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Sample records for accelerating epistasis analysis

  1. Epistasis analysis using artificial intelligence.

    PubMed

    Moore, Jason H; Hill, Doug P

    2015-01-01

    Here we introduce artificial intelligence (AI) methodology for detecting and characterizing epistasis in genetic association studies. The ultimate goal of our AI strategy is to analyze genome-wide genetics data as a human would using sources of expert knowledge as a guide. The methodology presented here is based on computational evolution, which is a type of genetic programming. The ability to generate interesting solutions while at the same time learning how to solve the problem at hand distinguishes computational evolution from other genetic programming approaches. We provide a general overview of this approach and then present a few examples of its application to real data. PMID:25403541

  2. Dynamic Network-Based Epistasis Analysis: Boolean Examples

    PubMed Central

    Azpeitia, Eugenio; Benítez, Mariana; Padilla-Longoria, Pablo; Espinosa-Soto, Carlos; Alvarez-Buylla, Elena R.

    2011-01-01

    In this article we focus on how the hierarchical and single-path assumptions of epistasis analysis can bias the inference of gene regulatory networks. Here we emphasize the critical importance of dynamic analyses, and specifically illustrate the use of Boolean network models. Epistasis in a broad sense refers to gene interactions, however, as originally proposed by Bateson, epistasis is defined as the blocking of a particular allelic effect due to the effect of another allele at a different locus (herein, classical epistasis). Classical epistasis analysis has proven powerful and useful, allowing researchers to infer and assign directionality to gene interactions. As larger data sets are becoming available, the analysis of classical epistasis is being complemented with computer science tools and system biology approaches. We show that when the hierarchical and single-path assumptions are not met in classical epistasis analysis, the access to relevant information and the correct inference of gene interaction topologies is hindered, and it becomes necessary to consider the temporal dynamics of gene interactions. The use of dynamical networks can overcome these limitations. We particularly focus on the use of Boolean networks that, like classical epistasis analysis, relies on logical formalisms, and hence can complement classical epistasis analysis and relax its assumptions. We develop a couple of theoretical examples and analyze them from a dynamic Boolean network model perspective. Boolean networks could help to guide additional experiments and discern among alternative regulatory schemes that would be impossible or difficult to infer without the elimination of these assumption from the classical epistasis analysis. We also use examples from the literature to show how a Boolean network-based approach has resolved ambiguities and guided epistasis analysis. Our article complements previous accounts, not only by focusing on the implications of the hierarchical and

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

    PubMed Central

    Xie, Dan; Liang, Meimei; Xiong, Momiao

    2016-01-01

    To date, most genetic analyses of phenotypes have focused on analyzing single traits or analyzing each phenotype independently. However, joint epistasis analysis of multiple complementary traits will increase statistical power and improve our understanding of the complicated genetic structure of the complex diseases. Despite their importance in uncovering the genetic structure of complex traits, the statistical methods for identifying epistasis in multiple phenotypes remains fundamentally unexplored. To fill this gap, we formulate a test for interaction between two genes in multiple quantitative trait analysis as a multiple functional regression (MFRG) in which the genotype functions (genetic variant profiles) are defined as a function of the genomic position of the genetic variants. We use large-scale simulations to calculate Type I error rates for testing interaction between two genes with multiple phenotypes and to compare the power with multivariate pairwise interaction analysis and single trait interaction analysis by a single variate functional regression model. To further evaluate performance, the MFRG for epistasis analysis is applied to five phenotypes of exome sequence data from the NHLBI’s Exome Sequencing Project (ESP) to detect pleiotropic epistasis. A total of 267 pairs of genes that formed a genetic interaction network showed significant evidence of epistasis influencing five traits. The results demonstrate that the joint interaction analysis of multiple phenotypes has a much higher power to detect interaction than the interaction analysis of a single trait and may open a new direction to fully uncovering the genetic structure of multiple phenotypes. PMID:27104857

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

    PubMed

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

    2016-04-01

    To date, most genetic analyses of phenotypes have focused on analyzing single traits or analyzing each phenotype independently. However, joint epistasis analysis of multiple complementary traits will increase statistical power and improve our understanding of the complicated genetic structure of the complex diseases. Despite their importance in uncovering the genetic structure of complex traits, the statistical methods for identifying epistasis in multiple phenotypes remains fundamentally unexplored. To fill this gap, we formulate a test for interaction between two genes in multiple quantitative trait analysis as a multiple functional regression (MFRG) in which the genotype functions (genetic variant profiles) are defined as a function of the genomic position of the genetic variants. We use large-scale simulations to calculate Type I error rates for testing interaction between two genes with multiple phenotypes and to compare the power with multivariate pairwise interaction analysis and single trait interaction analysis by a single variate functional regression model. To further evaluate performance, the MFRG for epistasis analysis is applied to five phenotypes of exome sequence data from the NHLBI's Exome Sequencing Project (ESP) to detect pleiotropic epistasis. A total of 267 pairs of genes that formed a genetic interaction network showed significant evidence of epistasis influencing five traits. The results demonstrate that the joint interaction analysis of multiple phenotypes has a much higher power to detect interaction than the interaction analysis of a single trait and may open a new direction to fully uncovering the genetic structure of multiple phenotypes. PMID:27104857

  5. Identifiability and inference of pathway motifs by epistasis analysis.

    PubMed

    Phenix, Hilary; Perkins, Theodore; Kærn, Mads

    2013-06-01

    The accuracy of genetic network inference is limited by the assumptions used to determine if one hypothetical model is better than another in explaining experimental observations. Most previous work on epistasis analysis-in which one attempts to infer pathway relationships by determining equivalences among traits following mutations-has been based on Boolean or linear models. Here, we delineate the ultimate limits of epistasis-based inference by systematically surveying all two-gene network motifs and use symbolic algebra with arbitrary regulation functions to examine trait equivalences. Our analysis divides the motifs into equivalence classes, where different genetic perturbations result in indistinguishable experimental outcomes. We demonstrate that this partitioning can reveal important information about network architecture, and show, using simulated data, that it greatly improves the accuracy of genetic network inference methods. Because of the minimal assumptions involved, equivalence partitioning has broad applicability for gene network inference. PMID:23822501

  6. Identifiability and inference of pathway motifs by epistasis analysis

    NASA Astrophysics Data System (ADS)

    Phenix, Hilary; Perkins, Theodore; Kærn, Mads

    2013-06-01

    The accuracy of genetic network inference is limited by the assumptions used to determine if one hypothetical model is better than another in explaining experimental observations. Most previous work on epistasis analysis—in which one attempts to infer pathway relationships by determining equivalences among traits following mutations—has been based on Boolean or linear models. Here, we delineate the ultimate limits of epistasis-based inference by systematically surveying all two-gene network motifs and use symbolic algebra with arbitrary regulation functions to examine trait equivalences. Our analysis divides the motifs into equivalence classes, where different genetic perturbations result in indistinguishable experimental outcomes. We demonstrate that this partitioning can reveal important information about network architecture, and show, using simulated data, that it greatly improves the accuracy of genetic network inference methods. Because of the minimal assumptions involved, equivalence partitioning has broad applicability for gene network inference.

  7. Parallelizing Epistasis Detection in GWAS on FPGA and GPU-Accelerated Computing Systems.

    PubMed

    González-Domínguez, Jorge; Wienbrandt, Lars; Kässens, Jan Christian; Ellinghaus, David; Schimmler, Manfred; Schmidt, Bertil

    2015-01-01

    High-throughput genotyping technologies (such as SNP-arrays) allow the rapid collection of up to a few million genetic markers of an individual. Detecting epistasis (based on 2-SNP interactions) in Genome-Wide Association Studies is an important but time consuming operation since statistical computations have to be performed for each pair of measured markers. Computational methods to detect epistasis therefore suffer from prohibitively long runtimes; e.g., processing a moderately-sized dataset consisting of about 500,000 SNPs and 5,000 samples requires several days using state-of-the-art tools on a standard 3 GHz CPU. In this paper, we demonstrate how this task can be accelerated using a combination of fine-grained and coarse-grained parallelism on two different computing systems. The first architecture is based on reconfigurable hardware (FPGAs) while the second architecture uses multiple GPUs connected to the same host. We show that both systems can achieve speedups of around four orders-of-magnitude compared to the sequential implementation. This significantly reduces the runtimes for detecting epistasis to only a few minutes for moderately-sized datasets and to a few hours for large-scale datasets. PMID:26451813

  8. JBASE: Joint Bayesian Analysis of Subphenotypes and Epistasis

    PubMed Central

    Colak, Recep; Kim, TaeHyung; Kazan, Hilal; Oh, Yoomi; Cruz, Miguel; Valladares-Salgado, Adan; Peralta, Jesus; Escobedo, Jorge; Parra, Esteban J.; Kim, Philip M.; Goldenberg, Anna

    2016-01-01

    Motivation: Rapid advances in genotyping and genome-wide association studies have enabled the discovery of many new genotype–phenotype associations at the resolution of individual markers. However, these associations explain only a small proportion of theoretically estimated heritability of most diseases. In this work, we propose an integrative mixture model called JBASE: joint Bayesian analysis of subphenotypes and epistasis. JBASE explores two major reasons of missing heritability: interactions between genetic variants, a phenomenon known as epistasis and phenotypic heterogeneity, addressed via subphenotyping. Results: Our extensive simulations in a wide range of scenarios repeatedly demonstrate that JBASE can identify true underlying subphenotypes, including their associated variants and their interactions, with high precision. In the presence of phenotypic heterogeneity, JBASE has higher Power and lower Type 1 Error than five state-of-the-art approaches. We applied our method to a sample of individuals from Mexico with Type 2 diabetes and discovered two novel epistatic modules, including two loci each, that define two subphenotypes characterized by differences in body mass index and waist-to-hip ratio. We successfully replicated these subphenotypes and epistatic modules in an independent dataset from Mexico genotyped with a different platform. Availability and implementation: JBASE is implemented in C++, supported on Linux and is available at http://www.cs.toronto.edu/∼goldenberg/JBASE/jbase.tar.gz. The genotype data underlying this study are available upon approval by the ethics review board of the Medical Centre Siglo XXI. Please contact Dr Miguel Cruz at mcruzl@yahoo.com for assistance with the application. Contact: anna.goldenberg@utoronto.ca Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26411870

  9. Epistasis in Monkeyflowers

    PubMed Central

    Kelly, John K.

    2005-01-01

    Epistasis contributes significantly to intrapopulation variation in floral morphology, development time, and male fitness components of Mimulus guttatus. This is demonstrated with a replicated line-cross experiment involving slightly over 7000 plants. The line-cross methodology is based on estimates for means. It thus has greater power than the variance partitioning approaches historically used to estimate epistasis within populations. The replication of the breeding design across many pairs of randomly extracted, inbred lines is necessary given the diversity of multilocus genotypes residing within an outbred deme. Male fitness is shown to exhibit synergistic epistasis, an accelerating decline in fitness with inbreeding. Synergism is a necessary, but not sufficient, condition for a mutational deterministic hypothesis for the evolutionary maintenance of sexual reproduction. Unlike male fitness measures, flower morphology and development time yield positive evidence of epistasis but not of synergism. The results for these traits suggest that epistatic effects are variable across genetic backgrounds or sets of interacting loci. PMID:15944350

  10. Analysis of epistasis for diabetic nephropathy among type 2 diabetic patients.

    PubMed

    Hsieh, Chang-Hsun; Liang, Kung-Hao; Hung, Yi-Jen; Huang, Li-Chin; Pei, Dee; Liao, Ya-Tang; Kuo, Shi-Wen; Bey, Monica Shian-Jy; Chen, Jui-Lin; Chen, Ellson Y

    2006-09-15

    Diabetic nephropathy (DN) is one of the most serious complications of diabetes, accounting for the majority of patients with end-stage renal disease. The molecular pathogenesis of DN involves multiple pathways in a complex, partially resolved manner. The paper presents an exploratory epistatic study for DN. Association analysis were performed on 231 SNP loci in a cohort of 264 type 2 diabetes patients, followed by the epistasis analysis using the multifactor dimensionality reduction and the genetic algorithm with Boolean algebra. A two-locus epistatic effect of EGFR and RXRG was identified, with a cross-validation consistency of 91.7%. PMID:16893912

  11. Epistasis Test in Meta-Analysis: A Multi-Parameter Markov Chain Monte Carlo Model for Consistency of Evidence.

    PubMed

    Lin, Chin; Chu, Chi-Ming; Su, Sui-Lung

    2016-01-01

    Conventional genome-wide association studies (GWAS) have been proven to be a successful strategy for identifying genetic variants associated with complex human traits. However, there is still a large heritability gap between GWAS and transitional family studies. The "missing heritability" has been suggested to be due to lack of studies focused on epistasis, also called gene-gene interactions, because individual trials have often had insufficient sample size. Meta-analysis is a common method for increasing statistical power. However, sufficient detailed information is difficult to obtain. A previous study employed a meta-regression-based method to detect epistasis, but it faced the challenge of inconsistent estimates. Here, we describe a Markov chain Monte Carlo-based method, called "Epistasis Test in Meta-Analysis" (ETMA), which uses genotype summary data to obtain consistent estimates of epistasis effects in meta-analysis. We defined a series of conditions to generate simulation data and tested the power and type I error rates in ETMA, individual data analysis and conventional meta-regression-based method. ETMA not only successfully facilitated consistency of evidence but also yielded acceptable type I error and higher power than conventional meta-regression. We applied ETMA to three real meta-analysis data sets. We found significant gene-gene interactions in the renin-angiotensin system and the polycyclic aromatic hydrocarbon metabolism pathway, with strong supporting evidence. In addition, glutathione S-transferase (GST) mu 1 and theta 1 were confirmed to exert independent effects on cancer. We concluded that the application of ETMA to real meta-analysis data was successful. Finally, we developed an R package, etma, for the detection of epistasis in meta-analysis [etma is available via the Comprehensive R Archive Network (CRAN) at https://cran.r-project.org/web/packages/etma/index.html]. PMID:27045371

  12. Epistasis Test in Meta-Analysis: A Multi-Parameter Markov Chain Monte Carlo Model for Consistency of Evidence

    PubMed Central

    Lin, Chin; Chu, Chi-Ming; Su, Sui-Lung

    2016-01-01

    Conventional genome-wide association studies (GWAS) have been proven to be a successful strategy for identifying genetic variants associated with complex human traits. However, there is still a large heritability gap between GWAS and transitional family studies. The “missing heritability” has been suggested to be due to lack of studies focused on epistasis, also called gene–gene interactions, because individual trials have often had insufficient sample size. Meta-analysis is a common method for increasing statistical power. However, sufficient detailed information is difficult to obtain. A previous study employed a meta-regression-based method to detect epistasis, but it faced the challenge of inconsistent estimates. Here, we describe a Markov chain Monte Carlo-based method, called “Epistasis Test in Meta-Analysis” (ETMA), which uses genotype summary data to obtain consistent estimates of epistasis effects in meta-analysis. We defined a series of conditions to generate simulation data and tested the power and type I error rates in ETMA, individual data analysis and conventional meta-regression-based method. ETMA not only successfully facilitated consistency of evidence but also yielded acceptable type I error and higher power than conventional meta-regression. We applied ETMA to three real meta-analysis data sets. We found significant gene–gene interactions in the renin–angiotensin system and the polycyclic aromatic hydrocarbon metabolism pathway, with strong supporting evidence. In addition, glutathione S-transferase (GST) mu 1 and theta 1 were confirmed to exert independent effects on cancer. We concluded that the application of ETMA to real meta-analysis data was successful. Finally, we developed an R package, etma, for the detection of epistasis in meta-analysis [etma is available via the Comprehensive R Archive Network (CRAN) at https://cran.r-project.org/web/packages/etma/index.html]. PMID:27045371

  13. Genome-wide analysis of epistasis in body mass index using multiple human populations

    PubMed Central

    Wei, Wen-Hua; Hemani, Gib; Gyenesei, Attila; Vitart, Veronique; Navarro, Pau; Hayward, Caroline; Cabrera, Claudia P; Huffman, Jennifer E; Knott, Sara A; Hicks, Andrew A; Rudan, Igor; Pramstaller, Peter P; Wild, Sarah H; Wilson, James F; Campbell, Harry; Hastie, Nicholas D; Wright, Alan F; Haley, Chris S

    2012-01-01

    We surveyed gene–gene interactions (epistasis) in human body mass index (BMI) in four European populations (n<1200) via exhaustive pair-wise genome scans where interactions were computed as F ratios by testing a linear regression model fitting two single-nucleotide polymorphisms (SNPs) with interactions against the one without. Before the association tests, BMI was corrected for sex and age, normalised and adjusted for relatedness. Neither single SNPs nor SNP interactions were genome-wide significant in either cohort based on the consensus threshold (P=5.0E−08) and a Bonferroni corrected threshold (P=1.1E−12), respectively. Next we compared sub genome-wide significant SNP interactions (P<5.0E−08) across cohorts to identify common epistatic signals, where SNPs were annotated to genes to test for gene ontology (GO) enrichment. Among the epistatic genes contributing to the commonly enriched GO terms, 19 were shared across study cohorts of which 15 are previously published genome-wide association loci, including CDH13 (cadherin 13) associated with height and SORCS2 (sortilin-related VPS10 domain containing receptor 2) associated with circulating insulin-like growth factor 1 and binding protein 3. Interactions between the 19 shared epistatic genes and those involving BMI candidate loci (P<5.0E−08) were tested across cohorts and found eight replicated at the SNP level (P<0.05) in at least one cohort, which were further tested and showed limited replication in a separate European population (n>5000). We conclude that genome-wide analysis of epistasis in multiple populations is an effective approach to provide new insights into the genetic regulation of BMI but requires additional efforts to confirm the findings. PMID:22333899

  14. Deep epistasis in human metabolism

    PubMed Central

    Imielinski, Marcin; Belta, Calin

    2010-01-01

    We extend and apply a method that we have developed for deriving high-order epistatic relationships in large biochemical networks to a published genome-scale model of human metabolism. In our analysis we compute 33 328 reaction sets whose knockout synergistically disables one or more of 43 important metabolic functions. We also design minimal knockouts that remove flux through fumarase, an enzyme that has previously been shown to play an important role in human cancer. Most of these knockout sets employ more than eight mutually buffering reactions, spanning multiple cellular compartments and metabolic subsystems. These reaction sets suggest that human metabolic pathways possess a striking degree of parallelism, inducing “deep” epistasis between diversely annotated genes. Our results prompt specific chemical and genetic perturbation follow-up experiments that could be used to query in vivo pathway redundancy. They also suggest directions for future statistical studies of epistasis in genetic variation data sets. PMID:20590333

  15. Deep epistasis in human metabolism

    NASA Astrophysics Data System (ADS)

    Imielinski, Marcin; Belta, Calin

    2010-06-01

    We extend and apply a method that we have developed for deriving high-order epistatic relationships in large biochemical networks to a published genome-scale model of human metabolism. In our analysis we compute 33 328 reaction sets whose knockout synergistically disables one or more of 43 important metabolic functions. We also design minimal knockouts that remove flux through fumarase, an enzyme that has previously been shown to play an important role in human cancer. Most of these knockout sets employ more than eight mutually buffering reactions, spanning multiple cellular compartments and metabolic subsystems. These reaction sets suggest that human metabolic pathways possess a striking degree of parallelism, inducing "deep" epistasis between diversely annotated genes. Our results prompt specific chemical and genetic perturbation follow-up experiments that could be used to query in vivo pathway redundancy. They also suggest directions for future statistical studies of epistasis in genetic variation data sets.

  16. Epistasis in protein evolution.

    PubMed

    Starr, Tyler N; Thornton, Joseph W

    2016-07-01

    The structure, function, and evolution of proteins depend on physical and genetic interactions among amino acids. Recent studies have used new strategies to explore the prevalence, biochemical mechanisms, and evolutionary implications of these interactions-called epistasis-within proteins. Here we describe an emerging picture of pervasive epistasis in which the physical and biological effects of mutations change over the course of evolution in a lineage-specific fashion. Epistasis can restrict the trajectories available to an evolving protein or open new paths to sequences and functions that would otherwise have been inaccessible. We describe two broad classes of epistatic interactions, which arise from different physical mechanisms and have different effects on evolutionary processes. Specific epistasis-in which one mutation influences the phenotypic effect of few other mutations-is caused by direct and indirect physical interactions between mutations, which nonadditively change the protein's physical properties, such as conformation, stability, or affinity for ligands. In contrast, nonspecific epistasis describes mutations that modify the effect of many others; these typically behave additively with respect to the physical properties of a protein but exhibit epistasis because of a nonlinear relationship between the physical properties and their biological effects, such as function or fitness. Both types of interaction are rampant, but specific epistasis has stronger effects on the rate and outcomes of evolution, because it imposes stricter constraints and modulates evolutionary potential more dramatically; it therefore makes evolution more contingent on low-probability historical events and leaves stronger marks on the sequences, structures, and functions of protein families. PMID:26833806

  17. Dynamic Epistasis under Varying Environmental Perturbations

    PubMed Central

    Barker, Brandon; Xu, Lin; Gu, Zhenglong

    2015-01-01

    Epistasis describes the phenomenon that mutations at different loci do not have independent effects with regard to certain phenotypes. Understanding the global epistatic landscape is vital for many genetic and evolutionary theories. Current knowledge for epistatic dynamics under multiple conditions is limited by the technological difficulties in experimentally screening epistatic relations among genes. We explored this issue by applying flux balance analysis to simulate epistatic landscapes under various environmental perturbations. Specifically, we looked at gene-gene epistatic interactions, where the mutations were assumed to occur in different genes. We predicted that epistasis tends to become more positive from glucose-abundant to nutrient-limiting conditions, indicating that selection might be less effective in removing deleterious mutations in the latter. We also observed a stable core of epistatic interactions in all tested conditions, as well as many epistatic interactions unique to each condition. Interestingly, genes in the stable epistatic interaction network are directly linked to most other genes whereas genes with condition-specific epistasis form a scale-free network. Furthermore, genes with stable epistasis tend to have similar evolutionary rates, whereas this co-evolving relationship does not hold for genes with condition-specific epistasis. Our findings provide a novel genome-wide picture about epistatic dynamics under environmental perturbations. PMID:25625594

  18. How mutational epistasis impairs predictability in protein evolution and design.

    PubMed

    Miton, Charlotte M; Tokuriki, Nobuhiko

    2016-07-01

    There has been much debate about the extent to which mutational epistasis, that is, the dependence of the outcome of a mutation on the genetic background, constrains evolutionary trajectories. The degree of unpredictability introduced by epistasis, due to the non-additivity of functional effects, strongly hinders the strategies developed in protein design and engineering. While many studies have addressed this issue through systematic characterization of evolutionary trajectories within individual enzymes, the field lacks a consensus view on this matter. In this work, we performed a comprehensive analysis of epistasis by analyzing the mutational effects from nine adaptive trajectories toward new enzymatic functions. We quantified epistasis by comparing the effect of mutations occurring between two genetic backgrounds: the starting enzyme (for example, wild type) and the intermediate variant on which the mutation occurred during the trajectory. We found that most trajectories exhibit positive epistasis, in which the mutational effect is more beneficial when it occurs later in the evolutionary trajectory. Approximately half (49%) of functional mutations were neutral or negative on the wild-type background, but became beneficial at a later stage in the trajectory, indicating that these functional mutations were not predictable from the initial starting point. While some cases of strong epistasis were associated with direct interaction between residues, many others were caused by long-range indirect interactions between mutations. Our work highlights the prevalence of epistasis in enzyme adaptive evolution, in particular positive epistasis, and suggests the necessity of incorporating mutational epistasis in protein engineering and design to create highly efficient catalysts. PMID:26757214

  19. Integrated pathway and epistasis analysis reveals interactive effect of genetic variants at TERF1 and AFAP1L2 loci on melanoma risk.

    PubMed

    Brossard, Myriam; Fang, Shenying; Vaysse, Amaury; Wei, Qingyi; Chen, Wei V; Mohamdi, Hamida; Maubec, Eve; Lavielle, Nolwenn; Galan, Pilar; Lathrop, Mark; Avril, Marie-Françoise; Lee, Jeffrey E; Amos, Christopher I; Demenais, Florence

    2015-10-15

    Genome-wide association studies (GWASs) have characterized 13 loci associated with melanoma, which only account for a small part of melanoma risk. To identify new genes with too small an effect to be detected individually but which collectively influence melanoma risk and/or show interactive effects, we used a two-step analysis strategy including pathway analysis of genome-wide SNP data, in a first step, and epistasis analysis within significant pathways, in a second step. Pathway analysis, using the gene-set enrichment analysis (GSEA) approach and the gene ontology (GO) database, was applied to the outcomes of MELARISK (3,976 subjects) and MDACC (2,827 subjects) GWASs. Cross-gene SNP-SNP interaction analysis within melanoma-associated GOs was performed using the INTERSNP software. Five GO categories were significantly enriched in genes associated with melanoma (false discovery rate ≤ 5% in both studies): response to light stimulus, regulation of mitotic cell cycle, induction of programmed cell death, cytokine activity and oxidative phosphorylation. Epistasis analysis, within each of the five significant GOs, showed significant evidence for interaction for one SNP pair at TERF1 and AFAP1L2 loci (pmeta-int  = 2.0 × 10(-7) , which met both the pathway and overall multiple-testing corrected thresholds that are equal to 9.8 × 10(-7) and 2.0 × 10(-7) , respectively) and suggestive evidence for another pair involving correlated SNPs at the same loci (pmeta-int  = 3.6 × 10(-6) ). This interaction has important biological relevance given the key role of TERF1 in telomere biology and the reported physical interaction between TERF1 and AFAP1L2 proteins. This finding brings a novel piece of evidence for the emerging role of telomere dysfunction into melanoma development. PMID:25892537

  20. The decline in fitness with inbreeding: evidence for negative dominance-by-dominance epistasis in Drosophila melanogaster.

    PubMed

    Sharp, N P; Agrawal, A F

    2016-04-01

    Genetic interactions can play an important role in the evolution of reproductive strategies. In particular, negative dominance-by-dominance epistasis for fitness can theoretically favour sex and recombination. This form of epistasis can be detected statistically because it generates nonlinearity in the relationship between fitness and inbreeding coefficient. Measures of fitness in progressively inbred lines tend to show limited evidence for epistasis. However, tests of this kind can be biased against detecting an accelerating decline due to line losses at higher inbreeding levels. We tested for dominance-by-dominance epistasis in Drosophila melanogaster by examining viability at five inbreeding levels that were generated simultaneously, avoiding the bias against detecting nonlinearity that has affected previous studies. We find an accelerating rate of fitness decline with inbreeding, indicating that dominance-by-dominance epistasis is negative on average, which should favour sex and recombination. PMID:26709722

  1. Experimental evolution and epistasis in variable environments

    NASA Astrophysics Data System (ADS)

    Tans, Sander

    2014-03-01

    Environmental changes trigger cellular responses, but also impose selective pressures on the underlying regulatory systems. To disentangle this complex interplay we follow a synthetic biology approach. By linking the output of regulatory systems to bacterial growth, quantified temporally variable selective pressures can be applied to regulatory systems. This approach allows one to explore how networks evolve in complex variable environments. Epistatic interactions that underlie evolutionary constraint have mainly been studied for constant external conditions. However, environmental changes may modulate epistasis and hence affect genetic constraints. We investigate genetic constraints in the adaptive evolution of a novel regulatory function in variable environments, using the lac repressor, LacI, as a model system. We systematically reconstructed mutational trajectories from wild type LacI to three different variants that each exhibit an inverse response to the inducing ligand IPTG, and analyzed the higher-order interactions between genetic and environmental changes. We find epistasis to depend strongly on the environment. As a result, mutational steps essential to inversion but inaccessible by positive selection in one environment, become accessible in another. We present a graphical method to analyze the observed complex higher-order interactions between multiple mutations and environmental change, and show how they can be explained by a combination of mutational effects on allostery and thermodynamic stability. This dependency of genetic constraint on the environment should fundamentally affect evolutionary dynamics and phylogenetic analysis. NWO-FOM

  2. Weak Epistasis Generally Stabilizes Phenotypes in a Mouse Intercross

    PubMed Central

    Tyler, Anna L.; Donahue, Leah Rae; Churchill, Gary A.; Carter, Gregory W.

    2016-01-01

    The extent and strength of epistasis is commonly unresolved in genetic studies, and observed epistasis is often difficult to interpret in terms of biological consequences or overall genetic architecture. We investigated the prevalence and consequences of epistasis by analyzing four body composition phenotypes—body weight, body fat percentage, femoral density, and femoral circumference—in a large F2 intercross of B6-lit/lit and C3.B6-lit/lit mice. We used Combined Analysis of Pleiotropy and Epistasis (CAPE) to examine interactions for the four phenotypes simultaneously, which revealed an extensive directed network of genetic loci interacting with each other, circulating IGF1, and sex to influence these phenotypes. The majority of epistatic interactions had small effects relative to additive effects of individual loci, and tended to stabilize phenotypes towards the mean of the population rather than extremes. Interactive effects of two alleles inherited from one parental strain commonly resulted in phenotypes closer to the population mean than the additive effects from the two loci, and often much closer to the mean than either single-locus model. Alternatively, combinations of alleles inherited from different parent strains contribute to more extreme phenotypes not observed in either parental strain. This class of phenotype-stabilizing interactions has effects that are close to additive and are thus difficult to detect except in very large intercrosses. Nevertheless, we found these interactions to be useful in generating hypotheses for functional relationships between genetic loci. Our findings suggest that while epistasis is often weak and unlikely to account for a large proportion of heritable variance, even small-effect genetic interactions can facilitate hypotheses of underlying biology in well-powered studies. PMID:26828925

  3. Accelerating pulsar timing data analysis

    NASA Astrophysics Data System (ADS)

    van Haasteren, Rutger

    2013-02-01

    The analysis of pulsar timing data, especially in pulsar timing array (PTA) projects, has encountered practical difficulties: evaluating the likelihood and/or correlation-based statistics can become prohibitively computationally expensive for large data sets. In situations where a stochastic signal of interest has a power spectral density that dominates the noise in a limited bandwidth of the total frequency domain (e.g. the isotropic background of gravitational waves), a linear transformation exists that transforms the timing residuals to a basis in which virtually all the information about the stochastic signal of interest is contained in a small fraction of basis vectors. By only considering such a small subset of these `generalized residuals', the dimensionality of the data analysis problem is greatly reduced, which can cause a large speedup in the evaluation of the likelihood: the ABC-method (Acceleration By Compression). The compression fidelity, calculable with crude estimates of the signal and noise, can be used to determine how far a data set can be compressed without significant loss of information. Both direct tests on the likelihood, and Bayesian analysis of mock data, show that the signal can be recovered as well as with an analysis of uncompressed data. In the analysis of International PTA Mock Data Challenge data sets, speedups of a factor of 3 orders of magnitude are demonstrated. For realistic PTA data sets the acceleration may become greater than six orders of magnitude due to the low signal-to-noise ratio.

