some recent developments are added to this survey.

  14. Medfly (Diptera: Tephritidae) genetic sexing: large-scale field comparison of males-only and bisexual sterile fly releases in Guatemala.

    PubMed

    Rendón, P; McInnis, D; Lance, D; Stewart, J

    2004-10-01

    The effect of releases of bisexual (males and female) and unisexual (male only) sterilized medflies was compared in three large field evaluations over a 3-yr period (1995-1997) in southwestern Guatemala. The two strains tested were a genetic sexing strain, Vienna-4/Tol-94, carrying the temperature sensitive tsl gene to eliminate females in the egg stage, and the standard bisexual Petapa strain. Flies were mass-reared, sterilized by irradiation as pupae, shipped to a field center, and released by air as young adults over 2 km by 2 km core areas in the centers of separate 6 km by 6 km test plots. Strain performance was monitored weekly by trapping sterile and wild male adults in core and buffer areas and by collecting eggs from coffee berries to determine induced sterility. Results indicated a several-fold advantage for the males-only strain as measured by the level of induced sterility, especially at the very high release ratios of 100:1 recorded in 1997. During that final test year, sterile-fly release rates were increased to provide high sterile:wild (S:W) fly ratios in the field, and egg sterility reached levels in excess of 70% in plots were the male-only strain was used. However, in the plots where the bisexual strain was released, induced sterility only reached 12% despite S:W ratios above 1,000:1. PMID:15568342

  15. Large-scale functional brain networks in human non-rapid eye movement sleep: insights from combined electroencephalographic/functional magnetic resonance imaging studies.

    PubMed

    Spoormaker, Victor I; Czisch, Michael; Maquet, Pierre; Jäncke, Lutz

    2011-10-13

    This paper reviews the existing body of knowledge on the neural correlates of spontaneous oscillations, functional connectivity and brain plasticity in human non-rapid eye movement (NREM) sleep. The first section reviews the evidence that specific sleep events as slow waves and spindles are associated with transient increases in regional brain activity. The second section describes the changes in functional connectivity during NREM sleep, with a particular focus on changes within a low-frequency, large-scale functional brain network. The third section will discuss the possibility that spontaneous oscillations and differential functional connectivity are related to brain plasticity and systems consolidation, with a particular focus on motor skill acquisition. Implications for the mode of information processing per sleep stage and future experimental studies are discussed. PMID:21893524

  16. A LARGE-SCALE CLUSTER RANDOMIZED TRIAL TO DETERMINE THE EFFECTS OF COMMUNITY-BASED DIETARY SODIUM REDUCTION – THE CHINA RURAL HEALTH INITIATIVE SODIUM REDUCTION STUDY

    PubMed Central

    Li, Nicole; Yan, Lijing L.; Niu, Wenyi; Labarthe, Darwin; Feng, Xiangxian; Shi, Jingpu; Zhang, Jianxin; Zhang, Ruijuan; Zhang, Yuhong; Chu, Hongling; Neiman, Andrea; Engelgau, Michael; Elliott, Paul; Wu, Yangfeng; Neal, Bruce

    2013-01-01

    Background Cardiovascular diseases are the leading cause of death and disability in China. High blood pressure caused by excess intake of dietary sodium is widespread and an effective sodium reduction program has potential to improve cardiovascular health. Design This study is a large-scale, cluster-randomized, trial done in five Northern Chinese provinces. Two counties have been selected from each province and 12 townships in each county making a total of 120 clusters. Within each township one village has been selected for participation with 1:1 randomization stratified by county. The sodium reduction intervention comprises community health education and a food supply strategy based upon providing access to salt substitute. Subsidization of the price of salt substitute was done in 30 intervention villages selected at random. Control villages continued usual practices. The primary outcome for the study is dietary sodium intake level estimated from assays of 24 hour urine. Trial status The trial recruited and randomized 120 townships in April 2011. The sodium reduction program was commenced in the 60 intervention villages between May and June of that year with outcome surveys scheduled for October to December 2012. Baseline data collection shows that randomisation achieved good balance across groups. Discussion The establishment of the China Rural Health Initiative has enabled the launch of this large-scale trial designed to identify a novel, scalable strategy for reduction of dietary sodium and control of blood pressure. If proved effective, the intervention could plausibly be implemented at low cost in large parts of China and other countries worldwide. PMID:24176436

  17. Knowledge-Guided Robust MRI Brain Extraction for Diverse Large-Scale Neuroimaging Studies on Humans and Non-Human Primates

    PubMed Central

    Wang, Yaping; Nie, Jingxin; Yap, Pew-Thian; Li, Gang; Shi, Feng; Geng, Xiujuan; Guo, Lei; Shen, Dinggang

    2014-01-01

    Accurate and robust brain extraction is a critical step in most neuroimaging analysis pipelines. In particular, for the large-scale multi-site neuroimaging studies involving a significant number of subjects with diverse age and diagnostic groups, accurate and robust extraction of the brain automatically and consistently is highly desirable. In this paper, we introduce population-specific probability maps to guide the brain extraction of diverse subject groups, including both healthy and diseased adult human populations, both developing and aging human populations, as well as non-human primates. Specifically, the proposed method combines an atlas-based approach, for coarse skull-stripping, with a deformable-surface-based approach that is guided by local intensity information and population-specific prior information learned from a set of real brain images for more localized refinement. Comprehensive quantitative evaluations were performed on the diverse large-scale populations of ADNI dataset with over 800 subjects (55∼90 years of age, multi-site, various diagnosis groups), OASIS dataset with over 400 subjects (18∼96 years of age, wide age range, various diagnosis groups), and NIH pediatrics dataset with 150 subjects (5∼18 years of age, multi-site, wide age range as a complementary age group to the adult dataset). The results demonstrate that our method consistently yields the best overall results across almost the entire human life span, with only a single set of parameters. To demonstrate its capability to work on non-human primates, the proposed method is further evaluated using a rhesus macaque dataset with 20 subjects. Quantitative comparisons with popularly used state-of-the-art methods, including BET, Two-pass BET, BET-B, BSE, HWA, ROBEX and AFNI, demonstrate that the proposed method performs favorably with superior performance on all testing datasets, indicating its robustness and effectiveness. PMID:24489639

  18. Large Scale Commodity Clusters for Lattice QCD

    SciTech Connect

    A. Pochinsky; W. Akers; R. Brower; J. Chen; P. Dreher; R. Edwards; S. Gottlieb; D. Holmgren; P. Mackenzie; J. Negele; D. Richards; J. Simone; W. Watson

    2002-06-01

    We describe the construction of large scale clusters for lattice QCD computing being developed under the umbrella of the U.S. DoE SciDAC initiative. We discuss the study of floating point and network performance that drove the design of the cluster, and present our plans for future multi-Terascale facilities.

  19. Large-scale genetic fine mapping and genotype-phenotype associations implicate polymorphism in the IL2RA region in type 1 diabetes.

    PubMed

    Lowe, Christopher E; Cooper, Jason D; Brusko, Todd; Walker, Neil M; Smyth, Deborah J; Bailey, Rebecca; Bourget, Kirsi; Plagnol, Vincent; Field, Sarah; Atkinson, Mark; Clayton, David G; Wicker, Linda S; Todd, John A

    2007-09-01

    Genome-wide association studies are now identifying disease-associated chromosome regions. However, even after convincing replication, the localization of the causal variant(s) requires comprehensive resequencing, extensive genotyping and statistical analyses in large sample sets leading to targeted functional studies. Here, we have localized the type 1 diabetes (T1D) association in the interleukin 2 receptor alpha (IL2RA) gene region to two independent groups of SNPs, spanning overlapping regions of 14 and 40 kb, encompassing IL2RA intron 1 and the 5' regions of IL2RA and RBM17 (odds ratio = 2.04, 95% confidence interval = 1.70-2.45; P = 1.92 x 10(-28); control frequency = 0.635). Furthermore, we have associated IL2RA T1D susceptibility genotypes with lower circulating levels of the biomarker, soluble IL-2RA (P = 6.28 x 10(-28)), suggesting that an inherited lower immune responsiveness predisposes to T1D. PMID:17676041

  20. Large-scale functional connectivity networks in the rodent brain.

    PubMed

    Gozzi, Alessandro; Schwarz, Adam J

    2016-02-15

    Resting-state functional Magnetic Resonance Imaging (rsfMRI) of the human brain has revealed multiple large-scale neural networks within a hierarchical and complex structure of coordinated functional activity. These distributed neuroanatomical systems provide a sensitive window on brain function and its disruption in a variety of neuropathological conditions. The study of macroscale intrinsic connectivity networks in preclinical species, where genetic and environmental conditions can be controlled and manipulated with high specificity, offers the opportunity to elucidate the biological determinants of these alterations. While rsfMRI methods are now widely used in human connectivity research, these approaches have only relatively recently been back-translated into laboratory animals. Here we review recent progress in the study of functional connectivity in rodent species, emphasising the ability of this approach to resolve large-scale brain networks that recapitulate neuroanatomical features of known functional systems in the human brain. These include, but are not limited to, a distributed set of regions identified in rats and mice that may represent a putative evolutionary precursor of the human default mode network (DMN). The impact and control of potential experimental and methodological confounds are also critically discussed. Finally, we highlight the enormous potential and some initial application of connectivity mapping in transgenic models as a tool to investigate the neuropathological underpinnings of the large-scale connectional alterations associated with human neuropsychiatric and neurological conditions. We conclude by discussing the translational potential of these methods in basic and applied neuroscience. PMID:26706448

  1. Large scale study on the variation of RF energy absorption in the head & brain regions of adults and children and evaluation of the SAM phantom conservativeness

    NASA Astrophysics Data System (ADS)

    Keshvari, J.; Kivento, M.; Christ, A.; Bit-Babik, G.

    2016-04-01

    This paper presents the results of two computational large scale studies using highly realistic exposure scenarios, MRI based human head and hand models, and two mobile phone models. The objectives are (i) to study the relevance of age when people are exposed to RF by comparing adult and child heads and (ii) to analyze and discuss the conservativeness of the SAM phantom for all age groups. Representative use conditions were simulated using detailed CAD models of two mobile phones operating between 900 MHz and 1950 MHz including configurations with the hand holding the phone, which were not considered in most previous studies. The peak spatial-average specific absorption rate (psSAR) in the head and the pinna tissues is assessed using anatomically accurate head and hand models. The first of the two mentioned studies involved nine head-, four hand- and two phone-models, the second study included six head-, four hand- and three simplified phone-models (over 400 configurations in total). In addition, both studies also evaluated the exposure using the SAM phantom. Results show no systematic differences between psSAR induced in the adult and child heads. The exposure level and its variation for different age groups may be different for particular phones, but no correlation between psSAR and model age was found. The psSAR from all exposure conditions was compared to the corresponding configurations using SAM, which was found to be conservative in the large majority of cases.

  2. Evaluating cloud processes in large-scale models: Of idealized case studies, parameterization testbeds and single-column modelling on climate time-scales

    NASA Astrophysics Data System (ADS)

    Neggers, Roel

    2016-04-01

    Boundary-layer schemes have always formed an integral part of General Circulation Models (GCMs) used for numerical weather and climate prediction. The spatial and temporal scales associated with boundary-layer processes and clouds are typically much smaller than those at which GCMs are discretized, which makes their representation through parameterization a necessity. The need for generally applicable boundary-layer parameterizations has motivated many scientific studies, which in effect has created its own active research field in the atmospheric sciences. Of particular interest has been the evaluation of boundary-layer schemes at "process-level". This means that parameterized physics are studied in isolated mode from the larger-scale circulation, using prescribed forcings and excluding any upscale interaction. Although feedbacks are thus prevented, the benefit is an enhanced model transparency, which might aid an investigator in identifying model errors and understanding model behavior. The popularity and success of the process-level approach is demonstrated by the many past and ongoing model inter-comparison studies that have been organized by initiatives such as GCSS/GASS. A red line in the results of these studies is that although most schemes somehow manage to capture first-order aspects of boundary layer cloud fields, there certainly remains room for improvement in many areas. Only too often are boundary layer parameterizations still found to be at the heart of problems in large-scale models, negatively affecting forecast skills of NWP models or causing uncertainty in numerical predictions of future climate. How to break this parameterization "deadlock" remains an open problem. This presentation attempts to give an overview of the various existing methods for the process-level evaluation of boundary-layer physics in large-scale models. This includes i) idealized case studies, ii) longer-term evaluation at permanent meteorological sites (the testbed approach

  3. Modelling large-scale spatial variability of soil properties with sequential stochastic simulation conditioned by universal kriging in a Hungarian study site

    NASA Astrophysics Data System (ADS)

    Szatmári, Gábor; Barta, Károly; Pásztor, László

    2015-04-01

    Modelling of large-scale spatial variability of soil properties is a promising subject in soil science, as well as in general environmental research, since the resulted model(s) can be applied to solve various problems. In addition to "purely" map an environmental element, the spatial uncertainty of the map product can deduced, specific areas could be identified and/or delineated (contaminated or endangered regions, plots for fertilization, etc.). Geostatistics, which can be regarded as a subset of statistics specialized in analysis and interpretation of geographically referenced data, offer a huge amount of tools to solve these tasks. Numerous spatial modeling methods have been developed in the past decades based on the regionalized variable theory. One of these techniques is sequential stochastic simulation, which can be conditioned with universal kriging (also referred to as regression kriging). As opposed to universal kriging (UK), sequential simulation conditioned with universal kriging (SSUK) provides not just one but several alternative and equally probable "maps", i.e. realizations. The realizations reproduce the global statistics (e.g. sample histogram, variogram), i.e. they reflect/model the reality in a certain global (and not local!) sense. In this paper we present and test SSUK developed in R-code and its utilizations in a water erosion affected study area. Furthermore, we compare the results from UK and SSUK. For this purpose, two soil variables were selected: soil organic matter (SOM) content and rooting depth (RD). SSUK approach is illustrated with a legacy soil dataset from a study area endangered by water erosion in Central Hungary. Legacy soil data was collected in the end of the 1980s in the framework of the National Land Evaluation Programme. Spatially exhaustive covariates were derived from a digital elevation model and from the land-use-map of the study area. SSUK was built upon a UK prediction system for both variables and 200 realizations

  4. Analysis of precipitation data from in situ and large-scale source in a tropical mountain environment. Study case of the Cordillera Blanca region, Peru.

    NASA Astrophysics Data System (ADS)

    Mourre, Lise; Junquas, Clémentine; Condom, Thomas; Lebel, Thierry

    2014-05-01

    The study area, the watershed of the Rio Santa in Peru, accuses a strong longitudinal climatic gradient, from the humid Amazonian lowlands to the drier Pacific coast, associated with an altitudinal gradient, with the highest point of the watershed at 6,768 meters asl. The Cordillera Blanca situated in this area, had more than 600 km² of glacier coverage at the end of the 20th century, with more than half that belongs to the watershed of the Rio Santa. The application of a hydrological model in this area requires the analysis and regionalization of precipitation, a key variable for the establishment of a water balance. In this context, different sources of precipitation data are useful in order to catch the spatial and temporal variability: in situ meteorological stations, TRMM 3B42 and 3B43 product satellite data and outputs of WRF model (Weather Research and Forecasting Model) at 3 km of spatial resolution. Precipitations are dependent on both the large-scale atmospheric circulation and local parameters such as topography or albedo. As all these variables cannot be properly taken into account in large scale models, it is important to evaluate the contribution of regional models in the analysis and the understanding of the spatial heterogeneity of precipitation across a watershed. To investigate the spatial and temporal variability of precipitations, two approaches have been adopted in this work. In a first approach the spatial repartition of precipitation is described from station data. The second approach is focused on the assessment of a high-scale regional climate model (WRF) and the TRMM satellite data to reproduce spatially and temporally in situ observed precipitations. This comparison was carried out for different time-scale variability: on a monthly time scale with the observation of the seasonal cycle, on the daily time scale to study the occurrence of precipitation, and finally with the hourly data to study the representation of diurnal cycle. First

  5. Microfluidic large-scale integration.

    PubMed

    Thorsen, Todd; Maerkl, Sebastian J; Quake, Stephen R

    2002-10-18

    We developed high-density microfluidic chips that contain plumbing networks with thousands of micromechanical valves and hundreds of individually addressable chambers. These fluidic devices are analogous to electronic integrated circuits fabricated using large-scale integration. A key component of these networks is the fluidic multiplexor, which is a combinatorial array of binary valve patterns that exponentially increases the processing power of a network by allowing complex fluid manipulations with a minimal number of inputs. We used these integrated microfluidic networks to construct the microfluidic analog of a comparator array and a microfluidic memory storage device whose behavior resembles random-access memory. PMID:12351675

  6. A comparative study of outlier detection for large-scale traffic data by one-class SVM and kernel density estimation

    NASA Astrophysics Data System (ADS)

    Ngan, Henry Y. T.; Yung, Nelson H. C.; Yeh, Anthony G. O.

    2015-02-01

    This paper aims at presenting a comparative study of outlier detection (OD) for large-scale traffic data. The traffic data nowadays are massive in scale and collected in every second throughout any modern city. In this research, the traffic flow dynamic is collected from one of the busiest 4-armed junction in Hong Kong in a 31-day sampling period (with 764,027 vehicles in total). The traffic flow dynamic is expressed in a high dimension spatial-temporal (ST) signal format (i.e. 80 cycles) which has a high degree of similarities among the same signal and across different signals in one direction. A total of 19 traffic directions are identified in this junction and lots of ST signals are collected in the 31-day period (i.e. 874 signals). In order to reduce its dimension, the ST signals are firstly undergone a principal component analysis (PCA) to represent as (x,y)-coordinates. Then, these PCA (x,y)-coordinates are assumed to be conformed as Gaussian distributed. With this assumption, the data points are further to be evaluated by (a) a correlation study with three variant coefficients, (b) one-class support vector machine (SVM) and (c) kernel density estimation (KDE). The correlation study could not give any explicit OD result while the one-class SVM and KDE provide average 59.61% and 95.20% DSRs, respectively.

  7. In vitro Stability of Heat Shock Protein 27 in Serum and Plasma Under Different Pre-analytical Conditions: Implications for Large-Scale Clinical Studies.