  4. Confronting the missing epistasis problem: on the reproducibility of gene-gene interactions.

    PubMed

    Murk, William; Bracken, Michael B; DeWan, Andrew T

    2015-08-01

    Epistasis (gene-gene interaction) is thought to play an integral role in the genetic basis of complex traits, and a significant amount of research has been invested into identifying this phenomenon in human disease. However, the overall success of empirical studies of epistasis in humans is unclear, as such studies are rarely systematically evaluated. Here, we have selected asthma as an example of a well-studied, complex human disease, and provide a critical analysis and replication attempt of nearly all prior reports of epistasis for this disease. Of 191 previously reported interactions, we find that 39.8% were not originally identified using an explicit test for interaction and thus may not have been true epistatic effects to begin with. Moreover, directions of effect were not described for 46.1% of the interactions, which prevents their rigorous replication. In the original studies, attempts at replication were made for 15.2% of the interactions, and 7.3% were actually replicated. In the current study, we were able to evaluate 85.9% of the interactions using a large asthma dataset from the GABRIEL Consortium. None of these interactions could be replicated based on strict criteria. However, we found nominally significant (p < 0.05) evidence in support of 23.8% of the evaluated interactions. Although many reports of epistasis are not robustly supported in the published literature, our results suggest that at least some of these reports may have been true-positive examples of epistasis. In general, improvements in empirical studies of epistasis are called for, in order to better understand the importance of this phenomenon in human disease. PMID:25998948

  5. A survey about methods dedicated to epistasis detection.

    PubMed

    Niel, Clément; Sinoquet, Christine; Dina, Christian; Rocheleau, Ghislain

    2015-01-01

    During the past decade, findings of genome-wide association studies (GWAS) improved our knowledge and understanding of disease genetics. To date, thousands of SNPs have been associated with diseases and other complex traits. Statistical analysis typically looks for association between a phenotype and a SNP taken individually via single-locus tests. However, geneticists admit this is an oversimplified approach to tackle the complexity of underlying biological mechanisms. Interaction between SNPs, namely epistasis, must be considered. Unfortunately, epistasis detection gives rise to analytic challenges since analyzing every SNP combination is at present impractical at a genome-wide scale. In this review, we will present the main strategies recently proposed to detect epistatic interactions, along with their operating principle. Some of these methods are exhaustive, such as multifactor dimensionality reduction, likelihood ratio-based tests or receiver operating characteristic curve analysis; some are non-exhaustive, such as machine learning techniques (random forests, Bayesian networks) or combinatorial optimization approaches (ant colony optimization, computational evolution system). PMID:26442103

  6. A survey about methods dedicated to epistasis detection

    PubMed Central

    Niel, Clément; Sinoquet, Christine; Dina, Christian; Rocheleau, Ghislain

    2015-01-01

    During the past decade, findings of genome-wide association studies (GWAS) improved our knowledge and understanding of disease genetics. To date, thousands of SNPs have been associated with diseases and other complex traits. Statistical analysis typically looks for association between a phenotype and a SNP taken individually via single-locus tests. However, geneticists admit this is an oversimplified approach to tackle the complexity of underlying biological mechanisms. Interaction between SNPs, namely epistasis, must be considered. Unfortunately, epistasis detection gives rise to analytic challenges since analyzing every SNP combination is at present impractical at a genome-wide scale. In this review, we will present the main strategies recently proposed to detect epistatic interactions, along with their operating principle. Some of these methods are exhaustive, such as multifactor dimensionality reduction, likelihood ratio-based tests or receiver operating characteristic curve analysis; some are non-exhaustive, such as machine learning techniques (random forests, Bayesian networks) or combinatorial optimization approaches (ant colony optimization, computational evolution system). PMID:26442103

  7. Hugoniot analysis of the ram accelerator

    NASA Astrophysics Data System (ADS)

    Knowlen, C.; Bruckner, A. P.

    The thermodynamic properties of a combustible propellant gas, after it has been processed by a ram accelerator propulsive mode, are related by a 'ram accelerator Hugoniot' expression. These end states are determined from the 1-D conservation equations in a manner similar to that used for detonation waves, but with the addition of a force term in the momentum equation. Establishment of a region of potentially accessible thermodynamic end states that are consistent with ram accelerator operation at and above the Chapman-Jouguet detonation speed indicates that there are no fundamental constraints on accelerating projectiles over a wide range of Mach numbers in a single propellant mixture. Interpreting experimental data in the context of a generalized ram accelerator process leads to relatively simple propulsive models which can predict the projectile acceleration of any propulsive mode. The projectile velocity and acceleration histories determined by the Hugoniot analysis for the thermally choked ram accelerator mode are in excellent agreement with experiments.

  8. Epistasis and its consequences for the evolution of natural populations.

    PubMed

    Fenster, C B; Galloway, L F; Chao, L

    1997-07-01

    Throughout the neodarwinian synthesis, theorists have debated the role of gene interactions, or epistasis, in the evolutionary process. Unfortunately, empirical measurement of the role of epistasis in the evolution of natural populations has, until now, been difficult. Two developments in empirical approaches have occurred: (1) application of theory to the evolution of natural populations, and (2) the concurrent development of molecular marker-assisted techniques to understand the architecture of quantitative genetic variation. Thus, exciting developments in both theory and empirical data collection provide the stimulus for documenting the role of epistasis in the evolutionary process. PMID:21238076

  9. Rapid appearance of epistasis during adaptive divergence following colonization.

    PubMed Central

    Carroll, Scott P; Dingle, Hugh; Famula, Thomas R

    2003-01-01

    Theory predicts that short-term adaptation within populations depends on additive (A) genetic effects, while gene-gene interactions 'epistasis (E)' are important only in long-term evolution. However, few data exist on the genetic architecture of adaptive variation, and the relative importance of A versus non-additive genetic effects continues to be a central controversy of evolutionary biology after more than 70 years of debate. To examine this issue directly, we conducted hybridization experiments between two populations of wild soapberry bugs that have strongly differentiated in 100 or fewer generations following a host plant shift. Contrary to expectation, we found that between-population E and dominance (D) have appeared quickly in the evolution of new phenotypes. Rather than thousands of generations, adaptive gene differences between populations have evolved in tens. Such complex genetic variation could underlie the seemingly extreme rates of evolution that are increasingly reported in many taxa. In the case of the soapberry bug, extraordinary ecological opportunity, rather than mortality, may have created hard selection for genetic variants. Because ultimate division of populations into genetic species depends on epistatic loss of hybrid compatibility, local adaptation based on E may accelerate macro-evolutionary diversification. PMID:12952643

  10. Protein evolution. Pervasive degeneracy and epistasis in a protein-protein interface.

    PubMed

    Podgornaia, Anna I; Laub, Michael T

    2015-02-01

    Mapping protein sequence space is a difficult problem that necessitates the analysis of 20(N) combinations for sequences of length N. We systematically mapped the sequence space of four key residues in the Escherichia coli protein kinase PhoQ that drive recognition of its substrate PhoP. We generated a library containing all 160,000 variants of PhoQ at these positions and used a two-step selection coupled to next-generation sequencing to identify 1659 functional variants. Our results reveal extensive degeneracy in the PhoQ-PhoP interface and epistasis, with the effect of individual substitutions often highly dependent on context. Together, epistasis and the genetic code create a pattern of connectivity of functional variants in sequence space that likely constrains PhoQ evolution. Consequently, the diversity of PhoQ orthologs is substantially lower than that of functional PhoQ variants. PMID:25657251

  11. A pharmaco-epistasis strategy reveals a new cell size controlling pathway in yeast

    PubMed Central

    Moretto, Fabien; Sagot, Isabelle; Daignan-Fornier, Bertrand; Pinson, Benoît

    2013-01-01

    Cell size is a complex quantitative trait resulting from interactions between intricate genetic networks and environmental conditions. Here, taking advantage of previous studies that uncovered hundreds of genes affecting budding yeast cell size homeostasis, we performed a wide pharmaco-epistasis analysis using drugs mimicking cell size mutations. Simple epistasis relationship emerging from this approach allowed us to characterize a new cell size homeostasis pathway comprising the sirtuin Sir2, downstream effectors including the large ribosomal subunit (60S) and the transcriptional regulators Swi4 and Swi6. We showed that this Sir2/60S signaling route acts independently of other previously described cell size controlling pathways and may integrate the metabolic status of the cell through NAD+ intracellular concentration. Finally, although Sir2 and the 60S subunits regulate both cell size and replicative aging, we found that there is no clear causal relationship between these two complex traits. This study sheds light on a pathway of >50 genes and illustrates how pharmaco-epistasis applied to yeast offers a potent experimental framework to explore complex genotype/phenotype relationships. PMID:24217298

  12. Naturally segregating loci exhibit epistasis for fitness

    PubMed Central

    Monnahan, Patrick J.; Kelly, John K.

    2015-01-01

    The extent to which gene interaction or epistasis contributes to fitness variation within populations remains poorly understood, despite its importance to a myriad of evolutionary questions. Here, we report a multi-year field study estimating fitness of Mimulus guttatus genetic lines in which pairs of naturally segregating loci exist in an otherwise uniform background. An allele at QTL x5b—a locus originally mapped for its effect on flower size—positively affects survival if combined with one genotype at quantitative trait locus x10a (aa) but has negative effects when combined with the other genotypes (Aa and AA). The viability differences between genotypes parallel phenotypic differences for the time and node at which a plant flowers. Viability is negatively correlated with fecundity across genotypes, indicating antagonistic pleiotropy for fitness components. This trade-off reduces the genetic variance for total fitness relative to the individual fitness components and thus may serve to maintain variation. Additionally, we find that the effects of each locus and their interaction often vary with the environment. PMID:26246336

  13. The effect of epistasis on sexually antagonistic genetic variation

    PubMed Central

    Arnqvist, Göran; Vellnow, Nikolas; Rowe, Locke

    2014-01-01

    There is increasing evidence of segregating sexually antagonistic (SA) genetic variation for fitness in laboratory and wild populations, yet the conditions for the maintenance of such variation can be restrictive. Epistatic interactions between genes can contribute to the maintenance of genetic variance in fitness and we suggest that epistasis between SA genes should be pervasive. Here, we explore its effect on SA genetic variation in fitness using a two locus model with negative epistasis. Our results demonstrate that epistasis often increases the parameter space showing polymorphism for SA loci. This is because selection in one locus is affected by allele frequencies at the other, which can act to balance net selection in males and females. Increased linkage between SA loci had more marginal effects. We also show that under some conditions, large portions of the parameter space evolve to a state where male benefit alleles are fixed at one locus and female benefit alleles at the other. This novel effect of epistasis on SA loci, which we term the ‘equity effect’, may have important effects on population differentiation and may contribute to speciation. More generally, these results support the suggestion that epistasis contributes to population divergence. PMID:24870040

  14. Genotypic Context and Epistasis in Individuals and Populations.

    PubMed

    Sackton, Timothy B; Hartl, Daniel L

    2016-07-14

    Genes encode components of coevolved and interconnected networks. The effect of genotype on phenotype therefore depends on genotypic context through gene interactions known as epistasis. Epistasis is important in predicting phenotype from genotype for an individual. It is also examined in population studies to identify genetic risk factors in complex traits and to predict evolution under selection. Paradoxically, the effects of genotypic context in individuals and populations are distinct and sometimes contradictory. We argue that predicting genotype from phenotype for individuals based on population studies is difficult and, especially in human genetics, likely to result in underestimating the effects of genotypic context. PMID:27419868

  15. An efficient algorithm to perform multiple testing in epistasis screening

    PubMed Central

    2013-01-01

    Background Research in epistasis or gene-gene interaction detection for human complex traits has grown over the last few years. It has been marked by promising methodological developments, improved translation efforts of statistical epistasis to biological epistasis and attempts to integrate different omics information sources into the epistasis screening to enhance power. The quest for gene-gene interactions poses severe multiple-testing problems. In this context, the maxT algorithm is one technique to control the false-positive rate. However, the memory needed by this algorithm rises linearly with the amount of hypothesis tests. Gene-gene interaction studies will require a memory proportional to the squared number of SNPs. A genome-wide epistasis search would therefore require terabytes of memory. Hence, cache problems are likely to occur, increasing the computation time. In this work we present a new version of maxT, requiring an amount of memory independent from the number of genetic effects to be investigated. This algorithm was implemented in C++ in our epistasis screening software MBMDR-3.0.3. We evaluate the new implementation in terms of memory efficiency and speed using simulated data. The software is illustrated on real-life data for Crohn’s disease. Results In the case of a binary (affected/unaffected) trait, the parallel workflow of MBMDR-3.0.3 analyzes all gene-gene interactions with a dataset of 100,000 SNPs typed on 1000 individuals within 4 days and 9 hours, using 999 permutations of the trait to assess statistical significance, on a cluster composed of 10 blades, containing each four Quad-Core AMD Opteron(tm) Processor 2352 2.1 GHz. In the case of a continuous trait, a similar run takes 9 days. Our program found 14 SNP-SNP interactions with a multiple-testing corrected p-value of less than 0.05 on real-life Crohn’s disease (CD) data. Conclusions Our software is the first implementation of the MB-MDR methodology able to solve large-scale SNP

  16. Accelerator physics analysis with an integrated toolkit

    SciTech Connect

    Holt, J.A.; Michelotti, L.; Satogata, T.

    1992-08-01

    Work is in progress on an integrated software toolkit for linear and nonlinear accelerator design, analysis, and simulation. As a first application, ``beamline`` and ``MXYZPTLK`` (differential algebra) class libraries, were used with an X Windows graphics library to build an user-friendly, interactive phase space tracker which, additionally, finds periodic orbits. This program was used to analyse a theoretical lattice which contains octupoles and decapoles to find the 20th order, stable and unstable periodic orbits and to explore the local phase space structure.

  17. Acceleration of Data Analysis Applications using GPUs

    NASA Astrophysics Data System (ADS)

    Fillmore, D.; Messmer, P.; Mullowney, P.; Amyx, K.

    2008-12-01

    The vast amount of data collected by present and future scientific instruments, sensors and numerical models requires a significant increase in computing power for analysis. In many cases, processing time on a single workstation becomes impractical. While clusters of commodity processors can be utilized to accelerate some of these tasks, the relatively high software development cost, as well as acquisition and operational costs, make them less attractive for broad use. Over the past few years, another class of architectures has gained some popularity, namely heterogeneous architectures, which consist of general purpose processors connected to specialized processors. One of the most prominent examples are Graphics Processing Units (GPUs), which offer a tremendous amount of floating-point processing power due to demand for high-quality graphics in the computer game market. However, in order to harness this processing power, software developers have to develop with a detailed understanding of the underlying hardware. This burden on the developer is often hardly justifiable considering the rapid evolution of the hardware. In this talk, we will introduce GPULib, an open source library that enables scientists to accelerate their data analysis tasks using the GPUs already installed in their system from within high-level languages like IDL or MATLAB, and present examples and possible speedup from real-world data analysis applications. This work is funded through NASA Phase II SBIR Grant NNG06CA13C.

  18. Accelerating DNA analysis applications on GPU clusters

    SciTech Connect

    Tumeo, Antonino; Villa, Oreste

    2010-06-13

    DNA analysis is an emerging application of high performance bioinformatic. Modern sequencing machinery are able to provide, in few hours, large input streams of data which needs to be matched against exponentially growing databases known fragments. The ability to recognize these patterns effectively and fastly may allow extending the scale and the reach of the investigations performed by biology scientists. Aho-Corasick is an exact, multiple pattern matching algorithm often at the base of this application. High performance systems are a promising platform to accelerate this algorithm, which is computationally intensive but also inherently parallel. Nowadays, high performance systems also include heterogeneous processing elements, such as Graphic Processing Units (GPUs), to further accelerate parallel algorithms. Unfortunately, the Aho-Corasick algorithm exhibits large performance variabilities, depending on the size of the input streams, on the number of patterns to search and on the number of matches, and poses significant challenges on current high performance software and hardware implementations. An adequate mapping of the algorithm on the target architecture, coping with the limit of the underlining hardware, is required to reach the desired high throughputs. Load balancing also plays a crucial role when considering the limited bandwidth among the nodes of these systems. In this paper we present an efficient implementation of the Aho-Corasick algorithm for high performance clusters accelerated with GPUs. We discuss how we partitioned and adapted the algorithm to fit the Tesla C1060 GPU and then present a MPI based implementation for a heterogeneous high performance cluster. We compare this implementation to MPI and MPI with pthreads based implementations for a homogeneous cluster of x86 processors, discussing the stability vs. the performance and the scaling of the solutions, taking into consideration aspects such as the bandwidth among the different nodes.

  19. Epistasis and the selective advantage of sex and recombination

    NASA Astrophysics Data System (ADS)

    de Oliveira, Viviane M.; da Silva, Juliana K.; Campos, Paulo R. A.

    2008-09-01

    The understanding of the central mechanisms favoring sex and recombination in real populations is one of the fundamental issues in evolutionary biology. Based on a previous stochastic formulation for the study of sex, here we aim to investigate the conditions under which epistasis favors the fixation of the sexual mode of reproduction in a given population. In addition, we try to identify the evolutionary forces which contribute to this process. One considers a finite population model which assumes the existence of a recombination modifier allele that can activate the recombination mechanism. We have found that sex is very little favored in a scenario of antagonistic epistasis, and this advantage only occurs in a narrow range of values of the selection coefficient sd . On the other hand, synergistic epistasis favors recombination in a very broad domain. However, the major mechanism contributing to the spreading of the modifier allele depends on the range of values of sd . At large sd , background selection favors recombination since it increases the efficacy of selection, while at low sd Muller’s ratchet is the leading mechanism.

  20. Epistasis between mutations is host-dependent for an RNA virus

    PubMed Central

    Lalić, Jasna; Elena, Santiago F.

    2013-01-01

    How, and to what extent, does the environment influence the way mutations interact? Do environmental changes affect both the sign and the magnitude of epistasis? Are there any correlations between environments in the variability, sign or magnitude of epistasis? Very few studies have tackled these questions. Here, we addressed them in the context of viral emergence. Most emerging viruses are RNA viruses with small genomes, overlapping reading frames and multifunctional proteins for which epistasis is abundant. Understanding the effect of host species in the sign and magnitude of epistasis will provide insights into the evolutionary ecology of infectious diseases and the predictability of viral emergence. PMID:22809724

  1. Accelerating Large Data Analysis By Exploiting Regularities

    NASA Technical Reports Server (NTRS)

    Moran, Patrick J.; Ellsworth, David

    2003-01-01

    We present techniques for discovering and exploiting regularity in large curvilinear data sets. The data can be based on a single mesh or a mesh composed of multiple submeshes (also known as zones). Multi-zone data are typical to Computational Fluid Dynamics (CFD) simulations. Regularities include axis-aligned rectilinear and cylindrical meshes as well as cases where one zone is equivalent to a rigid-body transformation of another. Our algorithms can also discover rigid-body motion of meshes in time-series data. Next, we describe a data model where we can utilize the results from the discovery process in order to accelerate large data visualizations. Where possible, we replace general curvilinear zones with rectilinear or cylindrical zones. In rigid-body motion cases we replace a time-series of meshes with a transformed mesh object where a reference mesh is dynamically transformed based on a given time value in order to satisfy geometry requests, on demand. The data model enables us to make these substitutions and dynamic transformations transparently with respect to the visualization algorithms. We present results with large data sets where we combine our mesh replacement and transformation techniques with out-of-core paging in order to achieve significant speed-ups in analysis.

  2. Dispersion Analysis of the Pulseline Accelerator

    SciTech Connect

    Caporaso, G J; Briggs, R J; Poole, B R; Nelson, S D

    2005-05-10

    The authors analyze the sheath helix model of the pulseline accelerator. They find the dispersion relation for a shielded helix with a dielectric material between the shield and the helix and compare it against the results from 3-D electromagnetic simulations. Expressions for the fields near the beam axis are obtained. A scheme to taper the properties of the helix to maintain synchronism with the accelerated ions is described. An approximate circuit model of the system that includes beam loading is derived.

  3. Gait analysis using gravitational acceleration measured by wearable sensors.

    PubMed

    Takeda, Ryo; Tadano, Shigeru; Todoh, Masahiro; Morikawa, Manabu; Nakayasu, Minoru; Yoshinari, Satoshi

    2009-02-01

    A novel method for measuring human gait posture using wearable sensor units is proposed. The sensor units consist of a tri-axial acceleration sensor and three gyro sensors aligned on three axes. The acceleration and angular velocity during walking were measured with seven sensor units worn on the abdomen and the lower limb segments (both thighs, shanks and feet). The three-dimensional positions of each joint are calculated from each segment length and joint angle. Joint angle can be estimated mechanically from the gravitational acceleration along the anterior axis of the segment. However, the acceleration data during walking includes three major components; translational acceleration, gravitational acceleration and external noise. Therefore, an optimization analysis was represented to separate only the gravitational acceleration from the acceleration data. Because the cyclic patterns of acceleration data can be found during constant walking, a FFT analysis was applied to obtain some characteristic frequencies in it. A pattern of gravitational acceleration was assumed using some parts of these characteristic frequencies. Every joint position was calculated from the pattern under the condition of physiological motion range of each joint. An optimized pattern of the gravitational acceleration was selected as a solution of an inverse problem. Gaits of three healthy volunteers were measured by walking for 20s on a flat floor. As a result, the acceleration data of every segment was measured simultaneously. The characteristic three-dimensional walking could be shown by the expression using a stick figure model. In addition, the trajectories of the knee joint in the horizontal plane could be checked by visual imaging on a PC. Therefore, this method provides important quantitive information for gait diagnosis. PMID:19121522

  4. Simple genomes, complex interactions: Epistasis in RNA virus

    NASA Astrophysics Data System (ADS)

    Elena, Santiago F.; Solé, Ricard V.; Sardanyés, Josep

    2010-06-01

    Owed to their reduced size and low number of proteins encoded, RNA viruses and other subviral pathogens are often considered as being genetically too simple. However, this structural simplicity also creates the necessity for viral RNA sequences to encode for more than one protein and for proteins to carry out multiple functions, all together resulting in complex patterns of genetic interactions. In this work we will first review the experimental studies revealing that the architecture of viral genomes is dominated by antagonistic interactions among loci. Second, we will also review mathematical models and provide a description of computational tools for the study of RNA virus dynamics and evolution. As an application of these tools, we will finish this review article by analyzing a stochastic bit-string model of in silico virus replication. This model analyzes the interplay between epistasis and the mode of replication on determining the population load of deleterious mutations. The model suggests that, for a given mutation rate, the deleterious mutational load is always larger when epistasis is predominantly antagonistic than when synergism is the rule. However, the magnitude of this effect is larger if replication occurs geometrically than if it proceeds linearly.

  5. Impact of epistasis and pleiotropy on evolutionary adaptation

    PubMed Central

    Østman, Bjørn; Hintze, Arend; Adami, Christoph

    2012-01-01

    Evolutionary adaptation is often likened to climbing a hill or peak. While this process is simple for fitness landscapes where mutations are independent, the interaction between mutations (epistasis) as well as mutations at loci that affect more than one trait (pleiotropy) are crucial in complex and realistic fitness landscapes. We investigate the impact of epistasis and pleiotropy on adaptive evolution by studying the evolution of a population of asexual haploid organisms (haplotypes) in a model of N interacting loci, where each locus interacts with K other loci. We use a quantitative measure of the magnitude of epistatic interactions between substitutions, and find that it is an increasing function of K. When haplotypes adapt at high mutation rates, more epistatic pairs of substitutions are observed on the line of descent than expected. The highest fitness is attained in landscapes with an intermediate amount of ruggedness that balance the higher fitness potential of interacting genes with their concomitant decreased evolvability. Our findings imply that the synergism between loci that interact epistatically is crucial for evolving genetic modules with high fitness, while too much ruggedness stalls the adaptive process. PMID:21697174

  6. The Red Queen lives: Epistasis between linked resistance loci.

    PubMed

    Metzger, César M J A; Luijckx, Pepijn; Bento, Gilberto; Mariadassou, Mahendra; Ebert, Dieter

    2016-02-01

    A popular theory explaining the maintenance of genetic recombination (sex) is the Red Queen Theory. This theory revolves around the idea that time-lagged negative frequency-dependent selection by parasites favors rare host genotypes generated through recombination. Although the Red Queen has been studied for decades, one of its key assumptions has remained unsupported. The signature host-parasite specificity underlying the Red Queen, where infection depends on a match between host and parasite genotypes, relies on epistasis between linked resistance loci for which no empirical evidence exists. We performed 13 genetic crosses and tested over 7000 Daphnia magna genotypes for resistance to two strains of the bacterial pathogen Pasteuria ramosa. Results reveal the presence of strong epistasis between three closely linked resistance loci. One locus masks the expression of the other two, while these two interact to produce a single resistance phenotype. Changing a single allele on one of these interacting loci can reverse resistance against the tested parasites. Such a genetic mechanism is consistent with host and parasite specificity assumed by the Red Queen Theory. These results thus provide evidence for a fundamental assumption of this theory and provide a genetic basis for understanding the Red Queen dynamics in the Daphnia-Pasteuria system. PMID:26763092

  7. Diminishing-returns epistasis among random beneficial mutations in a multicellular fungus.

    PubMed

    Schoustra, Sijmen; Hwang, Sungmin; Krug, Joachim; de Visser, J Arjan G M

    2016-08-31

    Adaptive evolution ultimately is fuelled by mutations generating novel genetic variation. Non-additivity of fitness effects of mutations (called epistasis) may affect the dynamics and repeatability of adaptation. However, understanding the importance and implications of epistasis is hampered by the observation of substantial variation in patterns of epistasis across empirical studies. Interestingly, some recent studies report increasingly smaller benefits of beneficial mutations once genotypes become better adapted (called diminishing-returns epistasis) in unicellular microbes and single genes. Here, we use Fisher's geometric model (FGM) to generate analytical predictions about the relationship between the effect size of mutations and the extent of epistasis. We then test these predictions using the multicellular fungus Aspergillus nidulans by generating a collection of 108 strains in either a poor or a rich nutrient environment that each carry a beneficial mutation and constructing pairwise combinations using sexual crosses. Our results support the predictions from FGM and indicate negative epistasis among beneficial mutations in both environments, which scale with mutational effect size. Hence, our findings show the importance of diminishing-returns epistasis among beneficial mutations also for a multicellular organism, and suggest that this pattern reflects a generic constraint operating at diverse levels of biological organization. PMID:27559062

  8. Analysis of accelerated motion in the theory of relativity

    NASA Technical Reports Server (NTRS)

    Jones, R. T.

    1976-01-01

    Conventional treatments of accelerated motion in the theory of relativity have led to certain difficulties of interpretation. Certain reversals in the apparent gravitational field of an accelerated body may be avoided by simpler analysis based on the use of restricted conformal transformations. In the conformal theory the velocity of light remains constant even for experimenters in accelerated motion. The problem considered is that of rectilinear motion with a variable velocity. The motion takes place along the x or x' axis of two coordinate systems.

  9. A new tool for accelerator system modeling and analysis

    SciTech Connect

    Gillespie, G.H.; Hill, B.W.; Jameson, R.A.

    1994-09-01

    A novel computer code is being developed to generate system level designs of radiofrequency ion accelerators. The goal of the Accelerator System Model (ASM) code is to create a modeling and analysis tool that is easy to use, automates many of the initial design calculations, supports trade studies used in assessing alternate designs and yet is flexible enough to incorporate new technology concepts as they emerge. Hardware engineering parameters and beam dynamics are modeled at comparable levels of fidelity. Existing scaling models of accelerator subsystems were sued to produce a prototype of ASM (version 1.0) working within the Shell for Particle Accelerator Related Codes (SPARC) graphical user interface. A small user group has been testing and evaluating the prototype for about a year. Several enhancements and improvements are now being developed. The current version (1.1) of ASM is briefly described and an example of the modeling and analysis capabilities is illustrated.

  10. Failure Mode Effects Analysis for an Accelerator Control System

    SciTech Connect

    Hartman, Steven M

    2009-01-01

    Failure mode effects analysis (FMEA) has been used in industry for design, manufacturing and assembly process quality control. It describes a formal approach for categorizing how a process may fail and for prioritizing failures based on their severity, frequency and likelihood of detection. Experience conducting a partial FMEA of an accelerator subsystem and its related control system will be reviewed. The applicability of the FMEA process to an operational accelerator control system will be discussed.

  11. Statistical modeling of interlocus interactions in a complex disease: rejection of the multiplicative model of epistasis in type 1 diabetes.

    PubMed Central

    Cordell, H J; Todd, J A; Hill, N J; Lord, C J; Lyons, P A; Peterson, L B; Wicker, L S; Clayton, D G

    2001-01-01

    In general, common diseases do not follow a Mendelian inheritance pattern. To identify disease mechanisms and etiology, their genetic dissection may be assisted by evaluation of linkage in mouse models of human disease. Statistical modeling of multiple-locus linkage data from the nonobese diabetic (NOD) mouse model of type 1 diabetes has previously provided evidence for epistasis between alleles of several Idd (insulin-dependent diabetes) loci. The construction of NOD congenic strains containing selected segments of the diabetes-resistant strain genome allows analysis of the joint effects of alleles of different loci in isolation, without the complication of other segregating Idd loci. In this article, we analyze data from congenic strains carrying two chromosome intervals (a double congenic strain) for two pairs of loci: Idd3 and Idd10 and Idd3 and Idd5. The joint action of both pairs is consistent with models of additivity on either the log odds of the penetrance, or the liability scale, rather than with the previously proposed multiplicative model of epistasis. For Idd3 and Idd5 we would also not reject a model of additivity on the penetrance scale, which might indicate a disease model mediated by more than one pathway leading to beta-cell destruction and development of diabetes. However, there has been confusion between different definitions of interaction or epistasis as used in the biological, statistical, epidemiological, and quantitative and human genetics fields. The degree to which statistical analyses can elucidate underlying biologic mechanisms may be limited and may require prior knowledge of the underlying etiology. PMID:11333244

  12. Dominant-and-recessive epistasis in a homeotic mosquito mutant.

    PubMed

    Bhalla, S C

    1976-12-01

    Following selection for 15 generations a pure strain of a homeotic mutant spur was isolated from a Brazilian population of the mosquito Culex pipiens fatigans. Monohybrid crosses showed a 13:3 segregation indicating dominant-and-recessive epistasis for wild-type vs. spur. This implies that a dominant allele at one locus and a recessive at the other interact to produce the mutant phenotype. Dihybrid crosses with linkage group II markers yellow and ruby gave 39:13:9:3 ratios indicating independent segregation. However, the dihybrid cross with linkage group I marker maroon showed a highly significant departure from 39:13:9:3 ratio. Data available indicate that the phenotype spur is controlled by a dominant epistat in linkage group III and a recessive epistat (approximately 31.9 crossover units from maroon) in linkage group I. PMID:1022329

  13. A robustness study of parametric and non-parametric tests in model-based multifactor dimensionality reduction for epistasis detection

    PubMed Central

    2013-01-01

    Background Applying a statistical method implies identifying underlying (model) assumptions and checking their validity in the particular context. One of these contexts is association modeling for epistasis detection. Here, depending on the technique used, violation of model assumptions may result in increased type I error, power loss, or biased parameter estimates. Remedial measures for violated underlying conditions or assumptions include data transformation or selecting a more relaxed modeling or testing strategy. Model-Based Multifactor Dimensionality Reduction (MB-MDR) for epistasis detection relies on association testing between a trait and a factor consisting of multilocus genotype information. For quantitative traits, the framework is essentially Analysis of Variance (ANOVA) that decomposes the variability in the trait amongst the different factors. In this study, we assess through simulations, the cumulative effect of deviations from normality and homoscedasticity on the overall performance of quantitative Model-Based Multifactor Dimensionality Reduction (MB-MDR) to detect 2-locus epistasis signals in the absence of main effects. Methodology Our simulation study focuses on pure epistasis models with varying degrees of genetic influence on a quantitative trait. Conditional on a multilocus genotype, we consider quantitative trait distributions that are normal, chi-square or Student’s t with constant or non-constant phenotypic variances. All data are analyzed with MB-MDR using the built-in Student’s t-test for association, as well as a novel MB-MDR implementation based on Welch’s t-test. Traits are either left untransformed or are transformed into new traits via logarithmic, standardization or rank-based transformations, prior to MB-MDR modeling. Results Our simulation results show that MB-MDR controls type I error and false positive rates irrespective of the association test considered. Empirically-based MB-MDR power estimates for MB-MDR with Welch

  14. Acceleration of reverse analysis method using hyperbolic activation function

    NASA Astrophysics Data System (ADS)

    Pwasong, Augustine; Sathasivam, Saratha

    2015-10-01

    Hyperbolic activation function is examined for its ability to accelerate the performance of doing data mining by using a technique named as Reverse Analysis method. In this paper, we describe how Hopfield network perform better with hyperbolic activation function and able to induce logical rules from large database by using reverse analysis method: given the values of the connections of a network, we can hope to know what logical rules are entrenched in the database. We limit our analysis to Horn clauses.

  15. Further analysis of MHD acceleration for a hypersonic wind tunnel

    SciTech Connect

    Christiansen, M.J.; Schmidt, H.J.; Chapman, J.N.

    1995-12-31

    A previously completed MHD study of the use of an MHD accelerator with seeded air from a state-of-the-art arc heater, was generally hailed as showing that the system studied has some promise of meeting the most critical hypersonic testing requirements. However, some concerns existed about certain aspects of the results. This paper discusses some of these problems and presents analysis of potential solutions. Specifically the problems addressed are; reducing the amount of seed in the flow, reducing test chamber temperatures, and reducing the oxygen dissociation. Modeling techniques are used to study three design variables of the MHD accelerator. The accelerator channel inlet Mach number, the accelerator channel divergence angle, and the magnetic field strength are all studied. These variables are all optimized to meet the goals for seed, temperature, and dissociated oxygen reduction. The results of this paper are encouraging, showing that all three goals can be met. General relationships are observed as to how the design variables affect the performance of the MHD accelerator facility. This paper expands on the results presented in the UTSI report and further supports the feasibility of MHD acceleration as a means to provide hypersonic flight simulation.