    PubMed

    Zimmermann, Matthias; Traxler, Denise; Simader, Elisabeth; Bekos, Christine; Dieplinger, Benjamin; Lainscak, Mitja; Ankersmit, Hendrik Jan; Mueller, Thomas

    2016-07-01

    The effects of storage temperatures, repeated freeze-thaw cycles, or delays in separating plasma or serum from blood samples are largely unknown for heat shock protein 27 (HSP27). We evaluated (1) the imprecision of the HSP27 assay used in this study; (2) the in vitro stability of HSP27 in blood samples stored at 4°C for up to 6 hr with immediate and delayed serum/plasma separation from cells; and (3) the in vitro stability of HSP27 in blood samples stored at -80°C after repeated freeze-thaw cycles. The ELISA to detect HSP27 in this study showed a within-run CV of <9% and a total CV of <15%. After 4-6 hr of storage at 4°C, HSP27 concentrations remained stable when using serum tubes irrespective of sample handling, but HSP27 concentrations decreased by 25-45% when using EDTA plasma tubes. Compared with baseline HSP27, one freeze-thaw cycle had no effect on serum concentrations. However, plasma concentrations increased by 3.1-fold after one freeze-thaw cycle and by 7.3-fold after five freeze-thaw cycles. In conclusion, serum is an appropriate biological sample type for use in epidemiological and large-scale clinical studies. PMID:27139608

  8. A large-scale multicentre study in Belgium of dose area product values and effective doses in interventional cardiology using contemporary X-ray equipment.

    PubMed

    Bogaert, E; Bacher, K; Thierens, H

    2008-01-01

    In this paper, a large-scale multicentre patient dose study performed in eight Belgian interventional cardiology departments is presented. Effective dose (E) was calculated based on a detailed dose-area product (DAP)-registration during each procedure and by using conversion coefficients generated by the Monte Carlo-based computer program PCXMC. Conversion coefficients were found to be 0.177 mSv Gycm(-2) for systems that do not use any additional copper filtration in cineradiography and 0.207 mSv Gycm(-2) for systems that use additional copper filtration in cineradiography. Mean E values of 9.6 and 15.3 mSv for diagnostic and therapeutic procedures, respectively, were obtained. DAP distributions were investigated in order to derive dose reference levels: 71 and 106 Gycm2 for diagnostic and therapeutic procedures, respectively, are proposed. Significant differences were observed in DAP distributions taking into account whether additional copper filtration was used in the cineradiography mode. Apart from the skin, the organs most at risk are lungs and heart. The probability of fatal cancer for the studied population amounted to 1.1x10(-4) and 2.1x10(-4) for diagnostic and therapeutic procedures, respectively, for the age distribution of the patients considered in this multicentre study. PMID:17681964

  9. A systematic review of the effect of red blood cell transfusion on mortality: evidence from large-scale observational studies published between 2006 and 2010

    PubMed Central

    Hopewell, Sally; Omar, Omar; Hyde, Chris; Yu, Ly-Mee; Doree, Carolyn; Murphy, Mike F

    2013-01-01

    Objective To carry out a systematic review of recently published large-scale observational studies assessing the effects of red blood cell transfusion (RBCT) on mortality, with particular emphasis on the statistical methods used to adjust for confounding. Given the limited number of randomised trials of the efficacy of RBCT, clinicians often use evidence from observational studies. However, confounding factors, for example, individuals receiving blood generally being sicker than those who do not, make their interpretation challenging. Design Systematic review. Information sources We searched MEDLINE and EMBASE for studies published from 1 January 2006 to 31 December 2010. Eligibility criteria for included studies We included prospective cohort, case–control studies or retrospective analyses of databases or disease registers where the effect of risk factors for mortality or survival was examined. Studies must have included more than 1000 participants receiving RBCT for any cause. We assessed the effects of RBCT versus no RBCT and different volumes and age of RBCT. Results –32 studies were included in the review; 23 assessed the effects of RBCT versus no RBCT; 5 assessed different volumes and 4 older versus newer RBCT. There was a considerable variability in the patient populations, study designs and level of statistical adjustment. Overall, most studies showed a higher rate of mortality when comparing patients who received RBCT with those who did not, even when these rates were adjusted for confounding; the majority of these increases were statistically significant. The same pattern was observed in studies where protection from bias was likely to be greater, such as prospective studies. Conclusions Recent observational studies do show a consistently adverse effect of RBCT on mortality. Whether this is a true effect remains uncertain as it is possible that even the best conducted adjustments cannot completely eliminate the impact of confounding. PMID:23645909

  10. Decision aid on breast cancer screening reduces attendance rate: results of a large-scale, randomized, controlled study by the DECIDEO group.

    PubMed

    Bourmaud, Aurelie; Soler-Michel, Patricia; Oriol, Mathieu; Regnier, Véronique; Tinquaut, Fabien; Nourissat, Alice; Bremond, Alain; Moumjid, Nora; Chauvin, Franck

    2016-03-15

    Controversies regarding the benefits of breast cancer screening programs have led to the promotion of new strategies taking into account individual preferences, such as decision aid. The aim of this study was to assess the impact of a decision aid leaflet on the participation of women invited to participate in a national breast cancer screening program. This Randomized, multicentre, controlled trial. Women aged 50 to 74 years, were randomly assigned to receive either a decision aid or the usual invitation letter. Primary outcome was the participation rate 12 months after the invitation. 16 000 women were randomized and 15 844 included in the modified intention-to-treat analysis. The participation rate in the intervention group was 40.25% (3174/7885 women) compared with 42.13% (3353/7959) in the control group (p = 0.02). Previous attendance for screening (RR = 6.24; [95%IC: 5.75-6.77]; p < 0.0001) and medium household income (RR = 1.05; [95%IC: 1.01-1.09]; p = 0.0074) were independently associated with attendance for screening. This large-scale study demonstrates that the decision aid reduced the participation rate. The decision aid activate the decision making process of women toward non-attendance to screening. These results show the importance of promoting informed patient choices, especially when those choices cannot be anticipated. PMID:26883201

  11. Decision aid on breast cancer screening reduces attendance rate: results of a large-scale, randomized, controlled study by the DECIDEO group

    PubMed Central

    Bourmaud, Aurelie; Soler-Michel, Patricia; Oriol, Mathieu; Regnier, Véronique; Tinquaut, Fabien; Nourissat, Alice; Bremond, Alain; Moumjid, Nora; Chauvin, Franck

    2016-01-01

    Controversies regarding the benefits of breast cancer screening programs have led to the promotion of new strategies taking into account individual preferences, such as decision aid. The aim of this study was to assess the impact of a decision aid leaflet on the participation of women invited to participate in a national breast cancer screening program. This Randomized, multicentre, controlled trial. Women aged 50 to 74 years, were randomly assigned to receive either a decision aid or the usual invitation letter. Primary outcome was the participation rate 12 months after the invitation. 16 000 women were randomized and 15 844 included in the modified intention-to-treat analysis. The participation rate in the intervention group was 40.25% (3174/7885 women) compared with 42.13% (3353/7959) in the control group (p = 0.02). Previous attendance for screening (RR = 6.24; [95%IC: 5.75-6.77]; p < 0.0001) and medium household income (RR = 1.05; [95%IC: 1.01-1.09]; p = 0.0074) were independently associated with attendance for screening. This large-scale study demonstrates that the decision aid reduced the participation rate. The decision aid activate the decision making process of women toward non-attendance to screening. These results show the importance of promoting informed patient choices, especially when those choices cannot be anticipated. PMID:26883201

  12. LARGE-SCALE CORONAL PROPAGATING FRONTS IN SOLAR ERUPTIONS AS OBSERVED BY THE ATMOSPHERIC IMAGING ASSEMBLY ON BOARD THE SOLAR DYNAMICS OBSERVATORY—AN ENSEMBLE STUDY

    SciTech Connect

    Nitta, Nariaki V.; Schrijver, Carolus J.; Title, Alan M.; Liu, Wei

    2013-10-10

    This paper presents a study of a large sample of global disturbances in the solar corona with characteristic propagating fronts as intensity enhancement, similar to the phenomena that have often been referred to as Extreme Ultraviolet Imaging Telescope (EIT) waves or extreme-ultraviolet (EUV) waves. Now EUV images obtained by the Atmospheric Imaging Assembly (AIA) on board the Solar Dynamics Observatory provide a significantly improved view of these large-scale coronal propagating fronts (LCPFs). Between 2010 April and 2013 January, a total of 171 LCPFs have been identified through visual inspection of AIA images in the 193 Å channel. Here we focus on the 138 LCPFs that are seen to propagate across the solar disk, first studying how they are associated with flares, coronal mass ejections (CMEs), and type II radio bursts. We measure the speed of the LCPF in various directions until it is clearly altered by active regions or coronal holes. The highest speed is extracted for each LCPF. It is often considerably higher than EIT waves. We do not find a pattern where faster LCPFs decelerate and slow LCPFs accelerate. Furthermore, the speeds are not strongly correlated with the flare intensity or CME magnitude, nor do they show an association with type II bursts. We do not find a good correlation either between the speeds of LCPFs and CMEs in a subset of 86 LCPFs observed by one or both of the Solar and Terrestrial Relations Observatory spacecraft as limb events.

  13. PDMS microwells for multi-parametric monitoring of single mitochondria on a large scale: a study of their individual membrane potential and endogenous NADH.

    PubMed

    Vajrala, Venkata Suresh; Suraniti, Emmanuel; Rigoulet, Michel; Devin, Anne; Sojic, Neso; Arbault, Stéphane

    2016-08-01

    Microwell arrays have been developed to monitor simultaneously, and on a large scale, multiple metabolic responses of single mitochondria. Wells of 50 to 1000 μm-diameter were prepared based on easy structuration of thin polydimethylsiloxane layers (PDMS; 100 μm thickness). Their surface treatment with oxygen plasma allowed the immobilization in situ and observation with time of populations of single isolated mitochondria. Their metabolic activities could be monitored individually by fluorescence microscopy under several activation/inhibition conditions. We measured the concomitant variations of two main metabolic parameters - the endogenous NADH level and the internal membrane potential difference Δψ owing to a cationic fluorescent probe (TMRM) - at energized, uncoupled and inhibited stages of the mitochondrial respiratory chain. Microwell arrays allowed analyses on large populations, and consequently statistical studies with a single organelle resolution. Thus, we observed rapid individual polarizations and depolarizations of mitochondria following their supply with the energetic substrate, while an averaged global polarization (increase of TMRM fluorescence within mitochondria) and NADH increase were detected for the whole population. In addition, statistical correlation studies show that the NADH content of all mitochondria tends toward a metabolic limit and that their polarization-depolarization ability is ubiquitous. These results demonstrate that PDMS microwell platforms provide an innovative approach to better characterize the individual metabolic status of isolated mitochondria, possibly as a function of their cell or organ origin or in different physio-pathological situations. PMID:27384613

  14. Sound to Language: Different Cortical Processing for First and Second Languages in Elementary School Children as Revealed by a Large-Scale Study Using fNIRS

    PubMed Central

    Ojima, Shiro; Matsuba-Kurita, Hiroko; Dan, Ippeita; Tsuzuki, Daisuke; Katura, Takusige; Hagiwara, Hiroko

    2011-01-01

    A large-scale study of 484 elementary school children (6–10 years) performing word repetition tasks in their native language (L1-Japanese) and a second language (L2-English) was conducted using functional near-infrared spectroscopy. Three factors presumably associated with cortical activation, language (L1/L2), word frequency (high/low), and hemisphere (left/right), were investigated. L1 words elicited significantly greater brain activation than L2 words, regardless of semantic knowledge, particularly in the superior/middle temporal and inferior parietal regions (angular/supramarginal gyri). The greater L1-elicited activation in these regions suggests that they are phonological loci, reflecting processes tuned to the phonology of the native language, while phonologically unfamiliar L2 words were processed like nonword auditory stimuli. The activation was bilateral in the auditory and superior/middle temporal regions. Hemispheric asymmetry was observed in the inferior frontal region (right dominant), and in the inferior parietal region with interactions: low-frequency words elicited more right-hemispheric activation (particularly in the supramarginal gyrus), while high-frequency words elicited more left-hemispheric activation (particularly in the angular gyrus). The present results reveal the strong involvement of a bilateral language network in children’s brains depending more on right-hemispheric processing while acquiring unfamiliar/low-frequency words. A right-to-left shift in laterality should occur in the inferior parietal region, as lexical knowledge increases irrespective of language. PMID:21350046

  15. Association of Perceived Stress with Stressful Life Events, Lifestyle and Sociodemographic Factors: A Large-Scale Community-Based Study Using Logistic Quantile Regression

    PubMed Central

    Feizi, Awat; Aliyari, Roqayeh; Roohafza, Hamidreza

    2012-01-01

    Objective. The present paper aimed at investigating the association between perceived stress and major life events stressors in Iranian general population. Methods. In a cross-sectional large-scale community-based study, 4583 people aged 19 and older, living in Isfahan, Iran, were investigated. Logistic quantile regression was used for modeling perceived stress, measured by GHQ questionnaire, as the bounded outcome (dependent), variable, and as a function of most important stressful life events, as the predictor variables, controlling for major lifestyle and sociodemographic factors. This model provides empirical evidence of the predictors' effects heterogeneity depending on individual location on the distribution of perceived stress. Results. The results showed that among four stressful life events, family conflicts and social problems were more correlated with level of perceived stress. Higher levels of education were negatively associated with perceived stress and its coefficients monotonically decrease beyond the 30th percentile. Also, higher levels of physical activity were associated with perception of low levels of stress. The pattern of gender's coefficient over the majority of quantiles implied that females are more affected by stressors. Also high perceived stress was associated with low or middle levels of income. Conclusions. The results of current research suggested that in a developing society with high prevalence of stress, interventions targeted toward promoting financial and social equalities, social skills training, and healthy lifestyle may have the potential benefits for large parts of the population, most notably female and lower educated people. PMID:23091560

  16. Challenges for Large Scale Simulations

    NASA Astrophysics Data System (ADS)

    Troyer, Matthias

    2010-03-01

    With computational approaches becoming ubiquitous the growing impact of large scale computing on research influences both theoretical and experimental work. I will review a few examples in condensed matter physics and quantum optics, including the impact of computer simulations in the search for supersolidity, thermometry in ultracold quantum gases, and the challenging search for novel phases in strongly correlated electron systems. While only a decade ago such simulations needed the fastest supercomputers, many simulations can now be performed on small workstation clusters or even a laptop: what was previously restricted to a few experts can now potentially be used by many. Only part of the gain in computational capabilities is due to Moore's law and improvement in hardware. Equally impressive is the performance gain due to new algorithms - as I will illustrate using some recently developed algorithms. At the same time modern peta-scale supercomputers offer unprecedented computational power and allow us to tackle new problems and address questions that were impossible to solve numerically only a few years ago. While there is a roadmap for future hardware developments to exascale and beyond, the main challenges are on the algorithmic and software infrastructure side. Among the problems that face the computational physicist are: the development of new algorithms that scale to thousands of cores and beyond, a software infrastructure that lifts code development to a higher level and speeds up the development of new simulation programs for large scale computing machines, tools to analyze the large volume of data obtained from such simulations, and as an emerging field provenance-aware software that aims for reproducibility of the complete computational workflow from model parameters to the final figures. Interdisciplinary collaborations and collective efforts will be required, in contrast to the cottage-industry culture currently present in many areas of computational

  17. Interactions between psychological stress and drinking status in relation to diet among middle-aged men and women: a large-scale cross-sectional study in Japan.

    PubMed

    Endoh, Kaori; Kuriki, Kiyonori; Kasezawa, Nobuhiko; Tohyama, Kazushige; Goda, Toshinao

    2015-01-01

    The aim of this study was to investigate the interaction between psychological stress (PS) and drinking status in relation to diet among middle-aged Japanese men and women in a large-scale cross-sectional study. The study population included 5,587 middle-aged Japanese men and 2,718 middle-aged Japanese women who underwent annual health checkups. The subjects were divided into 2 groups (non-drinkers and drinkers) and classified as having low, moderate, or high self-reported PS levels. Energy-adjusted food and nutrient consumption was assessed with a validated food frequency questionnaire. Using a general linear model, food and nutrient consumption was estimated for each self-reported PS level in the 2 groups (non-drinkers and drinkers) and the interactions between self-reported PS levels and drinking status were calculated. In men, pork and beef; squid, octopus, shrimp, and clams; eggs; mushrooms; Japanese-style sweets; ice cream; bread; Chinese noodles; coffee; and soda as foods and protein, animal protein, fat, animal fat, carbohydrate, monounsaturated fatty acid, polyunsaturated fatty acid (PUFA), n-3 PUFA, n-6 PUFA, cholesterol, vitamin D, vitamin B2, vitamin B6, vitamin B12, niacin, pantothenic acid, magnesium, phosphorus, and zinc as nutrients significantly interacted with self-reported PS levels and drinking status (p for interaction <0.05 for all). No specific interactions were found in women. These findings suggest interactions between PS levels and drinking status with consumption of some foods and nutrients, especially macronutrient intake, in men but not in women. PMID:26027597

  18. Recurrent TERT promoter mutations identified in a large-scale study of multiple tumor types are associated with increased TERT expression and telomerase activation

    PubMed Central

    Huang, Dong-Sheng; Wang, Zhaohui; He, Xu-Jun; Diplas, Bill H.; Yang, Rui; Killela, Patrick J.; Liang, Junbo; Meng, Qun; Ye, Zai-Yuan; Wang, Wei; Jiang, Xiao-Ting; Xu, Li; He, Xiang-Lei; Zhao, Zhong-Sheng; Xu, Wen-Juan; Wang, Hui-Ju; Ma, Ying-Yu; Xia, Ying-Jie; Li, Li; Zhang, Ru-Xuan; Jin, Tao; Zhao, Zhong-Kuo; Xu, Ji; Yu, Sheng; Wu, Fang; Wang, Si-Zhen; Jiao, Yu-Chen; Yan, Hai; Tao, Hou-Quan