  16. Magnitude and sign epistasis among deleterious mutations in a positive-sense plant RNA virus

    PubMed Central

    Lalić, J; Elena, S F

    2012-01-01

    How epistatic interactions between mutations determine the genetic architecture of fitness is of central importance in evolution. The study of epistasis is particularly interesting for RNA viruses because of their genomic compactness, lack of genetic redundancy, and apparent low complexity. Moreover, interactions between mutations in viral genomes determine traits such as resistance to antiviral drugs, virulence and host range. In this study we generated 53 Tobacco etch potyvirus genotypes carrying pairs of single-nucleotide substitutions and measured their separated and combined deleterious fitness effects. We found that up to 38% of pairs had significant epistasis for fitness, including both positive and negative deviations from the null hypothesis of multiplicative effects. Interestingly, the sign of epistasis was correlated with viral protein–protein interactions in a model network, being predominantly positive between linked pairs of proteins and negative between unlinked ones. Furthermore, 55% of significant interactions were cases of reciprocal sign epistasis (RSE), indicating that adaptive landscapes for RNA viruses maybe highly rugged. Finally, we found that the magnitude of epistasis correlated negatively with the average effect of mutations. Overall, our results are in good agreement to those previously reported for other viruses and further consolidate the view that positive epistasis is the norm for small and compact genomes that lack genetic robustness. PMID:22491062

  17. Cancer type-dependent genetic interactions between cancer driver alterations indicate plasticity of epistasis across cell types.

    PubMed

    Park, Solip; Lehner, Ben

    2015-07-01

    Cancers, like many diseases, are normally caused by combinations of genetic alterations rather than by changes affecting single genes. It is well established that the genetic alterations that drive cancer often interact epistatically, having greater or weaker consequences in combination than expected from their individual effects. In a stringent statistical analysis of data from > 3,000 tumors, we find that the co-occurrence and mutual exclusivity relationships between cancer driver alterations change quite extensively in different types of cancer. This cannot be accounted for by variation in tumor heterogeneity or unrecognized cancer subtypes. Rather, it suggests that how genomic alterations interact cooperatively or partially redundantly to driver cancer changes in different types of cancers. This re-wiring of epistasis across cell types is likely to be a basic feature of genetic architecture, with important implications for understanding the evolution of multicellularity and human genetic diseases. In addition, if this plasticity of epistasis across cell types is also true for synthetic lethal interactions, a synthetic lethal strategy to kill cancer cells may frequently work in one type of cancer but prove ineffective in another. PMID:26227665

  18. Cancer type-dependent genetic interactions between cancer driver alterations indicate plasticity of epistasis across cell types

    PubMed Central

    Park, Solip; Lehner, Ben

    2015-01-01

    Cancers, like many diseases, are normally caused by combinations of genetic alterations rather than by changes affecting single genes. It is well established that the genetic alterations that drive cancer often interact epistatically, having greater or weaker consequences in combination than expected from their individual effects. In a stringent statistical analysis of data from > 3,000 tumors, we find that the co-occurrence and mutual exclusivity relationships between cancer driver alterations change quite extensively in different types of cancer. This cannot be accounted for by variation in tumor heterogeneity or unrecognized cancer subtypes. Rather, it suggests that how genomic alterations interact cooperatively or partially redundantly to driver cancer changes in different types of cancers. This re-wiring of epistasis across cell types is likely to be a basic feature of genetic architecture, with important implications for understanding the evolution of multicellularity and human genetic diseases. In addition, if this plasticity of epistasis across cell types is also true for synthetic lethal interactions, a synthetic lethal strategy to kill cancer cells may frequently work in one type of cancer but prove ineffective in another. PMID:26227665

  19. New accelerators for femtosecond beam pump-and-probe analysis

    NASA Astrophysics Data System (ADS)

    Uesaka, Mitsuru; Sakumi, Akira; Hosokai, Tomonao; Kinoshita, Kenichi; Yamaoka, Nobuaki; Zhidkov, Alexei; Ohkubo, Takeru; Ueda, Toru; Muroya, Yusa; Katsumura, Yosuke; Iijima, Hokuto; Tomizawa, Hiromitsu; Kumagai, Noritaka

    2005-12-01

    Femtosecond electron beams are novel tool for pump-probe analysis of condensed matter. Progress in developing femtosecond electron beams with the use of both conventional accelerators and laser-plasma accelerators is discussed. In conventional accelerators, the critical issue is timing jitter and drift of the linac-laser synchronization system. Sophisticated electronic devices are developed to reduce the jitter to 330 fs (rms); the precise control of temperature at several parts of the accelerator lessens the drift to 1 ps (rms). We also report on a full-optical X-ray and e-beam system based on the laser-plasma cathode by using a 12 TW 50 fs laser, which enables 40 MeV (at maximum), 40 fs (cal.), 100 pC and quasi-monochromatic single electron bunches. Since the synchronization is done by a passive optical beam-splitter, this system intrinsically has no jitter and drift. It could achieve tens of femtoseconds time-resolved analysis in the near future.

  20. Epistasis and the Dynamics of Reversion in Molecular Evolution.

    PubMed

    McCandlish, David M; Shah, Premal; Plotkin, Joshua B

    2016-07-01

    Recent studies of protein evolution contend that the longer an amino acid substitution is present at a site, the less likely it is to revert to the amino acid previously occupying that site. Here we study this phenomenon of decreasing reversion rates rigorously and in a much more general context. We show that, under weak mutation and for arbitrary fitness landscapes, reversion rates decrease with time for any site that is involved in at least one epistatic interaction. Specifically, we prove that, at stationarity, the hazard function of the distribution of waiting times until reversion is strictly decreasing for any such site. Thus, in the presence of epistasis, the longer a particular character has been absent from a site, the less likely the site will revert to its prior state. We also explore several examples of this general result, which share a common pattern whereby the probability of having reverted increases rapidly at short times to some substantial value before becoming almost flat after a few substitutions at other sites. This pattern indicates a characteristic tendency for reversion to occur either almost immediately after the initial substitution or only after a very long time. PMID:27194749

  1. RATES OF FITNESS DECLINE AND REBOUND SUGGEST PERVASIVE EPISTASIS

    PubMed Central

    Perfeito, L; Sousa, A; Bataillon, T; Gordo, I

    2014-01-01

    Unraveling the factors that determine the rate of adaptation is a major question in evolutionary biology. One key parameter is the effect of a new mutation on fitness, which invariably depends on the environment and genetic background. The fate of a mutation also depends on population size, which determines the amount of drift it will experience. Here, we manipulate both population size and genotype composition and follow adaptation of 23 distinct Escherichia coli genotypes. These have previously accumulated mutations under intense genetic drift and encompass a substantial fitness variation. A simple rule is uncovered: the net fitness change is negatively correlated with the fitness of the genotype in which new mutations appear—a signature of epistasis. We find that Fisher's geometrical model can account for the observed patterns of fitness change and infer the parameters of this model that best fit the data, using Approximate Bayesian Computation. We estimate a genomic mutation rate of 0.01 per generation for fitness altering mutations, albeit with a large confidence interval, a mean fitness effect of mutations of −0.01, and an effective number of traits nine in mutS− E. coli. This framework can be extended to confront a broader range of models with data and test different classes of fitness landscape models. PMID:24372601

  2. Automatic Beam Path Analysis of Laser Wakefield Particle Acceleration Data

    SciTech Connect

    Rubel, Oliver; Geddes, Cameron G.R.; Cormier-Michel, Estelle; Wu, Kesheng; Prabhat,; Weber, Gunther H.; Ushizima, Daniela M.; Messmer, Peter; Hagen, Hans; Hamann, Bernd; Bethel, E. Wes

    2009-10-19

    Numerical simulations of laser wakefield particle accelerators play a key role in the understanding of the complex acceleration process and in the design of expensive experimental facilities. As the size and complexity of simulation output grows, an increasingly acute challenge is the practical need for computational techniques that aid in scientific knowledge discovery. To that end, we present a set of data-understanding algorithms that work in concert in a pipeline fashion to automatically locate and analyze high energy particle bunches undergoing acceleration in very large simulation datasets. These techniques work cooperatively by first identifying features of interest in individual timesteps, then integrating features across timesteps, and based on the information derived perform analysis of temporally dynamic features. This combination of techniques supports accurate detection of particle beams enabling a deeper level of scientific understanding of physical phenomena than hasbeen possible before. By combining efficient data analysis algorithms and state-of-the-art data management we enable high-performance analysis of extremely large particle datasets in 3D. We demonstrate the usefulness of our methods for a variety of 2D and 3D datasets and discuss the performance of our analysis pipeline.

  3. The Impact of Macroscopic Epistasis on Long-Term Evolutionary Dynamics

    PubMed Central

    Good, Benjamin H.; Desai, Michael M.

    2015-01-01

    Genetic interactions can strongly influence the fitness effects of individual mutations, yet the impact of these epistatic interactions on evolutionary dynamics remains poorly understood. Here we investigate the evolutionary role of epistasis over 50,000 generations in a well-studied laboratory evolution experiment in Escherichia coli. The extensive duration of this experiment provides a unique window into the effects of epistasis during long-term adaptation to a constant environment. Guided by analytical results in the weak-mutation limit, we develop a computational framework to assess the compatibility of a given epistatic model with the observed patterns of fitness gain and mutation accumulation through time. We find that a decelerating fitness trajectory alone provides little power to distinguish between competing models, including those that lack any direct epistatic interactions between mutations. However, when combined with the mutation trajectory, these observables place strong constraints on the set of possible models of epistasis, ruling out many existing explanations of the data. Instead, we find that the data are consistent with a “two-epoch” model of adaptation, in which an initial burst of diminishing-returns epistasis is followed by a steady accumulation of mutations under a constant distribution of fitness effects. Our results highlight the need for additional DNA sequencing of these populations, as well as for more sophisticated models of epistasis that are compatible with all of the experimental data. PMID:25395665

  4. Measuring epistasis in fitness landscapes: The correlation of fitness effects of mutations.

    PubMed

    Ferretti, Luca; Schmiegelt, Benjamin; Weinreich, Daniel; Yamauchi, Atsushi; Kobayashi, Yutaka; Tajima, Fumio; Achaz, Guillaume

    2016-05-01

    Genotypic fitness landscapes are constructed by assessing the fitness of all possible combinations of a given number of mutations. In the last years, several experimental fitness landscapes have been completely resolved. As fitness landscapes are high-dimensional, simple measures of their structure are used as statistics in empirical applications. Epistasis is one of the most relevant features of fitness landscapes. Here we propose a new natural measure of the amount of epistasis based on the correlation of fitness effects of mutations. This measure has a natural interpretation, captures well the interaction between mutations and can be obtained analytically for most landscape models. We discuss how this measure is related to previous measures of epistasis (number of peaks, roughness/slope, fraction of sign epistasis, Fourier-Walsh spectrum) and how it can be easily extended to landscapes with missing data or with fitness ranks only. Furthermore, the dependence of the correlation of fitness effects on mutational distance contains interesting information about the patterns of epistasis. This dependence can be used to uncover the amount and nature of epistatic interactions in a landscape or to discriminate between different landscape models. PMID:26854875

  5. Epistasis in intra- and inter-gene pool crosses of the common bean.

    PubMed

    Borel, J C; Ramalho, M A P; Abreu, A F B

    2016-01-01

    Epistasis has been shown to have an important role in the genetic control of several quantitative traits in the common bean. This study aimed to investigate the occurrence of epistasis in intra- and inter-pool gene crosses of the common bean. Four elite lines adapted to Brazilian conditions were used as parents, two from the Andean gene pool (ESAL 686; BRS Radiante) and two from the Mesoamerican gene pool (BRSMG Majestoso; BRS Valente). Four F2 populations were obtained: "A" (ESAL 686 x BRS Radiante), "B" (BRSMG Majestoso x BRS Valente), "C" (BRS Radiante x BRSMG Majestoso), and "D" (BRS Valente x ESAL 686). A random sample of F2 plants from each population was backcrossed to parents and F1 individuals, according to the triple test cross. Three types of progenies from each population were evaluated in contiguous trials. Seed yield and 100-seed weight were evaluated. Dominance genetic variance was predominant in most cases. However, the estimates of genetic variance may be biased by the occurrence of linkage disequilibrium and epistasis. Epistasis was detected for both traits; however, the occurrence differed among the populations and between the two traits. The results of this study reinforce the hypothesis that epistasis is present in the genetic control of traits in the common bean and suggest that the phenomenon is more frequent in inter-gene pool crosses than in intra-gene pool crosses. PMID:26985920

  6. Review: High-performance computing to detect epistasis in genome scale data sets.

    PubMed

    Upton, Alex; Trelles, Oswaldo; Cornejo-García, José Antonio; Perkins, James Richard

    2016-05-01

    It is becoming clear that most human diseases have a complex etiology that cannot be explained by single nucleotide polymorphisms (SNPs) or simple additive combinations; the general consensus is that they are caused by combinations of multiple genetic variations. The limited success of some genome-wide association studies is partly a result of this focus on single genetic markers. A more promising approach is to take into account epistasis, by considering the association of multiple SNP interactions with disease. However, as genomic data continues to grow in resolution, and genome and exome sequencing become more established, the number of combinations of variants to consider increases rapidly. Two potential solutions should be considered: the use of high-performance computing, which allows us to consider a larger number of variables, and heuristics to make the solution more tractable, essential in the case of genome sequencing. In this review, we look at different computational methods to analyse epistatic interactions within disease-related genetic data sets created by microarray technology. We also review efforts to use epistatic analysis results to produce biomarkers for diagnostic tests and give our views on future directions in this field in light of advances in sequencing technology and variants in non-coding regions. PMID:26272945

  7. Mitochondrial–Nuclear Epistasis Impacts Fitness and Mitochondrial Physiology of Interpopulation Caenorhabditis briggsae Hybrids

    PubMed Central

    Chang, Chih-Chiun; Rodriguez, Joel; Ross, Joseph

    2015-01-01

    In order to identify the earliest genetic changes that precipitate species formation, it is useful to study genetic incompatibilities that cause only mild dysfunction when incompatible alleles are combined in an interpopulation hybrid. Such hybridization within the nematode species Caenorhabditis briggsae has been suggested to result in selection against certain combinations of nuclear and mitochondrial alleles, raising the possibility that mitochondrial–nuclear (mitonuclear) epistasis reduces hybrid fitness. To test this hypothesis, cytoplasmic–nuclear hybrids (cybrids) were created to purposefully disrupt any epistatic interactions. Experimental analysis of the cybrids suggests that mitonuclear discord can result in decreased fecundity, increased lipid content, and increased mitochondrial reactive oxygen species levels. Many of these effects were asymmetric with respect to cross direction, as expected if cytoplasmic–nuclear Dobzhansky-Muller incompatibilities exist. One such effect is consistent with the interpretation that disrupting coevolved mitochondrial and nuclear loci impacts mitochondrial function and organismal fitness. These findings enhance efforts to study the genesis, identity, and maintenance of genetic incompatibilities that precipitate the speciation process. PMID:26585825

  8. Shadows of complexity: what biological networks reveal about epistasis and pleiotropy.

    PubMed

    Tyler, Anna L; Asselbergs, Folkert W; Williams, Scott M; Moore, Jason H

    2009-02-01

    Pleiotropy, in which one mutation causes multiple phenotypes, has traditionally been seen as a deviation from the conventional observation in which one gene affects one phenotype. Epistasis, or gene-gene interaction, has also been treated as an exception to the Mendelian one gene-one phenotype paradigm. This simplified perspective belies the pervasive complexity of biology and hinders progress toward a deeper understanding of biological systems. We assert that epistasis and pleiotropy are not isolated occurrences, but ubiquitous and inherent properties of biomolecular networks. These phenomena should not be treated as exceptions, but rather as fundamental components of genetic analyses. A systems level understanding of epistasis and pleiotropy is, therefore, critical to furthering our understanding of human genetics and its contribution to common human disease. Finally, graph theory offers an intuitive and powerful set of tools with which to study the network bases of these important genetic phenomena. PMID:19204994

  9. Accelerated Gibbs Sampling for Infinite Sparse Factor Analysis

    SciTech Connect

    Andrzejewski, D M

    2011-09-12

    The Indian Buffet Process (IBP) gives a probabilistic model of sparse binary matrices with an unbounded number of columns. This construct can be used, for example, to model a fixed numer of observed data points (rows) associated with an unknown number of latent features (columns). Markov Chain Monte Carlo (MCMC) methods are often used for IBP inference, and in this technical note, we provide a detailed review of the derivations of collapsed and accelerated Gibbs samplers for the linear-Gaussian infinite latent feature model. We also discuss and explain update equations for hyperparameter resampling in a 'full Bayesian' treatment and present a novel slice sampler capable of extending the accelerated Gibbs sampler to the case of infinite sparse factor analysis by allowing the use of real-valued latent features.

  10. Analysis of accelerants and fire debris using aroma detection technology

    SciTech Connect

    Barshick, S.A.

    1997-01-17

    The purpose of this work was to investigate the utility of electronic aroma detection technologies for the detection and identification of accelerant residues in suspected arson debris. Through the analysis of known accelerant residues, a trained neural network was developed for classifying suspected arson samples. Three unknown fire debris samples were classified using this neural network. The item corresponding to diesel fuel was correctly identified every time. For the other two items, wide variations in sample concentration and excessive water content, producing high sample humidities, were shown to influence the sensor response. Sorbent sampling prior to aroma detection was demonstrated to reduce these problems and to allow proper neural network classification of the remaining items corresponding to kerosene and gasoline.

  11. GPU accelerated dynamic functional connectivity analysis for functional MRI data.

    PubMed

    Akgün, Devrim; Sakoğlu, Ünal; Esquivel, Johnny; Adinoff, Bryon; Mete, Mutlu

    2015-07-01

    Recent advances in multi-core processors and graphics card based computational technologies have paved the way for an improved and dynamic utilization of parallel computing techniques. Numerous applications have been implemented for the acceleration of computationally-intensive problems in various computational science fields including bioinformatics, in which big data problems are prevalent. In neuroimaging, dynamic functional connectivity (DFC) analysis is a computationally demanding method used to investigate dynamic functional interactions among different brain regions or networks identified with functional magnetic resonance imaging (fMRI) data. In this study, we implemented and analyzed a parallel DFC algorithm based on thread-based and block-based approaches. The thread-based approach was designed to parallelize DFC computations and was implemented in both Open Multi-Processing (OpenMP) and Compute Unified Device Architecture (CUDA) programming platforms. Another approach developed in this study to better utilize CUDA architecture is the block-based approach, where parallelization involves smaller parts of fMRI time-courses obtained by sliding-windows. Experimental results showed that the proposed parallel design solutions enabled by the GPUs significantly reduce the computation time for DFC analysis. Multicore implementation using OpenMP on 8-core processor provides up to 7.7× speed-up. GPU implementation using CUDA yielded substantial accelerations ranging from 18.5× to 157× speed-up once thread-based and block-based approaches were combined in the analysis. Proposed parallel programming solutions showed that multi-core processor and CUDA-supported GPU implementations accelerated the DFC analyses significantly. Developed algorithms make the DFC analyses more practical for multi-subject studies with more dynamic analyses. PMID:25805449

  12. Analysis of Cultural Heritage by Accelerator Techniques and Analytical Imaging

    NASA Astrophysics Data System (ADS)

    Ide-Ektessabi, Ari; Toque, Jay Arre; Murayama, Yusuke

    2011-12-01

    In this paper we present the result of experimental investigation using two very important accelerator techniques: (1) synchrotron radiation XRF and XAFS; and (2) accelerator mass spectrometry and multispectral analytical imaging for the investigation of cultural heritage. We also want to introduce a complementary approach to the investigation of artworks which is noninvasive and nondestructive that can be applied in situ. Four major projects will be discussed to illustrate the potential applications of these accelerator and analytical imaging techniques: (1) investigation of Mongolian Textile (Genghis Khan and Kublai Khan Period) using XRF, AMS and electron microscopy; (2) XRF studies of pigments collected from Korean Buddhist paintings; (3) creating a database of elemental composition and spectral reflectance of more than 1000 Japanese pigments which have been used for traditional Japanese paintings; and (4) visible light-near infrared spectroscopy and multispectral imaging of degraded malachite and azurite. The XRF measurements of the Japanese and Korean pigments could be used to complement the results of pigment identification by analytical imaging through spectral reflectance reconstruction. On the other hand, analysis of the Mongolian textiles revealed that they were produced between 12th and 13th century. Elemental analysis of the samples showed that they contained traces of gold, copper, iron and titanium. Based on the age and trace elements in the samples, it was concluded that the textiles were produced during the height of power of the Mongol empire, which makes them a valuable cultural heritage. Finally, the analysis of the degraded and discolored malachite and azurite demonstrates how multispectral analytical imaging could be used to complement the results of high energy-based techniques.

  13. A multi-beamlet analysis of the MITICA accelerator

    SciTech Connect

    Fonnesu, N. Agostinetti, P.; Serianni, G.; Veltri, P.; Kisaki, M.

    2015-04-08

    The thermo-mechanical analysis and the mechanical design of the accelerator of MITICA (i.e. the full size prototype of the ITER neutral beam injector under construction at RFX [1]) are based on the calculation of the power deposition induced by particle impacts. This calculation is performed by EAMCC [2], a relativistic particle tracking code based on the Monte-Carlo method for describing collisions inside the accelerator, under prescribed electric and magnetic fields. The magnetic field maps are produced by 3D codes, while the electric field maps come from the 2D axi-symmetric code SLACCAD [3]. In order to perform a multi-beamlet analysis, which allows to take into account the beamlet-beamlet repulsion, and to consider other effects neglected under the hypothesis of axi-symmetric beam, a fully 3D version of the code is required. In this paper, a modified version of EAMCC, fully 3D, capable of modifying the mesh of the 3D maps and of dealing with uneven meshes is presented. A finer mesh is used just in the regions where a more detailed description of the fields is required, for a more realistic simulation. A comparison between the original code and the modified version is presented at first, as a validation of the modifications introduced in the latter. Subsequently, the main results of a single-beamlet analysis performed with the two versions of the code are shown and the differences between the 2D and the 3D simulations discussed. The last part is dedicated to the multi-beamlet simulation of the accelerator.

  14. [Analysis of human tissue samples for volatile fire accelerants].

    PubMed

    Treibs, Rudolf

    2014-01-01

    In police investigations of fires, the cause of a fire and the fire debris analysis regarding traces of fire accelerants are important aspects for forensic scientists. Established analytical procedures were recently applied to the remains of fire victims. When examining lung tissue samples, vapors inhaled from volatile ignitable liquids could be identified and differentiated from products of pyrolysis caused by the fire. In addition to the medico-legal results this evidence allowed to draw conclusions as to whether the fire victim was still alive when the fire started. PMID:24855737

  15. The Benefits of Acceleration: An Outcomes Analysis of Dual Enrollment

    ERIC Educational Resources Information Center

    Morrison, Michael C.

    2007-01-01

    This study adds to the growing body of research with a focus on (1) the characteristics of accelerated (dual enrolled) students versus their counterparts who did not participate in accelerated programs; (2) differences in academic outcomes of accelerated and non-accelerated students; and (3) differences in days to complete the associate degree for…

  16. Ant Species Differences Determined by Epistasis between Brood and Worker Genomes

    PubMed Central

    Linksvayer, Timothy A.

    2007-01-01

    Epistasis arising from physiological interactions between gene products often contributes to species differences, particularly those involved in reproductive isolation. In social organisms, phenotypes are influenced by the genotypes of multiple interacting individuals. In theory, social interactions can give rise to an additional type of epistasis between the genomes of social partners that can contribute to species differences. Using a full-factorial cross-fostering design with three species of closely related Temnothorax ants, I found that adult worker size was determined by an interaction between the genotypes of developing brood and care-giving workers, i.e. intergenomic epistasis. Such intergenomic social epistasis provides a strong signature of coevolution between social partners. These results demonstrate that just as physiologically interacting genes coevolve, diverge, and contribute to species differences, so do socially interacting genes. Coevolution and conflict between social partners, especially relatives such as parents and offspring, has long been recognized as having widespread evolutionary effects. This coevolutionary process may often result in coevolved socially-interacting gene complexes that contribute to species differences. PMID:17912371

  17. Direct and indirect genetic effects of sex-specific mitonuclear epistasis on reproductive ageing.

    PubMed

    Immonen, E; Collet, M; Goenaga, J; Arnqvist, G

    2016-03-01

    Mitochondria are involved in ageing and their function requires coordinated action of both mitochondrial and nuclear genes. Epistasis between the two genomes can influence lifespan but whether this also holds for reproductive senescence is unclear. Maternal inheritance of mitochondria predicts sex differences in the efficacy of selection on mitonuclear genotypes that should result in differences between females and males in mitochondrial genetic effects. Mitonuclear genotype of a focal individual may also indirectly affect trait expression in the mating partner. We tested these predictions in the seed beetle Callosobruchus maculatus, using introgression lines harbouring distinct mitonuclear genotypes. Our results reveal both direct and indirect sex-specific effects of mitonuclear epistasis on reproductive ageing. Females harbouring coadapted mitonuclear genotypes showed higher lifetime fecundity due to slower senescence relative to novel mitonuclear combinations. We found no evidence for mitonuclear coadaptation in males. Mitonuclear epistasis not only affected age-specific ejaculate weight, but also influenced male age-dependent indirect effects on traits expressed by their female partners (fecundity, egg size, longevity). These results demonstrate important consequences of sex-specific mitonuclear epistasis for both mating partners, consistent with a role for mitonuclear genetic constraints upon sex-specific adaptive evolution. PMID:26732015

  18. Evolution and polymorphism in the multilocus Levene model with no or weak epistasis

    PubMed Central

    Bürger, Reinhard

    2010-01-01

    Evolution and the maintenance of polymorphism under the multilocus Levene model with soft selection are studied. The number of loci and alleles, the number of demes, the linkage map, and the degree of dominance are arbitrary, but epistasis is absent or weak. We prove that, without epistasis and under mild, generic conditions, every trajectory converges to a stationary point in linkage equilibrium. Consequently, the equilibrium and stability structure can be determined by investigating the much simpler gene-frequency dynamics on the linkage-equilibrium manifold. For a haploid species an analogous result is shown. For weak epistasis, global convergence to quasi-linkage equilibrium is established. As an application, the maintenance of multilocus polymorphism is explored if the degree of dominance is intermediate at every locus and epistasis is absent or weak. If there are at least two demes, then arbitrarily many multiallelic loci can be maintained polymorphic at a globally asymptotically stable equilibrium. Because this holds for an open set of parameters, such equilibria are structurally stable. If the degree of dominance is not only intermediate but also deme independent, and loci are diallelic, an open set of parameters yielding an internal equilibrium exists only if the number of loci is strictly less than the number of demes. Otherwise, a fully polymorphic equilibrium exists only nongenerically, and if it exists, it consists of a manifold of equilibria. Its dimension is determined. In the absence of genotype-by-environment interaction, however, a manifold of equilibria occurs for an open set of parameters. In this case, the equilibrium structure is not robust to small deviations from no genotype-by-environment interaction. In a quantitative-genetic setting, the assumptions of no epistasis and intermediate dominance are equivalent to assuming that in every deme directional selection acts on a trait that is determined additively, i.e., by nonepistatic loci with

  19. Cosmic acceleration without dark energy: background tests and thermodynamic analysis

    SciTech Connect

    Lima, J.A.S.; Graef, L.L.; Pavón, D.; Basilakos, Spyros E-mail: leilagraef@usp.br E-mail: svasil@academyofathens.gr

    2014-10-01

    A cosmic scenario with gravitationally induced particle creation is proposed. In this model the Universe evolves from an early to a late time de Sitter era, with the recent accelerating phase driven only by the negative creation pressure associated with the cold dark matter component. The model can be interpreted as an attempt to reduce the so-called cosmic sector (dark matter plus dark energy) and relate the two cosmic accelerating phases (early and late time de Sitter expansions). A detailed thermodynamic analysis including possible quantum corrections is also carried out. For a very wide range of the free parameters, it is found that the model presents the expected behavior of an ordinary macroscopic system in the sense that it approaches thermodynamic equilibrium in the long run (i.e., as it nears the second de Sitter phase). Moreover, an upper bound is found for the Gibbons–Hawking temperature of the primordial de Sitter phase. Finally, when confronted with the recent observational data, the current 'quasi'-de Sitter era, as predicted by the model, is seen to pass very comfortably the cosmic background tests.

  20. Cosmic acceleration without dark energy: background tests and thermodynamic analysis

    NASA Astrophysics Data System (ADS)

    Lima, J. A. S.; Graef, L. L.; Pavón, D.; Basilakos, Spyros

    2014-10-01

    A cosmic scenario with gravitationally induced particle creation is proposed. In this model the Universe evolves from an early to a late time de Sitter era, with the recent accelerating phase driven only by the negative creation pressure associated with the cold dark matter component. The model can be interpreted as an attempt to reduce the so-called cosmic sector (dark matter plus dark energy) and relate the two cosmic accelerating phases (early and late time de Sitter expansions). A detailed thermodynamic analysis including possible quantum corrections is also carried out. For a very wide range of the free parameters, it is found that the model presents the expected behavior of an ordinary macroscopic system in the sense that it approaches thermodynamic equilibrium in the long run (i.e., as it nears the second de Sitter phase). Moreover, an upper bound is found for the Gibbons-Hawking temperature of the primordial de Sitter phase. Finally, when confronted with the recent observational data, the current `quasi'-de Sitter era, as predicted by the model, is seen to pass very comfortably the cosmic background tests.

  1. SIMS analysis of high-performance accelerator niobium

    SciTech Connect

    Maheshwari, P.; Stevie, F. A.; Myneni, Ganapati Rao; Rigsbee, J, M.; Dhakal, Pashupati; Ciovati, Gianluigi; Griffis, D. P.

    2014-11-01

    Niobium is used to fabricate superconducting radio frequency accelerator modules because of its high critical temperature, high critical magnetic field, and easy formability. Recent experiments have shown a very significant improvement in performance (over 100%) after a high-temperature bake at 1400 degrees C for 3h. SIMS analysis of this material showed the oxygen profile was significantly deeper than the native oxide with a shape that is indicative of diffusion. Positive secondary ion mass spectra showed the presence of Ti with a depth profile similar to that of O. It is suspected that Ti is associated with the performance improvement. The source of Ti contamination in the anneal furnace has been identified, and a new furnace was constructed without Ti. Initial results from the new furnace do not show the yield improvement. Further analyses should determine the relationship of Ti to cavity performance.

  2. Bayesian Analysis of Peak Ground Acceleration Attenuation Relationship

    SciTech Connect

    Mu Heqing; Yuen Kaveng

    2010-05-21

    Estimation of peak ground acceleration is one of the main issues in civil and earthquake engineering practice. The Boore-Joyner-Fumal empirical formula is well known for this purpose. In this paper we propose to use the Bayesian probabilistic model class selection approach to obtain the most suitable prediction model class for the seismic attenuation formula. The optimal model class is robust in the sense that it has balance between the data fitting capability and the sensitivity to noise. A database of strong-motion records is utilized for the analysis. It turns out that the optimal model class is simpler than the full order attenuation model suggested by Boore, Joyner and Fumal (1993).