    2015-01-01

    Background Several somatic mutation hotspots were recently identified in the TERT promoter region in human cancers. Large scale studies of these mutations in multiple tumor types are limited, in particular in Asian populations. This study aimed to: analyze TERT promoter mutations in multiple tumor types in a large Chinese patient cohort, investigate novel tumor types and assess the functional significance of the mutations. Methods TERT promoter mutation status was assessed by Sanger sequencing for 13 different tumor types and 799 tumor tissues from Chinese cancer patients. Thymic epithelial tumors, gastrointestinal leiomyoma, and gastric schwannoma were included, for which the TERT promoter has not been previously sequenced. Functional studies included TERT expression by RT-qPCR, telomerase activity by the TRAP assay, and promoter activity by the luciferase reporter assay. Results TERT promoter mutations were highly frequent in glioblastoma (83.9%), urothelial carcinoma (64.5%), oligodendroglioma (70.0%), medulloblastoma (33.3%), and hepatocellular carcinoma (31.4%). C228T and C250T were the most common mutations. In urothelial carcinoma, several novel rare mutations were identified. TERT promoter mutations were absent in GIST, thymic epithelial tumors, gastrointestinal leiomyoma, gastric schwannoma, cholangiocarcinoma, gastric and pancreatic cancer. TERT promoter mutations highly correlated with upregulated TERT mRNA expression and telomerase activity in adult gliomas. These mutations differentially enhanced the transcriptional activity of the TERT core promoter. Conclusions TERT promoter mutations are frequent in multiple tumor types and have similar distributions in Chinese cancer patients. The functional significance of these mutations reflect the importance to telomere maintenance and hence tumorigenesis, making them potential therapeutic targets. PMID:25843513

  19. An expert-based job exposure matrix for large scale epidemiologic studies of primary hip and knee osteoarthritis: The Lower Body JEM

    PubMed Central

    2014-01-01

    Background When conducting large scale epidemiologic studies, it is a challenge to obtain quantitative exposure estimates, which do not rely on self-report where estimates may be influenced by symptoms and knowledge of disease status. In this study we developed a job exposure matrix (JEM) for use in population studies of the work-relatedness of hip and knee osteoarthritis. Methods Based on all 2227 occupational titles in the Danish version of the International Standard Classification of Occupations (D-ISCO 88), we constructed 121 job groups comprising occupational titles with expected homogeneous exposure patterns in addition to a minimally exposed job group, which was not included in the JEM. The job groups were allocated the mean value of five experts’ ratings of daily duration (hours/day) of standing/walking, kneeling/squatting, and whole-body vibration as well as total load lifted (kg/day), and frequency of lifting loads weighing ≥20 kg (times/day). Weighted kappa statistics were used to evaluate inter-rater agreement on rankings of the job groups for four of these exposures (whole-body vibration could not be evaluated due to few exposed job groups). Two external experts checked the face validity of the rankings of the mean values. Results A JEM was constructed and English ISCO codes were provided where possible. The experts’ ratings showed fair to moderate agreement with respect to rankings of the job groups (mean weighted kappa values between 0.36 and 0.49). The external experts agreed on 586 of the 605 rankings. Conclusion The Lower Body JEM based on experts’ ratings was established. Experts agreed on rankings of the job groups, and rankings based on mean values were in accordance with the opinion of external experts. PMID:24927760

  20. Developing a "Semi-Systematic" Approach to Using Large-Scale Data-Sets for Small-Scale Interventions: The "Baby Matterz" Initiative as a Case Study

    ERIC Educational Resources Information Center

    O'Brien, Mark

    2011-01-01

    The appropriateness of using statistical data to inform the design of any given service development or initiative often depends upon judgements regarding scale. Large-scale data sets, perhaps national in scope, whilst potentially important in informing the design, implementation and roll-out of experimental initiatives, will often remain unused…

  1. Impact of tissue atrophy on high-pass filtered MRI signal phase-based assessment in large-scale group-comparison studies: A simulation study

    NASA Astrophysics Data System (ADS)

    Schweser, Ferdinand; Dwyer, Michael G.; Deistung, Andreas; Reichenbach, Jürgen R.; Zivadinov, Robert

    2013-10-01

    The assessment of abnormal accumulation of tissue iron in the basal ganglia nuclei and in white matter plaques using the gradient echo magnetic resonance signal phase has become a research focus in many neurodegenerative diseases such as multiple sclerosis or Parkinson’s disease. A common and natural approach is to calculate the mean high-pass-filtered phase of previously delineated brain structures. Unfortunately, the interpretation of such an analysis requires caution: in this paper we demonstrate that regional gray matter atrophy, which is concomitant with many neurodegenerative diseases, may itself directly result in a phase shift seemingly indicative of increased iron concentration even without any real change in the tissue iron concentration. Although this effect is relatively small results of large-scale group comparisons may be driven by anatomical changes rather than by changes of the iron concentration.

  2. Effects of sex and proficiency in second language processing as revealed by a large-scale fNIRS study of school-aged children.

    PubMed

    Sugiura, Lisa; Ojima, Shiro; Matsuba-Kurita, Hiroko; Dan, Ippeita; Tsuzuki, Daisuke; Katura, Takusige; Hagiwara, Hiroko

    2015-10-01

    Previous neuroimaging studies in adults have revealed that first and second languages (L1/L2) share similar neural substrates, and that proficiency is a major determinant of the neural organization of L2 in the lexical-semantic and syntactic domains. However, little is known about neural substrates of children in the phonological domain, or about sex differences. Here, we conducted a large-scale study (n = 484) of school-aged children using functional near-infrared spectroscopy and a word repetition task, which requires a great extent of phonological processing. We investigated cortical activation during word processing, emphasizing sex differences, to clarify similarities and differences between L1 and L2, and proficiency-related differences during early L2 learning. L1 and L2 shared similar neural substrates with decreased activation in L2 compared to L1 in the posterior superior/middle temporal and angular/supramarginal gyri for both sexes. Significant sex differences were found in cortical activation within language areas during high-frequency word but not during low-frequency word processing. During high-frequency word processing, widely distributed areas including the angular/supramarginal gyri were activated in boys, while more restricted areas, excluding the angular/supramarginal gyri were activated in girls. Significant sex differences were also found in L2 proficiency-related activation: activation significantly increased with proficiency in boys, whereas no proficiency-related differences were found in girls. Importantly, cortical sex differences emerged with proficiency. Based on previous research, the present results indicate that sex differences are acquired or enlarged during language development through different cognitive strategies between sexes, possibly reflecting their different memory functions. PMID:26147179

  3. A Small-scale Physical Model of the Lower Mississippi River for Studying the Potential of Medium- and Large-scale Diversions

    NASA Astrophysics Data System (ADS)

    Willson, C. S.

    2011-12-01

    Over the past several thousand years the Mississippi River has formed one of the world's largest deltas and much of the Louisiana coast. However, in the last 100 years or so, anthropogenic controls have been placed on the system to maintain important navigation routes and for flood control resulting in the loss of the natural channel shifting necessary for replenishment of the deltaic coast with fresh sediment and resources. In addition, the high relative sea level rise in the lowermost portion of the river is causing a change in the distributary flow patterns of the river and deposition center. River and sediment diversions are being proposed as way to re-create some of the historical distribution of river water and sediments into the delta region. In response to a need for improving the understanding of the potential for medium- and large-scale river and sediment diversions, the state of Louisiana funded the construction of a small-scale physical model (SSPM) of the lower ~76 river miles (RM). The SSPM is a 1:12,000 horizontal, 1:500 vertical, highly-distorted, movable bed physical model designed to provide qualitative and semi-quantitative results regarding bulk noncohesive sediment transport characteristics in the river and through medium- and large-scale diversion structures. The SSPM was designed based on Froude similarity for the hydraulics and Shields similarity for sand transport and has a sediment time scale of 1 year prototype to 30 minutes model allowing for decadal length studies of the land building potential of diversions. Annual flow and sediment hydrographs were developed from historical records and a uniform relative sea level rise of 3 feet in 100 years is used to account for the combined effects of eustatic sea level rise and subsidence. Data collected during the experiments include river stages, dredging amounts and high-resolution video of transport patterns within the main channel and photographs of the sand deposition patterns in the

  4. Assembly of 500,000 inter-specific catfish expressed sequence tags and large scale gene-associated marker development for whole genome association studies

    SciTech Connect

    Catfish Genome Consortium; Wang, Shaolin; Peatman, Eric; Abernathy, Jason; Waldbieser, Geoff; Lindquist, Erika; Richardson, Paul; Lucas, Susan; Wang, Mei; Li, Ping; Thimmapuram, Jyothi; Liu, Lei; Vullaganti, Deepika; Kucuktas, Huseyin; Murdock, Christopher; Small, Brian C; Wilson, Melanie; Liu, Hong; Jiang, Yanliang; Lee, Yoona; Chen, Fei; Lu, Jianguo; Wang, Wenqi; Xu, Peng; Somridhivej, Benjaporn; Baoprasertkul, Puttharat; Quilang, Jonas; Sha, Zhenxia; Bao, Baolong; Wang, Yaping; Wang, Qun; Takano, Tomokazu; Nandi, Samiran; Liu, Shikai; Wong, Lilian; Kaltenboeck, Ludmilla; Quiniou, Sylvie; Bengten, Eva; Miller, Norman; Trant, John; Rokhsar, Daniel; Liu, Zhanjiang

    2010-03-23

    Background-Through the Community Sequencing Program, a catfish EST sequencing project was carried out through a collaboration between the catfish research community and the Department of Energy's Joint Genome Institute. Prior to this project, only a limited EST resource from catfish was available for the purpose of SNP identification. Results-A total of 438,321 quality ESTs were generated from 8 channel catfish (Ictalurus punctatus) and 4 blue catfish (Ictalurus furcatus) libraries, bringing the number of catfish ESTs to nearly 500,000. Assembly of all catfish ESTs resulted in 45,306 contigs and 66,272 singletons. Over 35percent of the unique sequences had significant similarities to known genes, allowing the identification of 14,776 unique genes in catfish. Over 300,000 putative SNPs have been identified, of which approximately 48,000 are high-quality SNPs identified from contigs with at least four sequences and the minor allele presence of at least two sequences in the contig. The EST resource should be valuable for identification of microsatellites, genome annotation, large-scale expression analysis, and comparative genome analysis. Conclusions-This project generated a large EST resource for catfish that captured the majority of the catfish transcriptome. The parallel analysis of ESTs from two closely related Ictalurid catfishes should also provide powerful means for the evaluation of ancient and recent gene duplications, and for the development of high-density microarrays in catfish. The inter- and intra-specific SNPs identified from all catfish EST dataset assembly will greatly benefit the catfish introgression breeding program and whole genome association studies.

  5. A large-scale field study examining effects of exposure to clothianidin seed-treated canola on honey bee colony health, development, and overwintering success.

    PubMed

    Cutler, G Christopher; Scott-Dupree, Cynthia D; Sultan, Maryam; McFarlane, Andrew D; Brewer, Larry

    2014-01-01

    In summer 2012, we initiated a large-scale field experiment in southern Ontario, Canada, to determine whether exposure to clothianidin seed-treated canola (oil seed rape) has any adverse impacts on honey bees. Colonies were placed in clothianidin seed-treated or control canola fields during bloom, and thereafter were moved to an apiary with no surrounding crops grown from seeds treated with neonicotinoids. Colony weight gain, honey production, pest incidence, bee mortality, number of adults, and amount of sealed brood were assessed in each colony throughout summer and autumn. Samples of honey, beeswax, pollen, and nectar were regularly collected, and samples were analyzed for clothianidin residues. Several of these endpoints were also measured in spring 2013. Overall, colonies were vigorous during and after the exposure period, and we found no effects of exposure to clothianidin seed-treated canola on any endpoint measures. Bees foraged heavily on the test fields during peak bloom and residue analysis indicated that honey bees were exposed to low levels (0.5-2 ppb) of clothianidin in pollen. Low levels of clothianidin were detected in a few pollen samples collected toward the end of the bloom from control hives, illustrating the difficulty of conducting a perfectly controlled field study with free-ranging honey bees in agricultural landscapes. Overwintering success did not differ significantly between treatment and control hives, and was similar to overwintering colony loss rates reported for the winter of 2012-2013 for beekeepers in Ontario and Canada. Our results suggest that exposure to canola grown from seed treated with clothianidin poses low risk to honey bees. PMID:25374790

  6. Use of isotopic spike from Tropical Storm to understand water exchange on large scale: study case of Rafael Storm in the Lesser Antilles archipelago, October 2012.

    NASA Astrophysics Data System (ADS)

    Lambs, Luc

    2014-05-01

    Aim The tracking of the rainfall from Tropical Storm Raphael of mid October 2012 was used to better understand how the eco-hydrology and the water cycle function in wet areas, such as mangrove growing in salty ponds on a number of tropical islands. Location Guadeloupe and Saint Martin Islands in the Leeward Islands archipelago, Lesser Antilles. Methods Compared to normal tropical rainfall, tropical storms display distinct depleted heavy stable water isotopes which can be used as isotopic spikes to understand these special rainfall inflows. Rainfall, groundwater, river and pond water were sampled before, during and after the storm. Results In Guadeloupe where the tropical storm started, the rainfall isotopic signal reached values of d18O= -9 to -8 o on October 12-14th 2012, whereas the normal range is d18O= -4 to -2 o as measured from 2009 to 2012. It was possible to detect such a depleted signal in the groundwater and in the mangrove forest during the days after the storm event. Main conclusions The use of such natural isotopic spikes provides an opportunity to obtain a dynamic and time reference on a large scale for the study of the hydro-ecosystems and the effects on the impacted tropical islands. A few days after the cyclone, the isotopic spikes were found in river, groundwater and mangrove water pools with values up to d18O= -8.6 o . For the water basins on the windward side, the downhill salty pond water was almost completely renewed. By contrast, only 20 to 50 % of the water in the ponds located on the leeward side was renewed. No specific elevation in the d-excess values was noted, certainly due to the relatively long distance from the eye of the storm (180 to 300 km), which meant that there was no spray water evaporative process.

  7. Large-scale molecular dynamics study of jet breakup and ejecta production from shock-loaded copper with a hybrid method

    NASA Astrophysics Data System (ADS)

    Durand, O.; Soulard, L.

    2012-02-01

    Ejecta production from the free surface of metals under shock loading is investigated using large-scale molecular dynamics (MD) simulations performed with a new (hybrid) method. A copper crystal, in contact with vacuum and with a sinusoidal surface finish representative of the roughness produced by a machine polishing, is divided in two zones, bulk and surface, calculated with, respectively, Hugoniostat and NVE ensembles. The bulk part is simulated using the Hugoniostat technique, which allows a very large number of particles to reach a Hugoniot equilibrium state in a short physical time by the mean of a quasi-equilibrium MD simulation. The surface part is simulated with the NVE ensemble (microcanonical ensemble in which the total number N of particles, the total volume V, and the total energy E of the system are constant) in order to account for the non-equilibrium character of the ejection process. With this method, the morphology and the size distribution of the ejecta cloud generated by a system with 125 × 106 atoms are studied over 1 ns. The simulations show that the ejection phenomenon tends toward a steady state on long times (typically above 200 ps). The ejected particles remain spherical with time and their size distribution exhibits a power law scaling followed by a large-size residual in the large size limit. This behavior is in good agreement with most of distributions measured in fragmentation processes. In particular, the power law scaling reflects a self-similar behavior which seems to be successfully reproduced within the framework of a 2D percolation model although a direct analogy is still difficult to establish.

  8. Assembly of 500,000 inter-specific catfish expressed sequence tags and large scale gene-associated marker development for whole genome association studies

    PubMed Central

    2010-01-01

    Background Through the Community Sequencing Program, a catfish EST sequencing project was carried out through a collaboration between the catfish research community and the Department of Energy's Joint Genome Institute. Prior to this project, only a limited EST resource from catfish was available for the purpose of SNP identification. Results A total of 438,321 quality ESTs were generated from 8 channel catfish (Ictalurus punctatus) and 4 blue catfish (Ictalurus furcatus) libraries, bringing the number of catfish ESTs to nearly 500,000. Assembly of all catfish ESTs resulted in 45,306 contigs and 66,272 singletons. Over 35% of the unique sequences had significant similarities to known genes, allowing the identification of 14,776 unique genes in catfish. Over 300,000 putative SNPs have been identified, of which approximately 48,000 are high-quality SNPs identified from contigs with at least four sequences and the minor allele presence of at least two sequences in the contig. The EST resource should be valuable for identification of microsatellites, genome annotation, large-scale expression analysis, and comparative genome analysis. Conclusions This project generated a large EST resource for catfish that captured the majority of the catfish transcriptome. The parallel analysis of ESTs from two closely related Ictalurid catfishes should also provide powerful means for the evaluation of ancient and recent gene duplications, and for the development of high-density microarrays in catfish. The inter- and intra-specific SNPs identified from all catfish EST dataset assembly will greatly benefit the catfish introgression breeding program and whole genome association studies. PMID:20096101

  9. A large-scale field study examining effects of exposure to clothianidin seed-treated canola on honey bee colony health, development, and overwintering success

    PubMed Central

    Scott-Dupree, Cynthia D.; Sultan, Maryam; McFarlane, Andrew D.; Brewer, Larry

    2014-01-01

    In summer 2012, we initiated a large-scale field experiment in southern Ontario, Canada, to determine whether exposure to clothianidin seed-treated canola (oil seed rape) has any adverse impacts on honey bees. Colonies were placed in clothianidin seed-treated or control canola fields during bloom, and thereafter were moved to an apiary with no surrounding crops grown from seeds treated with neonicotinoids. Colony weight gain, honey production, pest incidence, bee mortality, number of adults, and amount of sealed brood were assessed in each colony throughout summer and autumn. Samples of honey, beeswax, pollen, and nectar were regularly collected, and samples were analyzed for clothianidin residues. Several of these endpoints were also measured in spring 2013. Overall, colonies were vigorous during and after the exposure period, and we found no effects of exposure to clothianidin seed-treated canola on any endpoint measures. Bees foraged heavily on the test fields during peak bloom and residue analysis indicated that honey bees were exposed to low levels (0.5–2 ppb) of clothianidin in pollen. Low levels of clothianidin were detected in a few pollen samples collected toward the end of the bloom from control hives, illustrating the difficulty of conducting a perfectly controlled field study with free-ranging honey bees in agricultural landscapes. Overwintering success did not differ significantly between treatment and control hives, and was similar to overwintering colony loss rates reported for the winter of 2012–2013 for beekeepers in Ontario and Canada. Our results suggest that exposure to canola grown from seed treated with clothianidin poses low risk to honey bees. PMID:25374790

  10. NASA's Arctic-Boreal Vulnerability Experiment: A large-scale study of environmental change in Western North America and its implications for ecological systems and society

    NASA Astrophysics Data System (ADS)

    Kasischke, E. S.; Hayes, D. J.; Griffith, P. C.; Larson, E. K.; Wickland, D. E.