  3. 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

  4. Epistasis among eNOS, MMP-9 and VEGF maternal genotypes in hypertensive disorders of pregnancy.

    PubMed

    Luizon, Marcelo R; Sandrim, Valeria C; Palei, Ana Ct; Lacchini, Riccardo; Cavalli, Ricardo C; Duarte, Geraldo; Tanus-Santos, Jose E

    2012-09-01

    Polymorphisms of the endothelial nitric oxide synthase (eNOS), matrix metalloproteinase-9 (MMP-9) and vascular endothelial growth factor (VEGF) genes were shown to be associated with hypertensive disorders of pregnancy. However, epistasis is suggested to be an important component of the genetic susceptibility to preeclampsia (PE). The aim of this study was to characterize the interactions among these genes in PE and gestational hypertension (GH). Seven clinically relevant polymorphisms of eNOS (T-786C, rs2070744, a variable number of tandem repeats in intron 4 and Glu298Asp, rs1799983), MMP-9 (C-1562T, rs3918242 and -90(CA)₁₃-₂₅, rs2234681) and VEGF (C-2578A, rs699947 and G-634C, rs2010963) were genotyped by TaqMan allelic discrimination assays or PCR and fragment separation by electrophoresis in 122 patients with PE, 107 patients with GH and a control group of 102 normotensive pregnant (NP) women. A robust multifactor dimensionality reduction analysis was used to characterize gene-gene interactions. Although no significant genotype combinations were observed for the comparison between the GH and NP groups (P>0.05), the combination of MMP-9-1562CC with VEGF-634GG was more frequent in NP women than in women with PE (P<0.05). Moreover, the combination of MMP-9-1562CC with VEGF-634CC or MMP-9-1562CT with VEGF-634CC or-634GG was more frequent in women with PE than in NP women (P<0.05). These results are obscured when single polymorphisms in these genes are considered and suggest that specific genotype combinations of MMP-9 and VEGF contribute to PE susceptibility. PMID:22573202

  5. 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

  6. Transition of Iodine Analysis to Accelerator Mass Spectrometry

    SciTech Connect

    Watrous, Matthew George; Adamic, Mary Louise; Olson, John Eric; Baeck, D. L.; Fox, R. V.; Hahn, P. A.; Jenson, D. D.; Lister, T. E.

    2015-09-01

    The goal of the project, New Paradigms for Isotope Ratio Mass Spectrometry: Raising the Scientific Profile and Improved Performance for Accelerator Mass Spectrometry (AMS) and Thermal Ionization Mass Spectrometry (TIMS), is to ensure that the ongoing isotope ratio determination capability within the U.S. Department of Energy complex is the world’s best for application to nonproliferation. This report spells out the progress of Task 4, Transition of TIMS to AMS for Iodine Analysis, of the larger project. The subtasks under Task 4 and the accomplishments throughout the three year project life cycle are presented in this report. Progress was made in optimization of chemical extraction, determination of a detection limit for 127Iodine, production of standard materials for AMS analysis quality assurance, facilitation of knowledge exchange with respect to analyzing iodine on an AMS, cross comparison with a world-leading AMS laboratory, supercritical fluid extraction of iodine for AMS analysis and electrodeposition of seawater as a direct method of preparation for iodine analysis by AMS--all with the goal of minimizing the time required to stand up an AMS capability for iodine analysis of exposed air filters at INL. An effective extraction method has been developed and demonstrated for iodine analysis of exposed air filters. Innovative techniques to accomplish the cathode preparation for AMS analysis were developed and demonstrated and published. The known gap of a lack of available materials for reference standards in the analysis of iodine by AMS was filled by the preparation of homogenous materials that were calibrated against NIST materials. A minimum limit on the amount of abundant isotope in a sample was determined for AMS analysis. The knowledge exchange occurred with fantastic success. Scientists engaged the international AMS community at conferences, as well as in their laboratories for collaborative work. The supercritical fluid extraction work has positive

  7. Transition of Iodine Analysis to Accelerator Mass Spectrometry

    SciTech Connect

    M. L. Adamic; J. E. Olson; D. D. Jenson; J. G. Eisenmenger; M. G. Watrous

    2012-09-01

    This NA 22 funded research project investigated the transition of iodine isotopic analyses from thermal ionization mass spectrometry (TIMS) to an accelerator mass spectrometry (AMS) system. Previous work (Fiscal Year 2010) had demonstrated comparable data from TIMS and AMS. With AMS providing comparable data with improved background levels and vastly superior sample throughput, improvement in the sample extraction from environmental sample matrices was needed to bring sample preparation throughput closer to the operation level of the instrument. Previous research used an extraction chemistry that was not optimized for yield or refined for reduced labor to prove the principle. This research was done to find an extraction with better yield using less labor per sample to produce a sample ready for the AMS instrument. An extraction method using tetramethyl ammonium hydroxide (TMAH) was developed for removal of iodine species from high volume air filters. The TMAH with gentle heating was superior to the following three extraction methods: ammonium hydroxide aided by sonication, acidic and basic extraction aided by microwave, and ethanol mixed with sodium hydroxide. Taking the iodine from the extraction solvent to being ready for AMS analysis was accomplished by a direct precipitation, as well as, using silver wool to harvest the iodine from the TMAH. Portions of the same filters processed in FY 2010 were processed again with the improved extraction scheme followed by successful analysis by AMS at the Swiss Federal Institute of Technology. The data favorably matched the data obtained in 2010. The time required for analysis has been reduced over the aqueous extraction/AMS approach developed in FY 2010. For a hypothetical batch of 30 samples, the AMS methodology is about 10 times faster than the traditional gas phase chemistry and TIMS analysis. As an additional benefit, background levels for the AMS method are about 1000 times lower than TIMS. This results from the

  8. Statistical analysis of accelerated temperature aging of semiconductor devices

    NASA Astrophysics Data System (ADS)

    Johnson, W. A.; Milles, M. F.

    1981-05-01

    A number of semiconductor devices taken from a distribution were operated at several elevated temperatures to induce failure in all devices within a reasonable time. Assuming general characteristics of the device failure probability density function (pdf) and its temperature dependence, the expected cumulative failure function (cff) for devices in normal operation were estimated based on statistical inference, taking the average probability of a random device (from the same distribution but operated at a normal temperature) failing as a function of time. A review of the mathematical formalism employed in semiconductor reliability discussions is included. Three failure pdf's at particular usefulness to this analysis--exponential, normal, and lognormal - are discussed. The cff, at times orders of magnitude loss then, at times comparable to the desired system useful, life (*10 to the 4th power to 10 to the 5th power hr) is considered. A review of accelerated temperature aging is presented, and the assumption concerning the general characteristics of the failure pdf, which are fundamental to this analysis, are emphasized.

  9. Durability analysis of composite structures using the accelerated testing methodology

    NASA Astrophysics Data System (ADS)

    Kuraishi, Akira

    The applications of composite materials are increasing significantly due to their excellent properties and design flexibility, and composite materials have completely replaced conventional metals in several applications. However, much larger opportunities will be likely to occur when physical bases for durability characterization become established. Polymeric composite materials are in general viscoelastic, and their stiffness and strength depend on temperature and loading rate. These effects play an important role in the long-term durability of the composite materials, and therefore it is important to develop a durability analysis method for composite structures that considers these effects. The present approach is based on three components, a new accelerated material characterization methodology, statistical analysis of this methodology, and conventional design tools tailored for the temperature and loading rate dependence. The material characterization methodology uses series of short-term tests at elevated temperatures to predict life for wide ranges of temperature and loading conditions. This methodology is based on the empirical relation between the effects of temperature and loading rate on the stiffness and strength of polymeric composite materials. The statistical analysis allows us to create the confidence interval of the prediction, which is essential in generating the design allowables. Common design tools such as failure criteria and cumulative damage laws can be tailored to consider the temperature and loading rate dependence. These components are integrated into the proposed durability analysis and design method for composite structures. The durability design of a composite rotor for the flywheel energy storage system is shown as an example. This example demonstrates that the proposed design method is not significantly different from conventional designs in terms of complexity and required effort.

  10. Accelerated Sensitivity Analysis in High-Dimensional Stochastic Reaction Networks

    PubMed Central

    Arampatzis, Georgios; Katsoulakis, Markos A.; Pantazis, Yannis

    2015-01-01

    Existing sensitivity analysis approaches are not able to handle efficiently stochastic reaction networks with a large number of parameters and species, which are typical in the modeling and simulation of complex biochemical phenomena. In this paper, a two-step strategy for parametric sensitivity analysis for such systems is proposed, exploiting advantages and synergies between two recently proposed sensitivity analysis methodologies for stochastic dynamics. The first method performs sensitivity analysis of the stochastic dynamics by means of the Fisher Information Matrix on the underlying distribution of the trajectories; the second method is a reduced-variance, finite-difference, gradient-type sensitivity approach relying on stochastic coupling techniques for variance reduction. Here we demonstrate that these two methods can be combined and deployed together by means of a new sensitivity bound which incorporates the variance of the quantity of interest as well as the Fisher Information Matrix estimated from the first method. The first step of the proposed strategy labels sensitivities using the bound and screens out the insensitive parameters in a controlled manner. In the second step of the proposed strategy, a finite-difference method is applied only for the sensitivity estimation of the (potentially) sensitive parameters that have not been screened out in the first step. Results on an epidermal growth factor network with fifty parameters and on a protein homeostasis with eighty parameters demonstrate that the proposed strategy is able to quickly discover and discard the insensitive parameters and in the remaining potentially sensitive parameters it accurately estimates the sensitivities. The new sensitivity strategy can be several times faster than current state-of-the-art approaches that test all parameters, especially in “sloppy” systems. In particular, the computational acceleration is quantified by the ratio between the total number of parameters over

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

    PubMed Central

    McKinney, Brett A.; Lareau, Caleb; Oberg, Ann L.; Kennedy, Richard B.; Ovsyannikova, Inna G.; Poland, Gregory A.

    2016-01-01

    Although many diseases and traits show large heritability, few genetic variants have been found to strongly separate phenotype groups by genotype. Complex regulatory networks of variants and expression of multiple genes lead to small individual-variant effects and difficulty replicating the effect of any single variant in an affected pathway. Interaction network modeling of GWAS identifies effects ignored by univariate models, but population differences may still cause specific genes to not replicate. Integrative network models may help detect indirect effects of variants in the underlying biological pathway. In this study, we used gene-level functional interaction information from the Integrative Multi-species Prediction (IMP) tool to reveal important genes associated with a complex phenotype through evidence from epistasis networks and pathway enrichment. We test this method for augmenting variant-based network analyses with functional interactions by applying it to a smallpox vaccine immune response GWAS. The integrative analysis spotlights the role of genes related to retinoid X receptor alpha (RXRA), which has been implicated in a previous epistasis network analysis of smallpox vaccine. PMID:27513748

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

    PubMed

    McKinney, Brett A; Lareau, Caleb; Oberg, Ann L; Kennedy, Richard B; Ovsyannikova, Inna G; Poland, Gregory A

    2016-01-01

    Although many diseases and traits show large heritability, few genetic variants have been found to strongly separate phenotype groups by genotype. Complex regulatory networks of variants and expression of multiple genes lead to small individual-variant effects and difficulty replicating the effect of any single variant in an affected pathway. Interaction network modeling of GWAS identifies effects ignored by univariate models, but population differences may still cause specific genes to not replicate. Integrative network models may help detect indirect effects of variants in the underlying biological pathway. In this study, we used gene-level functional interaction information from the Integrative Multi-species Prediction (IMP) tool to reveal important genes associated with a complex phenotype through evidence from epistasis networks and pathway enrichment. We test this method for augmenting variant-based network analyses with functional interactions by applying it to a smallpox vaccine immune response GWAS. The integrative analysis spotlights the role of genes related to retinoid X receptor alpha (RXRA), which has been implicated in a previous epistasis network analysis of smallpox vaccine. PMID:27513748

  13. Solar wind conditions leading to efficient radiation belt electron acceleration: A superposed epoch analysis

    SciTech Connect

    Li, W.; Thorne, R. M.; Bortnik, J.; Baker, D. N.; Reeves, G. D.; Kanekal, S. G.; Spence, H. E.; Green, J. C.

    2015-09-07

    In this study by determining preferential solar wind conditions leading to efficient radiation belt electron acceleration is crucial for predicting radiation belt electron dynamics. Using Van Allen Probes electron observations (>1 MeV) from 2012 to 2015, we identify a number of efficient and inefficient acceleration events separately to perform a superposed epoch analysis of the corresponding solar wind parameters and geomagnetic indices. By directly comparing efficient and inefficient acceleration events, we clearly show that prolonged southward Bz, high solar wind speed, and low dynamic pressure are critical for electron acceleration to >1 MeV energies in the heart of the outer radiation belt. We also evaluate chorus wave evolution using the superposed epoch analysis for the identified efficient and inefficient acceleration events and find that chorus wave intensity is much stronger and lasts longer during efficient electron acceleration events, supporting the scenario that chorus waves play a key role in MeV electron acceleration.

  14. Epistasis between adults and larvae underlies caste fate and fitness in a clonal ant.

    PubMed

    Teseo, Serafino; Châline, Nicolas; Jaisson, Pierre; Kronauer, Daniel J C

    2014-01-01

    In social species, the phenotype and fitness of an individual depend in part on the genotype of its social partners. However, how these indirect genetic effects affect genotype fitness in competitive situations is poorly understood in animal societies. We therefore studied phenotypic plasticity and fitness of two clones of the ant Cerapachys biroi in monoclonal and chimeric colonies. Here we show that, while clone B has lower fitness in isolation, surprisingly, it consistently outcompetes clone A in chimeras. The reason is that, in chimeras, clone B produces more individuals specializing in reproduction rather than cooperative tasks, behaving like a facultative social parasite. A cross-fostering experiment shows that the proportion of these individuals depends on intergenomic epistasis between larvae and nursing adults, explaining the flexible allocation strategy of clone B. Our results suggest that intergenomic epistasis can be the proximate mechanism for social parasitism in ants, revealing striking analogies between social insects and social microbes. PMID:24561920

  15. ViSEN: methodology and software for visualization of statistical epistasis networks.

    PubMed

    Hu, Ting; Chen, Yuanzhu; Kiralis, Jeff W; Moore, Jason H

    2013-04-01

    The nonlinear interaction effect among multiple genetic factors, i.e. epistasis, has been recognized as a key component in understanding the underlying genetic basis of complex human diseases and phenotypic traits. Due to the statistical and computational complexity, most epistasis studies are limited to interactions with an order of two. We developed ViSEN to analyze and visualize epistatic interactions of both two-way and three-way. ViSEN not only identifies strong interactions among pairs or trios of genetic attributes, but also provides a global interaction map that shows neighborhood and clustering structures. This visualized information could be very helpful to infer the underlying genetic architecture of complex diseases and to generate plausible hypotheses for further biological validations. ViSEN is implemented in Java and freely available at https://sourceforge.net/projects/visen/. PMID:23468157

  16. Estimation and interpretation of genetic effects with epistasis using the NOIA model.

    PubMed

    Alvarez-Castro, José M; Carlborg, Orjan; Rönnegård, Lars

    2012-01-01

    We introduce this communication with a brief outline of the historical landmarks in genetic modeling, especially concerning epistasis. Then, we present methods for the use of genetic modeling in QTL analyses. In particular, we summarize the essential expressions of the natural and orthogonal interactions (NOIA) model of genetic effects. Our motivation for reviewing that theory here is twofold. First, this review presents a digest of the expressions for the application of the NOIA model, which are often mixed with intermediate and additional formulae in the original articles. Second, we make the required theory handy for the reader to relate the genetic concepts to the particular mathematical expressions underlying them. We illustrate those relations by providing graphical interpretations and a diagram summarizing the key features for applying genetic modeling with epistasis in comprehensive QTL analyses. Finally, we briefly review some examples of the application of NOIA to real data and the way it improves the interpretability of the results. PMID:22565838

  17. Lorentz Force Detuning Analysis of the SNS Accelerating Cavities

    SciTech Connect

    R. Mitchell; K. Matsumoto; G. Ciovati; K. Davis; K. Macha; R. Sundelin

    2001-09-01

    The Spallation Neutron Source (SNS) project incorporates a superconducting radio-frequency (SRF) accelerator for the final section of the pulsed mode linac Cavities with geometrical {beta} values of {beta} = 0.61 and {beta} = 0.81 are utilized in the SRF section, and are constructed out of thin-walled niobium with stiffener rings welded between the cells near the iris. The welded titanium helium vessel and tuner assembly restrains the cavity beam tubes Cavities with {beta} values less than one have relatively steep and flat side-walls making the cavities susceptible to Ised RF induces cyclic Lorentz pressures that mechanically excite the cavities, producing a dynamic Lorentz force detuning different from a continuous RF system. The amplitude of the dynamic detuning for a given cavity design is a function of the mechanical damping, stiffness of the tuner/helium vessel assembly, RF pulse profile, and the RF pulse rate. This paper presents analysis and testing results to date, and indicates areas where more investigation is required.

  18. Transition of Iodine Analysis to Accelerator Mass Spectrometry

    SciTech Connect

    J. E. Delmore

    2010-09-01

    Funding was received from NA-22 to investigate transitioning iodine isotopic analyses to an accelerator mass spectrometry (AMS) system. The present method uses gas-phase chemistry followed by thermal ionization mass spectrometry (TIMS). It was anticipated that the AMS approach could provide comparable data, with improved background levels and superior sample throughput. An aqueous extraction method was developed for removal of iodine species from high-volume air filters. Ethanol and sodium hydroxide, plus heating and ultrasonic treatment, were used to successfully extract iodine from loaded high-volume air filters. Portions of the same filters were also processed in the traditional method and analyzed by TIMS for comparison. Aliquot parts of the aqueous extracts were analyzed by AMS at the Swiss Federal Institute of Technology. Idaho National Laboratory (INL) personnel visited several AMS laboratories in the US, Spain, and Switzerland. Experience with AMS systems from several manufacturers was gained, and relationships were developed with key personnel at the laboratories. Three batches of samples were analyzed in Switzerland, and one in Spain. Results show that the INL extraction method successfully extracted enough iodine from high-volume air filters to allow AMS analysis. Comparison of the AMS and TIMS data is very encouraging; while the TIMS showed about forty percent more atoms of 129I, the 129/127 ratios tracked each other very well between the two methods. The time required for analysis is greatly reduced for the aqueous extraction/AMS approach. For a hypothetical batch of thirty samples, the AMS methodology is about five times faster than the traditional gas-phase chemistry and TIMS analysis. As an additional benefit, background levels for the AMS method are about 1000 times lower than for TIMS. This results from the fundamental mechanisms of ionization in the AMS system and cleanup of molecular interferences. We showed that an aqueous extraction of high

  19. Plasticity and epistasis strongly affect bacterial fitness after losing multiple metabolic genes.

    PubMed

    D'Souza, Glen; Waschina, Silvio; Kaleta, Christoph; Kost, Christian

    2015-05-01

    Many bacterial lineages lack seemingly essential metabolic genes. Previous work suggested selective benefits could drive the loss of biosynthetic functions from bacterial genomes when the corresponding metabolites are sufficiently available in the environment. However, the factors that govern this "genome streamlining" remain poorly understood. Here we determine the effect of plasticity and epistasis on the fitness of Escherichia coli genotypes from whose genome biosynthetic genes for one, two, or three different amino acids have been deleted. Competitive fitness experiments between auxotrophic mutants and prototrophic wild-type cells in one of two carbon environments revealed that plasticity and epistasis strongly affected the mutants' fitness individually and interactively. Positive and negative epistatic interactions were prevalent, yet on average cancelled each other out. Moreover, epistasis correlated negatively with the expected effects of combined auxotrophy-causing mutations, thus producing a pattern of diminishing returns. Moreover, computationally analyzing 1,432 eubacterial metabolic networks revealed that most pairs of auxotrophies co-occurred significantly more often than expected by chance, suggesting epistatic interactions and/or environmental factors favored these combinations. Our results demonstrate that both the genetic background and environmental conditions determine the adaptive value of a loss-of-biochemical-function mutation and that fitness gains decelerate, as more biochemical functions are lost. PMID:25765095

  20. Genetic control of soybean seed isoflavone content: importance of statistical model and epistasis in complex traits.

    PubMed

    Gutierrez-Gonzalez, Juan Jose; Wu, Xiaolei; Zhang, Juan; Lee, Jeong-Dong; Ellersieck, Mark; Shannon, J Grover; Yu, Oliver; Nguyen, Henry T; Sleper, David A

    2009-10-01

    A major objective for geneticists is to decipher genetic architecture of traits associated with agronomic importance. However, a majority of such traits are complex, and their genetic dissection has been traditionally hampered not only by the number of minor-effect quantitative trait loci (QTL) but also by genome-wide interacting loci with little or no individual effect. Soybean (Glycine max [L.] Merr.) seed isoflavonoids display a broad range of variation, even in genetically stabilized lines that grow in a fixed environment, because their synthesis and accumulation are affected by many biotic and abiotic factors. Due to this complexity, isoflavone QTL mapping has often produced conflicting results especially with variable growing conditions. Herein, we comparatively mapped soybean seed isoflavones genistein, daidzein, and glycitein by using several of the most commonly used mapping approaches: interval mapping, composite interval mapping, multiple interval mapping and a mixed-model based composite interval mapping. In total, 26 QTLs, including many novel regions, were found bearing additive main effects in a population of RILs derived from the cross between Essex and PI 437654. Our comparative approach demonstrates that statistical mapping methodologies are crucial for QTL discovery in complex traits. Despite a previous understanding of the influence of additive QTL on isoflavone production, the role of epistasis is not well established. Results indicate that epistasis, although largely dependent on the environment, is a very important genetic component underlying seed isoflavone content, and suggest epistasis as a key factor causing the observed phenotypic variability of these traits in diverse environments. PMID:19626310

  1. Epistasis Constrains Mutational Pathways of Hemoglobin Adaptation in High-Altitude Pikas

    PubMed Central

    Tufts, Danielle M.; Natarajan, Chandrasekhar; Revsbech, Inge G.; Projecto-Garcia, Joana; Hoffmann, Federico G.; Weber, Roy E.; Fago, Angela; Moriyama, Hideaki; Storz, Jay F.

    2015-01-01

    A fundamental question in evolutionary genetics concerns the roles of mutational pleiotropy and epistasis in shaping trajectories of protein evolution. This question can be addressed most directly by using site-directed mutagenesis to explore the mutational landscape of protein function in experimentally defined regions of sequence space. Here, we evaluate how pleiotropic trade-offs and epistatic interactions influence the accessibility of alternative mutational pathways during the adaptive evolution of hemoglobin (Hb) function in high-altitude pikas (Mammalia: Lagomorpha). By combining ancestral protein resurrection with a combinatorial protein-engineering approach, we examined the functional effects of sequential mutational steps in all possible pathways that produced an increased Hb–O2 affinity. These experiments revealed that the effects of mutations on Hb–O2 affinity are highly dependent on the temporal order in which they occur: Each of three β-chain substitutions produced a significant increase in Hb–O2 affinity on the ancestral genetic background, but two of these substitutions produced opposite effects when they occurred as later steps in the pathway. The experiments revealed pervasive epistasis for Hb–O2 affinity, but affinity-altering mutations produced no significant pleiotropic trade-offs. These results provide insights into the properties of adaptive substitutions in naturally evolved proteins and suggest that the accessibility of alternative mutational pathways may be more strongly constrained by sign epistasis for positively selected biochemical phenotypes than by antagonistic pleiotropy. PMID:25415962

  2. Systemic properties of metabolic networks lead to an epistasis-based model for heterosis.

    PubMed

    Fiévet, Julie B; Dillmann, Christine; de Vienne, Dominique

    2010-01-01

    The genetic and molecular approaches to heterosis usually do not rely on any model of the genotype-phenotype relationship. From the generalization of Kacser and Burns' biochemical model for dominance and epistasis to networks with several variable enzymes, we hypothesized that metabolic heterosis could be observed because the response of the flux towards enzyme activities and/or concentrations follows a multi-dimensional hyperbolic-like relationship. To corroborate this, we used the values of systemic parameters accounting for the kinetic behaviour of four enzymes of the upstream part of glycolysis, and simulated genetic variability by varying in silico enzyme concentrations. Then we "crossed" virtual parents to get 1,000 hybrids, and showed that best-parent heterosis was frequently observed. The decomposition of the flux value into genetic effects, with the help of a novel multilocus epistasis index, revealed that antagonistic additive-by-additive epistasis effects play the major role in this framework of the genotype-phenotype relationship. This result is consistent with various observations in quantitative and evolutionary genetics, and provides a model unifying the genetic effects underlying heterosis. PMID:19916003

  3. Feature-based Analysis of Plasma-based Particle Acceleration Data

    SciTech Connect

    Ruebel, Oliver; Geddes, Cameron G.R.; Chen, Min; Cormier-Michel, Estelle; Bethel, E. Wes

    2013-07-05

    Plasma-based particle accelerators can produce and sustain thousands of times stronger acceleration fields than conventional particle accelerators, providing a potential solution to the problem of the growing size and cost of conventional particle accelerators. To facilitate scientific knowledge discovery from the ever growing collections of accelerator simulation data generated by accelerator physicists to investigate next-generation plasma-based particle accelerator designs, we describe a novel approach for automatic detection and classification of particle beams and beam substructures due to temporal differences in the acceleration process, here called acceleration features. The automatic feature detection in combination with a novel visualization tool for fast, intuitive, query-based exploration of acceleration features enables an effective top-down data exploration process, starting from a high-level, feature-based view down to the level of individual particles. We describe the application of our analysis in practice to analyze simulations of single pulse and dual and triple colliding pulse accelerator designs, and to study the formation and evolution of particle beams, to compare substructures of a beam and to investigate transverse particle loss.

  4. Feature-based analysis of plasma-based particle acceleration data.

    PubMed

    Rübel, Oliver; Geddes, Cameron G R; Chen, Min; Cormier-Michel, Estelle; Bethel, E Wes

    2014-02-01

    Plasma-based particle accelerators can produce and sustain thousands of times stronger acceleration fields than conventional particle accelerators, providing a potential solution to the problem of the growing size and cost of conventional particle accelerators. To facilitate scientific knowledge discovery from the ever growing collections of accelerator simulation data generated by accelerator physicists to investigate next-generation plasma-based particle accelerator designs, we describe a novel approach for automatic detection and classification of particle beams and beam substructures due to temporal differences in the acceleration process, here called acceleration features. The automatic feature detection in combination with a novel visualization tool for fast, intuitive, query-based exploration of acceleration features enables an effective top-down data exploration process, starting from a high-level, feature-based view down to the level of individual particles. We describe the application of our analysis in practice to analyze simulations of single pulse and dual and triple colliding pulse accelerator designs, and to study the formation and evolution of particle beams, to compare substructures of a beam, and to investigate transverse particle loss. PMID:24356363

  5. Using Biological Knowledge to Uncover the Mystery in the Search for Epistasis in Genome-Wide Association Studies

    PubMed Central

    Ritchie, Marylyn D.

    2011-01-01

    The search for the missing heritability in genome-wide association studies (GWAS) has become an important focus for the human genetics community. One suspected location of these genetic effects is in gene-gene interactions, or epistasis. The computational burden of exploring gene-gene interactions in the wealth of data generated in GWAS, along with small to moderate sample sizes, have led to epistasis being an afterthought, rather than a primary focus of GWAS analyses. In this review, we discuss some potential approaches to filter a GWAS dataset to a smaller, more manageable dataset where searching for epistasis is considerably more feasible. We describe a number of alternative approaches, but primarily focus on the use of prior biological knowledge from databases in the public domain to guide the search for epistasis. The manner in which prior knowledge is incorporated into a GWA study can be many and these data can be extracted from a variety of database sources. We discuss a number of these approaches and propose that a comprehensive approach will likely be most fruitful for searching for epistasis in large-scale genomic studies of the current state-of-the-art and into the future. PMID:21158748

  6. X Chromosome SNPs Were Heavily Involved In Epistasis Effects Of Net Merit Component Traits In Contemporary U.S. Holstein Cows

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Pairwise epistasis effects of net merit and its eight component traits were tested in 1654 contemporary U.S. Holstein cows using the BovineSNP50 (45,878 SNPs). A large number of epistasis effects exceeded the genome-wide significance of 5% type-I error with the Bonferroni correction and a QTL map of...

  7. A Massively Parallel Solver for the Mechanical Harmonic Analysis of Accelerator Cavities

    SciTech Connect

    O. Kononenko

    2015-02-17

    ACE3P is a 3D massively parallel simulation suite that developed at SLAC National Accelerator Laboratory that can perform coupled electromagnetic, thermal and mechanical study. Effectively utilizing supercomputer resources, ACE3P has become a key simulation tool for particle accelerator R and D. A new frequency domain solver to perform mechanical harmonic response analysis of accelerator components is developed within the existing parallel framework. This solver is designed to determine the frequency response of the mechanical system to external harmonic excitations for time-efficient accurate analysis of the large-scale problems. Coupled with the ACE3P electromagnetic modules, this capability complements a set of multi-physics tools for a comprehensive study of microphonics in superconducting accelerating cavities in order to understand the RF response and feedback requirements for the operational reliability of a particle accelerator. (auth)

  8. TRI-SERVICE SITE CHARACTERIZATION AND ANALYSIS PENETROMETER SYSTEM (SCAPS) ACCELERATED SENSOR DEVELOPMENT PROJECT

    EPA Science Inventory

    In 1994, the Strategic Environmental Research and Development Program (SERDP) funded a Tri-Service effort to accelerate the development and fielding of environmental sensing technologies to extend the capabilities of the Site Characterization and Analysis Penetrometer System (SCA...

  9. Association Mapping for Epistasis and Environmental Interaction of Yield Traits in 323 Cotton Cultivars under 9 Different Environments

    PubMed Central

    Pan, Zhaoe; Wang, Xiwen; He, Shoupu; Xiao, Songhua; Shi, Weijun; Zhou, Zhongli; Pang, Baoyin; Wang, Liru; Liu, Jianguang; Ma, Jun; Du, Xiongming; Zhu, Jun

    2014-01-01

    Improving yield is a major objective for cotton breeding schemes, and lint yield and its three component traits (boll number, boll weight and lint percentage) are complex traits controlled by multiple genes and various environments. Association mapping was performed to detect markers associated with these four traits using 651 simple sequence repeats (SSRs). A mixed linear model including epistasis and environmental interaction was used to screen the loci associated with these four yield traits by 323 accessions of Gossypium hirsutum L. evaluated in nine different environments. 251 significant loci were detected to be associated with lint yield and its three components, including 69 loci with individual effects and all involved in epistasis interactions. These significant loci explain ∼ 62.05% of the phenotypic variance (ranging from 49.06% ∼ 72.29% for these four traits). It was indicated by high contribution of environmental interaction to the phenotypic variance for lint yield and boll numbers, that genetic effects of SSR loci were susceptible to environment factors. Shared loci were also observed among these four traits, which may be used for simultaneous improvement in cotton breeding for yield traits. Furthermore, consistent and elite loci were screened with −Log10 (P-value) >8.0 based on predicted effects of loci detected in different environments. There was one locus and 6 pairs of epistasis for lint yield, 4 loci and 10 epistasis for boll number, 15 loci and 2 epistasis for boll weight, and 2 loci and 5 epistasis for lint percentage, respectively. These results provided insights into the genetic basis of lint yield and its components and may be useful for marker-assisted breeding to improve cotton production. PMID:24810754

  10. Analysis and Design of Optical Bragg Acceleration Structures

    SciTech Connect

    Mizrahi, Amit; Schaechter, Levi

    2004-12-07

    It is demonstrated that a Bragg waveguide consisting of a series of dielectric layers may form an excellent optical acceleration structure. Confinement of the accelerating fields is achieved for both planar and cylindrical configurations by adjusting the first dielectric layer width. A typical structure made of Silica and Zirconia may support gradients of the order of 1 GV/m with an interaction impedance of a few hundreds of Ohms and with an energy velocity of less than 0.5c. An interaction impedance of about one thousand Ohms may be obtained by replacing the Zirconia with a (fictitious) material of {epsilon} = 25. Special attention is paid to the wake-field developing in such a structure. In case of a relatively small number of layers, a qualitative approach shows that the emitted power is inversely proportional to the number of micro-bunches. Quantitative results are given for a higher number of dielectric layers, showing that in comparison to a structure bounded by metallic walls, the emitted power is significantly smaller due to propagation bands allowing electromagnetic energy to escape. The efficiency of the acceleration structures is investigated and shown to have an optimum as a function of the vacuum core dimension.

  11. Analysis of Capillary Guided Laser Plasma Accelerator Experiments at LBNL

    SciTech Connect

    Nakamura, K.; Esarey, E.; Leemans, W. P.; Gonsalves, A. J.; Panasenko, D.; Toth, Cs.; Geddes, C. G. R.; Schroeder, C. B.; Lin, C.