    2013-12-01

    Climate change in high northern latitudes is unfolding faster than anywhere else on Earth, resulting in widespread changes in landscape structure and ecosystem function in the Arctic-Boreal Region (ABR). Recognizing its sensitivity, vulnerability and global importance, national- and international-level scientific efforts are now advancing our ability to observe, understand and model the complex, multi-scale processes that drive the ABR's natural and social systems. Long at the edge of our mental map of the world, environmental change in the ABR is increasingly becoming the focus of numerous policy discussions at the highest levels of decision-making. To improve our understanding of environmental change and its impacts in the ABR, the Terrestrial Ecology Program of the U.S. National Aeronautics and Space Administration (NASA) is planning its next major field campaign for Western Canada and Alaska. The field campaign will be based on the Arctic-Boreal Vulnerability Experiment (ABoVE) concept as described in the Revised Executive Summary from the ABoVE Scoping Study Report. The original Scoping Study Report provided the proof-of-concept demonstration of scientific importance and feasibility for this large-scale study. In early 2013, NASA announced the selection of the ABoVE Science Definition Team, which is charged with developing the Concise Experiment Plan for the campaign. Here, we outline the conceptual basis for ABoVE and present the compelling rationale explaining the scientific and societal importance of the study. We present the current status of the planning process, which includes development of the science questions to drive ABoVE research; the study design for the field campaign to address them; and the interagency and international collaborations necessary for implementation. The ABoVE study will focus on 1) developing a fuller understanding of ecosystem vulnerability to climate change in the ABR, and 2) providing the scientific information required to

  11. Large Scale Homing in Honeybees

    PubMed Central

    Pahl, Mario; Zhu, Hong; Tautz, Jürgen; Zhang, Shaowu

    2011-01-01

    Honeybee foragers frequently fly several kilometres to and from vital resources, and communicate those locations to their nest mates by a symbolic dance language. Research has shown that they achieve this feat by memorizing landmarks and the skyline panorama, using the sun and polarized skylight as compasses and by integrating their outbound flight paths. In order to investigate the capacity of the honeybees' homing abilities, we artificially displaced foragers to novel release spots at various distances up to 13 km in the four cardinal directions. Returning bees were individually registered by a radio frequency identification (RFID) system at the hive entrance. We found that homing rate, homing speed and the maximum homing distance depend on the release direction. Bees released in the east were more likely to find their way back home, and returned faster than bees released in any other direction, due to the familiarity of global landmarks seen from the hive. Our findings suggest that such large scale homing is facilitated by global landmarks acting as beacons, and possibly the entire skyline panorama. PMID:21602920

  12. Bridging local scale ground-based tree assessments to large scale inventory and remote sensing data to quantify landscape representativeness of an atmospheric study tower

    NASA Astrophysics Data System (ADS)

    Bizjack, M.; Brooks, B.; Dietze, M. C.; Serbin, S. P.

    2012-12-01

    identify locations that are not well represented. Quantifying small and large scale representativeness of these towers allows studies that use tower data to quantify the confidence in representation of data used in model validation.

  13. Analysis and experimental study on formation conditions of large-scale barrier-free diffuse atmospheric pressure air plasmas in repetitive pulse mode

    SciTech Connect

    Li, Lee Liu, Lun; Liu, Yun-Long; Bin, Yu; Ge, Ya-Feng; Lin, Fo-Chang

    2014-01-14

    Atmospheric air diffuse plasmas have enormous application potential in various fields of science and technology. Without dielectric barrier, generating large-scale air diffuse plasmas is always a challenging issue. This paper discusses and analyses the formation mechanism of cold homogenous plasma. It is proposed that generating stable diffuse atmospheric plasmas in open air should meet the three conditions: high transient power with low average power, excitation in low average E-field with locally high E-field region, and multiple overlapping electron avalanches. Accordingly, an experimental configuration of generating large-scale barrier-free diffuse air plasmas is designed. Based on runaway electron theory, a low duty-ratio, high voltage repetitive nanosecond pulse generator is chosen as a discharge excitation source. Using the wire-electrodes with small curvature radius, the gaps with highly non-uniform E-field are structured. Experimental results show that the volume-scaleable, barrier-free, homogeneous air non-thermal plasmas have been obtained between the gap spacing with the copper-wire electrodes. The area of air cold plasmas has been up to hundreds of square centimeters. The proposed formation conditions of large-scale barrier-free diffuse air plasmas are proved to be reasonable and feasible.

  14. Analysis and experimental study on formation conditions of large-scale barrier-free diffuse atmospheric pressure air plasmas in repetitive pulse mode

    NASA Astrophysics Data System (ADS)

    Li, Lee; Liu, Lun; Liu, Yun-Long; Bin, Yu; Ge, Ya-Feng; Lin, Fo-Chang

    2014-01-01

    Atmospheric air diffuse plasmas have enormous application potential in various fields of science and technology. Without dielectric barrier, generating large-scale air diffuse plasmas is always a challenging issue. This paper discusses and analyses the formation mechanism of cold homogenous plasma. It is proposed that generating stable diffuse atmospheric plasmas in open air should meet the three conditions: high transient power with low average power, excitation in low average E-field with locally high E-field region, and multiple overlapping electron avalanches. Accordingly, an experimental configuration of generating large-scale barrier-free diffuse air plasmas is designed. Based on runaway electron theory, a low duty-ratio, high voltage repetitive nanosecond pulse generator is chosen as a discharge excitation source. Using the wire-electrodes with small curvature radius, the gaps with highly non-uniform E-field are structured. Experimental results show that the volume-scaleable, barrier-free, homogeneous air non-thermal plasmas have been obtained between the gap spacing with the copper-wire electrodes. The area of air cold plasmas has been up to hundreds of square centimeters. The proposed formation conditions of large-scale barrier-free diffuse air plasmas are proved to be reasonable and feasible.

  15. Development of an ion-pair liquid chromatography-high resolution mass spectrometry method for determination of organophosphate pesticide metabolites in large-scale biomonitoring studies.

    PubMed

    Cequier, Enrique; Sakhi, Amrit Kaur; Haug, Line Småstuen; Thomsen, Cathrine

    2016-07-01

    Organophosphate based pesticides are widely used in the agricultural sector, and exposure to these chemicals is common for the general population. Pesticides are toxic due to the inhibition of acetylcholinesterases, and the potential for adverse health effects have been investigated in past and recent studies. Human biomonitoring of organophosphate pesticide exposure is carried out through the determination of the metabolites in urine (dialkylphosphates, DAPs). Hereby we present a new method for determination of the 6 non-specific metabolites dimethyl phosphate (DMP), diethyl phosphate (DEP), dimethyl thiophosphate (DMTP), diethyl thiophosphate (DETP), dimethyl dithiophosphate (DMDTP), and diethyl dithiophosphate (DEDTP) in urine based on off-line solid phase extraction (anion exchange, 96-well plates) followed by ion-pair ultra-performance liquid chromatography time-of-flight mass spectrometry. Recoveries and accuracies in control urine spiked at 5ng/mL ranged from 48% to109% and from 91% to 115%, respectively. The method limits of detection for the DAPs were 1.2ng/mL for DMP, 0.38ng/mL for DEP, 0.20ng/mL for DMTP, 0.33ng/mL for DETP, 0.64ng/mL for DMDTP, and 0.15ng/mL for DEDTP. The method was applied to samples from a Norwegian mother/child study group (n=48/56) and the DAPs detection frequencies in urine from mothers and children were about: 40% for DMP, 95% for DEP, 96% for DMTP, 50% for DETP, 15% for DMDTP, and 1% for DEDTP. In both mothers and children, the most abundant DAPs were DMTP (median 2.4/5.2ng/mL) and DEP (median 2.6/3.4ng/mL) followed by DMP (median 1.5/2.1ng/mL). The SG corrected concentrations of DEP and DETP in mothers were statistically higher than in children (p-value<0.05; Mann-Whitney test) which might suggest a higher exposure to pesticides in these mothers, or significant differences in toxicokinetics between adults and children. The method was proven robust and suitable for large-scale biomonitoring studies. PMID:27264744

  16. Large Scale Nanolaminate Deformable Mirror

    SciTech Connect

    Papavasiliou, A; Olivier, S; Barbee, T; Miles, R; Chang, K

    2005-11-30

    This work concerns the development of a technology that uses Nanolaminate foils to form light-weight, deformable mirrors that are scalable over a wide range of mirror sizes. While MEMS-based deformable mirrors and spatial light modulators have considerably reduced the cost and increased the capabilities of adaptive optic systems, there has not been a way to utilize the advantages of lithography and batch-fabrication to produce large-scale deformable mirrors. This technology is made scalable by using fabrication techniques and lithography that are not limited to the sizes of conventional MEMS devices. Like many MEMS devices, these mirrors use parallel plate electrostatic actuators. This technology replicates that functionality by suspending a horizontal piece of nanolaminate foil over an electrode by electroplated nickel posts. This actuator is attached, with another post, to another nanolaminate foil that acts as the mirror surface. Most MEMS devices are produced with integrated circuit lithography techniques that are capable of very small line widths, but are not scalable to large sizes. This technology is very tolerant of lithography errors and can use coarser, printed circuit board lithography techniques that can be scaled to very large sizes. These mirrors use small, lithographically defined actuators and thin nanolaminate foils allowing them to produce deformations over a large area while minimizing weight. This paper will describe a staged program to develop this technology. First-principles models were developed to determine design parameters. Three stages of fabrication will be described starting with a 3 x 3 device using conventional metal foils and epoxy to a 10-across all-metal device with nanolaminate mirror surfaces.

  17. Large-Scale Information Systems

    SciTech Connect

    D. M. Nicol; H. R. Ammerlahn; M. E. Goldsby; M. M. Johnson; D. E. Rhodes; A. S. Yoshimura

    2000-12-01

    Large enterprises are ever more dependent on their Large-Scale Information Systems (LSLS), computer systems that are distinguished architecturally by distributed components--data sources, networks, computing engines, simulations, human-in-the-loop control and remote access stations. These systems provide such capabilities as workflow, data fusion and distributed database access. The Nuclear Weapons Complex (NWC) contains many examples of LSIS components, a fact that motivates this research. However, most LSIS in use grew up from collections of separate subsystems that were not designed to be components of an integrated system. For this reason, they are often difficult to analyze and control. The problem is made more difficult by the size of a typical system, its diversity of information sources, and the institutional complexities associated with its geographic distribution across the enterprise. Moreover, there is no integrated approach for analyzing or managing such systems. Indeed, integrated development of LSIS is an active area of academic research. This work developed such an approach by simulating the various components of the LSIS and allowing the simulated components to interact with real LSIS subsystems. This research demonstrated two benefits. First, applying it to a particular LSIS provided a thorough understanding of the interfaces between the system's components. Second, it demonstrated how more rapid and detailed answers could be obtained to questions significant to the enterprise by interacting with the relevant LSIS subsystems through simulated components designed with those questions in mind. In a final, added phase of the project, investigations were made on extending this research to wireless communication networks in support of telemetry applications.

  18. Large scale and cloud scale dynamics and microphysics in the formation and evolution of a TTL cirrus : a case modelling study

    NASA Astrophysics Data System (ADS)

    Podglajen, Aurélien; Plougonven, Riwal; Hertzog, Albert; Legras, Bernard

    2015-04-01

    Cirrus clouds in the tropical tropopause layer (TTL) control dehydration of air masses entering the stratosphere and strongly contribute to the local radiative heating. In this study, we aim at understanding, through a real case simulation, the dynamics controlling the formation and life cycle of a cirrus cloud event in the TTL. We also aim at quantifying the chemical and radiative impacts of the clouds. To do this, we use the Weather Research and Forecast (WRF) model to simulate a large scale TTL cirrus event happening in January 2009 (27-29) over the Eastern Pacific, which has been extensively described through satellite observations (Taylor et al., 2011). Comparison of simulated and observed high clouds shows a fair agreement, and validates the reference simulation regarding cloud extension, location and life time. The simulation and Lagrangian trajectories within the simulation are then used to characterize the evolution of the cloud : displacement, Lagrangian life time and links with dynamics. The efficiency of dehydration by such clouds is also examined. Sensitivity tests were performed to evaluate the importance of different microphysics schemes and initial and boundary conditions to accurately simulate the cirrus. As expected, both were found to have strong impacts. In particular, there were substantial differences between simulations using different initial and boundary conditions from atmospheric analyses (NCEP CFSR and ECMWF). This illustrates the primordial role of accurate vapour and dynamics for realistic cirrus modelling, on top of the need for appropriate microphysics. Last, we examined the effects of cloud radiative heating. Long wave radiative heating in cirrus clouds has been invoked to induce a cloud scale circulation that would lengthen the cloud lifetime, and increase the size of its dehydration area (Dinh et al. 2010). To try to diagnose this, we have carried out simulations using different radiative schemes, including or suppressing the

  19. Cooking practices, air quality, and the acceptability of advanced cookstoves in Haryana, India: an exploratory study to inform large-scale interventions

    PubMed Central

    Mukhopadhyay, Rupak; Sambandam, Sankar; Pillarisetti, Ajay; Jack, Darby; Mukhopadhyay, Krishnendu; Balakrishnan, Kalpana; Vaswani, Mayur; Bates, Michael N.; Kinney, Patrick L.; Arora, Narendra; Smith, Kirk R.

    2012-01-01

    Background In India, approximately 66% of households rely on dung or woody biomass as fuels for cooking. These fuels are burned under inefficient conditions, leading to household air pollution (HAP) and exposure to smoke containing toxic substances. Large-scale intervention efforts need to be informed by careful piloting to address multiple methodological and sociocultural issues. This exploratory study provides preliminary data for such an exercise from Palwal District, Haryana, India. Methods Traditional cooking practices were assessed through semi-structured interviews in participating households. Philips and Oorja, two brands of commercially available advanced cookstoves with small blowers to improve combustion, were deployed in these households. Concentrations of particulate matter (PM) with a diameter <2.5 μm (PM2.5) and carbon monoxide (CO) related to traditional stove use were measured using real-time and integrated personal, microenvironmental samplers for optimizing protocols to evaluate exposure reduction. Qualitative data on acceptability of advanced stoves and objective measures of stove usage were also collected. Results Twenty-eight of the thirty-two participating households had outdoor primary cooking spaces. Twenty households had liquefied petroleum gas (LPG) but preferred traditional stoves as the cost of LPG was higher and because meals cooked on traditional stoves were perceived to taste better. Kitchen area concentrations and kitchen personal concentrations assessed during cooking events were very high, with respective mean PM2.5 concentrations of 468 and 718 µg/m3. Twenty-four hour outdoor concentrations averaged 400 µg/m3. Twenty-four hour personal CO concentrations ranged between 0.82 and 5.27 ppm. The Philips stove was used more often and for more hours than the Oorja. Conclusions The high PM and CO concentrations reinforce the need for interventions that reduce HAP exposure in the aforementioned community. Of the two stoves tested

  20. A robust methodology for conducting large-scale assessments of current and future water availability and use: A case study in Tasmania, Australia

    NASA Astrophysics Data System (ADS)

    Post, D. A.; Chiew, F. H. S.; Teng, J.; Viney, N. R.; Ling, F. L. N.; Harrington, G.; Crosbie, R. S.; Graham, B.; Marvanek, S.; McLoughlin, R.

    2012-01-01

    SummaryThis paper describes a robust methodology for determining current surface and groundwater availability and use, as well as future changes due to climate and landuse changes. It is based on the methodology developed by CSIRO to deliver on four large-scale water availability assessments conducted in the Murray-Darling Basin, Northern Australia, south-west Western Australia, and Tasmania. It will focus on the application of the technique and results from Tasmania, providing a representative example of the approach used. The genesis of this work was the explicit desire by Australian State and Commonwealth governments to use the outputs of these water availability assessments for assisting the formation of state and federal government water policy. For example, the results of the work have already been utilised as a key technical input to decision making on funding for proposed irrigation projects in Tasmania. Outputs from the other three study areas have been used to assist in developing a water resources plan for the Murray-Darling Basin, to guide infrastructure development in northern Australia, and to plan for reductions in water availability due to climate change in south-west Western Australia. The methodology assesses current water availability through the application of rainfall-runoff and river models, and recharge and groundwater models. These were calibrated to streamflow records and groundwater levels, and parameterised using estimates of current surface and groundwater extractions and use. Having derived an estimate of current water availability, the impacts of future climate change on water availability were determined through deriving projected changes in rainfall and potential evaporation from 15 IPCC AR4 global climate models. The changes in rainfall were then dynamically downscaled using the CSIRO-CCAM model over the study area (50,000 km 2). The future climate sequence was then derived by modifying the historical 84-year climate sequence based

  1. Estimation of seawater-groundwater exchange rate: case study in a tidal flat with a large-scale seepage face (Laizhou Bay, China)

    NASA Astrophysics Data System (ADS)

    Ma, Qian; Li, Hailong; Wang, Xuejing; Wang, Chaoyue; Wan, Li; Wang, Xusheng; Jiang, Xiaowei

    2015-03-01

    The exchange rate between seawater and groundwater in a tidal flat was investigated at Laizhou Bay, China, where there are large-scale seepage faces with horizontal extension of several hundred meters developed during low tides. Taking into account the effects of seepage face and density, a simple and efficient method for estimating seawater-groundwater exchange rate is proposed, based on field measurements of groundwater hydraulic head, temperature and salinity. First, the exchange rate at each well was obtained using the generalized Darcy's law, then the results were interpolated and integrated along the whole transect. The total submarine groundwater discharge (SGD) and inflow were estimated to be 8.8 and 15.3 m3 d-1 m-1, respectively. The spatial distributions of SGD and inflow were different from those of sandy or gravel beaches possibly owing to the low-permeability sediment (silty sand with mud), very gentle slope, and the large-scale seepage faces. A freshwater discharge tube was identified near the low-tide line, as evidenced by significant increase in outflow and low salinity of groundwater observed there. The SGD from the seepage faces accounted for ˜21 % of the total SGD. The outflow rate that occurred from the seepage faces, and the ratio of the outflow from the seepage faces to the total outflow, decreased seaward significantly and monotonically.