    2009-01-22

    Laser wakefield acceleration experiments were carried out by using a hydrogen-filled capillary discharge waveguide. For a 15 mm long, 200 {mu}m diameter capillary, quasi-monoenergetic e-beams up to 300 MeV were observed. By de-tuning discharge delay from optimum guiding performance, self-trapping was found to be stabilized. For a 33 mm long, 300 {mu}m capillary, a parameter regime with high energy electron beams, up to 1 GeV, was found. In this regime, the electron beam peak energy was correlated with the amount of trapped electrons.

  12. Analysis of Capillary Guided Laser Plasma Accelerator Experiments at LBNL

    SciTech Connect

    Advanced Light Source; Nakamura, Kei; Gonsalves, Anthony; Panasenko, Dmitriy; Lin, Chen; Toth, Csaba; Geddes, Cameron; Schroeder, Carl; Esarey, Eric; Leemans, Wim

    2008-09-29

    Laser wakefield acceleration experiments were carried out by using a hydrogen-filledcapillary discharge waveguide. For a 15 mm long, 200 mu m diameter capillary, quasi-monoenergetic e-beams up to 300 MeV were observed. By de-tuning discharge delay from optimum guiding performance, self-trapping was found to be stabilized. For a 33 mm long, 300 mu m capillary, a parameter regime with high energy electron beams, up to 1 GeV, was found. In this regime, the electron beam peak energy was correlated with the amount of trapped electrons.

  13. Use of Tritium Accelerator Mass Spectrometry for Tree Ring Analysis

    PubMed Central

    LOVE, ADAM H.; HUNT, JAMES R.; ROBERTS, MARK L.; SOUTHON, JOHN R.; CHIARAPPA - ZUCCA, MARINA L.; DINGLEY, KAREN H.

    2010-01-01

    Public concerns over the health effects associated with low-level and long-term exposure to tritium released from industrial point sources have generated the demand for better methods to evaluate historical tritium exposure levels for these communities. The cellulose of trees accurately reflects the tritium concentration in the source water and may contain the only historical record of tritium exposure. The tritium activity in the annual rings of a tree was measured using accelerator mass spectrometry to reconstruct historical annual averages of tritium exposure. Milligram-sized samples of the annual tree rings from a Tamarix located at the Nevada Test Site are used for validation of this methodology. The salt cedar was chosen since it had a single source of tritiated water that was well-characterized as it varied over time. The decay-corrected tritium activity of the water in which the salt cedar grew closely agrees with the organically bound tritium activity in its annual rings. This demonstrates that the milligram-sized samples used in tritium accelerator mass spectrometry are suited for reconstructing anthropogenic tritium levels in the environment. PMID:12144257

  14. Use of tritium accelerator mass spectrometry for tree ring analysis.

    PubMed

    Love, Adam H; Hunt, James R; Roberts, Mark L; Southon, John R; Chiarapp-Zucca, Marina L; Dingley, Karen H

    2002-07-01

    Public concerns over the health effects associated with low-level and long-term exposure to tritium released from industrial point sources have generated the demand for better methods to evaluate historical tritium exposure levels for these communities. The cellulose of trees accurately reflects the tritium concentration in the source water and may contain the only historical record of tritium exposure. The tritium activity in the annual rings of a tree was measured using accelerator mass spectrometry to reconstruct historical annual averages of tritium exposure. Milligram-sized samples of the annual tree rings from a Tamarix located at the Nevada Test Site are used for validation of this methodology. The salt cedar was chosen since it had a single source of tritiated water that was well-characterized as it varied over time. The decay-corrected tritium activity of the water in which the salt cedar grew closely agrees with the organically bound tritium activity in its annual rings. This demonstrates that the milligram-sized samples used in tritium accelerator mass spectrometry are suited for reconstructing anthropogenic tritium levels in the environment. PMID:12144257

  15. A fast and powerful W-test for pairwise epistasis testing.

    PubMed

    Wang, Maggie Haitian; Sun, Rui; Guo, Junfeng; Weng, Haoyi; Lee, Jack; Hu, Inchi; Sham, Pak Chung; Zee, Benny Chung-Ying

    2016-07-01

    Epistasis plays an essential role in the development of complex diseases. Interaction methods face common challenge of seeking a balance between persistent power, model complexity, computation efficiency, and validity of identified bio-markers. We introduce a novel W-test to identify pairwise epistasis effect, which measures the distributional difference between cases and controls through a combined log odds ratio. The test is model-free, fast, and inherits a Chi-squared distribution with data adaptive degrees of freedom. No permutation is needed to obtain the P-values. Simulation studies demonstrated that the W-test is more powerful in low frequency variants environment than alternative methods, which are the Chi-squared test, logistic regression and multifactor-dimensionality reduction (MDR). In two independent real bipolar disorder genome-wide associations (GWAS) datasets, the W-test identified significant interactions pairs that can be replicated, including SLIT3-CENPN, SLIT3-TMEM132D, CNTNAP2-NDST4 and CNTCAP2-RTN4R The genes in the pairs play central roles in neurotransmission and synapse formation. A majority of the identified loci are undiscoverable by main effect and are low frequency variants. The proposed method offers a powerful alternative tool for mapping the genetic puzzle underlying complex disorders. PMID:27112568

  16. Environmental Interactions and Epistasis Are Revealed in the Proteomic Responses to Complex Stimuli

    PubMed Central

    Samir, Parimal; Rahul; Slaughter, James C.; Link, Andrew J.

    2015-01-01

    Ultimately, the genotype of a cell and its interaction with the environment determine the cell’s biochemical state. While the cell’s response to a single stimulus has been studied extensively, a conceptual framework to model the effect of multiple environmental stimuli applied concurrently is not as well developed. In this study, we developed the concepts of environmental interactions and epistasis to explain the responses of the S. cerevisiae proteome to simultaneous environmental stimuli. We hypothesize that, as an abstraction, environmental stimuli can be treated as analogous to genetic elements. This would allow modeling of the effects of multiple stimuli using the concepts and tools developed for studying gene interactions. Mirroring gene interactions, our results show that environmental interactions play a critical role in determining the state of the proteome. We show that individual and complex environmental stimuli behave similarly to genetic elements in regulating the cellular responses to stimuli, including the phenomena of dominance and suppression. Interestingly, we observed that the effect of a stimulus on a protein is dominant over other stimuli if the response to the stimulus involves the protein. Using publicly available transcriptomic data, we find that environmental interactions and epistasis regulate transcriptomic responses as well. PMID:26247773

  17. A fast and powerful W-test for pairwise epistasis testing

    PubMed Central

    Wang, Maggie Haitian; Sun, Rui; Guo, Junfeng; Weng, Haoyi; Lee, Jack; Hu, Inchi; Sham, Pak Chung; Zee, Benny Chung-Ying

    2016-01-01

    Epistasis plays an essential role in the development of complex diseases. Interaction methods face common challenge of seeking a balance between persistent power, model complexity, computation efficiency, and validity of identified bio-markers. We introduce a novel W-test to identify pairwise epistasis effect, which measures the distributional difference between cases and controls through a combined log odds ratio. The test is model-free, fast, and inherits a Chi-squared distribution with data adaptive degrees of freedom. No permutation is needed to obtain the P-values. Simulation studies demonstrated that the W-test is more powerful in low frequency variants environment than alternative methods, which are the Chi-squared test, logistic regression and multifactor-dimensionality reduction (MDR). In two independent real bipolar disorder genome-wide associations (GWAS) datasets, the W-test identified significant interactions pairs that can be replicated, including SLIT3-CENPN, SLIT3-TMEM132D, CNTNAP2-NDST4 and CNTCAP2-RTN4R. The genes in the pairs play central roles in neurotransmission and synapse formation. A majority of the identified loci are undiscoverable by main effect and are low frequency variants. The proposed method offers a powerful alternative tool for mapping the genetic puzzle underlying complex disorders. PMID:27112568

  18. Survival of the Curviest: Noise-Driven Selection for Synergistic Epistasis.

    PubMed

    Wilkins, Jon F; McHale, Peter T; Gervin, Joshua; Lander, Arthur D

    2016-04-01

    A major goal of human genetics is to elucidate the genetic architecture of human disease, with the goal of fueling improvements in diagnosis and the understanding of disease pathogenesis. The degree to which epistasis, or non-additive effects of risk alleles at different loci, accounts for common disease traits is hotly debated, in part because the conditions under which epistasis evolves are not well understood. Using both theory and evolutionary simulation, we show that the occurrence of common diseases (i.e. unfit phenotypes with frequencies on the order of 1%) can, under the right circumstances, be expected to be driven primarily by synergistic epistatic interactions. Conditions that are necessary, collectively, for this outcome include a strongly non-linear phenotypic landscape, strong (but not too strong) selection against the disease phenotype, and "noise" in the genotype-phenotype map that is both environmental (extrinsic, time-correlated) and developmental (intrinsic, uncorrelated) and, in both cases, neither too little nor too great. These results suggest ways in which geneticists might identify, a priori, those disease traits for which an "epistatic explanation" should be sought, and in the process better focus ongoing searches for risk alleles. PMID:27123867

  19. Cuckoo search epistasis: a new method for exploring significant genetic interactions.

    PubMed

    Aflakparast, M; Salimi, H; Gerami, A; Dubé, M-P; Visweswaran, S; Masoudi-Nejad, A

    2014-06-01

    The advent of high-throughput sequencing technology has resulted in the ability to measure millions of single-nucleotide polymorphisms (SNPs) from thousands of individuals. Although these high-dimensional data have paved the way for better understanding of the genetic architecture of common diseases, they have also given rise to challenges in developing computational methods for learning epistatic relationships among genetic markers. We propose a new method, named cuckoo search epistasis (CSE) for identifying significant epistatic interactions in population-based association studies with a case-control design. This method combines a computationally efficient Bayesian scoring function with an evolutionary-based heuristic search algorithm, and can be efficiently applied to high-dimensional genome-wide SNP data. The experimental results from synthetic data sets show that CSE outperforms existing methods including multifactorial dimensionality reduction and Bayesian epistasis association mapping. In addition, on a real genome-wide data set related to Alzheimer's disease, CSE identified SNPs that are consistent with previously reported results, and show the utility of CSE for application to genome-wide data. PMID:24549111

  20. Epistasis and the Structure of Fitness Landscapes: Are Experimental Fitness Landscapes Compatible with Fisher's Geometric Model?

    PubMed

    Blanquart, François; Bataillon, Thomas

    2016-06-01

    The fitness landscape defines the relationship between genotypes and fitness in a given environment and underlies fundamental quantities such as the distribution of selection coefficient and the magnitude and type of epistasis. A better understanding of variation in landscape structure across species and environments is thus necessary to understand and predict how populations will adapt. An increasing number of experiments investigate the properties of fitness landscapes by identifying mutations, constructing genotypes with combinations of these mutations, and measuring the fitness of these genotypes. Yet these empirical landscapes represent a very small sample of the vast space of all possible genotypes, and this sample is often biased by the protocol used to identify mutations. Here we develop a rigorous statistical framework based on Approximate Bayesian Computation to address these concerns and use this flexible framework to fit a broad class of phenotypic fitness models (including Fisher's model) to 26 empirical landscapes representing nine diverse biological systems. Despite uncertainty owing to the small size of most published empirical landscapes, the inferred landscapes have similar structure in similar biological systems. Surprisingly, goodness-of-fit tests reveal that this class of phenotypic models, which has been successful so far in interpreting experimental data, is a plausible in only three of nine biological systems. More precisely, although Fisher's model was able to explain several statistical properties of the landscapes-including the mean and SD of selection and epistasis coefficients-it was often unable to explain the full structure of fitness landscapes. PMID:27052568

  1. Survival of the Curviest: Noise-Driven Selection for Synergistic Epistasis

    PubMed Central

    Gervin, Joshua; Lander, Arthur D.

    2016-01-01

    A major goal of human genetics is to elucidate the genetic architecture of human disease, with the goal of fueling improvements in diagnosis and the understanding of disease pathogenesis. The degree to which epistasis, or non-additive effects of risk alleles at different loci, accounts for common disease traits is hotly debated, in part because the conditions under which epistasis evolves are not well understood. Using both theory and evolutionary simulation, we show that the occurrence of common diseases (i.e. unfit phenotypes with frequencies on the order of 1%) can, under the right circumstances, be expected to be driven primarily by synergistic epistatic interactions. Conditions that are necessary, collectively, for this outcome include a strongly non-linear phenotypic landscape, strong (but not too strong) selection against the disease phenotype, and “noise” in the genotype-phenotype map that is both environmental (extrinsic, time-correlated) and developmental (intrinsic, uncorrelated) and, in both cases, neither too little nor too great. These results suggest ways in which geneticists might identify, a priori, those disease traits for which an “epistatic explanation” should be sought, and in the process better focus ongoing searches for risk alleles. PMID:27123867

  2. Physical analysis of the radiation shielding for the medical accelerators

    NASA Astrophysics Data System (ADS)

    Li, Q. F.; Xing, Q. Z.; Kong, C. C.

    2009-02-01

    Radiation safety standards today require comprehensive shielding protection schemes for all particle accelerators. The original shielding system of BJ-20 (BeiJing-20 MeV), the high-energy medical electron linac, was designed only for the 18 MeV level. And the dose caused by the lost electrons in the 270° bending magnet system was neglected. In this paper, the leakage dose of BJ-20 is carefully analyzed. The radiation leakage dose distribution of the photons coming from the accelerator head is obtained for energy levels of 6, 12, 14, and 18 MeV. The dose of the photoneutrons is especially analyzed for the 18 MeV level. The result gives that even neglecting the dose from the 270° bending magnet system, the shielding system is still not enough for the energy levels lower than 18 MeV. The radiation leakage produced by electrons that are lost in the 270° bending magnet system has been particularly studied. Using beam transport theory and Monte Carlo sampling methods, which have been combined in calculations, we have obtained the distribution of the energy, position, and direction of the lost electrons. These data were then further processed by the Monte Carlo N-particle (MCNP) code as input data. The results show that when the electron loss rate in the 270° bending magnet system is 13.5%, the radiation leakage dose of the photons generated by the lost electrons is 0.1% higher than that at the isocenter, and the corresponding relative leakage dose of the photoneutrons reaches 0.045% around an angle of 170° at 18 MeV level. Both of these parameters exceed radioprotection safety standards for medical accelerators. The original shielding design is therefore not suitable and is also incomplete since the radiation produced by the electrons being lost in the 270° bending magnet system was neglected and the leakage dose for the low-energy levels was not considered in the original design. Our calculations provide a very useful tool for further optimization and design

  3. Solar wind conditions leading to efficient radiation belt electron acceleration: A superposed epoch analysis

    DOE PAGESBeta

    Li, W.; Thorne, R. M.; Bortnik, J.; Baker, D. N.; Reeves, G. D.; Kanekal, S. G.; Spence, H. E.; Green, J. C.

    2015-09-07

    In this study by determining preferential solar wind conditions leading to efficient radiation belt electron acceleration is crucial for predicting radiation belt electron dynamics. Using Van Allen Probes electron observations (>1 MeV) from 2012 to 2015, we identify a number of efficient and inefficient acceleration events separately to perform a superposed epoch analysis of the corresponding solar wind parameters and geomagnetic indices. By directly comparing efficient and inefficient acceleration events, we clearly show that prolonged southward Bz, high solar wind speed, and low dynamic pressure are critical for electron acceleration to >1 MeV energies in the heart of the outermore » radiation belt. We also evaluate chorus wave evolution using the superposed epoch analysis for the identified efficient and inefficient acceleration events and find that chorus wave intensity is much stronger and lasts longer during efficient electron acceleration events, supporting the scenario that chorus waves play a key role in MeV electron acceleration.« less

  4. Analysis of ICRF-Accelerated Ions in ASDEX Upgrade

    SciTech Connect

    Mantsinen, M. J.; Eriksson, L.-G.; Noterdaeme, J.-M.

    2007-09-28

    MHD-induced losses of fast ions with energy in the MeV range have been observed during high-power ICRF heating of hydrogen minority ions in the ASDEX Upgrade tokamak (R{sub 0}{approx_equal}1.65 m, a{approx_equal}0.5 m). ICRF heating and ICRF-driven fast ions in discharges exhibiting fast ion losses due to toroidal Alfven eigenmodes and a new core-localised MHD instability are analysed. It is found that the lost ions are ICRF-accelerated trapped protons with energy in the range of 0.3-1.6 MeV, orbit widths of 20-35 cm, and turning points at r/a>0.5 and at major radii close to the cyclotron resonance {omega} = {omega}{sub cH}(R). The presence of such protons is consistent with ICRF modelling.

  5. RAPID COMMUNICATION: Analysis of photoneutron spectra produced in medical accelerators

    NASA Astrophysics Data System (ADS)

    Ongaro, Carla; Zanini, Alba; Nastasi, U.; Ródenas, José; Ottaviano, Giuseppe; Manfredotti, Claudio

    2000-12-01

    A complete method is presented for the evaluation of photoneutron spectra produced in linear accelerators for cancer radiotherapy. It consists of a computer simulation code based on the MCNP4B Monte Carlo code, in which the new routine GAMMAN was implemented, allowing the accurate study of photoneutron production in high Z elements. In addition an experimental method based on a passive bubble spectrometer allows direct measurements of the photoneutron spectrum at the patient plane, also under the photon beam. The results are presented both for a 15 MeV linac with a traditional collimator system and for an 18 MeV linac equipped with a multileaf collimator, used in conformational radiotherapy.

  6. Omega3P: A Parallel Finite-Element Eigenmode Analysis Code for Accelerator Cavities

    SciTech Connect

    Lee, Lie-Quan; Li, Zenghai; Ng, Cho; Ko, Kwok; /SLAC

    2009-03-04

    Omega3P is a parallel eigenmode calculation code for accelerator cavities in frequency domain analysis using finite-element methods. In this report, we will present detailed finite-element formulations and resulting eigenvalue problems for lossless cavities, cavities with lossy materials, cavities with imperfectly conducting surfaces, and cavities with waveguide coupling. We will discuss the parallel algorithms for solving those eigenvalue problems and demonstrate modeling of accelerator cavities through different examples.

  7. Analysis of human accelerated DNA regions using archaic hominin genomes.

    PubMed

    Burbano, Hernán A; Green, Richard E; Maricic, Tomislav; Lalueza-Fox, Carles; de la Rasilla, Marco; Rosas, Antonio; Kelso, Janet; Pollard, Katherine S; Lachmann, Michael; Pääbo, Svante

    2012-01-01

    Several previous comparisons of the human genome with other primate and vertebrate genomes identified genomic regions that are highly conserved in vertebrate evolution but fast-evolving on the human lineage. These human accelerated regions (HARs) may be regions of past adaptive evolution in humans. Alternatively, they may be the result of non-adaptive processes, such as biased gene conversion. We captured and sequenced DNA from a collection of previously published HARs using DNA from an Iberian Neandertal. Combining these new data with shotgun sequence from the Neandertal and Denisova draft genomes, we determine at least one archaic hominin allele for 84% of all positions within HARs. We find that 8% of HAR substitutions are not observed in the archaic hominins and are thus recent in the sense that the derived allele had not come to fixation in the common ancestor of modern humans and archaic hominins. Further, we find that recent substitutions in HARs tend to have come to fixation faster than substitutions elsewhere in the genome and that substitutions in HARs tend to cluster in time, consistent with an episodic rather than a clock-like process underlying HAR evolution. Our catalog of sequence changes in HARs will help prioritize them for functional studies of genomic elements potentially responsible for modern human adaptations. PMID:22412940

  8. Comprehensive identification and analysis of human accelerated regulatory DNA

    PubMed Central

    Gittelman, Rachel M.; Hun, Enna; Ay, Ferhat; Madeoy, Jennifer; Pennacchio, Len; Noble, William S.; Hawkins, R. David; Akey, Joshua M.

    2015-01-01

    It has long been hypothesized that changes in gene regulation have played an important role in human evolution, but regulatory DNA has been much more difficult to study compared with protein-coding regions. Recent large-scale studies have created genome-scale catalogs of DNase I hypersensitive sites (DHSs), which demark potentially functional regulatory DNA. To better define regulatory DNA that has been subject to human-specific adaptive evolution, we performed comprehensive evolutionary and population genetics analyses on over 18 million DHSs discovered in 130 cell types. We identified 524 DHSs that are conserved in nonhuman primates but accelerated in the human lineage (haDHS), and estimate that 70% of substitutions in haDHSs are attributable to positive selection. Through extensive computational and experimental analyses, we demonstrate that haDHSs are often active in brain or neuronal cell types; play an important role in regulating the expression of developmentally important genes, including many transcription factors such as SOX6, POU3F2, and HOX genes; and identify striking examples of adaptive regulatory evolution that may have contributed to human-specific phenotypes. More generally, our results reveal new insights into conserved and adaptive regulatory DNA in humans and refine the set of genomic substrates that distinguish humans from their closest living primate relatives. PMID:26104583

  9. Comprehensive identification and analysis of human accelerated regulatory DNA.

    PubMed

    Gittelman, Rachel M; Hun, Enna; Ay, Ferhat; Madeoy, Jennifer; Pennacchio, Len; Noble, William S; Hawkins, R David; Akey, Joshua M

    2015-09-01

    It has long been hypothesized that changes in gene regulation have played an important role in human evolution, but regulatory DNA has been much more difficult to study compared with protein-coding regions. Recent large-scale studies have created genome-scale catalogs of DNase I hypersensitive sites (DHSs), which demark potentially functional regulatory DNA. To better define regulatory DNA that has been subject to human-specific adaptive evolution, we performed comprehensive evolutionary and population genetics analyses on over 18 million DHSs discovered in 130 cell types. We identified 524 DHSs that are conserved in nonhuman primates but accelerated in the human lineage (haDHS), and estimate that 70% of substitutions in haDHSs are attributable to positive selection. Through extensive computational and experimental analyses, we demonstrate that haDHSs are often active in brain or neuronal cell types; play an important role in regulating the expression of developmentally important genes, including many transcription factors such as SOX6, POU3F2, and HOX genes; and identify striking examples of adaptive regulatory evolution that may have contributed to human-specific phenotypes. More generally, our results reveal new insights into conserved and adaptive regulatory DNA in humans and refine the set of genomic substrates that distinguish humans from their closest living primate relatives. PMID:26104583

  10. Analysis of Human Accelerated DNA Regions Using Archaic Hominin Genomes

    PubMed Central

    Burbano, Hernán A.; Green, Richard E.; Maricic, Tomislav; Lalueza-Fox, Carles; de la Rasilla, Marco; Rosas, Antonio; Kelso, Janet; Pollard, Katherine S.; Lachmann, Michael; Pääbo, Svante

    2012-01-01

    Several previous comparisons of the human genome with other primate and vertebrate genomes identified genomic regions that are highly conserved in vertebrate evolution but fast-evolving on the human lineage. These human accelerated regions (HARs) may be regions of past adaptive evolution in humans. Alternatively, they may be the result of non-adaptive processes, such as biased gene conversion. We captured and sequenced DNA from a collection of previously published HARs using DNA from an Iberian Neandertal. Combining these new data with shotgun sequence from the Neandertal and Denisova draft genomes, we determine at least one archaic hominin allele for 84% of all positions within HARs. We find that 8% of HAR substitutions are not observed in the archaic hominins and are thus recent in the sense that the derived allele had not come to fixation in the common ancestor of modern humans and archaic hominins. Further, we find that recent substitutions in HARs tend to have come to fixation faster than substitutions elsewhere in the genome and that substitutions in HARs tend to cluster in time, consistent with an episodic rather than a clock-like process underlying HAR evolution. Our catalog of sequence changes in HARs will help prioritize them for functional studies of genomic elements potentially responsible for modern human adaptations. PMID:22412940

  11. Superconducting Accelerating Cavity Pressure Sensitivity Analysis and Stiffening

    SciTech Connect

    Rodnizki, J; Ben Aliz, Y; Grin, A; Horvitz, Z; Perry, A; Weissman, L; Davis, G Kirk; Delayen, Jean R.

    2014-12-01

    The Soreq Applied Research Accelerator Facility (SARAF) design is based on a 40 MeV 5 mA light ions superconducting RF linac. Phase-I of SARAF delivers up to 2 mA CW proton beams in an energy range of 1.5 - 4.0 MeV. The maximum beam power that we have reached is 5.7 kW. Today, the main limiting factor to reach higher ion energy and beam power is related to the HWR sensitivity to the liquid helium coolant pressure fluctuations. The HWR sensitivity to helium pressure is about 60 Hz/mbar. The cavities had been designed, a decade ago, to be soft in order to enable tuning of their novel shape. However, the cavities turned out to be too soft. In this work we found that increasing the rigidity of the cavities in the vicinity of the external drift tubes may reduce the cavity sensitivity by a factor of three. A preliminary design to increase the cavity rigidity is presented.

  12. Hamiltonian analysis for linearly acceleration-dependent Lagrangians

    NASA Astrophysics Data System (ADS)

    Cruz, Miguel; Gómez-Cortés, Rosario; Molgado, Alberto; Rojas, Efraín

    2016-06-01

    We study the constrained Ostrogradski-Hamilton framework for the equations of motion provided by mechanical systems described by second-order derivative actions with a linear dependence in the accelerations. We stress out the peculiar features provided by the surface terms arising for this type of theories and we discuss some important properties for this kind of actions in order to pave the way for the construction of a well defined quantum counterpart by means of canonical methods. In particular, we analyse in detail the constraint structure for these theories and its relation to the inherent conserved quantities where the associated energies together with a Noether charge may be identified. The constraint structure is fully analyzed without the introduction of auxiliary variables, as proposed in recent works involving higher order Lagrangians. Finally, we also provide some examples where our approach is explicitly applied and emphasize the way in which our original arrangement results in propitious for the Hamiltonian formulation of covariant field theories.

  13. [Preparation of Rubber Accelerator Zinc Diethyldithiocarbamate and Its Spectral Analysis].

    PubMed

    Zhang, Zhi-liang; Jia, Tai-xuan; Jiang, Yue-hua; Peng, Hong-yan; Xu, Guang-pu; Li, Hong-liang

    2015-08-01

    In the study, rubber accelerator Zinc diethyldithiocarbamate (EZ) was synthesized firstly. Complex EZ of single crystal was cultivated by solvent evaporation method. EZ was detected and characterized by XRD single crystal diffraction, FTIR and TG-DSC. The micro-structure and intrinsic regularity were revealed. Its highly efficient performance of rubber vulcanization promotion was decided due to its orientation structure? and high order. The result of TG-DSC showed that complex EZ was possessed with a little CS2. The chemical bond types in EZ were revealed by FTIR, the same as single crystal? diffraction testing by different way. The decomposition temperature of EZ was very high. It could provided reference with research on rubber vulcanizing properties by EZ on rubber vulcanizing machine. This study can help the enterprises to designate the working standard tracing detection of EZ industrialized production. Performance index of EZ was judged. The project of EZ industry standard can be declared by the enterprises, written a draft standard on the basis experimental data. PMID:26672276

  14. Data acquisition, control, and analysis for the Argonne Advanced Accelerator Test Facility (AATF)

    SciTech Connect

    Schoessow, P.

    1989-01-01

    The AATF has been used to study wakefield acceleration and focusing in plasmas and rf structures. A PC-based system is described which incorporates the functions of beamline control and acquisition, storage, and preliminary analysis of video images from luminescent screen beam diagnostics. General features of the offline analysis of wakefield data are also discussed. 4 refs., 3 figs.

  15. Analysis of Voltage Signals from Superconducting Accelerator Magnets

    SciTech Connect

    Lizarazo, J.; Caspi, S.; Ferracin, P.; Joseph, J.; Lietzke, A. F.; Sabbi, G. L.; Wang, X.

    2009-10-30

    We present two techniques used in the analysis of voltage tap data collected during recent tests of superconducting magnets developed by the Superconducting Magnet Program at Lawrence Berkeley National Laboratory. The first technique was used on a quadrupole to provide information about quench origins that could not be obtained using the time-of-flight method. The second technique illustrates the use of data from transient flux imbalances occurring during magnet ramping to diagnose changes in the current-temperature margin of a superconducting cable. In both cases, the results of this analysis contributed to make improvements on subsequent magnets.

  16. Metabolic epistasis among apoptosis-inducing factor and the mitochondrial import factor CHCHD4

    PubMed Central

    Modjtahedi, Nazanine; Hangen, Emilie; Gonin, Patrick; Kroemer, Guido

    2015-01-01

    Abstract Hypomorphic mutation of apoptosis-inducing factor (AIF) in the whole body or organ-specific knockout of AIF compromises the activity of respiratory chain complexes I and IV, as it confers resistance to obesity and diabetes induced by high-fat diet. The mitochondrial defect induced by AIF deficiency can be explained by reduced AIF-dependent mitochondrial import of CHCHD4, which in turn is required for optimal import and assembly of respiratory chain complexes. Here we show that, as compared to wild type control littermates, mice with a heterozygous knockout of CHCHD4 exhibit reduced weight gain when fed with a Western style high-fat diet. This finding suggests widespread metabolic epistasis among AIF and CHCHD4. Targeting either of these proteins or their functional interaction might constitute a novel strategy to combat obesity. PMID:26178476

  17. Genecentric: a package to uncover graph-theoretic structure in high-throughput epistasis data

    PubMed Central

    2013-01-01

    Background New technology has resulted in high-throughput screens for pairwise genetic interactions in yeast and other model organisms. For each pair in a collection of non-essential genes, an epistasis score is obtained, representing how much sicker (or healthier) the double-knockout organism will be compared to what would be expected from the sickness of the component single knockouts. Recent algorithmic work has identified graph-theoretic patterns in this data that can indicate functional modules, and even sets of genes that may occur in compensatory pathways, such as a BPM-type schema first introduced by Kelley and Ideker. However, to date, any algorithms for finding such patterns in the data were implemented internally, with no software being made publically available. Results Genecentric is a new package that implements a parallelized version of the Leiserson et al. algorithm (J Comput Biol 18:1399-1409, 2011) for generating generalized BPMs from high-throughput genetic interaction data. Given a matrix of weighted epistasis values for a set of double knock-outs, Genecentric returns a list of generalized BPMs that may represent compensatory pathways. Genecentric also has an extension, GenecentricGO, to query FuncAssociate (Bioinformatics 25:3043-3044, 2009) to retrieve GO enrichment statistics on generated BPMs. Python is the only dependency, and our web site provides working examples and documentation. Conclusion We find that Genecentric can be used to find coherent functional and perhaps compensatory gene sets from high throughput genetic interaction data. Genecentric is made freely available for download under the GPLv2 from http://bcb.cs.tufts.edu/genecentric. PMID:23331614

  18. Incorporating epistasis interaction of genetic susceptibility single nucleotide polymorphisms in a lung cancer risk prediction model.

    PubMed

    Marcus, Michael W; Raji, Olaide Y; Duffy, Stephen W; Young, Robert P; Hopkins, Raewyn J; Field, John K

    2016-07-01

    Incorporation of genetic variants such as single nucleotide polymorphisms (SNPs) into risk prediction models may account for a substantial fraction of attributable disease risk. Genetic data, from 2385 subjects recruited into the Liverpool Lung Project (LLP) between 2000 and 2008, consisting of 20 SNPs independently validated in a candidate-gene discovery study was used. Multifactor dimensionality reduction (MDR) and random forest (RF) were used to explore evidence of epistasis among 20 replicated SNPs. Multivariable logistic regression was used to identify similar risk predictors for lung cancer in the LLP risk model for the epidemiological model and extended model with SNPs. Both models were internally validated using the bootstrap method and model performance was assessed using area under the curve (AUC) and net reclassification improvement (NRI). Using MDR and RF, the overall best classifier of lung cancer status were SNPs rs1799732 (DRD2), rs5744256 (IL-18), rs2306022 (ITGA11) with training accuracy of 0.6592 and a testing accuracy of 0.6572 and a cross-validation consistency of 10/10 with permutation testing P<0.0001. The apparent AUC of the epidemiological model was 0.75 (95% CI 0.73-0.77). When epistatic data were incorporated in the extended model, the AUC increased to 0.81 (95% CI 0.79-0.83) which corresponds to 8% increase in AUC (DeLong's test P=2.2e-16); 17.5% by NRI. After correction for optimism, the AUC was 0.73 for the epidemiological model and 0.79 for the extended model. Our results showed modest improvement in lung cancer risk prediction when the SNP epistasis factor was added. PMID:27121382

  19. Incorporating epistasis interaction of genetic susceptibility single nucleotide polymorphisms in a lung cancer risk prediction model

    PubMed Central

    MARCUS, MICHAEL W.; RAJI, OLAIDE Y.; DUFFY, STEPHEN W.; YOUNG, ROBERT P.; HOPKINS, RAEWYN J.; FIELD, JOHN K.