  2. Unfolding large-scale maps.

    PubMed

    Jenkins, Glyn

    2003-12-01

    This is an account of the development and use of genetic maps, from humble beginnings at the hands of Thomas Hunt Morgan, to the sophistication of genome sequencing. The review charters the emergence of molecular marker maps exploiting DNA polymorphism, the renaissance of cytogenetics through the use of fluorescence in situ hybridisation, and the discovery and isolation of genes by map-based cloning. The historical significance of sequencing of DNA prefaces a section describing the sequencing of genomes, the ascendancy of particular model organisms, and the utility and limitations of comparative genomic and functional genomic approaches to further our understanding of the control of biological processes. Emphasis is given throughout the treatise as to how the structure and biological behaviour of the DNA molecule underpin the technological development and biological applications of maps. PMID:14663511

  3. Roary: rapid large-scale prokaryote pan genome analysis

    PubMed Central

    Page, Andrew J.; Cummins, Carla A.; Hunt, Martin; Wong, Vanessa K.; Reuter, Sandra; Holden, Matthew T.G.; Fookes, Maria; Falush, Daniel; Keane, Jacqueline A.; Parkhill, Julian

    2015-01-01

    Summary: A typical prokaryote population sequencing study can now consist of hundreds or thousands of isolates. Interrogating these datasets can provide detailed insights into the genetic structure of prokaryotic genomes. We introduce Roary, a tool that rapidly builds large-scale pan genomes, identifying the core and accessory genes. Roary makes construction of the pan genome of thousands of prokaryote samples possible on a standard desktop without compromising on the accuracy of results. Using a single CPU Roary can produce a pan genome consisting of 1000 isolates in 4.5 hours using 13 GB of RAM, with further speedups possible using multiple processors. Availability and implementation: Roary is implemented in Perl and is freely available under an open source GPLv3 license from http://sanger-pathogens.github.io/Roary Contact: roary@sanger.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26198102

  4. First-principles studies on vacancy-modified interstitial diffusion mechanism of oxygen in nickel, associated with large-scale atomic simulation techniques

    SciTech Connect

    Fang, H. Z.; Shang, S. L.; Wang, Y.; Liu, Z. K.; Alfonso, D.; Alman, D. E.; Shin, Y. K.; Zou, C. Y.; Duin, A. C. T. van; Lei, Y. K.; Wang, G. F.

    2014-01-28

    This paper is concerned with the prediction of oxygen diffusivities in fcc nickel from first-principles calculations and large-scale atomic simulations. Considering only the interstitial octahedral to tetrahedral to octahedral minimum energy pathway for oxygen diffusion in fcc lattice, greatly underestimates the migration barrier and overestimates the diffusivities by several orders of magnitude. The results indicate that vacancies in the Ni-lattice significantly impact the migration barrier of oxygen in nickel. Incorporation of the effect of vacancies results in predicted diffusivities consistent with available experimental data. First-principles calculations show that at high temperatures the vacancy concentration is comparable to the oxygen solubility, and there is a strong binding energy and a redistribution of charge density between the oxygen atom and vacancy. Consequently, there is a strong attraction between the oxygen and vacancy in the Ni lattice, which impacts diffusion.

  5. Distribution probability of large-scale landslides in central Nepal

    NASA Astrophysics Data System (ADS)

    Timilsina, Manita; Bhandary, Netra P.; Dahal, Ranjan Kumar; Yatabe, Ryuichi

    2014-12-01

    Large-scale landslides in the Himalaya are defined as huge, deep-seated landslide masses that occurred in the geological past. They are widely distributed in the Nepal Himalaya. The steep topography and high local relief provide high potential for such failures, whereas the dynamic geology and adverse climatic conditions play a key role in the occurrence and reactivation of such landslides. The major geoscientific problems related with such large-scale landslides are 1) difficulties in their identification and delineation, 2) sources of small-scale failures, and 3) reactivation. Only a few scientific publications have been published concerning large-scale landslides in Nepal. In this context, the identification and quantification of large-scale landslides and their potential distribution are crucial. Therefore, this study explores the distribution of large-scale landslides in the Lesser Himalaya. It provides simple guidelines to identify large-scale landslides based on their typical characteristics and using a 3D schematic diagram. Based on the spatial distribution of landslides, geomorphological/geological parameters and logistic regression, an equation of large-scale landslide distribution is also derived. The equation is validated by applying it to another area. For the new area, the area under the receiver operating curve of the landslide distribution probability in the new area is 0.699, and a distribution probability value could explain > 65% of existing landslides. Therefore, the regression equation can be applied to areas of the Lesser Himalaya of central Nepal with similar geological and geomorphological conditions.

  6. Investigating the Causal Relationship of C-Reactive Protein with 32 Complex Somatic and Psychiatric Outcomes: A Large-Scale Cross-Consortium Mendelian Randomization Study

    PubMed Central

    Prins, Bram. P.; Nolte, Ilja; Franceschini, Nora; Guterriez Achury, Javier; Mistry, Vanisha; Bradfield, Jonathan P.; Valdes, Ana M.; Bras, Jose; Shatunov, Aleksey; Lu, Chen; Han, Buhm; Raychaudhuri, Soumya; Bevan, Steve; Mayes, Maureen D.; Tsoi, Lam C.; Evangelou, Evangelos; Nair, Rajan P.; Grant, Struan F. A.; Polychronakos, Constantin; Radstake, Timothy R. D.; van Heel, David A.; Wood, Nicholas W.; Al-Chalabi, Ammar; Dehghan, Abbas; Hakonarson, Hakon; Markus, Hugh S.; Elder, James T.; Knight, Jo; Arking, Dan E.; Spector, Timothy D.; Koeleman, Bobby P. C.; van Duijn, Cornelia M.; Martin, Javier; Morris, Andrew P.; Weersma, Rinse K.; Wijmenga, Cisca; Munroe, Patricia B.; Perry, John R. B.; Pouget, Jennie G.; Jamshidi, Yalda; Snieder, Harold; Alizadeh, Behrooz Z.

    2016-01-01

    Background C-reactive protein (CRP) is associated with immune, cardiometabolic, and psychiatric traits and diseases. Yet it is inconclusive whether these associations are causal. Methods and Findings We performed Mendelian randomization (MR) analyses using two genetic risk scores (GRSs) as instrumental variables (IVs). The first GRS consisted of four single nucleotide polymorphisms (SNPs) in the CRP gene (GRSCRP), and the second consisted of 18 SNPs that were significantly associated with CRP levels in the largest genome-wide association study (GWAS) to date (GRSGWAS). To optimize power, we used summary statistics from GWAS consortia and tested the association of these two GRSs with 32 complex somatic and psychiatric outcomes, with up to 123,865 participants per outcome from populations of European ancestry. We performed heterogeneity tests to disentangle the pleiotropic effect of IVs. A Bonferroni-corrected significance level of less than 0.0016 was considered statistically significant. An observed p-value equal to or less than 0.05 was considered nominally significant evidence for a potential causal association, yet to be confirmed. The strengths (F-statistics) of the IVs were 31.92–3,761.29 and 82.32–9,403.21 for GRSCRP and GRSGWAS, respectively. CRP GRSGWAS showed a statistically significant protective relationship of a 10% genetically elevated CRP level with the risk of schizophrenia (odds ratio [OR] 0.86 [95% CI 0.79–0.94]; p < 0.001). We validated this finding with individual-level genotype data from the schizophrenia GWAS (OR 0.96 [95% CI 0.94–0.98]; p < 1.72 × 10−6). Further, we found that a standardized CRP polygenic risk score (CRPPRS) at p-value thresholds of 1 × 10−4, 0.001, 0.01, 0.05, and 0.1 using individual-level data also showed a protective effect (OR < 1.00) against schizophrenia; the first CRPPRS (built of SNPs with p < 1 × 10−4) showed a statistically significant (p < 2.45 × 10−4) protective effect with an OR of 0.97 (95

  7. Large-Scale Reform Comes of Age

    ERIC Educational Resources Information Center

    Fullan, Michael

    2009-01-01

    This article reviews the history of large-scale education reform and makes the case that large-scale or whole system reform policies and strategies are becoming increasingly evident. The review briefly addresses the pre 1997 period concluding that while the pressure for reform was mounting that there were very few examples of deliberate or…

  8. Large-scale infrared scene projectors

    NASA Astrophysics Data System (ADS)

    Murray, Darin A.

    1999-07-01

    Large-scale infrared scene projectors, typically have unique opto-mechanical characteristics associated to their application. This paper outlines two large-scale zoom lens assemblies with different environmental and package constraints. Various challenges and their respective solutions are discussed and presented.

  9. Population generation for large-scale simulation

    NASA Astrophysics Data System (ADS)

    Hannon, Andrew C.; King, Gary; Morrison, Clayton; Galstyan, Aram; Cohen, Paul

    2005-05-01

    Computer simulation is used to research phenomena ranging from the structure of the space-time continuum to population genetics and future combat.1-3 Multi-agent simulations in particular are now commonplace in many fields.4, 5 By modeling populations whose complex behavior emerges from individual interactions, these simulations help to answer questions about effects where closed form solutions are difficult to solve or impossible to derive.6 To be useful, simulations must accurately model the relevant aspects of the underlying domain. In multi-agent simulation, this means that the modeling must include both the agents and their relationships. Typically, each agent can be modeled as a set of attributes drawn from various distributions (e.g., height, morale, intelligence and so forth). Though these can interact - for example, agent height is related to agent weight - they are usually independent. Modeling relations between agents, on the other hand, adds a new layer of complexity, and tools from graph theory and social network analysis are finding increasing application.7, 8 Recognizing the role and proper use of these techniques, however, remains the subject of ongoing research. We recently encountered these complexities while building large scale social simulations.9-11 One of these, the Hats Simulator, is designed to be a lightweight proxy for intelligence analysis problems. Hats models a "society in a box" consisting of many simple agents, called hats. Hats gets its name from the classic spaghetti western, in which the heroes and villains are known by the color of the hats they wear. The Hats society also has its heroes and villains, but the challenge is to identify which color hat they should be wearing based on how they behave. There are three types of hats: benign hats, known terrorists, and covert terrorists. Covert terrorists look just like benign hats but act like terrorists. Population structure can make covert hat identification significantly more

  10. Composite and case study analyses of the large-scale environments associated with West Pacific Polar and subtropical vertical jet superposition events

    NASA Astrophysics Data System (ADS)

    Handlos, Zachary J.

    Though considerable research attention has been devoted to examination of the Northern Hemispheric polar and subtropical jet streams, relatively little has been directed toward understanding the circumstances that conspire to produce the relatively rare vertical superposition of these usually separate features. This dissertation investigates the structure and evolution of large-scale environments associated with jet superposition events in the northwest Pacific. An objective identification scheme, using NCEP/NCAR Reanalysis 1 data, is employed to identify all jet superpositions in the west Pacific (30-40°N, 135-175°E) for boreal winters (DJF) between 1979/80 - 2009/10. The analysis reveals that environments conducive to west Pacific jet superposition share several large-scale features usually associated with East Asian Winter Monsoon (EAWM) northerly cold surges, including the presence of an enhanced Hadley Cell-like circulation within the jet entrance region. It is further demonstrated that several EAWM indices are statistically significantly correlated with jet superposition frequency in the west Pacific. The life cycle of EAWM cold surges promotes interaction between tropical convection and internal jet dynamics. Low potential vorticity (PV), high theta e tropical boundary layer air, exhausted by anomalous convection in the west Pacific lower latitudes, is advected poleward towards the equatorward side of the jet in upper tropospheric isentropic layers resulting in anomalous anticyclonic wind shear that accelerates the jet. This, along with geostrophic cold air advection in the left jet entrance region that drives the polar tropopause downward through the jet core, promotes the development of the deep, vertical PV wall characteristic of superposed jets. West Pacific jet superpositions preferentially form within an environment favoring the aforementioned characteristics regardless of EAWM seasonal strength. Post-superposition, it is shown that the west Pacific

  11. Large-scale Forest Resource Dynamic Monitoring Using Worldview-2 data—A Case Study in Pingtan Island, Fujian Province, China

    NASA Astrophysics Data System (ADS)

    Wei, Huang; Xiaoqin, Wang; Yunzhi, Chen; Xiaocheng, Zhou; Nengwen, Xiao

    2014-03-01

    Due to its capacity to describe detailed information., high spatial resolution remote sensing technology has been used increasely in forest resource dynamic monitoring, especially at large scale. Based on 0.5m resolution Worldview-2 data and 1:10000 forest stand-wise vector data, monitoring on forest resource dynamic during 2010-2011 in Pingtan Island is carried out. Object-oriented classification method was adopted. Firstly, multi-resolution segmentation was done on Worldview-2 image, which produced two levels of objects. The boundary of objects at the first level corresponded to boundary of individual polygon in the forest stand-wise data coverage. The more homogeneous objects at the second level were smaller and within the objects at the first level. Then, hierarchical supervised classification was used to classify the second-level objects. The objects were assigned to seven different thematic layers according to the attribute of land use types of forest stand-wise data, then object samples were selected for supervised classification to identify the change of objects in each layer. Changed objects larger than 0.0667hm2 were preserved and used for dynamics analysis. The classification accuracy was assessed by field survey and one-by-one visual interpretation. The result indicated that the overall accuracy was 90.85%. Forest in Pingtan Island had changed greatly during 2010-2011, area of forest increase and decrease is 2314.7817 hm2 and 1089.6508 hm2 respectively.

  12. Food fortification as a complementary strategy for the elimination of micronutrient deficiencies: case studies of large scale food fortification in two Indian States.

    PubMed

    Bhagwat, Sadhana; Gulati, Deepti; Sachdeva, Ruchika; Sankar, Rajan

    2014-01-01

    The burden of micronutrient malnutrition is very high in India. Food fortification is one of the most cost-effective and sustainable strategies to deliver micronutrients to large population groups. Global Alliance for Improved Nutrition (GAIN) is supporting large-scale, voluntary, staple food fortification in Rajasthan and Madhya Pradesh because of the high burden of malnutrition, availability of industries capable of and willing to introduce fortified staples, consumption patterns of target foods and a conducive and enabling environment. High extraction wheat flour from roller flour mills, edible soybean oil and milk from dairy cooperatives were chosen as the vehicles for fortification. Micronutrients and levels of fortification were selected based on vehicle characteristics and consumption levels. Industry recruitment was done after a careful assessment of capability and willingness. Production units were equipped with necessary equipment for fortification. Staffs were trained in fortification and quality control. Social marketing and communication activities were carried out as per the strategy developed. A state food fortification alliance was formed in Madhya Pradesh with all relevant stakeholders. Over 260,000 MT of edible oil, 300,000 MT of wheat flour and 500,000 MT of milk are being fortified annually and marketed. Rajasthan is also distributing 840,000 MT of fortified wheat flour annually through its Public Distribution System and 1.1 million fortified Mid-day meals daily through the centralised kitchens. Concurrent monitoring in Rajasthan and Madhya has demonstrated high compliance with all quality standards in fortified foods. PMID:25384726

  13. Aggregation behavior of amphiphilic cyclodextrins in a nonpolar solvent: evidence of large-scale structures by atomistic molecular dynamics simulations and solution studies.

    PubMed

    Raffaini, Giuseppina; Ganazzoli, Fabio; Mazzaglia, Antonino

    2016-01-01

    Chemically modified cyclodextrins carrying both hydrophobic and hydrophilic substituents may form supramolecular aggregates or nanostructures of great interest. These systems have been usually investigated and characterized in water for their potential use as nanocarriers for drug delivery, but they can also aggregate in apolar solvents, as shown in the present paper through atomistic molecular dynamics simulations and dynamic light scattering measurements. The simulations, carried out with a large number of molecules in vacuo adopting an unbiased bottom-up approach, suggest the formation of bidimensional structures with characteristic length scales of the order of 10 nm, although some of these sizes are possibly affected by the assumed periodicity of the simulation cell, in particular at longer lengths. In any case, these nanostructures are stable at least from the kinetic viewpoint for relatively long times thanks to the large number of intermolecular interactions of dipolar and dispersive nature. The dynamic light scattering experiments indicate the presence of aggregates with a hydrodynamic radius of the order of 80 nm and a relatively modest polydispersity, even though smaller nanometer-sized aggregates cannot be fully ruled out. Taken together, these simulation and experimental results indicate that amphiphilically modified cyclodextrins do also form large-scale nanoaggregates even in apolar solvents. PMID:26877809

  14. Aggregation behavior of amphiphilic cyclodextrins in a nonpolar solvent: evidence of large-scale structures by atomistic molecular dynamics simulations and solution studies

    PubMed Central

    Ganazzoli, Fabio; Mazzaglia, Antonino

    2016-01-01

    Summary Chemically modified cyclodextrins carrying both hydrophobic and hydrophilic substituents may form supramolecular aggregates or nanostructures of great interest. These systems have been usually investigated and characterized in water for their potential use as nanocarriers for drug delivery, but they can also aggregate in apolar solvents, as shown in the present paper through atomistic molecular dynamics simulations and dynamic light scattering measurements. The simulations, carried out with a large number of molecules in vacuo adopting an unbiased bottom-up approach, suggest the formation of bidimensional structures with characteristic length scales of the order of 10 nm, although some of these sizes are possibly affected by the assumed periodicity of the simulation cell, in particular at longer lengths. In any case, these nanostructures are stable at least from the kinetic viewpoint for relatively long times thanks to the large number of intermolecular interactions of dipolar and dispersive nature. The dynamic light scattering experiments indicate the presence of aggregates with a hydrodynamic radius of the order of 80 nm and a relatively modest polydispersity, even though smaller nanometer-sized aggregates cannot be fully ruled out. Taken together, these simulation and experimental results indicate that amphiphilically modified cyclodextrins do also form large-scale nanoaggregates even in apolar solvents. PMID:26877809

  15. Large Scale Quantum Simulations of Nuclear Pasta

    NASA Astrophysics Data System (ADS)

    Fattoyev, Farrukh J.; Horowitz, Charles J.; Schuetrumpf, Bastian

    2016-03-01

    Complex and exotic nuclear geometries collectively referred to as ``nuclear pasta'' are expected to naturally exist in the crust of neutron stars and in supernovae matter. Using a set of self-consistent microscopic nuclear energy density functionals we present the first results of large scale quantum simulations of pasta phases at baryon densities 0 . 03 < ρ < 0 . 10 fm-3, proton fractions 0 . 05 study the role and impact of the nuclear symmetry energy on these pasta configurations. This work is supported in part by DOE Grants DE-FG02-87ER40365 (Indiana University) and DE-SC0008808 (NUCLEI SciDAC Collaboration).