    2016-01-01

    Incorporation of genetic variants such as single nucleotide polymorphisms (SNPs) into risk prediction models may account for a substantial fraction of attributable disease risk. Genetic data, from 2385 subjects recruited into the Liverpool Lung Project (LLP) between 2000 and 2008, consisting of 20 SNPs independently validated in a candidate-gene discovery study was used. Multifactor dimensionality reduction (MDR) and random forest (RF) were used to explore evidence of epistasis among 20 replicated SNPs. Multivariable logistic regression was used to identify similar risk predictors for lung cancer in the LLP risk model for the epidemiological model and extended model with SNPs. Both models were internally validated using the bootstrap method and model performance was assessed using area under the curve (AUC) and net reclassification improvement (NRI). Using MDR and RF, the overall best classifier of lung cancer status were SNPs rs1799732 (DRD2), rs5744256 (IL-18), rs2306022 (ITGA11) with training accuracy of 0.6592 and a testing accuracy of 0.6572 and a cross-validation consistency of 10/10 with permutation testing P<0.0001. The apparent AUC of the epidemiological model was 0.75 (95% CI 0.73–0.77). When epistatic data were incorporated in the extended model, the AUC increased to 0.81 (95% CI 0.79–0.83) which corresponds to 8% increase in AUC (DeLong's test P=2.2e-16); 17.5% by NRI. After correction for optimism, the AUC was 0.73 for the epidemiological model and 0.79 for the extended model. Our results showed modest improvement in lung cancer risk prediction when the SNP epistasis factor was added. PMID:27121382

  20. Enabling More than Moore: Accelerated Reliability Testing and Risk Analysis for Advanced Electronics Packaging

    NASA Technical Reports Server (NTRS)

    Ghaffarian, Reza; Evans, John W.

    2014-01-01

    For five decades, the semiconductor industry has distinguished itself by the rapid pace of improvement in miniaturization of electronics products-Moore's Law. Now, scaling hits a brick wall, a paradigm shift. The industry roadmaps recognized the scaling limitation and project that packaging technologies will meet further miniaturization needs or ak.a "More than Moore". This paper presents packaging technology trends and accelerated reliability testing methods currently being practiced. Then, it presents industry status on key advanced electronic packages, factors affecting accelerated solder joint reliability of area array packages, and IPC/JEDEC/Mil specifications for characterizations of assemblies under accelerated thermal and mechanical loading. Finally, it presents an examples demonstrating how Accelerated Testing and Analysis have been effectively employed in the development of complex spacecraft thereby reducing risk. Quantitative assessments necessarily involve the mathematics of probability and statistics. In addition, accelerated tests need to be designed which consider the desired risk posture and schedule for particular project. Such assessments relieve risks without imposing additional costs. and constraints that are not value added for a particular mission. Furthermore, in the course of development of complex systems, variances and defects will inevitably present themselves and require a decision concerning their disposition, necessitating quantitative assessments. In summary, this paper presents a comprehensive view point, from technology to systems, including the benefits and impact of accelerated testing in offsetting risk.

  1. Detecting chaos in particle accelerators through the frequency map analysis method

    SciTech Connect

    Papaphilippou, Yannis

    2014-06-01

    The motion of beams in particle accelerators is dominated by a plethora of non-linear effects, which can enhance chaotic motion and limit their performance. The application of advanced non-linear dynamics methods for detecting and correcting these effects and thereby increasing the region of beam stability plays an essential role during the accelerator design phase but also their operation. After describing the nature of non-linear effects and their impact on performance parameters of different particle accelerator categories, the theory of non-linear particle motion is outlined. The recent developments on the methods employed for the analysis of chaotic beam motion are detailed. In particular, the ability of the frequency map analysis method to detect chaotic motion and guide the correction of non-linear effects is demonstrated in particle tracking simulations but also experimental data.

  2. Automated detection and analysis of particle beams in laser-plasma accelerator simulations

    SciTech Connect

    Ushizima, Daniela Mayumi; Geddes, C.G.; Cormier-Michel, E.; Bethel, E. Wes; Jacobsen, J.; Prabhat, ,; R.ubel, O.; Weber, G,; Hamann, B.

    2010-05-21

    Numerical simulations of laser-plasma wakefield (particle) accelerators model the acceleration of electrons trapped in plasma oscillations (wakes) left behind when an intense laser pulse propagates through the plasma. The goal of these simulations is to better understand the process involved in plasma wake generation and how electrons are trapped and accelerated by the wake. Understanding of such accelerators, and their development, offer high accelerating gradients, potentially reducing size and cost of new accelerators. One operating regime of interest is where a trapped subset of electrons loads the wake and forms an isolated group of accelerated particles with low spread in momentum and position, desirable characteristics for many applications. The electrons trapped in the wake may be accelerated to high energies, the plasma gradient in the wake reaching up to a gigaelectronvolt per centimeter. High-energy electron accelerators power intense X-ray radiation to terahertz sources, and are used in many applications including medical radiotherapy and imaging. To extract information from the simulation about the quality of the beam, a typical approach is to examine plots of the entire dataset, visually determining the adequate parameters necessary to select a subset of particles, which is then further analyzed. This procedure requires laborious examination of massive data sets over many time steps using several plots, a routine that is unfeasible for large data collections. Demand for automated analysis is growing along with the volume and size of simulations. Current 2D LWFA simulation datasets are typically between 1GB and 100GB in size, but simulations in 3D are of the order of TBs. The increase in the number of datasets and dataset sizes leads to a need for automatic routines to recognize particle patterns as particle bunches (beam of electrons) for subsequent analysis. Because of the growth in dataset size, the application of machine learning techniques for

  3. Accelerating Climate Data Analysis and Visualization with Parallel Scripting

    NASA Astrophysics Data System (ADS)

    Mickelson, S. A.; Jacob, R. L.; Wilde, M.; Wozniak, J.; Dennis, J.

    2011-12-01

    Climate models are continuing to increase both in their resolution and the number of variables used, resulting in multi-terabyte model outputs. This large volume of data overwhelms the series of processing steps used to derive climate averages and produce visualizations. Since many of the tasks in the post- processing sequence are independent, we have applied task-parallel scripting to speed up the post-processing. We have re-written portions of the complex shell script that processes output from the Community Atmosphere Model in Swift, a high-level implicitly-parallel scripting language that uses data dependencies to automatically parallelize a workflow. This has resulted in valuable speedups in model analysis for this heavily-used procedure. We describe the structure, usage, performance, and our experiences with the resulting script.

  4. Beam Based HOM Analysis of Accelerating Structures at the TESLA Test Facility Linac

    SciTech Connect

    Wendt, M.; Schreiber, S.; Castro, P.; Gossel, A.; Huning, M.; Devanz, G.; Jablonka, M.; Magne, C.; Napoly, O.; Baboi, N.; /SLAC

    2005-08-09

    The beam emittance in future linear accelerators for high energy physics and SASE-FEL applications depends highly on the field performance in the accelerating structures, i.e. the damping of higher order modes (HOM). Besides theoretical and laboratory analysis, a beam based analysis technique was established [1] at the TESLA Test Facility (TTF) linac. It uses a charge modulated beam of variable modulation frequency to excite dipole modes. This causes a modulation of the transverse beam displacement, which is observed at a downstream BPM and associated with a direct analysis of the modes at the HOM-couplers. A brief introduction of eigenmodes of a resonator and the concept of the wake potential is given. Emphasis is put on beam instrumentation and signal analysis aspects, required for this beam based HOM measurement technique.

  5. Design and Analysis of a Micro-Optical Position Readout for Acceleration Sensing

    SciTech Connect

    Dickey, Fred M.; Holswade, Scott C.; Shagam, Richard N.

    1999-07-08

    Sandia National Laboratories is developing a MEMS-based trajectory safety subsystem, which allows enablement of critical functions only after a particular acceleration environment has been achieved. The device, known as an Environmental Sensing Device (ESD), consists of a suspended moving shuttle that translates a given distance when exposed to an appropriate acceleration environment. The shuttle contains an embedded code, consisting of grating structures, that is illuminated and optically read using a semiconductor laser and detector integrated together in a GaAs-based Photonic Integrated Circuit (PIC) flip-chip bonded to the assembly. This paper will describe the optical design and performance analysis of the embedded code features in the shuttle.

  6. An improved method for statistical analysis of raw accelerator mass spectrometry data

    SciTech Connect

    Gutjahr, A.; Phillips, F.; Kubik, P.W.; Elmore, D.

    1987-01-01

    Hierarchical statistical analysis is an appropriate method for statistical treatment of raw accelerator mass spectrometry (AMS) data. Using Monte Carlo simulations we show that this method yields more accurate estimates of isotope ratios and analytical uncertainty than the generally used propagation of errors approach. The hierarchical analysis is also useful in design of experiments because it can be used to identify sources of variability. 8 refs., 2 figs.

  7. Interjoint dynamic interaction during constrained human quiet standing examined by induced acceleration analysis.

    PubMed

    Sasagawa, Shun; Shinya, Masahiro; Nakazawa, Kimitaka

    2014-01-01

    Recent studies have demonstrated that human quiet standing is a multijoint movement, whereby the central nervous system (CNS) is required to deal with dynamic interactions among the joints to achieve optimal motor performance. The purpose of this study was to investigate how the CNS deals with such interjoint interaction during quiet standing by examining the relationship between the kinetics (torque) and kinematics (angular acceleration) within the multi-degree of freedom system. We modeled quiet standing as a double-link inverted pendulum involving both ankle and hip joints and conducted an "induced acceleration analysis." We found that the net ankle and hip torques induced angular accelerations of comparable magnitudes to the ankle (3.8 ± 1.4°/s(2) and 3.3 ± 1.2°/s(2)) and hip (9.1 ± 3.2°/s(2) and 10.5 ± 3.5°/s(2)) joints, respectively. Angular accelerations induced by the net ankle and hip torques were modulated in a temporally antiphase pattern to one another in each of the two joints. These quantitative and temporal relationships allowed the angular accelerations induced by the two net torques to countercompensate one another, thereby substantially (∼70%) reducing the resultant angular accelerations of the individual joints. These results suggest that, by taking advantage of the interjoint interaction, the CNS prevents the net torques from producing large amplitudes of the resultant angular accelerations when combined with the kinematic effects of all other torques in the chain. PMID:24089399

  8. DEVELOPMENT OF ACCELERATOR DATA REPORTING SYSTEM AND ITS APPLICATION TO TREND ANALYSIS OF BEAM CURRENT DATA

    SciTech Connect

    Padilla, M.J.; Blokland, W.

    2009-01-01

    Detailed ongoing information about the ion beam quality is crucial to the successful operation of the Spallation Neutron Source at Oak Ridge National Laboratory. In order to provide the highest possible neutron production time, ion beam quality is monitored to isolate possible problems or performance-related issues throughout the accelerator and accumulator ring. For example, beam current monitor (BCM) data is used to determine the quality of the beam transport through the accelerator. In this study, a reporting system infrastructure was implemented and used to generate a trend analysis report of the BCM data. The BCM data was analyzed to facilitate the identifi cation of monitor calibration issues, beam trends, beam abnormalities, beam deviations and overall beam quality. A comparison between transformed BCM report data and accelerator log entries shows promising results which represent correlations between the data and changes made within the accelerator. The BCM analysis report is one of many reports within a system that assist in providing overall beam quality information to facilitate successful beam operation. In future reports, additional data manipulation functions and analysis can be implemented and applied. Built-in and user-defi ned analytic functions are available throughout the reporting system and can be reused with new data.

  9. Interface for the rapid analysis of liquid samples by accelerator mass spectrometry

    SciTech Connect

    Turteltaub, Kenneth; Ognibene, Ted; Thomas, Avi; Daley, Paul F; Salazar Quintero, Gary A; Bench, Graham

    2014-02-04

    An interface for the analysis of liquid sample having carbon content by an accelerator mass spectrometer including a wire, defects on the wire, a system for moving the wire, a droplet maker for producing droplets of the liquid sample and placing the droplets of the liquid sample on the wire in the defects, a system that converts the carbon content of the droplets of the liquid sample to carbon dioxide gas in a helium stream, and a gas-accepting ion source connected to the accelerator mass spectrometer that receives the carbon dioxide gas of the sample in a helium stream and introduces the carbon dioxide gas of the sample into the accelerator mass spectrometer.

  10. Sensitivity Analysis of the Off-Normal Conditions of the SPIDER Accelerator

    SciTech Connect

    Veltri, P.; Agostinetti, P.; Antoni, V.; Chitarin, G.; Marconato, N.; Pilan, N.; Sartori, E.; Serianni, G.; Cavenago, M.

    2011-09-26

    In the context of the development of the 1 MV neutral beam injector for the ITER tokamak, the study on beam formation and acceleration has considerable importance. This effort includes the ion source and accelerator SPIDER (Source for Production of Ions of Deuterium Extracted from an Rf plasma) ion source, planned to be built in Padova, and designed to extract and accelerate a 355 A/m{sup 2} current of H{sup -}(or 285 A/m{sup 2} D{sup -}) up to 100 kV. Exhaustive simulations were already carried out during the accelerator optimization leading to the present design. However, as it is expected that the accelerator shall operate also in case of pre-programmed or undesired off-normal conditions, the investigation of a large set of off-normal scenarios is necessary. These analyses will also be useful for the evaluation of the real performances of the machine, and should help in interpreting experimental results, or in identifying dangerous operating conditions.The present contribution offers an overview of the results obtained during the investigation of these off-normal conditions, by means of different modeling tools and codes. The results, showed a good flexibility of the device in different operating conditions. Where the consequences of the abnormalities appeared to be problematic further analysis were addressed.

  11. A novel two-stage approach for epistasis detection in genome-wide case-control studies.

    PubMed

    Liao, Zhongli; Zeng, Qingguang; Liao, Bo; Li, Xiong

    2014-10-01

    A significant challenge in epistasis detection is the huge amount of data, which leads to combinatorial explosion. This study focuses on a two-stage approach for detecting epistasis only among single nucleotide polymorphisms (SNPs) that show some marginal effect. We present this two-stage approach based on the fusion of two criteria (TwoFC) to detect epistatic interactions. We fuse the G (2) test and absolute probability difference function as a scoring function to measure the strength of association between SNPs and disease status. The fused scoring function is an excellent measure of the strength of such an association. The two-stage strategy greatly reduces the computation load on epistasis detection. We use both simulated data sets and a real disease data set to evaluate our method. The results of an experiment on the simulated data sets show that TwoFC exhibits high power and sample efficiency. The results of an experiment on the real disease data set show that our method performs well even with large-scale data sets. PMID:24880910

  12. Epistasis between antibiotic resistance mutations and genetic background shape the fitness effect of resistance across species of Pseudomonas.

    PubMed

    Vogwill, T; Kojadinovic, M; MacLean, R C

    2016-05-11

    Antibiotic resistance often evolves by mutations at conserved sites in essential genes, resulting in parallel molecular evolution between divergent bacterial strains and species. Whether these resistance mutations are having parallel effects on fitness across bacterial taxa, however, is unclear. This is an important point to address, because the fitness effects of resistance mutations play a key role in the spread and maintenance of resistance in pathogen populations. We address this idea by measuring the fitness effect of a collection of rifampicin resistance mutations in the β subunit of RNA polymerase (rpoB) across eight strains that span the diversity of the genus Pseudomonas We find that almost 50% of rpoB mutations have background-dependent fitness costs, demonstrating that epistatic interactions between rpoB and the rest of the genome are common. Moreover, epistasis is typically strong, and it is the dominant genetic determinant of the cost of resistance mutations. To investigate the functional basis of epistasis, and because rpoB plays a central role in transcription, we measured the effects of common rpoB mutations on transcriptional efficiency across three strains of Pseudomonas Transcriptional efficiency correlates strongly to fitness across strains, and epistasis arises because individual rpoB mutations have differential effects on transcriptional efficiency in different genetic backgrounds. PMID:27170722

  13. Epistasis between antibiotic resistance mutations and genetic background shape the fitness effect of resistance across species of Pseudomonas

    PubMed Central

    Kojadinovic, M.; MacLean, R. C.

    2016-01-01

    Antibiotic resistance often evolves by mutations at conserved sites in essential genes, resulting in parallel molecular evolution between divergent bacterial strains and species. Whether these resistance mutations are having parallel effects on fitness across bacterial taxa, however, is unclear. This is an important point to address, because the fitness effects of resistance mutations play a key role in the spread and maintenance of resistance in pathogen populations. We address this idea by measuring the fitness effect of a collection of rifampicin resistance mutations in the β subunit of RNA polymerase (rpoB) across eight strains that span the diversity of the genus Pseudomonas. We find that almost 50% of rpoB mutations have background-dependent fitness costs, demonstrating that epistatic interactions between rpoB and the rest of the genome are common. Moreover, epistasis is typically strong, and it is the dominant genetic determinant of the cost of resistance mutations. To investigate the functional basis of epistasis, and because rpoB plays a central role in transcription, we measured the effects of common rpoB mutations on transcriptional efficiency across three strains of Pseudomonas. Transcriptional efficiency correlates strongly to fitness across strains, and epistasis arises because individual rpoB mutations have differential effects on transcriptional efficiency in different genetic backgrounds. PMID:27170722

  14. Rapid analysis of scattering from periodic dielectric structures using accelerated Cartesian expansions

    SciTech Connect

    Baczewski, Andrew David; Miller, Nicholas C.; Shanker, Balasubramaniam

    2012-03-22

    Here, the analysis of fields in periodic dielectric structures arise in numerous applications of recent interest, ranging from photonic bandgap structures and plasmonically active nanostructures to metamaterials. To achieve an accurate representation of the fields in these structures using numerical methods, dense spatial discretization is required. This, in turn, affects the cost of analysis, particularly for integral-equation-based methods, for which traditional iterative methods require Ο(Ν2) operations, Ν being the number of spatial degrees of freedom. In this paper, we introduce a method for the rapid solution of volumetric electric field integral equations used in the analysis of doubly periodic dielectric structures. The crux of our method is the accelerated Cartesian expansion algorithm, which is used to evaluate the requisite potentials in Ο(Ν) cost. Results are provided that corroborate our claims of acceleration without compromising accuracy, as well as the application of our method to a number of compelling photonics applications.

  15. Thermal performance analysis and measurements of the prototype cryomodules of European XFEL accelerator - part I

    NASA Astrophysics Data System (ADS)

    Wang, X. L.; Barbanotti, S.; Eschke, J.; Jensch, K.; Klos, R.; Maschmann, W.; Petersen, B.; Sawlanski, O.

    2014-11-01

    The European X-Ray Free Electron Laser (XFEL), the research facility currently under construction in the Hamburg area, Germany, is based on a superconducting linear accelerator that brings electrons to almost the speed of light. The linear accelerator consists of 100 accelerating cryomodules (CMs) operating at the temperature of 2 K. The thermal performances of the accelerator CMs are a key element to determine the heat load budget, the required capacity and the cost of the XFEL refrigerating system and to guarantee its efficient operation. The measurement of the thermal performances of the CMs is also an important step in the qualification of the CMs during the series production. This paper describes the thermal performance analysis of the European XFEL prototype cryomodules. The analysis takes into account all the main contributors (multilayer insulation, current leads, power couplers, support posts, and cavities) to the static and dynamic heat loads at various cryogenic temperature levels. Existing empirical databases are reviewed and used to evaluate the heat transfer through the multilayer insulation and numerical simulations are developed to investigate the heat loads generated from the different CM components.

  16. Analysis of the acceleration region in a circulating fluidized bed riser operating above fast fluidization velocities

    SciTech Connect

    Monazam, E.R.; Shadle, L.J.

    2008-11-05

    In commercial circulating fluidized bed (CFB) processes the acceleration zone greatly contributes to solids mixing, gas and solids dispersion, and particle residence times. A new analysis was developed to describe the relative gas-solids concentration in the acceleration region of a transport system with air as the fluidizing agent for Geldart-type B particles. A theoretical expression was derived from a drag relationship and momentum and continuity equations to describe the evolution of the gas-solids profile along the axial direction. The acceleration zone was characterized using nondimensional analysis of the continuum equations (balances of masses and momenta) that described multiphase flows. In addition to acceleration length, the boundary condition for the solids fraction at the bottom of the riser and the fully developed regions were measured using an industrial scale CFB of 0.3 m diameter and 15 m tall. The operating factors affecting the flow development in the acceleration region were determined for three materials of various sizes and densities in core annular and dilute regimes of the riser. Performance data were taken from statistically designed experiments over a wide range of Fr (0.5-39), Re (8-600), Ar (29-3600), load ratio (0.2-28), riser to particle diameter ratio (375-5000), and gas to solids density ratio (138-1381). In this one-dimensional system of equations, velocities and solid fractions were assumed to be constant over any cross section. The model and engineering correlations were compared with literature expressions to assess their validity and range of applicability. These expressions can be used as tools for simulation and design of a CFB riser and can also be easily coupled to a kinetics model for process simulation.

  17. Stability analysis of multigrid acceleration methods for the solution of partial differential equations

    NASA Technical Reports Server (NTRS)

    Fay, John F.

    1990-01-01

    A calculation is made of the stability of various relaxation schemes for the numerical solution of partial differential equations. A multigrid acceleration method is introduced, and its effects on stability are explored. A detailed stability analysis of a simple case is carried out and verified by numerical experiment. It is shown that the use of multigrids can speed convergence by several orders of magnitude without adversely affecting stability.

  18. Fluorescence2D: Software for Accelerated Acquisition and Analysis of Two-Dimensional Fluorescence Spectra

    PubMed Central

    Kovrigin, Evgenii L.

    2014-01-01

    The Fluorescence2D is free software that allows analysis of two-dimensional fluorescence spectra obtained using the accelerated “triangular” acquisition schemes. The software is a combination of Python and MATLAB-based programs that perform conversion of the triangular data, display of the two-dimensional spectra, extraction of 1D slices at different wavelengths, and output in various graphic formats. PMID:24984078

  19. The metabolic background is a global player in Saccharomyces gene expression epistasis.

    PubMed

    Alam, Mohammad Tauqeer; Zelezniak, Aleksej; Mülleder, Michael; Shliaha, Pavel; Schwarz, Roland; Capuano, Floriana; Vowinckel, Jakob; Radmaneshfar, Elahe; Krüger, Antje; Calvani, Enrica; Michel, Steve; Börno, Stefan; Christen, Stefan; Patil, Kiran Raosaheb; Timmermann, Bernd; Lilley, Kathryn S; Ralser, Markus

    2016-01-01

    The regulation of gene expression in response to nutrient availability is fundamental to the genotype-phenotype relationship. The metabolic-genetic make-up of the cell, as reflected in auxotrophy, is hence likely to be a determinant of gene expression. Here, we address the importance of the metabolic-genetic background by monitoring transcriptome, proteome and metabolome in a repertoire of 16 Saccharomyces cerevisiae laboratory backgrounds, combinatorially perturbed in histidine, leucine, methionine and uracil biosynthesis. The metabolic background affected up to 85% of the coding genome. Suggesting widespread confounding, these transcriptional changes show, on average, 83% overlap between unrelated auxotrophs and 35% with previously published transcriptomes generated for non-metabolic gene knockouts. Background-dependent gene expression correlated with metabolic flux and acted, predominantly through masking or suppression, on 88% of transcriptional interactions epistatically. As a consequence, the deletion of the same metabolic gene in a different background could provoke an entirely different transcriptional response. Propagating to the proteome and scaling up at the metabolome, metabolic background dependencies reveal the prevalence of metabolism-dependent epistasis at all regulatory levels. Urging a fundamental change of the prevailing laboratory practice of using auxotrophs and nutrient supplemented media, these results reveal epistatic intertwining of metabolism with gene expression on the genomic scale. PMID:27572163

  20. Epistasis and genotype-by-environment interaction of grain protein content in durum wheat

    PubMed Central

    2010-01-01

    Parental, F1 , F 2 , BC 1 and BC 2 generations of four crosses involving four cultivars of durum wheat (Triticum durum Desf.) were evaluated at two sites in Tunisia. A three-parameter model was found inadequate for all cases except crosses Chili x Cocorit 71 at site Sidi Thabet and Inrat 69 x Karim at both sites. In most cases a digenic epistatic model was sufficient to explain variation in generation means. Dominance effects (h) and additive x additive epistasis (i) (when significant) were more important than additive (d) effects and other epistatic components. Considering the genotype-by-environment interaction, the non-interactive model (m, d, h, e) was found adequate. Additive variance was higher than environmental variance in three crosses at both sites. The estimated values of narrow-sense heritability were dependent upon the cross and the sites and were 0%-85%. The results indicate that appropriate choice of environment and selection in later generations would increase grain protein content in durum wheat. PMID:21637615

  1. Relationship between leaf stages and epistasis for resistance to Stagonospora nodorum in durum wheat

    PubMed Central

    Bnejdi, Fethi; Saadoun, Mourad; Naouari, Mouna; El Gazzah, Mohamed

    2012-01-01

    Ten varieties and eight generations (2F1, 2F2, 2B1 and 2B2) of durum wheat derived from two crosses were evaluated for resistance to natural infection by Stagonospora nodorum blotch (SNB) at the 2–3 and 6–7 leaf stages at two sites over two years. There were significant differences in the incidence of SNB between leaf stages in most of the wheat varieties, with resistance being most evident at the 6–7 leaf stage. Separate analyses of the mean values for each generation showed that the genetic mechanism of defense against the pathogen depended upon the leaf stage. At the 2–3 leaf stage, only additive and dominance effects were implicated in the control of SNB for the two crosses at the two sites and for the two replications. For the 6–7 leaf stage, inheritance was more complicated and an epistatic effect was involved. Narrow-sense heritability values (range: 0.63–0.67) were consistent between crosses and leaf stages. These findings indicate a lack of resistance to SNB at the 2–3 leaf stage whereas resistance was observed at the 6–7 leaf stage and involved the genetic mechanisms of plant defense such as epistasis. PMID:22888293

  2. Wavelet Analysis of Acceleration Response of Beam Under the Moving Mass for Damage Assessment

    NASA Astrophysics Data System (ADS)

    Vaidya, Tanuja; Chatterjee, Animesh

    2016-04-01

    In the present study, acceleration response of cracked beam is analyzed by using the wavelet transform to detect the crack presence, its location and also to predict the crack severity. The equation of motion of beam under the moving mass is solved by using the fourth order Runge-Kutta method. A code is written by expanding the equation for first three vibration modes. Acceleration signal of the damaged beam under the moving mass contains the discontinuity at the crack location. This discontinuity contained in the acceleration signal is sufficiently visible but it is very small for some signals. Therefore, the acceleration signals are transformed using the wavelet analysis. A wavelet coefficient peak occurs at the location of discontinuity, so that we can identify the crack presence and its location. From the value of wavelet coefficient peak, we can also predict the crack effect with respect to the change in velocity of moving mass and change in crack depth. The main advantage of this method is that the wavelet coefficient peak is sufficiently higher even for the higher velocities and small size crack.

  3. Three dimensional gait analysis using wearable acceleration and gyro sensors based on quaternion calculations.

    PubMed

    Tadano, Shigeru; Takeda, Ryo; Miyagawa, Hiroaki

    2013-01-01

    This paper proposes a method for three dimensional gait analysis using wearable sensors and quaternion calculations. Seven sensor units consisting of a tri-axial acceleration and gyro sensors, were fixed to the lower limbs. The acceleration and angular velocity data of each sensor unit were measured during level walking. The initial orientations of the sensor units were estimated using acceleration data during upright standing position and the angular displacements were estimated afterwards using angular velocity data during gait. Here, an algorithm based on quaternion calculation was implemented for orientation estimation of the sensor units. The orientations of the sensor units were converted to the orientations of the body segments by a rotation matrix obtained from a calibration trial. Body segment orientations were then used for constructing a three dimensional wire frame animation of the volunteers during the gait. Gait analysis was conducted on five volunteers, and results were compared with those from a camera-based motion analysis system. Comparisons were made for the joint trajectory in the horizontal and sagittal plane. The average RMSE and correlation coefficient (CC) were 10.14 deg and 0.98, 7.88 deg and 0.97, 9.75 deg and 0.78 for the hip, knee and ankle flexion angles, respectively. PMID:23877128

  4. Three Dimensional Gait Analysis Using Wearable Acceleration and Gyro Sensors Based on Quaternion Calculations

    PubMed Central

    Tadano, Shigeru; Takeda, Ryo; Miyagawa, Hiroaki

    2013-01-01

    This paper proposes a method for three dimensional gait analysis using wearable sensors and quaternion calculations. Seven sensor units consisting of a tri-axial acceleration and gyro sensors, were fixed to the lower limbs. The acceleration and angular velocity data of each sensor unit were measured during level walking. The initial orientations of the sensor units were estimated using acceleration data during upright standing position and the angular displacements were estimated afterwards using angular velocity data during gait. Here, an algorithm based on quaternion calculation was implemented for orientation estimation of the sensor units. The orientations of the sensor units were converted to the orientations of the body segments by a rotation matrix obtained from a calibration trial. Body segment orientations were then used for constructing a three dimensional wire frame animation of the volunteers during the gait. Gait analysis was conducted on five volunteers, and results were compared with those from a camera-based motion analysis system. Comparisons were made for the joint trajectory in the horizontal and sagittal plane. The average RMSE and correlation coefficient (CC) were 10.14 deg and 0.98, 7.88 deg and 0.97, 9.75 deg and 0.78 for the hip, knee and ankle flexion angles, respectively. PMID:23877128

  5. Acceleration Studies

    NASA Technical Reports Server (NTRS)

    Rogers, Melissa J. B.

    1993-01-01

    Work to support the NASA MSFC Acceleration Characterization and Analysis Project (ACAP) was performed. Four tasks (analysis development, analysis research, analysis documentation, and acceleration analysis) were addressed by parallel projects. Work concentrated on preparation for and implementation of near real-time SAMS data analysis during the USMP-1 mission. User support documents and case specific software documentation and tutorials were developed. Information and results were presented to microgravity users. ACAP computer facilities need to be fully implemented and networked, data resources must be cataloged and accessible, future microgravity missions must be coordinated, and continued Orbiter characterization is necessary.

  6. Experimental design and analysis for accelerated degradation tests with Li-ion cells.

    SciTech Connect

    Doughty, Daniel Harvey; Thomas, Edward Victor; Jungst, Rudolph George; Roth, Emanuel Peter

    2003-08-01

    This document describes a general protocol (involving both experimental and data analytic aspects) that is designed to be a roadmap for rapidly obtaining a useful assessment of the average lifetime (at some specified use conditions) that might be expected from cells of a particular design. The proposed experimental protocol involves a series of accelerated degradation experiments. Through the acquisition of degradation data over time specified by the experimental protocol, an unambiguous assessment of the effects of accelerating factors (e.g., temperature and state of charge) on various measures of the health of a cell (e.g., power fade and capacity fade) will result. In order to assess cell lifetime, it is necessary to develop a model that accurately predicts degradation over a range of the experimental factors. In general, it is difficult to specify an appropriate model form without some preliminary analysis of the data. Nevertheless, assuming that the aging phenomenon relates to a chemical reaction with simple first-order rate kinetics, a data analysis protocol is also provided to construct a useful model that relates performance degradation to the levels of the accelerating factors. This model can then be used to make an accurate assessment of the average cell lifetime. The proposed experimental and data analysis protocols are illustrated with a case study involving the effects of accelerated aging on the power output from Gen-2 cells. For this case study, inadequacies of the simple first-order kinetics model were observed. However, a more complex model allowing for the effects of two concurrent mechanisms provided an accurate representation of the experimental data.

  7. Fourier analysis of parallel inexact Block-Jacobi splitting with transport synthetic acceleration in slab geometry

    SciTech Connect

    Rosa, M.; Warsa, J. S.; Chang, J. H.