  16. Large scale cryogenic fluid systems testing

    NASA Technical Reports Server (NTRS)

    1992-01-01

    NASA Lewis Research Center's Cryogenic Fluid Systems Branch (CFSB) within the Space Propulsion Technology Division (SPTD) has the ultimate goal of enabling the long term storage and in-space fueling/resupply operations for spacecraft and reusable vehicles in support of space exploration. Using analytical modeling, ground based testing, and on-orbit experimentation, the CFSB is studying three primary categories of fluid technology: storage, supply, and transfer. The CFSB is also investigating fluid handling, advanced instrumentation, and tank structures and materials. Ground based testing of large-scale systems is done using liquid hydrogen as a test fluid at the Cryogenic Propellant Tank Facility (K-site) at Lewis' Plum Brook Station in Sandusky, Ohio. A general overview of tests involving liquid transfer, thermal control, pressure control, and pressurization is given.

  17. Protocol Design for Large-Scale Cross-Sectional Studies of Sexual Abuse and Associated Factors in Individual Sports: Feasibility Study in Swedish Athletics

    PubMed Central

    Timpka, Toomas; Janson, Staffan; Jacobsson, Jenny; Ekberg, Joakim; Dahlström, Örjan; Kowalski, Jan; Bargoria, Victor; Mountjoy, Margo; Svedin, Carl G.

    2015-01-01

    To ensure health and well-being for their athletes, sports organizations must offer preventive measures against sexual abuse. The aim of this study was to design and evaluate feasibility of a research protocol for cross-sectional epidemiological studies of sexual abuse in athletics. Examination of the requirements on the study of sexual abuse in athletics was followed by iterated drafting of protocol specifications and formative evaluations. The feasibility of the resulting protocol was evaluated in a national-level study among elite athletics athletes (n = 507) in Sweden. The definition of sexual abuse, the ethical soundness of the protocol, reference populations and study of co-morbidity, and the means for athlete-level data collection were identified as particularly complex issues in the requirements analyses. The web-based survey defined by the protocol facilitates anonymous athlete self-reporting of data on exposure to sexual abuse. 198 athletes (39%) fully completed the feasibility survey. 89% (n = 177) reported that they agreed with that the questions in the survey were important, and 95% (n = 189) reported that they answered truthfully to all questions. Similarly, 91% (n = 180) reported that they did not agree with that the questions were unpleasant for them. However, 16% (n = 32) reported that they did not find the survey to be of personal value, and 12% (n = 23) reported that the survey had caused them to think about issues that they did not want to think about. Responding that participation was not personally gratifying was associated with training more hours (p = 0.01). There is a scarcity of research on the prevention of sexual abuse in individual sports. The present protocol should be regarded as a means to overcome this shortcoming in athletics. When implementing the protocol, it is necessary to encourage athlete compliance and to adapt the web-based survey to the particular infrastructural conditions in the sports setting at hand. Key points A

  18. Protocol design for large-scale cross-sectional studies of sexual abuse and associated factors in individual sports: feasibility study in Swedish athletics.

    PubMed

    Timpka, Toomas; Janson, Staffan; Jacobsson, Jenny; Ekberg, Joakim; Dahlström, Örjan; Kowalski, Jan; Bargoria, Victor; Mountjoy, Margo; Svedin, Carl G

    2015-03-01

    To ensure health and well-being for their athletes, sports organizations must offer preventive measures against sexual abuse. The aim of this study was to design and evaluate feasibility of a research protocol for cross-sectional epidemiological studies of sexual abuse in athletics. Examination of the requirements on the study of sexual abuse in athletics was followed by iterated drafting of protocol specifications and formative evaluations. The feasibility of the resulting protocol was evaluated in a national-level study among elite athletics athletes (n = 507) in Sweden. The definition of sexual abuse, the ethical soundness of the protocol, reference populations and study of co-morbidity, and the means for athlete-level data collection were identified as particularly complex issues in the requirements analyses. The web-based survey defined by the protocol facilitates anonymous athlete self-reporting of data on exposure to sexual abuse. 198 athletes (39%) fully completed the feasibility survey. 89% (n = 177) reported that they agreed with that the questions in the survey were important, and 95% (n = 189) reported that they answered truthfully to all questions. Similarly, 91% (n = 180) reported that they did not agree with that the questions were unpleasant for them. However, 16% (n = 32) reported that they did not find the survey to be of personal value, and 12% (n = 23) reported that the survey had caused them to think about issues that they did not want to think about. Responding that participation was not personally gratifying was associated with training more hours (p = 0.01). There is a scarcity of research on the prevention of sexual abuse in individual sports. The present protocol should be regarded as a means to overcome this shortcoming in athletics. When implementing the protocol, it is necessary to encourage athlete compliance and to adapt the web-based survey to the particular infrastructural conditions in the sports setting at hand. Key points

  19. Evaluation of large-scale genetic structure in complex demographic and historical scenarios: the mitochondrial DNA and Y-chromosome pools of the Iberian Atlantic façade.

    PubMed

    Pardiñas, Antonio F; Roca, Agustín; García-Vazquez, Eva; López, Belén

    2014-04-01

    Genetic structural patterns of human populations are usually a combination of long-term evolutionary forces and short-term social, cultural, and demographic processes. Recently, using mitochondrial DNA and Y-chromosome loci, various studies in northern Spain have found evidence that the geographical distribution of Iron Age tribal peoples might have influenced current patterns of genetic structuring in several autochthonous populations. Using the wealth of data that are currently available from the whole territory of the Iberian Peninsula, we have evaluated its genetic structuring in the spatial scale of the Atlantic façade. Hierarchical tree modeling procedures, combined with a classic analysis of molecular variance (AMOVA), were used to model known sociocultural divisions from the third century BCE to the eighth century CE, contrasting them with uniparental marker data. Our results show that, while mountainous and abrupt areas of the Iberian North bear the signals of long-term isolation in their maternal and paternal gene pools, the makeup of the Atlantic façade as a whole can be related to tribal population groups that predate the Roman conquest of the Peninsula. The maintenance through time of such a structure can be related to the numerous geographic barriers of the Iberian mainland, which have historically conditioned its settlement patterns and the occurrence of genetic drift processes. PMID:24375152

  20. Large-scale sequential quadratic programming algorithms

    SciTech Connect

    Eldersveld, S.K.

    1992-09-01

    The problem addressed is the general nonlinear programming problem: finding a local minimizer for a nonlinear function subject to a mixture of nonlinear equality and inequality constraints. The methods studied are in the class of sequential quadratic programming (SQP) algorithms, which have previously proved successful for problems of moderate size. Our goal is to devise an SQP algorithm that is applicable to large-scale optimization problems, using sparse data structures and storing less curvature information but maintaining the property of superlinear convergence. The main features are: 1. The use of a quasi-Newton approximation to the reduced Hessian of the Lagrangian function. Only an estimate of the reduced Hessian matrix is required by our algorithm. The impact of not having available the full Hessian approximation is studied and alternative estimates are constructed. 2. The use of a transformation matrix Q. This allows the QP gradient to be computed easily when only the reduced Hessian approximation is maintained. 3. The use of a reduced-gradient form of the basis for the null space of the working set. This choice of basis is more practical than an orthogonal null-space basis for large-scale problems. The continuity condition for this choice is proven. 4. The use of incomplete solutions of quadratic programming subproblems. Certain iterates generated by an active-set method for the QP subproblem are used in place of the QP minimizer to define the search direction for the nonlinear problem. An implementation of the new algorithm has been obtained by modifying the code MINOS. Results and comparisons with MINOS and NPSOL are given for the new algorithm on a set of 92 test problems.

  1. Supporting large-scale computational science

    SciTech Connect

    Musick, R

    1998-10-01

    A study has been carried out to determine the feasibility of using commercial database management systems (DBMSs) to support large-scale computational science. Conventional wisdom in the past has been that DBMSs are too slow for such data. Several events over the past few years have muddied the clarity of this mindset: 1. 2. 3. 4. Several commercial DBMS systems have demonstrated storage and ad-hoc quer access to Terabyte data sets. Several large-scale science teams, such as EOSDIS [NAS91], high energy physics [MM97] and human genome [Kin93] have adopted (or make frequent use of) commercial DBMS systems as the central part of their data management scheme. Several major DBMS vendors have introduced their first object-relational products (ORDBMSs), which have the potential to support large, array-oriented data. In some cases, performance is a moot issue. This is true in particular if the performance of legacy applications is not reduced while new, albeit slow, capabilities are added to the system. The basic assessment is still that DBMSs do not scale to large computational data. However, many of the reasons have changed, and there is an expiration date attached to that prognosis. This document expands on this conclusion, identifies the advantages and disadvantages of various commercial approaches, and describes the studies carried out in exploring this area. The document is meant to be brief, technical and informative, rather than a motivational pitch. The conclusions within are very likely to become outdated within the next 5-7 years, as market forces will have a significant impact on the state of the art in scientific data management over the next decade.

  2. Study of Potential Cost Reductions Resulting from Super-Large-Scale Manufacturing of PV Modules: Final Subcontract Report, 7 August 2003--30 September 2004

    SciTech Connect

    Keshner, M. S.; Arya, R.

    2004-10-01

    Hewlett Packard has created a design for a ''Solar City'' factory that will process 30 million sq. meters of glass panels per year and produce 2.1-3.6 GW of solar panels per year-100x the volume of a typical, thin-film, solar panel manufacturer in 2004. We have shown that with a reasonable selection of materials, and conservative assumptions, this ''Solar City'' can produce solar panels and hit the price target of $1.00 per peak watt (6.5x-8.5x lower than prices in 2004) as the total price for a complete and installed rooftop (or ground mounted) solar energy system. This breakthrough in the price of solar energy comes without the need for any significant new invention. It comes entirely from the manufacturing scale of a large plant and the cost savings inherent in operating at such a large manufacturing scale. We expect that further optimizations from these simple designs will lead to further improvements in cost. The manufacturing process and cost depend on the choice for the active layer that converts sunlight into electricity. The efficiency by which sunlight is converted into electricity can range from 7% to 15%. This parameter has a large effect on the overall price per watt. There are other impacts, as well, and we have attempted to capture them without creating undue distractions. Our primary purpose is to demonstrate the impact of large-scale manufacturing. This impact is largely independent of the choice of active layer. It is not our purpose to compare the pro's and con's for various types of active layers. Significant improvements in cost per watt can also come from scientific advances in active layers that lead to higher efficiency. But, again, our focus is on manufacturing gains and not on the potential advances in the basic technology.

  3. Introducing Large-Scale Innovation in Schools

    NASA Astrophysics Data System (ADS)

    Sotiriou, Sofoklis; Riviou, Katherina; Cherouvis, Stephanos; Chelioti, Eleni; Bogner, Franz X.

    2016-08-01

    Education reform initiatives tend to promise higher effectiveness in classrooms especially when emphasis is given to e-learning and digital resources. Practical changes in classroom realities or school organization, however, are lacking. A major European initiative entitled Open Discovery Space (ODS) examined the challenge of modernizing school education via a large-scale implementation of an open-scale methodology in using technology-supported innovation. The present paper describes this innovation scheme which involved schools and teachers all over Europe, embedded technology-enhanced learning into wider school environments and provided training to teachers. Our implementation scheme consisted of three phases: (1) stimulating interest, (2) incorporating the innovation into school settings and (3) accelerating the implementation of the innovation. The scheme's impact was monitored for a school year using five indicators: leadership and vision building, ICT in the curriculum, development of ICT culture, professional development support, and school resources and infrastructure. Based on about 400 schools, our study produced four results: (1) The growth in digital maturity was substantial, even for previously high scoring schools. This was even more important for indicators such as vision and leadership" and "professional development." (2) The evolution of networking is presented graphically, showing the gradual growth of connections achieved. (3) These communities became core nodes, involving numerous teachers in sharing educational content and experiences: One out of three registered users (36 %) has shared his/her educational resources in at least one community. (4) Satisfaction scores ranged from 76 % (offer of useful support through teacher academies) to 87 % (good environment to exchange best practices). Initiatives such as ODS add substantial value to schools on a large scale.

  4. Introducing Large-Scale Innovation in Schools

    NASA Astrophysics Data System (ADS)

    Sotiriou, Sofoklis; Riviou, Katherina; Cherouvis, Stephanos; Chelioti, Eleni; Bogner, Franz X.

    2016-02-01

    Education reform initiatives tend to promise higher effectiveness in classrooms especially when emphasis is given to e-learning and digital resources. Practical changes in classroom realities or school organization, however, are lacking. A major European initiative entitled Open Discovery Space (ODS) examined the challenge of modernizing school education via a large-scale implementation of an open-scale methodology in using technology-supported innovation. The present paper describes this innovation scheme which involved schools and teachers all over Europe, embedded technology-enhanced learning into wider school environments and provided training to teachers. Our implementation scheme consisted of three phases: (1) stimulating interest, (2) incorporating the innovation into school settings and (3) accelerating the implementation of the innovation. The scheme's impact was monitored for a school year using five indicators: leadership and vision building, ICT in the curriculum, development of ICT culture, professional development support, and school resources and infrastructure. Based on about 400 schools, our study produced four results: (1) The growth in digital maturity was substantial, even for previously high scoring schools. This was even more important for indicators such as vision and leadership" and "professional development." (2) The evolution of networking is presented graphically, showing the gradual growth of connections achieved. (3) These communities became core nodes, involving numerous teachers in sharing educational content and experiences: One out of three registered users (36 %) has shared his/her educational resources in at least one community. (4) Satisfaction scores ranged from 76 % (offer of useful support through teacher academies) to 87 % (good environment to exchange best practices). Initiatives such as ODS add substantial value to schools on a large scale.

  5. Needs, opportunities, and options for large scale systems research

    SciTech Connect

    Thompson, G.L.

    1984-10-01

    The Office of Energy Research was recently asked to perform a study of Large Scale Systems in order to facilitate the development of a true large systems theory. It was decided to ask experts in the fields of electrical engineering, chemical engineering and manufacturing/operations research for their ideas concerning large scale systems research. The author was asked to distribute a questionnaire among these experts to find out their opinions concerning recent accomplishments and future research directions in large scale systems research. He was also requested to convene a conference which included three experts in each area as panel members to discuss the general area of large scale systems research. The conference was held on March 26--27, 1984 in Pittsburgh with nine panel members, and 15 other attendees. The present report is a summary of the ideas presented and the recommendations proposed by the attendees.

  6. How weight change is modelled in population studies can affect research findings: empirical results from a large-scale cohort study

    PubMed Central

    Paige, E; Korda, R J; Banks, E; Rodgers, B

    2014-01-01

    Objectives To investigate how results of the association between education and weight change vary when weight change is defined and modelled in different ways. Design Longitudinal cohort study. Participants 60 404 men and women participating in the Social, Environmental and Economic Factors (SEEF) subcomponent of the 45 and Up Study—a population-based cohort study of people aged 45 years or older, residing in New South Wales, Australia. Outcome measures The main exposure was self-reported education, categorised into four groups. The outcome was annual weight change, based on change in self-reported weight between the 45 and Up Study baseline questionnaire and SEEF questionnaire (completed an average of 3.3 years later). Weight change was modelled in four different ways: absolute change (kg) modelled as (1) a continuous variable and (2) a categorical variable (loss, maintenance and gain), and relative (%) change modelled as (3) a continuous variable and (4) a categorical variable. Different cut-points for defining weight-change categories were also tested. Results When weight change was measured categorically, people with higher levels of education (compared with no school certificate) were less likely to lose or to gain weight. When weight change was measured as the average of a continuous measure, a null relationship between education and annual weight change was observed. No material differences in the education and weight-change relationship were found when comparing weight change defined as an absolute (kg) versus a relative (%) measure. Results of the logistic regression were sensitive to different cut-points for defining weight-change categories. Conclusions Using average weight change can obscure important directional relationship information and, where possible, categorical outcome measurements should be included in analyses. PMID:24907245

  7. Dietary habits and risk of lung cancer death in a large-scale cohort study (JACC Study) in Japan by sex and smoking habit.

    PubMed

    Ozasa, K; Watanabe, Y; Ito, Y; Suzuki, K; Tamakoshi, A; Seki, N; Nishino, Y; Kondo, T; Wakai, K; Ando, M; Ohno, Y

    2001-12-01

    Lung cancer has increased and is the leading cause of cancer death among Japanese males. The associations of dietary habits with the risk of lung cancer death were evaluated by sex and smoking habits in this study. In the Japan Collaborative Cohort (JACC) Study, a cohort established in 1988 - 90 and consisting of 42 940 males and 55 308 females was observed for lung cancer deaths up to the end of 1997. During the observation period, 446 males and 126 females died of lung cancer. A self-administered food frequency questionnaire was used as the baseline survey. Hazard ratios for dietary factors were calculated by Cox's proportional hazards model. Among males, a high intake of ham and sausages, cheese, green-leafy vegetables, oranges, and other fruits significantly and dose-dependently decreased the risk of lung cancer death. Among females, a high intake of miso-soup, ham and sausages, and liver significantly and almost dose-dependently increased the risk. Vegetables and fruits rich in antioxidative and carcinogenic agents reduced the risk of lung cancer deaths among male smokers more than among female nonsmokers. The results among female nonsmokers were partially consistent with the hypothesis that high fat consumption increases the risk of lung cancer, especially that of adenocarcinoma. PMID:11749690

  8. Synthesis of small and large scale dynamos

    NASA Astrophysics Data System (ADS)

    Subramanian, Kandaswamy

    Using a closure model for the evolution of magnetic correlations, we uncover an interesting plausible saturated state of the small-scale fluctuation dynamo (SSD) and a novel analogy between quantum mechanical tunnelling and the generation of large-scale fields. Large scale fields develop via the α-effect, but as magnetic helicity can only change on a resistive timescale, the time it takes to organize the field into large scales increases with magnetic Reynolds number. This is very similar to the results which obtain from simulations using the full MHD equations.