    2006-07-01

    A Fourier analysis is conducted for the discrete-ordinates (SN) approximation of the neutron transport problem solved with Richardson iteration (Source Iteration) and Richardson iteration preconditioned with Transport Synthetic Acceleration (TSA), using the Parallel Block-Jacobi (PBJ) algorithm. Both 'traditional' TSA (TTSA) and a 'modified' TSA (MTSA), in which only the scattering in the low order equations is reduced by some non-negative factor {beta} and < 1, are considered. The results for the un-accelerated algorithm show that convergence of the PBJ algorithm can degrade. The PBJ algorithm with TTSA can be effective provided the {beta} parameter is properly tuned for a given scattering ratio c, but is potentially unstable. Compared to TTSA, MTSA is less sensitive to the choice of {beta}, more effective for the same computational effort (c'), and it is unconditionally stable. (authors)

  8. Analysis of ballistic transport in nanoscale devices by using an accelerated finite element contact block reduction approach

    SciTech Connect

    Li, H.; Li, G.

    2014-08-28

    An accelerated Finite Element Contact Block Reduction (FECBR) approach is presented for computational analysis of ballistic transport in nanoscale electronic devices with arbitrary geometry and unstructured mesh. Finite element formulation is developed for the theoretical CBR/Poisson model. The FECBR approach is accelerated through eigen-pair reduction, lead mode space projection, and component mode synthesis techniques. The accelerated FECBR is applied to perform quantum mechanical ballistic transport analysis of a DG-MOSFET with taper-shaped extensions and a DG-MOSFET with Si/SiO{sub 2} interface roughness. The computed electrical transport properties of the devices obtained from the accelerated FECBR approach and associated computational cost as a function of system degrees of freedom are compared with those obtained from the original CBR and direct inversion methods. The performance of the accelerated FECBR in both its accuracy and efficiency is demonstrated.

  9. Analysis of ballistic transport in nanoscale devices by using an accelerated finite element contact block reduction approach

    NASA Astrophysics Data System (ADS)

    Li, H.; Li, G.

    2014-08-01

    An accelerated Finite Element Contact Block Reduction (FECBR) approach is presented for computational analysis of ballistic transport in nanoscale electronic devices with arbitrary geometry and unstructured mesh. Finite element formulation is developed for the theoretical CBR/Poisson model. The FECBR approach is accelerated through eigen-pair reduction, lead mode space projection, and component mode synthesis techniques. The accelerated FECBR is applied to perform quantum mechanical ballistic transport analysis of a DG-MOSFET with taper-shaped extensions and a DG-MOSFET with Si/SiO2 interface roughness. The computed electrical transport properties of the devices obtained from the accelerated FECBR approach and associated computational cost as a function of system degrees of freedom are compared with those obtained from the original CBR and direct inversion methods. The performance of the accelerated FECBR in both its accuracy and efficiency is demonstrated.

  10. A domestic cat X chromosome linkage map and the sex-linked orange locus: mapping of orange, multiple origins and epistasis over nonagouti.

    PubMed

    Schmidt-Küntzel, Anne; Nelson, George; David, Victor A; Schäffer, Alejandro A; Eizirik, Eduardo; Roelke, Melody E; Kehler, James S; Hannah, Steven S; O'Brien, Stephen J; Menotti-Raymond, Marilyn

    2009-04-01

    A comprehensive genetic linkage map of the domestic cat X chromosome was generated with the goal of localizing the genomic position of the classic X-linked orange (O) locus. Microsatellite markers with an average spacing of 3 Mb were selected from sequence traces of the cat 1.9x whole genome sequence (WGS), including the pseudoautosomal region 1 (PAR1). Extreme variation in recombination rates (centimorgans per megabase) was observed along the X chromosome, ranging from a virtual absence of recombination events in a region estimated to be >30 Mb to recombination frequencies of 15.7 cM/Mb in a segment estimated to be <0.3 Mb. This detailed linkage map was applied to position the X-linked orange gene, placing this locus on the q arm of the X chromosome, as opposed to a previously reported location on the p arm. Fine mapping placed the locus between markers at positions 106 and 116.8 Mb in the current 1.9x-coverage sequence assembly of the cat genome. Haplotype analysis revealed potential recombination events that could reduce the size of the candidate region to 3.5 Mb and suggested multiple origins for the orange phenotype in the domestic cat. Furthermore, epistasis of orange over nonagouti was demonstrated at the genetic level. PMID:19189955

  11. A Domestic cat X Chromosome Linkage Map and the Sex-Linked orange Locus: Mapping of orange, Multiple Origins and Epistasis Over nonagouti

    PubMed Central

    Schmidt-Küntzel, Anne; Nelson, George; David, Victor A.; Schäffer, Alejandro A.; Eizirik, Eduardo; Roelke, Melody E.; Kehler, James S.; Hannah, Steven S.; O'Brien, Stephen J.; Menotti-Raymond, Marilyn

    2009-01-01

    A comprehensive genetic linkage map of the domestic cat X chromosome was generated with the goal of localizing the genomic position of the classic X-linked orange (O) locus. Microsatellite markers with an average spacing of 3 Mb were selected from sequence traces of the cat 1.9× whole genome sequence (WGS), including the pseudoautosomal region 1 (PAR1). Extreme variation in recombination rates (centimorgans per megabase) was observed along the X chromosome, ranging from a virtual absence of recombination events in a region estimated to be >30 Mb to recombination frequencies of 15.7 cM/Mb in a segment estimated to be <0.3 Mb. This detailed linkage map was applied to position the X-linked orange gene, placing this locus on the q arm of the X chromosome, as opposed to a previously reported location on the p arm. Fine mapping placed the locus between markers at positions 106 and 116.8 Mb in the current 1.9×-coverage sequence assembly of the cat genome. Haplotype analysis revealed potential recombination events that could reduce the size of the candidate region to 3.5 Mb and suggested multiple origins for the orange phenotype in the domestic cat. Furthermore, epistasis of orange over nonagouti was demonstrated at the genetic level. PMID:19189955

  12. Failure modes and effects criticality analysis and accelerated life testing of LEDs for medical applications

    NASA Astrophysics Data System (ADS)

    Sawant, M.; Christou, A.

    2012-12-01

    While use of LEDs in Fiber Optics and lighting applications is common, their use in medical diagnostic applications is not very extensive. Since the precise value of light intensity will be used to interpret patient results, understanding failure modes [1-4] is very important. We used the Failure Modes and Effects Criticality Analysis (FMECA) tool to identify the critical failure modes of the LEDs. FMECA involves identification of various failure modes, their effects on the system (LED optical output in this context), their frequency of occurrence, severity and the criticality of the failure modes. The competing failure modes/mechanisms were degradation of: active layer (where electron-hole recombination occurs to emit light), electrodes (provides electrical contact to the semiconductor chip), Indium Tin Oxide (ITO) surface layer (used to improve current spreading and light extraction), plastic encapsulation (protective polymer layer) and packaging failures (bond wires, heat sink separation). A FMECA table is constructed and the criticality is calculated by estimating the failure effect probability (β), failure mode ratio (α), failure rate (λ) and the operating time. Once the critical failure modes were identified, the next steps were generation of prior time to failure distribution and comparing with our accelerated life test data. To generate the prior distributions, data and results from previous investigations were utilized [5-33] where reliability test results of similar LEDs were reported. From the graphs or tabular data, we extracted the time required for the optical power output to reach 80% of its initial value. This is our failure criterion for the medical diagnostic application. Analysis of published data for different LED materials (AlGaInP, GaN, AlGaAs), the Semiconductor Structures (DH, MQW) and the mode of testing (DC, Pulsed) was carried out. The data was categorized according to the materials system and LED structure such as AlGaInP-DH-DC, Al

  13. Will solid-state drives accelerate your bioinformatics? In-depth profiling, performance analysis and beyond.

    PubMed

    Lee, Sungmin; Min, Hyeyoung; Yoon, Sungroh

    2016-07-01

    A wide variety of large-scale data have been produced in bioinformatics. In response, the need for efficient handling of biomedical big data has been partly met by parallel computing. However, the time demand of many bioinformatics programs still remains high for large-scale practical uses because of factors that hinder acceleration by parallelization. Recently, new generations of storage devices have emerged, such as NAND flash-based solid-state drives (SSDs), and with the renewed interest in near-data processing, they are increasingly becoming acceleration methods that can accompany parallel processing. In certain cases, a simple drop-in replacement of hard disk drives by SSDs results in dramatic speedup. Despite the various advantages and continuous cost reduction of SSDs, there has been little review of SSD-based profiling and performance exploration of important but time-consuming bioinformatics programs. For an informative review, we perform in-depth profiling and analysis of 23 key bioinformatics programs using multiple types of devices. Based on the insight we obtain from this research, we further discuss issues related to design and optimize bioinformatics algorithms and pipelines to fully exploit SSDs. The programs we profile cover traditional and emerging areas of importance, such as alignment, assembly, mapping, expression analysis, variant calling and metagenomics. We explain how acceleration by parallelization can be combined with SSDs for improved performance and also how using SSDs can expedite important bioinformatics pipelines, such as variant calling by the Genome Analysis Toolkit and transcriptome analysis using RNA sequencing. We hope that this review can provide useful directions and tips to accompany future bioinformatics algorithm design procedures that properly consider new generations of powerful storage devices. PMID:26330577

  14. Converging Evidence for Epistasis between ANK3 and Potassium Channel Gene KCNQ2 in Bipolar Disorder

    PubMed Central

    Judy, Jennifer Toolan; Seifuddin, Fayaz; Pirooznia, Mehdi; Mahon, Pamela Belmonte; Jancic, Dubravka; Goes, Fernando S.; Schulze, Thomas; Cichon, Sven; Noethen, Markus; Rietschel, Marcella; DePaulo, J. Raymond; Potash, James B.; Zandi, Peter P.

    2013-01-01

    Genome-wide association studies (GWAS) have implicated ANK3 as a susceptibility gene for bipolar disorder (BP). We examined whether epistasis with ANK3 may contribute to the “missing heritability” in BP. We first identified via the STRING database 14 genes encoding proteins with prior biological evidence that they interact molecularly with ANK3. We then tested for statistical evidence of interactions between SNPs in these genes in association with BP in a discovery GWAS dataset and two replication GWAS datasets. The most significant interaction in the discovery GWAS was between SNPs in ANK3 and KCNQ2 (p = 3.18 × 10−8). A total of 31 pair-wise interactions involving combinations between two SNPs from KCNQ2 and 16 different SNPs in ANK3 were significant after permutation. Of these, 28 pair-wise interactions were significant in the first replication GWAS. None were significant in the second replication GWAS, but the two SNPs from KCNQ2 were found to significantly interact with five other SNPs in ANK3, suggesting possible allelic heterogeneity. KCNQ2 forms homo- and hetero-meric complexes with KCNQ3 that constitute voltage-gated potassium channels in neurons. ANK3 is an adaptor protein that, through its interaction with KCNQ2 and KCNQ3, directs the localization of this channel in the axon initial segment (AIS). At the AIS, the KCNQ2/3 complex gives rise to the M-current, which stabilizes the neuronal resting potential and inhibits repetitive firing of action potentials. Thus, these channels act as “dampening” components and prevent neuronal hyperactivity. The interactions between ANK3 and KCNQ2 merit further investigation, and if confirmed, may motivate a new line of research into a novel therapeutic target for BP. PMID:23730306

  15. Mitonuclear Epistasis for Development Time and Its Modification by Diet in Drosophila.

    PubMed

    Mossman, Jim A; Biancani, Leann M; Zhu, Chen-Tseh; Rand, David M

    2016-05-01

    Mitochondrial (mtDNA) and nuclear genes have to operate in a coordinated manner to maintain organismal function, and the regulation of this homeostasis presents a substantial source of potential epistatic (G × G) interactions. How these interactions shape the fitness landscape is poorly understood. Here we developed a novel mitonuclear epistasis model, using selected strains of the Drosophila Genetic Reference Panel (DGRP) and mitochondrial genomes from within Drosophila melanogaster and D. simulans to test the hypothesis that mtDNA × nDNA interactions influence fitness. In total we built 72 genotypes (12 nuclear backgrounds × 6 mtDNA haplotypes, with 3 from each species) to dissect the relationship between genotype and phenotype. Each genotype was assayed on four food environments. We found considerable variation in several phenotypes, including development time and egg-to-adult viability, and this variation was partitioned into genetic (G), environmental (E), and higher-order (G × G, G × E, and G × G × E) components. Food type had a significant impact on development time and also modified mitonuclear epistases, evidencing a broad spectrum of G × G × E across these genotypes. Nuclear background effects were substantial, followed by mtDNA effects and their G × G interaction. The species of mtDNA haplotype had negligible effects on phenotypic variation and there was no evidence that mtDNA variation has different effects on male and female fitness traits. Our results demonstrate that mitonuclear epistases are context dependent, suggesting the selective pressure acting on mitonuclear genotypes may vary with food environment in a genotype-specific manner. PMID:26966258

  16. Mitonuclear Epistasis for Development Time and Its Modification by Diet in Drosophila

    PubMed Central

    Biancani, Leann M.; Zhu, Chen-Tseh

    2016-01-01

    Mitochondrial (mtDNA) and nuclear genes have to operate in a coordinated manner to maintain organismal function, and the regulation of this homeostasis presents a substantial source of potential epistatic (G × G) interactions. How these interactions shape the fitness landscape is poorly understood. Here we developed a novel mitonuclear epistasis model, using selected strains of the Drosophila Genetic Reference Panel (DGRP) and mitochondrial genomes from within Drosophila melanogaster and D. simulans to test the hypothesis that mtDNA × nDNA interactions influence fitness. In total we built 72 genotypes (12 nuclear backgrounds × 6 mtDNA haplotypes, with 3 from each species) to dissect the relationship between genotype and phenotype. Each genotype was assayed on four food environments. We found considerable variation in several phenotypes, including development time and egg-to-adult viability, and this variation was partitioned into genetic (G), environmental (E), and higher-order (G × G, G × E, and G × G × E) components. Food type had a significant impact on development time and also modified mitonuclear epistases, evidencing a broad spectrum of G × G × E across these genotypes. Nuclear background effects were substantial, followed by mtDNA effects and their G × G interaction. The species of mtDNA haplotype had negligible effects on phenotypic variation and there was no evidence that mtDNA variation has different effects on male and female fitness traits. Our results demonstrate that mitonuclear epistases are context dependent, suggesting the selective pressure acting on mitonuclear genotypes may vary with food environment in a genotype-specific manner. PMID:26966258

  17. Quantification of the transferability of a designed protein specificity switch reveals extensive epistasis in molecular recognition

    SciTech Connect

    Melero, Cristina; Ollikainen, Noah; Harwood, Ian; Karpiak, Joel; Kortemme, Tanja

    2014-10-13

    Re-engineering protein–protein recognition is an important route to dissecting and controlling complex interaction networks. Experimental approaches have used the strategy of “second-site suppressors,” where a functional interaction is inferred between two proteins if a mutation in one protein can be compensated by a mutation in the second. Mimicking this strategy, computational design has been applied successfully to change protein recognition specificity by predicting such sets of compensatory mutations in protein–protein interfaces. To extend this approach, it would be advantageous to be able to “transplant” existing engineered and experimentally validated specificity changes to other homologous protein–protein complexes. Here, we test this strategy by designing a pair of mutations that modulates peptide recognition specificity in the Syntrophin PDZ domain, confirming the designed interaction biochemically and structurally, and then transplanting the mutations into the context of five related PDZ domain–peptide complexes. We find a wide range of energetic effects of identical mutations in structurally similar positions, revealing a dramatic context dependence (epistasis) of designed mutations in homologous protein–protein interactions. To better understand the structural basis of this context dependence, we apply a structure-based computational model that recapitulates these energetic effects and we use this model to make and validate forward predictions. The context dependence of these mutations is captured by computational predictions, our results both highlight the considerable difficulties in designing protein–protein interactions and provide challenging benchmark cases for the development of improved protein modeling and design methods that accurately account for the context.

  18. Quantification of the transferability of a designed protein specificity switch reveals extensive epistasis in molecular recognition

    DOE PAGESBeta

    Melero, Cristina; Ollikainen, Noah; Harwood, Ian; Karpiak, Joel; Kortemme, Tanja

    2014-10-13

    Re-engineering protein–protein recognition is an important route to dissecting and controlling complex interaction networks. Experimental approaches have used the strategy of “second-site suppressors,” where a functional interaction is inferred between two proteins if a mutation in one protein can be compensated by a mutation in the second. Mimicking this strategy, computational design has been applied successfully to change protein recognition specificity by predicting such sets of compensatory mutations in protein–protein interfaces. To extend this approach, it would be advantageous to be able to “transplant” existing engineered and experimentally validated specificity changes to other homologous protein–protein complexes. Here, we test thismore » strategy by designing a pair of mutations that modulates peptide recognition specificity in the Syntrophin PDZ domain, confirming the designed interaction biochemically and structurally, and then transplanting the mutations into the context of five related PDZ domain–peptide complexes. We find a wide range of energetic effects of identical mutations in structurally similar positions, revealing a dramatic context dependence (epistasis) of designed mutations in homologous protein–protein interactions. To better understand the structural basis of this context dependence, we apply a structure-based computational model that recapitulates these energetic effects and we use this model to make and validate forward predictions. The context dependence of these mutations is captured by computational predictions, our results both highlight the considerable difficulties in designing protein–protein interactions and provide challenging benchmark cases for the development of improved protein modeling and design methods that accurately account for the context.« less

  19. FAM-MDR: A Flexible Family-Based Multifactor Dimensionality Reduction Technique to Detect Epistasis Using Related Individuals

    PubMed Central

    Cattaert, Tom; Urrea, Víctor; Naj, Adam C.; De Lobel, Lizzy; De Wit, Vanessa; Fu, Mao; Mahachie John, Jestinah M.; Shen, Haiqing; Calle, M. Luz; Ritchie, Marylyn D.; Edwards, Todd L.; Van Steen, Kristel

    2010-01-01

    We propose a novel multifactor dimensionality reduction method for epistasis detection in small or extended pedigrees, FAM-MDR. It combines features of the Genome-wide Rapid Association using Mixed Model And Regression approach (GRAMMAR) with Model-Based MDR (MB-MDR). We focus on continuous traits, although the method is general and can be used for outcomes of any type, including binary and censored traits. When comparing FAM-MDR with Pedigree-based Generalized MDR (PGMDR), which is a generalization of Multifactor Dimensionality Reduction (MDR) to continuous traits and related individuals, FAM-MDR was found to outperform PGMDR in terms of power, in most of the considered simulated scenarios. Additional simulations revealed that PGMDR does not appropriately deal with multiple testing and consequently gives rise to overly optimistic results. FAM-MDR adequately deals with multiple testing in epistasis screens and is in contrast rather conservative, by construction. Furthermore, simulations show that correcting for lower order (main) effects is of utmost importance when claiming epistasis. As Type 2 Diabetes Mellitus (T2DM) is a complex phenotype likely influenced by gene-gene interactions, we applied FAM-MDR to examine data on glucose area-under-the-curve (GAUC), an endophenotype of T2DM for which multiple independent genetic associations have been observed, in the Amish Family Diabetes Study (AFDS). This application reveals that FAM-MDR makes more efficient use of the available data than PGMDR and can deal with multi-generational pedigrees more easily. In conclusion, we have validated FAM-MDR and compared it to PGMDR, the current state-of-the-art MDR method for family data, using both simulations and a practical dataset. FAM-MDR is found to outperform PGMDR in that it handles the multiple testing issue more correctly, has increased power, and efficiently uses all available information. PMID:20421984

  20. Dynamic analysis of an accelerator-driven fluid-fueled subcritical radioactive waste burning system

    SciTech Connect

    Woosley, M.L. Jr.; Rydin, R.A.

    1998-05-01

    The recent revival of interest in accelerator-driven subcritical fluid-fueled systems is documented. Several important applications of these systems are mentioned, and this is used to motivate the need for dynamic analysis of the nuclear kinetics of such systems. A physical description of the Los alamos National Laboratory accelerator-based conversion (ABC) concept is provided. This system is used as the basis for the kinetics study in this research. The current approach to the dynamic simulation of an accelerator-driven subcritical fluid-fueled system includes four functional elements: a discrete ordinates model is used to calculate the flux distribution for the source-driven system; a nodal convection model is used to calculate time-dependent isotope and temperature distributions that impact reactivity; a nodal importance weighting model is used to calculate the reactivity impact of temperature and isotope distributions and to feed this information back to the time-dependent nodal convection model; and a transient driver is used to simulate transients, model the balance of plant, and record simulation data. Specific transients that have been analyzed with the current modeling system are discussed. These transients include loss-of-flow and loss-of-cooling accidents, xenon and samarium transients, and cold-plug and overfueling events. The results of various transients have uncovered unpredictable behavior, unresolved design issues, and the need for active control. The need for the development of a nodal-coupling spatial kinetics model is mentioned.

  1. Preliminary Safety Analysis Report (PSAR), The NSLS 200 MeV Linear Electron Accelerator

    SciTech Connect

    Blumberg, L.N.; Ackerman, A.I.; Dickinson, T.; Heese, R.N.; Larson, R.A.; Neuls, C.W.; Pjerov, S.; Sheehan, J.F.

    1993-06-15

    The radiological, fire and electrical hazards posed by a 200 MeV electron Linear Accelerator, which the NSLS Department will install and commission within a newly assembled structure, are addressed in this Preliminary Safety Analysis Report. Although it is clear that this accelerator is intended to be the injector for a future experimental facility, we address only the Linac in the present PSAR since neither the final design nor the operating characteristics of the experimental facility are known at the present time. The fire detection and control system to be installed in the building is judged to be completely adequate in terms of the marginal hazard presented - no combustible materials other than the usual cabling associated with such a facility have been identified. Likewise, electrical hazards associated with power supplies for the beam transport magnets and accelerator components such as the accelerator klystrons and electron gun are classified as marginal in terms of potential personnel injury, cost of equipment lost, program downtime and public impact perceptions as defined in the BNL Environmental Safety and Health Manual and the probability of occurrence is deemed to be remote. No unusual features have been identified for the power supplies or electrical distribution system, and normal and customary electrical safety standards as practiced throughout the NSLS complex and the Laboratory are specified in this report. The radiation safety hazards are similarly judged to be marginal in terms of probability of occurrence and potential injury consequences since, for the low intensity operation proposed - a factor of 25 less than the maximum Linac capability specified by the vendor - the average beam power is only 0.4 watts. The shielding specifications given in this report will give adequate protection to both the general public and nonradiation workers in areas adjacent to the building as well as radiation workers within the controlled access building.

  2. Analysis of damaging effects of laser-plasma accelerated shrapnels on protecting glass shield

    NASA Astrophysics Data System (ADS)

    Martinkova, Michaela; Kalal, Milan; Shmatov, Mikhail L.

    2013-11-01

    Analysis of the damage caused by laser plasma accelerated fragments of metal target was performed. Measured as well as calculated parameters of craters and shrapnel found in BK7 glass blastshield are presented. Method applied for the measurement of parameters of craters is described. Potential damage of optical elements by the so-called striking cores (high-velocity stable objects arising due to collapse of cones or some other target parts toward their axes) that can be generated in IFE related experiments is evaluated.

  3. Elemental analysis of concrete samples using an accelerator-based PGNAA setup

    NASA Astrophysics Data System (ADS)

    Naqvi, A. A.; Nagadi, M. M.; Baghabra Al-Amoudi, Omar S.

    2004-09-01

    Elemental analysis of concrete samples was carried out using an accelerator-based prompt gamma ray neutron activation analysis (PGNAA) setup. The gamma rays were produced via the capture of thermal neutron in the concrete sample. The prompt gamma ray yield was measured for 12 cm long concrete samples as a function of sample radius over a range of 6-11.5 cm radii. The optimum yield of the prompt gamma rays from the concrete sample was measured from a sample with 11.5 cm radius. The gamma ray yield was also calculated for 12 cm long concrete samples with 6-11.5 cm radius using Monte Carlo simulations. The experimental results were in excellent agreement with the calculated yield of the prompt gamma rays from the samples. Result of this study has shown the useful application of an accelerator-based PGNAA setup in elemental analysis of concrete sample. The facility can be further used to determine the chloride and sulfate concentrations in concrete samples for corrosion studies of reinforcement steel in concrete structures.

  4. The relevance of particle flux monitors in accelerator-based activation analysis

    SciTech Connect

    Segebade, Chr.; Maimaitimin, M.; Sun Zaijing

    2013-04-19

    One of the most critical parameters in activation analysis is the flux density of the activating radiation, its spatial distribution in particular. The validity of the basic equation for calculating the activity induced to the exposed item depends upon the fulfilment of several conditions, the most relevant of them being equal doses of incident activating radiation received by the unknown sample, the calibration material and the reference material, respectively. This requirement is most problematic if accelerator-produced radiation is used for activation. Whilst nuclear research reactors usually are equipped with exposure positions that provide fairly homogenous activation fields for thermal neutron activation analysis accelerator-generated particle beams (neutrons, photons, charged particles) usually exhibit axial and, in particular, sharp radial flux gradients. Different experimental procedures have been developed to fulfil the condition mentioned above. In this paper, three variants of the application of flux monitors in photon activation analysis are discussed (external monitor, additive and inherent internal monitor). Experiments have indicated that the latter technique yields highest quality of the analytical results.

  5. The relevance of particle flux monitors in accelerator-based activation analysis

    NASA Astrophysics Data System (ADS)

    Segebade, Chr.; Maimaitimin, M.; Zaijing, Sun

    2013-04-01

    One of the most critical parameters in activation analysis is the flux density of the activating radiation, its spatial distribution in particular. The validity of the basic equation for calculating the activity induced to the exposed item depends upon the fulfilment of several conditions, the most relevant of them being equal doses of incident activating radiation received by the unknown sample, the calibration material and the reference material, respectively. This requirement is most problematic if accelerator-produced radiation is used for activation. Whilst nuclear research reactors usually are equipped with exposure positions that provide fairly homogenous activation fields for thermal neutron activation analysis accelerator-generated particle beams (neutrons, photons, charged particles) usually exhibit axial and, in particular, sharp radial flux gradients. Different experimental procedures have been developed to fulfil the condition mentioned above. In this paper, three variants of the application of flux monitors in photon activation analysis are discussed (external monitor, additive and inherent internal monitor). Experiments have indicated that the latter technique yields highest quality of the analytical results.

  6. Rapid analysis of scattering from periodic dielectric structures using accelerated Cartesian expansions

    DOE PAGESBeta

    Baczewski, Andrew David; Miller, Nicholas C.; Shanker, Balasubramaniam

    2012-03-22

    Here, the analysis of fields in periodic dielectric structures arise in numerous applications of recent interest, ranging from photonic bandgap structures and plasmonically active nanostructures to metamaterials. To achieve an accurate representation of the fields in these structures using numerical methods, dense spatial discretization is required. This, in turn, affects the cost of analysis, particularly for integral-equation-based methods, for which traditional iterative methods require Ο(Ν2) operations, Ν being the number of spatial degrees of freedom. In this paper, we introduce a method for the rapid solution of volumetric electric field integral equations used in the analysis of doubly periodic dielectricmore » structures. The crux of our method is the accelerated Cartesian expansion algorithm, which is used to evaluate the requisite potentials in Ο(Ν) cost. Results are provided that corroborate our claims of acceleration without compromising accuracy, as well as the application of our method to a number of compelling photonics applications.« less

  7. Uncertainty in the estimates of peak ground acceleration in seismic hazard analysis

    NASA Astrophysics Data System (ADS)

    Pavlenko, V. A.

    2015-11-01

    Probabilistic seismic hazard analysis has become a standard procedure preceding the antiseismic construction. An important component of the relevant calculations is the allowance for the uncertainty in the strong motion parameters (e.g., peak ground acceleration (PGA)). In the present-day approaches of probabilistic analysis, this uncertainty is modeled by a random variable (a residual) which has a lognormal distribution. With this model, the extrapolation into the area of long return periods yields nonzero probabilities of unrealistically high PGA. In the present work, the distribution of the logarithmic PGA residuals is modeled by different parametric distributions. From the set of these distributions, the one which provides the closest approximation of the empirical data is selected by the statistical criteria. The analysis shows that the generalized extreme value distribution (GEVD) most accurately reproduces the residuals of the logarithmic PGA, and the tail of the distribution is approximated by the generalized Pareto distribution (GPD).

  8. Shielding analysis at the upper section of the accelerator-driven system.

    PubMed

    Sasa, Toshinobu; Yang, Jin An; Oigawa, Hiroyuki

    2005-01-01

    The proton beam duct of the accelerator-driven system (ADS) acts as a streaming path for spallation neutrons and photons and causes the activation of the magnets and other devices above the subcritical core. We have performed a streaming analysis at the upper section of the lead-bismuth target/cooled ADS (800 MWth). MCNPX was used to calculate the radiation dose from streamed neutrons and photons through the beam duct. For the secondary photon production calculation, cross sections for several actinides were substituted with plutonium because of the lack of gamma production cross section. From the results of this analysis, the neutron dose from the beam duct is seen to be about 20 orders higher than that of the bulk shield. The magnets and shield plug are heavily irradiated by streaming neutrons according to the DCHAIN-SP analysis. PMID:16604639

  9. Using Uncertainty Analysis to Guide the Development of Accelerated Stress Tests (Presentation)

    SciTech Connect

    Kempe, M.

    2014-03-01

    Extrapolation of accelerated testing to the long-term results expected in the field has uncertainty associated with the acceleration factors and the range of possible stresses in the field. When multiple stresses (such as temperature and humidity) can be used to increase the acceleration, the uncertainty may be reduced according to which stress factors are used to accelerate the degradation.

  10. Analysis of walking variability through simultaneous evaluation of the head, lumbar, and lower-extremity acceleration in healthy youth

    PubMed Central

    Toda, Haruki; Nagano, Akinori; Luo, Zhiwei

    2016-01-01

    [Purpose] The purpose of this study was to clarify whether walking speed affects acceleration variability of the head, lumbar, and lower extremity by simultaneously evaluating of acceleration. [Subjects and Methods] Twenty young individuals recruited from among the staff at Kurashiki Heisei Hospital participated in this study. Eight accelerometers were used to measure the head, lumbar and lower extremity accelerations. The participants were instructed to walk at five walking speeds prescribed by a metronome. Acceleration variability was assessed by a cross-correlation analysis normalized using z-transform in order to evaluate stride-to-stride variability. [Results] Vertical acceleration variability was the smallest in all body parts, and walking speed effect had laterality. Antero-posterior acceleration variability was significantly associated with walking speed at sites other than the head. Medio-lateral acceleration variability of the bilateral hip alone was smaller than the antero-posterior variability. [Conclusion] The findings of this study suggest that the effect of walking speed changes on the stride-to-stride acceleration variability was individual for each body parts, and differs among directions. PMID:27390419

  11. GPU-Accelerated Analysis and Visualization of Large Structures Solved by Molecular Dynamics Flexible Fitting

    PubMed Central

    McGreevy, Ryan; Isralewitz, Barry

    2014-01-01

    Hybrid structure fitting methods combine data from cryo-electron microscopy and X-ray crystallography with molecular dynamics simulations for the determination of all-atom structures of large biomolecular complexes. Evaluating the quality-of-fit obtained from hybrid fitting is computationally demanding, particularly in the context of a multiplicity of structural conformations that must be evaluated. Existing tools for quality-of-fit analysis and visualization have previously targeted small structures and are too slow to be used interactively for large biomolecular complexes of particular interest today such as viruses or for long molecular dynamics trajectories as they arise in protein folding. We present new data-parallel and GPU-accelerated algorithms for rapid interactive computation of quality-of-fit metrics linking all-atom structures and molecular dynamics trajectories to experimentally determined density maps obtained from cryo-electron microscopy or X-ray crystallography. We evaluate the performance and accuracy of the new quality-of-fit analysis algorithms vis-a-vis existing tools, examine algorithm performance on GPU-accelerated desktop workstations and supercomputers, and describe new visualization techniques for results of hybrid structure fitting methods. PMID:25340325

  12. Problems and Pit-Falls in Testing for G × E and Epistasis in Candidate Gene Studies of Human Behavior

    PubMed Central

    Verhulst, Brad

    2014-01-01

    Conclusions about the genetic architecture of a phenotype relating to the contributions of genetic additivity, dominance, epistasis or genotype × environment interaction, depend upon the statistical and distributional properties of the measured trait. This dependence is frequently ignored in contemporary genetic studies and can radically change the conclusions that may be drawn from the data. The interdependence of the conclusions about genetic architecture and instruments used for behavioral measurement is explored by simulated studies of the interaction between candidate genes and measured environment in psychiatric genetics. Trait values are simulated (N = 100,000) under several commonly encountered scenarios and subjected to two simulated 20-item psychological tests each comprising items with different patterns of difficulty and sensitivity to variation (discriminating power) in the latent trait. Test scores are generated for each test by summing the binary responses across all items. The full model for digenic additive and non-additive genetic effects and G × E is fitted to the trait values and test scores under a range of different simulated genetic architectures. Untransformed test scores show complex patterns of epistasis and G × E even when the underlying effects of genes and environment are purely additive and the transformation of symptom counts does not fully recover the simulated underlying genetic architecture. Accordingly, failing to allow for the theory of measurement when analyzing details of genetic architecture may frequently lead to replicable over-reporting of interactions and mislead potential investigators and funding agencies. PMID:25195167

  13. Partial Dominance, Overdominance, Epistasis and QTL by Environment Interactions Contribute to Heterosis in Two Upland Cotton Hybrids.