  9. Are the studies on cancer risk from CT scans biased by indication? Elements of answer from a large-scale cohort study in France

    PubMed Central

    Journy, N; Rehel, J-L; Ducou Le Pointe, H; Lee, C; Brisse, H; Chateil, J-F; Caer-Lorho, S; Laurier, D; Bernier, M-O

    2015-01-01

    Background: Recent epidemiological results suggested an increase of cancer risk after receiving computed tomography (CT) scans in childhood or adolescence. Their interpretation is questioned due to the lack of information about the reasons for examination. Our objective was to estimate the cancer risk related to childhood CT scans, and examine how cancer-predisposing factors (PFs) affect assessment of the radiation-related risk. Methods: The cohort included 67 274 children who had a first scan before the age of 10 years from 2000 to 2010 in 23 French departments. Cumulative X-rays doses were estimated from radiology protocols. Cancer incidence was retrieved through the national registry of childhood cancers; PF from discharge diagnoses. Results: During a mean follow-up of 4 years, 27 cases of tumours of the central nervous system, 25 of leukaemia and 21 of lymphoma were diagnosed; 32% of them among children with PF. Specific patterns of CT exposures were observed according to PFs. Adjustment for PF reduced the excess risk estimates related to cumulative doses from CT scans. No significant excess risk was observed in relation to CT exposures. Conclusions: This study suggests that the indication for examinations, whether suspected cancer or PF management, should be considered to avoid overestimation of the cancer risks associated with CT scans. PMID:25314057

  10. The Psychiatric Genomics Consortium Posttraumatic Stress Disorder Workgroup: Posttraumatic Stress Disorder Enters the Age of Large-Scale Genomic Collaboration

    PubMed Central

    Logue, Mark W; Amstadter, Ananda B; Baker, Dewleen G; Duncan, Laramie; Koenen, Karestan C; Liberzon, Israel; Miller, Mark W; Morey, Rajendra A; Nievergelt, Caroline M; Ressler, Kerry J; Smith, Alicia K; Smoller, Jordan W; Stein, Murray B; Sumner, Jennifer A; Uddin, Monica

    2015-01-01

    The development of posttraumatic stress disorder (PTSD) is influenced by genetic factors. Although there have been some replicated candidates, the identification of risk variants for PTSD has lagged behind genetic research of other psychiatric disorders such as schizophrenia, autism, and bipolar disorder. Psychiatric genetics has moved beyond examination of specific candidate genes in favor of the genome-wide association study (GWAS) strategy of very large numbers of samples, which allows for the discovery of previously unsuspected genes and molecular pathways. The successes of genetic studies of schizophrenia and bipolar disorder have been aided by the formation of a large-scale GWAS consortium: the Psychiatric Genomics Consortium (PGC). In contrast, only a handful of GWAS of PTSD have appeared in the literature to date. Here we describe the formation of a group dedicated to large-scale study of PTSD genetics: the PGC-PTSD. The PGC-PTSD faces challenges related to the contingency on trauma exposure and the large degree of ancestral genetic diversity within and across participating studies. Using the PGC analysis pipeline supplemented by analyses tailored to address these challenges, we anticipate that our first large-scale GWAS of PTSD will comprise over 10 000 cases and 30 000 trauma-exposed controls. Following in the footsteps of our PGC forerunners, this collaboration—of a scope that is unprecedented in the field of traumatic stress—will lead the search for replicable genetic associations and new insights into the biological underpinnings of PTSD. PMID:25904361

  11. Estimating large-scale evapotranspiration in arid and semi-arid systems: A multi-site study linking MODIS and Ameriflux data

    NASA Astrophysics Data System (ADS)

    Bunting, D. P.; Glenn, E. P.; Kurc, S. A.; Scott, R. L.; Nagler, P. L.

    2010-12-01

    . Future research includes applying these empirical models to large river-reaches across the southwestern United States. Total annual ET can be estimated at river-reach or watershed scales provided that each region is classified appropriately and surface area is known. This approach is expected to improve accuracy of ET estimates at large scales.

  12. Large-scale field study on thin-layer capping of marine PCDD/F-contaminated sediments in Grenlandfjords, Norway: physicochemical effects.

    PubMed

    Cornelissen, Gerard; Amstaetter, Katja; Hauge, Audun; Schaanning, Morten; Beylich, Bjørnar; Gunnarsson, Jonas S; Breedveld, Gijs D; Oen, Amy M P; Eek, Espen

    2012-11-01

    A large-scale field experiment on in situ thin-layer capping was carried out in the polychlorinated dibenzodioxin and dibenzofuran (PCDD/F) contaminated Grenlandsfjords, Norway. The main focus of the trial was to test the effectiveness of active caps (targeted thickness of 2.5 cm) consisting of powdered activated carbon (AC) mixed into locally dredged clean clay. Nonactive caps (targed thickness of 5 cm) consisting of clay without AC as well as crushed limestone were also tested. Fields with areas of 10,000 to 40,000 m(2) were established at 30 to 100 m water depth. Auxiliary shaken laboratory batch experiments showed that 2% of the applied powdered AC substantially reduced PCDD/F porewater concentrations, by >90% for tetra-, penta- and hexa-clorinated congeners to 60-70% for octachlorinated ones. In-situ AC profiles revealed that the AC was mixed into the sediment to 3 to 5 cm depth in 20 months. Only around 25% of the AC was found inside the pilot fields. Sediment-to-water PCDD/F fluxes measured by in situ diffusion chambers were significantly lower at the capped fields than at reference fields in the same fjord, reductions being largest for the limestone (50-90%) followed by clay (50-70%), and the AC + clay (60%). Also reductions in overlying aqueous PCDD/F concentrations measured by passive samplers were significant in most cases (20-40% reduction), probably because of the large size of the trial fields. The AC was less effective in the field than in the laboratory, probably due to prolonged sediment-to-AC mass transfer times for PCDD/Fs and field factors such as integrity of the cap, new deposition of contaminated sediment particles, and bioturbation. The present field data indicate that slightly thicker layers of limestone and dredged clay can show as good physicochemical effectiveness as thin caps of AC mixed with clay, at least for PCDD/Fs during the first two years after cap placement. PMID:23046183

  13. Evaluation of a multi-atlas based method for segmentation of cardiac CTA data: a large-scale, multicenter, and multivendor study

    SciTech Connect

    Kirisli, H. A.; Schaap, M.; Klein, S.; Papadopoulou, S. L.; Bonardi, M.; Chen, C. H.; Weustink, A. C.; Mollet, N. R.; Vonken, E. J.; Geest, R. J. van der; Walsum, T. van; Niessen, W. J.

    2010-12-15

    Purpose: Computed tomography angiography (CTA) is increasingly used for the diagnosis of coronary artery disease (CAD). However, CTA is not commonly used for the assessment of ventricular and atrial function, although functional information extracted from CTA data is expected to improve the diagnostic value of the examination. In clinical practice, the extraction of ventricular and atrial functional information, such as stroke volume and ejection fraction, requires accurate delineation of cardiac chambers. In this paper, we investigated the accuracy and robustness of cardiac chamber delineation using a multiatlas based segmentation method on multicenter and multivendor CTA data. Methods: A fully automatic multiatlas based method for segmenting the whole heart (i.e., the outer surface of the pericardium) and cardiac chambers from CTA data is presented and evaluated. In the segmentation approach, eight atlas images are registered to a new patient's CTA scan. The eight corresponding manually labeled images are then propagated and combined using a per voxel majority voting procedure, to obtain a cardiac segmentation. Results: The method was evaluated on a multicenter/multivendor database, consisting of (1) a set of 1380 Siemens scans from 795 patients and (2) a set of 60 multivendor scans (Siemens, Philips, and GE) from different patients, acquired in six different institutions worldwide. A leave-one-out 3D quantitative validation was carried out on the eight atlas images; we obtained a mean surface-to-surface error of 0.94{+-}1.12 mm and an average Dice coefficient of 0.93 was achieved. A 2D quantitative evaluation was performed on the 60 multivendor data sets. Here, we observed a mean surface-to-surface error of 1.26{+-}1.25 mm and an average Dice coefficient of 0.91 was achieved. In addition to this quantitative evaluation, a large-scale 2D and 3D qualitative evaluation was performed on 1380 and 140 images, respectively. Experts evaluated that 49% of the 1380 images

  14. Large-scale regions of antimatter

    SciTech Connect

    Grobov, A. V. Rubin, S. G.

    2015-07-15

    Amodified mechanism of the formation of large-scale antimatter regions is proposed. Antimatter appears owing to fluctuations of a complex scalar field that carries a baryon charge in the inflation era.

  15. Progress in genetic association studies of plasma lipids

    PubMed Central

    Asselbergs, Folkert W.; Lovering, Ruth C.; Drenos, Fotios

    2013-01-01

    Purpose of review This review summarizes recently published large-scale efforts elucidating the genetic architecture of lipid levels. A supplemental file with all genetic loci is provided for research purposes and we performed bioinformatic analyses of the genetic variants to give an oversight of involved pathways. Recent findings In total, 52 genes for HDL cholesterol, 42 genes for LDL cholesterol, 59 genes for total cholesterol, and 39 genes for triglycerides have been identified. Genetic overlap is present between the different traits and similar pathways are involved. Most of the SNPs that were detected in the European studies could be replicated in other ethnicities and these SNPs show the same direction of effect suggesting that the underlying genetic architecture of blood lipids is similar between ethnicities. Summary Genetic studies have identified many loci associated with plasma lipids and have provided insight into the underlying mechanisms of lipid homeostasis. Future research is needed to determine whether these loci may be novel targets for lipid-lowering therapy and for reducing cardiovascular disease risk. In addition, the proportion of genetic variance explained by these lipid loci is still limited and new large-scale genetic studies are ongoing to identify additional common and rare variants associated with lipid levels. PMID:23385652

  16. Processes of diversification and dispersion of rice yellow mottle virus inferred from large-scale and high-resolution phylogeographical studies.

    PubMed

    Traore, O; Sorho, F; Pinel, A; Abubakar, Z; Banwo, O; Maley, J; Hebrard, E; Winter, S; Sere, Y; Konate, G; Fargette, D

    2005-06-01

    Phylogeography of Rice yellow mottle virus (RYMV) was reconstructed from the coat protein gene sequences of a selection of 173 isolates from the 14 countries of mainland Africa where the disease occurred and from the full sequences of 16 representative isolates. Genetic variation was linked to geographical distribution and not to host species as isolates from wild rice always clustered with isolates from cultivated rice of the same region. Genetic variation was not associated to agro-ecology, viral interference and insect vector species. Distinct RYMV lineages occurred in East, Central and West Africa, although the Central African lineage included isolates from Benin, Togo and Niger at the west, adjacent to countries of the West African lineage. Genetic subdivision at finer geographical scales was apparent within lineages of Central and West Africa, although less pronounced than in East Africa. Physical obstacles, but also habitat fragmentation, as exemplified by the small low-lying island of Pemba offshore Tanzania mainland, explained strain localization. Three new highly divergent strains were found in eastern Tanzania. By contrast, intensive surveys in Cote d'Ivoire and Guinea at the west of Africa did not reveal any new variant. Altogether, this supported the view that the Eastern Arc Mountains biodiversity hotspot was the centre of origin of RYMV and that the virus spread subsequently from east to west across Africa. In West Africa, specific strains occurred in the Inner Niger Delta and suggested it was a secondary centre of diversification. Processes for diversification and dispersion of RYMV are proposed. PMID:15910330

  17. Large-scale motions in a plane wall jet

    NASA Astrophysics Data System (ADS)

    Gnanamanickam, Ebenezer; Jonathan, Latim; Shibani, Bhatt

    2015-11-01

    The dynamic significance of large-scale motions in turbulent boundary layers have been the focus of several recent studies, primarily focussing on canonical flows - zero pressure gradient boundary layers, flows within pipes and channels. This work presents an investigation into the large-scale motions in a boundary layer that is used as the prototypical flow field for flows with large-scale mixing and reactions, the plane wall jet. An experimental investigation is carried out in a plane wall jet facility designed to operate at friction Reynolds numbers Reτ > 1000 , which allows for the development of a significant logarithmic region. The streamwise turbulent intensity across the boundary layer is decomposed into small-scale (less than one integral length-scale δ) and large-scale components. The small-scale energy has a peak in the near-wall region associated with the near-wall turbulent cycle as in canonical boundary layers. However, eddies of large-scales are the dominating eddies having significantly higher energy, than the small-scales across almost the entire boundary layer even at the low to moderate Reynolds numbers under consideration. The large-scales also appear to amplitude and frequency modulate the smaller scales across the entire boundary layer.

  18. Large-Scale Discovery and Validation Studies Demonstrate Significant Reductions in Circulating Levels of IL8, IL-1Ra, MCP-1, and MIP-1β in Patients With Type 1 Diabetes

    PubMed Central

    Purohit, Sharad; Sharma, Ashok; Hopkins, Diane; Steed, Leigh; Bode, Bruce; Anderson, Stephen W.; Reed, John Chip; Steed, R. Dennis; Yang, Tao

    2015-01-01

    Context: Previous studies have attempted to elucidate the potential role of various cytokines and chemokines in human type 1 diabetes (T1D); however, the precise role of these serum proteins in T1D is still controversial and undetermined primarily due to the small sample sizes of the previous studies. We profiled a panel of serum cytokines and chemokines using a large-scale, two-stage study design for the discovery and validation of the serum proteins associated with T1D. Participants: The participants were patients with T1D and islet autoantibody–negative control subjects from the Phenome and Genome of Diabetes Autoimmunity study. Main Outcome Measures: Thirteen cytokines and chemokines were measured in serum of 4424 subjects using multiplex immunoassays. Results: Using 1378 samples in Stage 1, we found that four of the 13 proteins are significantly lower in patients with T1D than controls (IL8: odds ratio [OR] = 0.40; P = 5.7 × 10−19; IL-1Ra: OR = 0.42; P = 1.1 × 10−13; MCP-1: OR = 0.60; P = 6.7 × 10−9; and MIP-1β: OR = 0.63; P = 4.2 × 10−7). Our confirmation data with 3046 samples in Stage 2 further confirmed the significant negative associations of these four proteins with T1D (IL8: OR = 0.43; P = 8.9 × 10−32; IL-1Ra: OR = 0.56, P = 3.7 × 10−27; MCP-1: OR = 0.61, P = 4.3 × 10−17; and MIP-1β: OR = 0.69, P = 2.4 × 10−13). Quartile analyses also suggested that significantly more T1D cases have protein levels in the bottom quartile than in the top quartile for all four proteins: IL8 (OR = 0.09), IL-1Ra (OR = 0.18), MCP-1 (OR = 0.38), and MIP-1β (OR = 0.44). Furthermore, the negative associations between T1D and serum levels of all four proteins are stronger in genetically high-risk groups compared with the moderate and low-risk groups. Conclusions: IL8, IL-1Ra, MCP-1, and MIP-1β are significantly lower in patients with T1D than controls. PMID:26158606

  19. Development and performance of a large-scale, transonic turbine blade cascade facility for aerodynamic studies of merging coolant-mainstream flows

    NASA Astrophysics Data System (ADS)

    Al-Sayeh, Amjad Isaaf

    1998-11-01

    A new, large scale, linear cascade facility of turbine blades has been developed for the experimental exploration of the aerodynamic aspects of film cooling technology. Primary interest is in the mixing of the ejected coolant with the mainstream, at both subsonic and supersonic mainstream Mach numbers at the cascade exit. In order to achieve a spatial resolution adequate for the exploration of details on the scale of the coolant ejection holes, the cascade dimensions were maximized, within the limitations of the air supply system. The cascade contains four blades (three passages) with 14.05 cm axial chord, 17.56 cm span and a design total turning angle of 130.6 degrees. Exit Mach numbers range from 0.6 to 1.5 and Reynolds numbers from 0.5 to 1.5 million. The air supply system capacity allows run times up to five minutes at maximum flow rates. A coolant supply system has been built to deliver mixtures of SFsb6 and air to simulate coolant/mainstream density ratios up to 2. The cascade contains several novel features. A full-perimeter bleed slot upstream of the blades is used to remove the approach boundary layer from all four walls, to improve the degree of two-dimensionality. The exit flow is bounded by two adjustable tailboards that are hinged at the trailing edges and actuated to set the exit flow direction according to the imposed pressure ratio. The boards are perforated and subjected to mass removal near the blades, to minimize the undesirable reflection of shocks and expansion waves. A probe actuator is incorporated that allows continuous positioning of probes in the exhaust stream, in both the streamwise and pitchwise directions. Diagnostic methods include extensive surface pressure taps on the approach and exhaust ducts and on the blade surfaces. The large size permitted as many as 19 taps on the trailing edge itself. Shadowgraph and schlieren are available. A three-prong wake probe has been constructed to simultaneously measure total and static pressures

  20. Application of large-scale parentage analysis for investigating natal dispersal in highly vagile vertebrates: a case study of American black bears (Ursus americanus).

    PubMed

    Moore, Jennifer A; Draheim, Hope M; Etter, Dwayne; Winterstein, Scott; Scribner, Kim T

    2014-01-01

    Understanding the factors that affect dispersal is a fundamental question in ecology and conservation biology, particularly as populations are faced with increasing anthropogenic impacts. Here we collected georeferenced genetic samples (n = 2,540) from three generations of black bears (Ursus americanus) harvested in a large (47,739 km2), geographically isolated population and used parentage analysis to identify mother-offspring dyads (n = 337). We quantified the effects of sex, age, habitat type and suitability, and local harvest density at the natal and settlement sites on the probability of natal dispersal, and on dispersal distances. Dispersal was male-biased (76% of males dispersed) but a small proportion (21%) of females also dispersed, and female dispersal distances (mean ± SE  =  48.9±7.7 km) were comparable to male dispersal distances (59.0±3.2 km). Dispersal probabilities and dispersal distances were greatest for bears in areas with high habitat suitability and low harvest density. The inverse relationship between dispersal and harvest density in black bears suggests that 1) intensive harvest promotes restricted dispersal, or 2) high black bear population density decreases the propensity to disperse. Multigenerational genetic data collected over large landscape scales can be a powerful means of characterizing dispersal patterns and causal associations with demographic and landscape features in wild populations of elusive and wide-ranging species. PMID:24621593

  1. Gravity and large-scale nonlocal bias

    NASA Astrophysics Data System (ADS)

    Chan, Kwan Chuen; Scoccimarro, Román; Sheth, Ravi K.

    2012-04-01

    For Gaussian primordial fluctuations the relationship between galaxy and matter overdensities, bias, is most often assumed to be local at the time of observation in the large-scale limit. This hypothesis is however unstable under time evolution, we provide proofs under several (increasingly more realistic) sets of assumptions. In the simplest toy model galaxies are created locally and linearly biased at a single formation time, and subsequently move with the dark matter (no velocity bias) conserving their comoving number density (no merging). We show that, after this formation time, the bias becomes unavoidably nonlocal and nonlinear at large scales. We identify the nonlocal gravitationally induced fields in which the galaxy overdensity can be expanded, showing that they can be constructed out of the invariants of the deformation tensor (Galileons), the main signature of which is a quadrupole field in second-order perturbation theory. In addition, we show that this result persists if we include an arbitrary evolution of the comoving number density of tracers. We then include velocity bias, and show that new contributions appear; these are related to the breaking of Galilean invariance of the bias relation, a dipole field being the signature at second order. We test these predictions by studying the dependence of halo overdensities in cells of fixed dark matter density: measurements in simulations show that departures from the mean bias relation are strongly correlated with the nonlocal gravitationally induced fields identified by our formalism, suggesting that the halo distribution at the present time is indeed more closely related to the mass distribution at an earlier rather than present time. However, the nonlocality seen in the simulations is not fully captured by assuming local bias in Lagrangian space. The effects on nonlocal bias seen in the simulations are most important for the most biased halos, as expected from our predictions. Accounting for these

  2. Large-Scale Statistics for Cu Electromigration

    NASA Astrophysics Data System (ADS)

    Hauschildt, M.; Gall, M.; Hernandez, R.

    2009-06-01

    stress gradient is established. We therefore conducted large-scale statistical experiments close to the critical current density-length product (jL)*. The results indicate that even at very small failure percentages, this critical product seems to extrapolate to about 2900±400 A/cm for SiCOH-based dielectrics, close to previously determined (jL)* products of about 3000±500 A/cm for the same technology node and dielectric material, acquired with single link interconnects. More detailed studies are currently ongoing to verify the extrapolation methods at small percentages. Furthermore, the scaling behavior of the early failure population was investigated.

  3. Curvature constraints from large scale structure

    NASA Astrophysics Data System (ADS)

    Di Dio, Enea; Montanari, Francesco; Raccanelli, Alvise; Durrer, Ruth; Kamionkowski, Marc; Lesgourgues, Julien

    2016-06-01

    We modified the CLASS code in order to include relativistic galaxy number counts in spatially curved geometries; we present the formalism and study the effect of relativistic corrections on spatial curvature. The new version of the code is now publicly available. Using a Fisher matrix analysis, we investigate how measurements of the spatial curvature parameter ΩK with future galaxy surveys are affected by relativistic effects, which influence observations of the large scale galaxy distribution. These effects include contributions from cosmic magnification, Doppler terms and terms involving the gravitational potential. As an application, we consider angle and redshift dependent power spectra, which are especially well suited for model independent cosmological constraints. We compute our results for a representative deep, wide and spectroscopic survey, and our results show the impact of relativistic corrections on spatial curvature parameter estimation. We show that constraints on the curvature parameter may be strongly biased if, in particular, cosmic magnification is not included in the analysis. Other relativistic effects turn out to be subdominant in the studied configuration. We analyze how the shift in the estimated best-fit value for the curvature and other cosmological parameters depends on the magnification bias parameter, and find that significant biases are to be expected if this term is not properly considered in the analysis.

  4. Unsaturated Hydraulic Conductivity for Evaporation in Large scale Heterogeneous Soils

    NASA Astrophysics Data System (ADS)

    Sun, D.; Zhu, J.

    2014-12-01

    In this study we aim to provide some practical guidelines of how the commonly used simple averaging schemes (arithmetic, geometric, or harmonic mean) perform in simulating large scale evaporation in a large scale heterogeneous landscape. Previous studies on hydraulic property upscaling focusing on steady state flux exchanges illustrated that an effective hydraulic property is usually more difficult to define for evaporation. This study focuses on upscaling hydraulic properties of large scale transient evaporation dynamics using the idea of the stream tube approach. Specifically, the two main objectives are: (1) if the three simple averaging schemes (i.e., arithmetic, geometric and harmonic means) of hydraulic parameters are appropriate in representing large scale evaporation processes, and (2) how the applicability of these simple averaging schemes depends on the time scale of evaporation processes in heterogeneous soils. Multiple realizations of local evaporation processes are carried out using HYDRUS-1D computational code (Simunek et al, 1998). The three averaging schemes of soil hydraulic parameters were used to simulate the cumulative flux exchange, which is then compared with the large scale average cumulative flux. The sensitivity of the relative errors to the time frame of evaporation processes is also discussed.

  5. Large-scale inhomogeneities and galaxy statistics

    NASA Technical Reports Server (NTRS)

    Schaeffer, R.; Silk, J.

    1984-01-01

    The density fluctuations associated with the formation of large-scale cosmic pancake-like and filamentary structures are evaluated using the Zel'dovich approximation for the evolution of nonlinear inhomogeneities in the expanding universe. It is shown that the large-scale nonlinear density fluctuations in the galaxy distribution due to pancakes modify the standard scale-invariant correlation function xi(r) at scales comparable to the coherence length of adiabatic fluctuations. The typical contribution of pancakes and filaments to the J3 integral, and more generally to the moments of galaxy counts in a volume of approximately (15-40 per h Mpc)exp 3, provides a statistical test for the existence of large scale inhomogeneities. An application to several recent three dimensional data sets shows that despite large observational uncertainties over the relevant scales characteristic features may be present that can be attributed to pancakes in most, but not all, of the various galaxy samples.

  6. The large-scale distribution of galaxies

    NASA Technical Reports Server (NTRS)

    Geller, Margaret J.

    1989-01-01

    The spatial distribution of galaxies in the universe is characterized on the basis of the six completed strips of the Harvard-Smithsonian Center for Astrophysics redshift-survey extension. The design of the survey is briefly reviewed, and the results are presented graphically. Vast low-density voids similar to the void in Bootes are found, almost completely surrounded by thin sheets of galaxies. Also discussed are the implications of the results for the survey sampling problem, the two-point correlation function of the galaxy distribution, the possibility of detecting large-scale coherent flows, theoretical models of large-scale structure, and the identification of groups and clusters of galaxies.

  7. EINSTEIN'S SIGNATURE IN COSMOLOGICAL LARGE-SCALE STRUCTURE

    SciTech Connect

    Bruni, Marco; Hidalgo, Juan Carlos; Wands, David

    2014-10-10

    We show how the nonlinearity of general relativity generates a characteristic nonGaussian signal in cosmological large-scale structure that we calculate at all perturbative orders in a large-scale limit. Newtonian gravity and general relativity provide complementary theoretical frameworks for modeling large-scale structure in ΛCDM cosmology; a relativistic approach is essential to determine initial conditions, which can then be used in Newtonian simulations studying the nonlinear evolution of the matter density. Most inflationary models in the very early universe predict an almost Gaussian distribution for the primordial metric perturbation, ζ. However, we argue that it is the Ricci curvature of comoving-orthogonal spatial hypersurfaces, R, that drives structure formation at large scales. We show how the nonlinear relation between the spatial curvature, R, and the metric perturbation, ζ, translates into a specific nonGaussian contribution to the initial comoving matter density that we calculate for the simple case of an initially Gaussian ζ. Our analysis shows the nonlinear signature of Einstein's gravity in large-scale structure.

  8. Accuracy of Electronic Health Record Data for Identifying Stroke Cases in Large-Scale Epidemiological Studies: A Systematic Review from the UK Biobank Stroke Outcomes Group

    PubMed Central

    Woodfield, Rebecca; Grant, Ian; Sudlow, Cathie L. M.

    2015-01-01

    Objective Long-term follow-up of population-based prospective studies is often achieved through linkages to coded regional or national health care data. Our knowledge of the accuracy of such data is incomplete. To inform methods for identifying stroke cases in UK Biobank (a prospective study of 503,000 UK adults recruited in middle-age), we systematically evaluated the accuracy of these data for stroke and its main pathological types (ischaemic stroke, intracerebral haemorrhage, subarachnoid haemorrhage), determining the optimum codes for case identification. Methods We sought studies published from 1990-November 2013, which compared coded data from death certificates, hospital admissions or primary care with a reference standard for stroke or its pathological types. We extracted information on a range of study characteristics and assessed study quality with the Quality Assessment of Diagnostic Studies tool (QUADAS-2). To assess accuracy, we extracted data on positive predictive values (PPV) and—where available—on sensitivity, specificity, and negative predictive values (NPV). Results 37 of 39 eligible studies assessed accuracy of International Classification of Diseases (ICD)-coded hospital or death certificate data. They varied widely in their settings, methods, reporting, quality, and in the choice and accuracy of codes. Although PPVs for stroke and its pathological types ranged from 6–97%, appropriately selected, stroke-specific codes (rather than broad cerebrovascular codes) consistently produced PPVs >70%, and in several studies >90%. The few studies with data on sensitivity, specificity and NPV showed higher sensitivity of hospital versus death certificate data for stroke, with specificity and NPV consistently >96%. Few studies assessed either primary care data or combinations of data sources. Conclusions Particular stroke-specific codes can yield high PPVs (>90%) for stroke/stroke types. Inclusion of primary care data and combining data sources should

  9. Management of large-scale technology

    NASA Technical Reports Server (NTRS)

    Levine, A.

    1985-01-01

    Two major themes are addressed in this assessment of the management of large-scale NASA programs: (1) how a high technology agency was a decade marked by a rapid expansion of funds and manpower in the first half and almost as rapid contraction in the second; and (2) how NASA combined central planning and control with decentralized project execution.

  10. A Large Scale Computer Terminal Output Controller.

    ERIC Educational Resources Information Center

    Tucker, Paul Thomas

    This paper describes the design and implementation of a large scale computer terminal output controller which supervises the transfer of information from a Control Data 6400 Computer to a PLATO IV data network. It discusses the cost considerations leading to the selection of educational television channels rather than telephone lines for…

  11. Large-scale CFB combustion demonstration project

    SciTech Connect

    Nielsen, P.T.; Hebb, J.L.; Aquino, R.

    1998-07-01

    The Jacksonville Electric Authority's large-scale CFB demonstration project is described. Given the early stage of project development, the paper focuses on the project organizational structure, its role within the Department of Energy's Clean Coal Technology Demonstration Program, and the projected environmental performance. A description of the CFB combustion process in included.

  12. Large-scale CFB combustion demonstration project

    SciTech Connect

    Nielsen, P.T.; Hebb, J.L.; Aquino, R.

    1998-04-01

    The Jacksonville Electric Authority`s large-scale CFB demonstration project is described. Given the early stage of project development, the paper focuses on the project organizational structure, its role within the Department of Energy`s Clean Coal Technology Demonstration Program, and the projected environmental performance. A description of the CFB combustion process is included.

  13. Evaluating Large-Scale Interactive Radio Programmes

    ERIC Educational Resources Information Center

    Potter, Charles; Naidoo, Gordon

    2009-01-01

    This article focuses on the challenges involved in conducting evaluations of interactive radio programmes in South Africa with large numbers of schools, teachers, and learners. It focuses on the role such large-scale evaluation has played during the South African radio learning programme's development stage, as well as during its subsequent…

  14. ARPACK: Solving large scale eigenvalue problems

    NASA Astrophysics Data System (ADS)

    Lehoucq, Rich; Maschhoff, Kristi; Sorensen, Danny; Yang, Chao

    2013-11-01

    ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. The package is designed to compute a few eigenvalues and corresponding eigenvectors of a general n by n matrix A. It is most appropriate for large sparse or structured matrices A where structured means that a matrix-vector product w

  15. Large-scale micropropagation system of plant cells.

    PubMed

    Honda, Hiroyuki; Kobayashi, Takeshi

    2004-01-01

    Plant micropropagation is an efficient method of propagating disease-free, genetically uniform and massive amounts of plants in vitro. The scale-up of the whole process for plant micropropagation should be established by an economically feasible technology for large-scale production of them in appropriate bioreactors. It is necessary to design suitable bioreactor configuration which can provide adequate mixing and mass transfer while minimizing the intensity of shear stress and hydrodynamic pressure. Automatic selection of embryogenic calli and regenerated plantlets using image analysis system should be associated with the system. The aim of this chapter is to identify the problems related to large-scale plant micropropagation via somatic embryogenesis, and to summarize the micropropagation technology and computer-aided image analysis. Viscous additive supplemented culture, which is including the successful results obtained by us for callus regeneration, is also introduced. PMID:15453194

  16. What Sort of Girl Wants to Study Physics After the Age of 16? Findings from a Large-scale UK Survey

    NASA Astrophysics Data System (ADS)

    Mujtaba, Tamjid; Reiss, Michael J.

    2013-11-01

    This paper investigates the characteristics of 15-year-old girls who express an intention to study physics post-16. This paper unpacks issues around within-girl group differences and similarities between boys and girls in survey responses about physics. The analysis is based on the year 10 (age 15 years) responses of 5,034 students from 137 UK schools as learners of physics during the academic year 2008-2009. A comparison between boys and girls indicates the pervasiveness of gender issues, with boys more likely to respond positively towards physics-specific constructs than girls. The analysis also indicates that girls and boys who expressed intentions to participate in physics post-16 gave similar responses towards their physics teachers and physics lessons and had comparable physics extrinsic motivation. Girls (regardless of their intention to participate in physics) were less likely than boys to be encouraged to study physics post-16 by teachers, family and friends. Despite this, there were a subset of girls still intending to study physics post-16. The crucial differences between the girls who intended to study physics post-16 and those who did not is that girls who intend to study physics post-16 had higher physics extrinsic motivation, more positive perceptions of physics teachers and lessons, greater competitiveness and a tendency to be less extrovert. This strongly suggests that higher extrinsic motivation in physics could be the crucial underlying key that encourages a subset of girls (as well as boys) in wanting to pursue physics post-16.

  17. Coupling between convection and large-scale circulation

    NASA Astrophysics Data System (ADS)

    Becker, T.; Stevens, B. B.; Hohenegger, C.

    2014-12-01

    The ultimate drivers of convection - radiation, tropospheric humidity and surface fluxes - are altered both by the large-scale circulation and by convection itself. A quantity to which all drivers of convection contribute is moist static energy, or gross moist stability, respectively. Therefore, a variance analysis of the moist static energy budget in radiative-convective equilibrium helps understanding the interaction of precipitating convection and the large-scale environment. In addition, this method provides insights concerning the impact of convective aggregation on this coupling. As a starting point, the interaction is analyzed with a general circulation model, but a model intercomparison study using a hierarchy of models is planned. Effective coupling parameters will be derived from cloud resolving models and these will in turn be related to assumptions used to parameterize convection in large-scale models.

  18. Do Large-Scale Topological Features Correlate with Flare Properties?

    NASA Astrophysics Data System (ADS)

    DeRosa, Marc L.; Barnes, Graham

    2016-05-01

    In this study, we aim to identify whether the presence or absence of particular topological features in the large-scale coronal magnetic field are correlated with whether a flare is confined or eruptive. To this end, we first determine the locations of null points, spine lines, and separatrix surfaces within the potential fields associated with the locations of several strong flares from the current and previous sunspot cycles. We then validate the topological skeletons against large-scale features in observations, such as the locations of streamers and pseudostreamers in coronagraph images. Finally, we characterize the topological environment in the vicinity of the flaring active regions and identify the trends involving their large-scale topologies and the properties of the associated flares.

  19. Toward system-level understanding of baculovirus–host cell interactions: from molecular fundamental studies to large-scale proteomics approaches

    PubMed Central

    Monteiro, Francisca; Carinhas, Nuno; Carrondo, Manuel J. T.; Bernal, Vicente; Alves, Paula M.

    2012-01-01

    Baculoviruses are insect viruses extensively exploited as eukaryotic protein expression vectors. Molecular biology studies have provided exciting discoveries on virus–host interactions, but the application of omic high-throughput techniques on the baculovirus–insect cell system has been hampered by the lack of host genome sequencing. While a broader, systems-level analysis of biological responses to infection is urgently needed, recent advances on proteomic studies have yielded new insights on the impact of infection on the host cell. These works are reviewed and critically assessed in the light of current biological knowledge of the molecular biology of baculoviruses and insect cells. PMID:23162544

  20. The Development of Extraversion and Ability: Analysis of Data from a Large-Scale Longitudinal Study of Children Tested at 10-11 and 14-15 Years.

    ERIC Educational Resources Information Center

    Anthony, W. S.

    1983-01-01

    Results of analysis of correlations collected by Cookson, following Eysenck and Cookson's study of personality and ability in young people, confirm the finding from previous Cattellian test data that the more intelligent children decline in relative extraversion scores and cast doubt on Eysenck's suggestion that introverts gradually show higher…

  1. Gaining Ground in the Middle Grades: Why Some Schools Do Better. A Large-Scale Study of Middle Grades Practices and Student Outcomes. Initial Research Report

    ERIC Educational Resources Information Center

    EdSource, 2010

    2010-01-01

    This study contributes to the field by identifying a broad range of traditional and newer middle grade policies and practices, and determining in California which of these differentiate higher- from lower-performing schools serving similar student populations, with performance measured by the state's standards-based tests. Based on a sample of 303…

  2. What Sort of Girl Wants to Study Physics after the Age of 16? Findings from a Large-Scale UK Survey

    ERIC Educational Resources Information Center

    Mujtaba, Tamjid; Reiss, Michael J.

    2013-01-01

    This paper investigates the characteristics of 15-year-old girls who express an intention to study physics post-16. This paper unpacks issues around within-girl group differences and similarities between boys and girls in survey responses about physics. The analysis is based on the year 10 (age 15 years) responses of 5,034 students from 137 UK…

  3. A large-scale operational study of home-based therapy with ready-to-use therapeutic food in childhood malnutriton in Malawi

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Home-based therapy with ready-to-use therapeutic food (RUTF) for the treatment of malnutrition has better outcomes in the research setting than standard therapy. This study examined outcomes of malnourished children aged 6-60 months enrolled in operational home-based therapy with RUTF. Children enro...

  4. A Large-Scale Investigation into the Relationship between Attendance and Attainment: A Study Using an Innovative, Electronic Attendance Monitoring System

    ERIC Educational Resources Information Center

    Newman-Ford, Loretta; Fitzgibbon, Karen; Lloyd, Stephen; Thomas, Stephen

    2008-01-01

    The literature available on the relationship between student attendance and attainment is inconsistent. Nevertheless, there is some empirical evidence to suggest that attendance is a determinant of academic performance and progression. Colby published results of a study which examined the relationship within a single year 1 undergraduate module,…