    PubMed

    Shang, Lianguang; Wang, Yumei; Cai, Shihu; Wang, Xiaocui; Li, Yuhua; Abduweli, Abdugheni; Hua, Jinping

    2016-03-01

    Based on two recombinant inbred line (RIL) populations, two corresponding backcross (BC) populations were constructed to elucidate the genetic basis of heterosis in Upland cotton (Gossypium hirsutum L.). The yield, and yield components, of these populations were evaluated in three environments. At the single-locus level, 78 and 66 quantitative trait loci (QTL) were detected using composite interval mapping in RIL and BC populations, respectively, and 29 QTL were identified based on mid-parental heterosis (MPH) data of two hybrids. Considering all traits together, a total of 50 (64.9%) QTL with partial dominance effect, and 27 (35.1%) QTL for overdominance effect were identified in two BC populations. At the two-locus level, 120 and 88 QTL with main effects (M-QTL), and 335 and 99 QTL involved in digenic interactions (E-QTL), were detected by inclusive composite interval mapping in RIL and BC populations, respectively. A large number of QTL by environment interactions (QEs) for M-QTL and E-QTL were detected in three environments. For most traits, average E-QTL explained a larger proportion of phenotypic variation than did M-QTL in two RIL populations and two BC populations. It was concluded that partial dominance, overdominance, epistasis, and QEs all contribute to heterosis in Upland cotton, and that partial dominance resulting from single loci and epistasis play a relatively more important role than other genetic effects in heterosis in Upland cotton. PMID:26715091

  14. Epistasis and the Structure of Fitness Landscapes: Are Experimental Fitness Landscapes Compatible with Fisher’s Geometric Model?

    PubMed Central

    Blanquart, François; Bataillon, Thomas

    2016-01-01

    The fitness landscape defines the relationship between genotypes and fitness in a given environment and underlies fundamental quantities such as the distribution of selection coefficient and the magnitude and type of epistasis. A better understanding of variation in landscape structure across species and environments is thus necessary to understand and predict how populations will adapt. An increasing number of experiments investigate the properties of fitness landscapes by identifying mutations, constructing genotypes with combinations of these mutations, and measuring the fitness of these genotypes. Yet these empirical landscapes represent a very small sample of the vast space of all possible genotypes, and this sample is often biased by the protocol used to identify mutations. Here we develop a rigorous statistical framework based on Approximate Bayesian Computation to address these concerns and use this flexible framework to fit a broad class of phenotypic fitness models (including Fisher’s model) to 26 empirical landscapes representing nine diverse biological systems. Despite uncertainty owing to the small size of most published empirical landscapes, the inferred landscapes have similar structure in similar biological systems. Surprisingly, goodness-of-fit tests reveal that this class of phenotypic models, which has been successful so far in interpreting experimental data, is a plausible in only three of nine biological systems. More precisely, although Fisher’s model was able to explain several statistical properties of the landscapes—including the mean and SD of selection and epistasis coefficients—it was often unable to explain the full structure of fitness landscapes. PMID:27052568

  15. Accelerating Policy Decisions to Adopt Haemophilus influenzae Type b Vaccine: A Global, Multivariable Analysis

    PubMed Central

    Shearer, Jessica C.; Stack, Meghan L.; Richmond, Marcie R.; Bear, Allyson P.; Hajjeh, Rana A.; Bishai, David M.

    2010-01-01

    Background Adoption of new and underutilized vaccines by national immunization programs is an essential step towards reducing child mortality. Policy decisions to adopt new vaccines in high mortality countries often lag behind decisions in high-income countries. Using the case of Haemophilus influenzae type b (Hib) vaccine, this paper endeavors to explain these delays through the analysis of country-level economic, epidemiological, programmatic and policy-related factors, as well as the role of the Global Alliance for Vaccines and Immunisation (GAVI Alliance). Methods and Findings Data for 147 countries from 1990 to 2007 were analyzed in accelerated failure time models to identify factors that are associated with the time to decision to adopt Hib vaccine. In multivariable models that control for Gross National Income, region, and burden of Hib disease, the receipt of GAVI support speeded the time to decision by a factor of 0.37 (95% CI 0.18–0.76), or 63%. The presence of two or more neighboring country adopters accelerated decisions to adopt by a factor of 0.50 (95% CI 0.33–0.75). For each 1% increase in vaccine price, decisions to adopt are delayed by a factor of 1.02 (95% CI 1.00–1.04). Global recommendations and local studies were not associated with time to decision. Conclusions This study substantiates previous findings related to vaccine price and presents new evidence to suggest that GAVI eligibility is associated with accelerated decisions to adopt Hib vaccine. The influence of neighboring country decisions was also highly significant, suggesting that approaches to support the adoption of new vaccines should consider supply- and demand-side factors. Please see later in the article for the Editors' Summary PMID:20305714

  16. Species-wide Genetic Incompatibility Analysis Identifies Immune Genes as Hotspots of Deleterious Epistasis

    PubMed Central

    Chae, Eunyoung; Bomblies, Kirsten; Kim, Sang-Tae; Karelina, Darya; Zaidem, Maricris; Ossowski, Stephan; Martín-Pizarro, Carmen; Laitinen, Roosa A. E.; Rowan, Beth A.; Tenenboim, Hezi; Lechner, Sarah; Demar, Monika; Habring-Müller, Anette; Lanz, Christa; Rätsch, Gunnar; Weigel, Detlef

    2014-01-01

    Summary Intraspecific genetic incompatibilities prevent the assembly of specific alleles into single genotypes and influence genome- and species-wide patterns of sequence variation. A common incompatibility in plants is hybrid necrosis, characterized by autoimmune responses due to epistatic interactions between natural genetic variants. By systematically testing thousands of F1 hybrids of Arabidopsis thaliana strains, we identified a small number of incompatibility hotspots in the genome, often in regions densely populated by NLR immune receptor genes. In several cases, these immune receptor loci interact with each other, suggestive of conflict within the immune system. A particularly dangerous locus is a highly variable cluster of NLR genes, DANGEROUS MIX2 (DM2), which causes multiple, independent incompatibilities with genes that encode a range of biochemical functions, including NLRs. Our findings suggest that deleterious interactions of immune receptors at the front lines of host-pathogen co-evolution limit the combinations of favorable disease resistance alleles accessible to plant genomes. PMID:25467443

  17. Waveband Analysis of Track Irregularities in High-Speed Railway from On-Board Acceleration Measurement

    NASA Astrophysics Data System (ADS)

    Lee, Jun Seok; Choi, Sunghoon; Kim, Sang-Soo; Kim, Young Guk; Kim, Seog Won; Park, Choonsoo

    This paper is focused on waveband analysis of the lateral and vertical track irregularities from the on-board acceleration measurement of in-service high-speed trains. The track irregularities play important roles to determine dynamic stability of vehicles and ride quality of passengers, so that their amplitude and wavelength should be monitored continuously and carefully. Measuring acceleration at the axle-box or bogie of the trains has been under consideration for low-cost implementation and robust to a harsh railway environment. To estimate the track irregularities, lateral and vertical vibration caused by the wheel/track interaction is measured by the axle-box and bogie mounted accelerometers of an in-service high-speed train. A Kalman filter is used to prevent unrealistic drifts in the estimation. By applying the waveband-pass and compensation filters to the estimated displacement, it is possible to estimate the track irregularities. A distance-wavelength representation is used to identify their waveband in an intuitive way. It is verified by comparing with a commercial track geometry measurement system. From their comparison, it confirms that the representation can produce a satisfactory result.

  18. Analysis of secondary particle behavior in multiaperture, multigrid accelerator for the ITER neutral beam injector.

    PubMed

    Mizuno, T; Taniguchi, M; Kashiwagi, M; Umeda, N; Tobari, H; Watanabe, K; Dairaku, M; Sakamoto, K; Inoue, T

    2010-02-01

    Heat load on acceleration grids by secondary particles such as electrons, neutrals, and positive ions, is a key issue for long pulse acceleration of negative ion beams. Complicated behaviors of the secondary particles in multiaperture, multigrid (MAMuG) accelerator have been analyzed using electrostatic accelerator Monte Carlo code. The analytical result is compared to experimental one obtained in a long pulse operation of a MeV accelerator, of which second acceleration grid (A2G) was removed for simplification of structure. The analytical results show that relatively high heat load on the third acceleration grid (A3G) since stripped electrons were deposited mainly on A3G. This heat load on the A3G can be suppressed by installing the A2G. Thus, capability of MAMuG accelerator is demonstrated for suppression of heat load due to secondary particles by the intermediate grids. PMID:20192410

  19. Analysis of secondary particle behavior in multiaperture, multigrid accelerator for the ITER neutral beam injector

    SciTech Connect

    Mizuno, T.; Taniguchi, M.; Kashiwagi, M.; Umeda, N.; Tobari, H.; Watanabe, K.; Dairaku, M.; Sakamoto, K.; Inoue, T.

    2010-02-15

    Heat load on acceleration grids by secondary particles such as electrons, neutrals, and positive ions, is a key issue for long pulse acceleration of negative ion beams. Complicated behaviors of the secondary particles in multiaperture, multigrid (MAMuG) accelerator have been analyzed using electrostatic accelerator Monte Carlo code. The analytical result is compared to experimental one obtained in a long pulse operation of a MeV accelerator, of which second acceleration grid (A2G) was removed for simplification of structure. The analytical results show that relatively high heat load on the third acceleration grid (A3G) since stripped electrons were deposited mainly on A3G. This heat load on the A3G can be suppressed by installing the A2G. Thus, capability of MAMuG accelerator is demonstrated for suppression of heat load due to secondary particles by the intermediate grids.

  20. Mapa-an object oriented code with a graphical user interface for accelerator design and analysis

    SciTech Connect

    Shasharina, S.G.; Cary, J.R.

    1997-02-01

    We developed a code for accelerator modeling which will allow users to create and analyze accelerators through a graphical user interface (GUI). The GUI can read an accelerator from files or create it by adding, removing and changing elements. It also creates 4D orbits and lifetime plots. The code includes a set of accelerator elements classes, C++ utility and GUI libraries. Due to the GUI, the code is easy to use and expand. {copyright} {ital 1997 American Institute of Physics.}

  1. Mapa-an object oriented code with a graphical user interface for accelerator design and analysis

    SciTech Connect

    Shasharina, Svetlana G.; Cary, John R.

    1997-02-01

    We developed a code for accelerator modeling which will allow users to create and analyze accelerators through a graphical user interface (GUI). The GUI can read an accelerator from files or create it by adding, removing and changing elements. It also creates 4D orbits and lifetime plots. The code includes a set of accelerator elements classes, C++ utility and GUI libraries. Due to the GUI, the code is easy to use and expand.

  2. On the Impact of a Quadratic Acceleration Term in the Analysis of Position Time Series

    NASA Astrophysics Data System (ADS)

    Bogusz, Janusz; Klos, Anna; Bos, Machiel Simon; Hunegnaw, Addisu; Teferle, Felix Norman

    2016-04-01

    The analysis of Global Navigation Satellite System (GNSS) position time series generally assumes that each of the coordinate component series is described by the sum of a linear rate (velocity) and various periodic terms. The residuals, the deviations between the fitted model and the observations, are then a measure of the epoch-to-epoch scatter and have been used for the analysis of the stochastic character (noise) of the time series. Often the parameters of interest in GNSS position time series are the velocities and their associated uncertainties, which have to be determined with the highest reliability. It is clear that not all GNSS position time series follow this simple linear behaviour. Therefore, we have added an acceleration term in the form of a quadratic polynomial function to the model in order to better describe the non-linear motion in the position time series. This non-linear motion could be a response to purely geophysical processes, for example, elastic rebound of the Earth's crust due to ice mass loss in Greenland, artefacts due to deficiencies in bias mitigation models, for example, of the GNSS satellite and receiver antenna phase centres, or any combination thereof. In this study we have simulated 20 time series with different stochastic characteristics such as white, flicker or random walk noise of length of 23 years. The noise amplitude was assumed at 1 mm/y-/4. Then, we added the deterministic part consisting of a linear trend of 20 mm/y (that represents the averaged horizontal velocity) and accelerations ranging from minus 0.6 to plus 0.6 mm/y2. For all these data we estimated the noise parameters with Maximum Likelihood Estimation (MLE) using the Hector software package without taken into account the non-linear term. In this way we set the benchmark to then investigate how the noise properties and velocity uncertainty may be affected by any un-modelled, non-linear term. The velocities and their uncertainties versus the accelerations for

  3. Final safety analysis report for the Ground Test Accelerator (GTA), Phase 2

    SciTech Connect

    1994-10-01

    This document is the first volume of a 3 volume safety analysis report on the Ground Test Accelerator (GTA). The GTA program at the Los Alamos National Laboratory (LANL) is the major element of the national Neutral Particle Beam (NPB) program, which is supported by the Strategic Defense Initiative Office (SDIO). A principal goal of the national NPB program is to assess the feasibility of using hydrogen and deuterium neutral particle beams outside the Earth`s atmosphere. The main effort of the NPB program at Los Alamos concentrates on developing the GTA. The GTA is classified as a low-hazard facility, except for the cryogenic-cooling system, which is classified as a moderate-hazard facility. This volume consists of an introduction, summary/conclusion, site description and assessment, description of facility, and description of operation.

  4. Final safety analysis report for the Ground Test Accelerator (GTA), Phase 2

    SciTech Connect

    1994-10-01

    This document is the third volume of a 3 volume safety analysis report on the Ground Test Accelerator (GTA). The GTA program at the Los Alamos National Laboratory (LANL) is the major element of the national Neutral Particle Beam (NPB) program, which is supported by the Strategic Defense Initiative Office (SDIO). A principal goal of the national NPB program is to assess the feasibility of using hydrogen and deuterium neutral particle beams outside the Earth`s atmosphere. The main effort of the NPB program at Los Alamos concentrates on developing the GTA. The GTA is classified as a low-hazard facility, except for the cryogenic-cooling system, which is classified as a moderate-hazard facility. This volume consists of appendices C through U of the report

  5. On a thermal analysis of a second stripper for rare isotope accelerator.

    SciTech Connect

    Momozaki, Y.; Nolen, J.; Nuclear Engineering Division

    2008-08-04

    This memo summarizes simple calculations and results of the thermal analysis on the second stripper to be used in the driver linac of Rare Isotope Accelerator (RIA). Both liquid (Sodium) and solid (Titanium and Vanadium) stripper concepts were considered. These calculations were intended to provide basic information to evaluate the feasibility of liquid (thick film) and solid (rotating wheel) second strippers. Nuclear physics calculations to estimate the volumetric heat generation in the stripper material were performed by 'LISE for Excel'. In the thermal calculations, the strippers were modeled as a thin 2D plate with uniform heat generation within the beam spot. Then, temperature distributions were computed by assuming that the heat spreads conductively in the plate in radial direction without radiative heat losses to surroundings.

  6. Accelerated Monte Carlo Simulation for Safety Analysis of the Advanced Airspace Concept

    NASA Technical Reports Server (NTRS)

    Thipphavong, David

    2010-01-01

    Safe separation of aircraft is a primary objective of any air traffic control system. An accelerated Monte Carlo approach was developed to assess the level of safety provided by a proposed next-generation air traffic control system. It combines features of fault tree and standard Monte Carlo methods. It runs more than one order of magnitude faster than the standard Monte Carlo method while providing risk estimates that only differ by about 10%. It also preserves component-level model fidelity that is difficult to maintain using the standard fault tree method. This balance of speed and fidelity allows sensitivity analysis to be completed in days instead of weeks or months with the standard Monte Carlo method. Results indicate that risk estimates are sensitive to transponder, pilot visual avoidance, and conflict detection failure probabilities.

  7. Accelerator-Based PIXE and STIM Analysis of Candidate Solar Sail Materials

    SciTech Connect

    Hollerman, W.A.; Stanaland, T.L.; Boudreaux, P.; Elberson, L.; Fontenot, J.; Gates, E.; Greco, R.; McBride, M.; Woodward, A.; Edwards, D.

    2003-08-26

    Solar sailing is a unique form of propulsion where a spacecraft gains momentum from incident photons. A totally reflective sail experiences a pressure of 9.1 {mu}Pa at a distance of 1 AU from the Sun. Since sails are not limited by reaction mass, they provide continual acceleration, reduced only by the lifetime of the lightweight film in the space environment and the distance to the Sun. Practical solar sails can expand the number of possible missions, enabling new concepts that are difficult by conventional means. One of the current challenges is to develop strong, lightweight, and radiation resistant sail materials. This paper will discuss initial results from a Particle Induced X-Ray Emission (PIXE) and Scanning Transmission Ion Microscopy (STIM) analysis of candidate solar sail materials.

  8. Detailed analysis of Honeywell In-Space Accelerometer data - STS-32. [crystal microstructure response to different types of residual acceleration

    NASA Technical Reports Server (NTRS)

    Rogers, Melissa J. B.; Alexander, J. I. D.; Schoess, Jeff

    1993-01-01

    The Honeywell In-Space Accelerometer (HISA) system collected data in the mid-deck area of the Shuttle Columbia during the flight of STS-32, January 1990. The resulting data were to be used to investigate the response of crystal microstructure to different types of residual acceleration. The HISA is designed to detect and record transient and oscillatory accelerations. The sampling and electronics package stored averaged accelerations over two sampling periods; two sampling rates were available: 1 Hz and 50 Hz. Analysis of the HISA data followed the CMMR Acceleration Data Processing Guide, considering in-house computer modelling of a float-zone indium crystal growth experiment. Characteristic examples of HISA data showing the response to the primary reaction control system, Orbiter Maneuvering System operations, and crew treadmill activity are presented. Various orbiter structural modes are excited by these and other activities.

  9. Groundwater modelling: Towards an estimation of the acceleration factors of iterative methods via an analysis of the transmissivity spatial variability

    NASA Astrophysics Data System (ADS)

    Benali, Abdelmajid

    2013-01-01

    When running a groundwater flow model, a recurrent and seemingly subsidiary question arises at the starting step of computations: what value of acceleration parameter do we need to optimize the numerical solver? A method is proposed to provide a practical estimate of the optimal acceleration parameter via a geostatistical analysis of the spatial variability of the logarithm of the transmissivity field Y. The background of the approach is illustrated on the successive over-relaxation method (SOR) used, either as a stand-alone solver, or as a symmetric preconditioner (SSOR) to the gradient conjugate method, or as a smoother in multigrid methods. It shows that this optimum acceleration factor is a function of the standard deviation and the correlation length of Y. This provides an easy-to-use heuristic procedure to estimate the acceleration factors, which could even be incorporated in the software package. A case study illustrates the steps needed to perform this estimation.

  10. Variability in Working Memory Performance Explained by Epistasis versus Polygenic Scores in the ZNF804A Pathway

    PubMed Central

    Morris, Derek; Anney, Richard; Gill, Michael; Corvin, Aiden; Donohoe, Gary

    2015-01-01

    Importance We investigated the variation in neuropsychological function explained by risk alleles at the psychosis susceptibility gene ZNF804A and its interacting partners using single nucleotide polymorphisms (SNPs), polygenic score and epistatic analyses. Of particular importance was the relative contribution of the polygenic score versus epistasis in variation explained. Objective The objectives were twofold: first, to assess the association between SNPs in ZNF804A and the ZNF804A polygenic score with measures of cognition in cases with psychosis. The second was to assess whether epistasis within the ZNF804A pathway could explain additional variation above and beyond that explained by the polygenic score. Design, Setting and Participants Patients with psychosis (N = 424) were assessed in areas of cognitive ability impaired in schizophrenia including IQ, memory, attention and social cognition. We used the Psychiatric GWAS Consortium (PGC1) schizophrenia GWAS to calculate a polygenic score based on identified risk variants within this genetic pathway. Cognitive measures significantly associated with the polygenic score were tested for an epistatic component using a training set (N = 170), which was used to develop linear regression models containing the polygenic score and two-SNP interactions. The best-fitting models were tested for replication in two independent test sets of cases: 1) 170 individuals with schizophrenia or schizoaffective disorder and 2) 84 patients with broad psychosis (including bipolar disorder, major depressive disorder and other psychosis). Results Higher polygenic scores were associated with poorer performance amongst patients on IQ, memory and social cognition, explaining 1-3% of variation on these scores (p-values ranged from 0.012-0.034). Using a narrow psychosis training set and independent test sets of narrow phenotype psychosis (schizophrenia and schizoaffective disorder), broad psychosis, and controls (N = 89) respectively, the

  11. Soil dynamics and accelerated erosion: a sensitivity analysis of the LPJ Dynamic vegetation model

    NASA Astrophysics Data System (ADS)

    Bouchoms, Samuel; Van Oost, Kristof; Vanacker, Veerle; Kaplan, Jed O.; Vanwalleghem, Tom

    2013-04-01

    It is widely accepted that humans have become a major geomorphic force by disturbing natural vegetation patterns. Land conversion for agriculture purposes removes the protection of soils by the natural vegetation and leads to increased soil erosion by one to two orders of magnitude, breaking the balance that exists between the loss of soils and its production. Accelerated erosion and deposition have a strong influence on evolution and heterogeneity of basic soil characteristics (soil thickness, hydrology, horizon development,…) as well as on organic matter storage and cycling. Yet, since they are operating at a long time scale, those processes are not represented in state-of-art Dynamic Global Vegetation Models, which is a clear lack when exploring vegetation dynamics over past centuries. The main objectives of this paper are (i) to test the sensitivity of a Dynamic Global Vegetation Model, in terms of NPP and organic matter turnover, variations in state variables in response to accelerated erosion and (ii) to assess the performance of the model under the impact of erosion for a case-study in Central Spain. We evaluated the Lund-Postdam-Jena Dynamic Vegetation Model (LPJ DVGM) (Sitch et al, 2003) which simulates vegetation growth and carbon pools at the surface and in the soil based on climatic, pedologic and topographic variables. We assessed its reactions to changes in key soil properties that are affected by erosion such as texture and soil depth. We present the results of where we manipulated soil texture and bulk density while keeping the environmental drivers of climate, slope and altitude constant. For parameters exhibiting a strong control on NPP or SOM, a factorial analysis was conducted to test for interaction effects. The simulations show an important dependence on the clay content, especially for the slow cycling carbon pools and the biomass production, though the underground litter seems to be mostly influenced by the silt content. The fast cycling C

  12. Accelerating Data Acquisition, Reduction, and Analysis at the Spallation Neutron Source

    SciTech Connect

    Campbell, Stuart I; Kohl, James Arthur; Granroth, Garrett E; Miller, Ross G; Doucet, Mathieu; Stansberry, Dale V; Proffen, Thomas E; Taylor, Russell J; Dillow, David

    2014-01-01

    ORNL operates the world's brightest neutron source, the Spallation Neutron Source (SNS). Funded by the US DOE Office of Basic Energy Science, this national user facility hosts hundreds of scientists from around the world, providing a platform to enable break-through research in materials science, sustainable energy, and basic science. While the SNS provides scientists with advanced experimental instruments, the deluge of data generated from these instruments represents both a big data challenge and a big data opportunity. For example, instruments at the SNS can now generate multiple millions of neutron events per second providing unprecedented experiment fidelity but leaving the user with a dataset that cannot be processed and analyzed in a timely fashion using legacy techniques. To address this big data challenge, ORNL has developed a near real-time streaming data reduction and analysis infrastructure. The Accelerating Data Acquisition, Reduction, and Analysis (ADARA) system provides a live streaming data infrastructure based on a high-performance publish subscribe system, in situ data reduction, visualization, and analysis tools, and integration with a high-performance computing and data storage infrastructure. ADARA allows users of the SNS instruments to analyze their experiment as it is run and make changes to the experiment in real-time and visualize the results of these changes. In this paper we describe ADARA, provide a high-level architectural overview of the system, and present a set of use-cases and real-world demonstrations of the technology.

  13. Analysis of graduates' perceptions of an accelerated bachelor of science program in nursing.

    PubMed

    Kemsley, Martha; McCausland, Linda; Feigenbaum, Janice; Riegle, Elizabeth

    2011-01-01

    Rapid expansion of second-degree programs as one approach to addressing the nursing shortage by increasing the number of graduates in shorter periods of time prompted the need for program evaluation to identify the outcomes, strengths, and best practices of these programs. This study used both quantitative and qualitative methods of inquiry to analyze the responses of 28 of 56 recent graduates of an accelerated baccalaureate program. Respondents rated components of the program from preadmission to graduation on a Likert scale and responded to open-ended questions regarding strengths and weaknesses of the program. Analysis included descriptive statistics for quantitative data and content analysis for qualitative data. The analysis showed a high degree of similarity between the quantitative and qualitative data. Highly rated program components, that is, opportunity for graduate course work and integration with graduate students, clinical skill practice and experiences, variety of teaching methodologies, peer and faculty support, were reflected in the themes of cohort bonding, variety of clinical experiences, and supportive faculty and staff. Outcomes of program satisfaction, National Council Licensure Examination pass rates, successful nursing employment, and graduate school attendance were supported by the data. PMID:21272836

  14. Final safety analysis report for the Ground Test Accelerator (GTA), Phase 2

    SciTech Connect

    1994-10-01

    This document is the second volume of a 3 volume safety analysis report on the Ground Test Accelerator (GTA). The GTA program at the Los Alamos National Laboratory (LANL) is the major element of the national Neutral Particle Beam (NPB) program, which is supported by the Strategic Defense Initiative Office (SDIO). A principal goal of the national NPB program is to assess the feasibility of using hydrogen and deuterium neutral particle beams outside the Earth`s atmosphere. The main effort of the NPB program at Los Alamos concentrates on developing the GTA. The GTA is classified as a low-hazard facility, except for the cryogenic-cooling system, which is classified as a moderate-hazard facility. This volume consists of failure modes and effects analysis; accident analysis; operational safety requirements; quality assurance program; ES&H management program; environmental, safety, and health systems critical to safety; summary of waste-management program; environmental monitoring program; facility expansion, decontamination, and decommissioning; summary of emergency response plan; summary plan for employee training; summary plan for operating procedures; glossary; and appendices A and B.

  15. The Valley-of-Death: reciprocal sign epistasis constrains adaptive trajectories in a constant, nutrient limiting environment.

    PubMed

    Chiotti, Kami E; Kvitek, Daniel J; Schmidt, Karen H; Koniges, Gregory; Schwartz, Katja; Donckels, Elizabeth A; Rosenzweig, Frank; Sherlock, Gavin

    2014-12-01

    The fitness landscape is a powerful metaphor for describing the relationship between genotype and phenotype for a population under selection. However, empirical data as to the topography of fitness landscapes are limited, owing to difficulties in measuring fitness for large numbers of genotypes under any condition. We previously reported a case of reciprocal sign epistasis (RSE), where two mutations individually increased yeast fitness in a glucose-limited environment, but reduced fitness when combined, suggesting the existence of two peaks on the fitness landscape. We sought to determine whether a ridge connected these peaks so that populations founded by one mutant could reach the peak created by the other, avoiding the low-fitness "Valley-of-Death" between them. Sequencing clones after 250 generations of further evolution provided no evidence for such a ridge, but did reveal many presumptive beneficial mutations, adding to a growing body of evidence that clonal interference pervades evolving microbial populations. PMID:25449178

  16. Sociocultural epistasis and cultural exaptation in footbinding, marriage form, and religious practices in early 20th-century Taiwan.

    PubMed

    Brown, Melissa J; Feldman, Marcus W

    2009-12-29

    Social theorists have long recognized that changes in social order have cultural consequences but have not been able to provide an individual-level mechanism of such effects. Explanations of human behavior have only just begun to explore the different evolutionary dynamics of social and cultural inheritance. Here we provide ethnographic evidence of how cultural evolution, at the level of individuals, can be influenced by social evolution. Sociocultural epistasis--association of cultural ideas with the hierarchical structure of social roles--influences cultural change in unexpected ways. We document the existence of cultural exaptation, where a custom's origin was not due to acceptance of the later associated ideas. A cultural exaptation can develop in the absence of a cultural idea favoring it, or even in the presence of a cultural idea against it. Such associations indicate a potentially larger role for social evolutionary dynamics in explaining individual human behavior than previously anticipated. PMID:20080786

  17. Epistasis and the Genetic Divergence of Photoperiodism between Populations of the Pitcher-Plant Mosquito, Wyeomyia Smithii

    PubMed Central

    Hard, J. J.; Bradshaw, W. E.; Holzapfel, C. M.

    1992-01-01

    Parallel crosses between each of two southern (ancestral) and one northern (derived) population of the pitcher-plant mosquito, Wyeomyia smithii, were made to determine the genetic components of population divergence in critical photoperiod, a phenological trait that measures adaptation to seasonality along a climatic gradient. Joint scaling tests were used to analyze means and variances of first- and second-generation hybrids in order to determine whether nonadditive genetic variance, especially epistatic variance, contributed to divergence in critical photoperiod. In both crosses, digenic epistatic effects were highly significant, indicating that genetic divergence cannot have resulted solely from differences in additively acting loci. For one cross that could be tested directly for such effects, higher order epistasis and/or linkage did not contribute to the divergence of critical photoperiod between the constituent populations. PMID:1353737

  18. Epistasis and the genetic divergence of photoperiodism between populations of the pitcher-plant mosquito, Wyeomyia smithii.

    PubMed

    Hard, J J; Bradshaw, W E; Holzapfel, C M

    1992-06-01

    Parallel crosses between each of two southern (ancestral) and one northern (derived) population of the pitcher-plant mosquito, Wyeomyia smithii, were made to determine the genetic components of population divergence in critical photoperiod, a phenological trait that measures adaptation to seasonality along a climatic gradient. Joint scaling tests were used to analyze means and variances of first- and second-generation hybrids in order to determine whether nonadditive genetic variance, especially epistatic variance, contributed to divergence in critical photoperiod. In both crosses, digenic epistatic effects were highly significant, indicating that genetic divergence cannot have resulted solely from differences in additively acting loci. For one cross that could be tested directly for such effects, higher order epistasis and/or linkage did not contribute to the divergence of critical photoperiod between the constituent populations. PMID:1353737

  19. Partial Dominance, Overdominance and Epistasis as the Genetic Basis of Heterosis in Upland Cotton (Gossypium hirsutum L.)

    PubMed Central

    Wang, Yumei; Hua, Jinping

    2015-01-01

    Determination of genetic basis of heterosis may promote hybrid production in Upland cotton (Gossypium hirsutum L.). This study was designed to explore the genetic mechanism of heterosis for yield and yield components in F2: 3 and F2: 4 populations derived from a hybrid ‘Xinza No. 1’. Replicated yield field trials of the progenies were conducted in 2008 and 2009. Phenotypic data analyses indicated overdominance in F1 for yield and yield components. Additive and dominance effects at single-locus level and digenic epistatic interactions at two-locus level were analyzed by 421 marker loci spanning 3814 cM of the genome. A total of 38 and 49 QTLs controlling yield and yield components were identified in F2: 3 and F2: 4 populations, respectively. Analyses of these QTLs indicated that the effects of partial dominance and overdominance contributed to heterosis in Upland cotton simultaneously. Most of the QTLs showed partial dominance whereas 13 QTLs showing overdominance in F2:3 population, and 19 QTLs showed overdominance in F2:4. Among them, 21 QTLs were common in both F2: 3 and F2: 4 populations. A large number of two-locus interactions for yield and yield components were detected in both generations. AA (additive × additive) epistasis accounted for majority portion of epistatic effects. Thirty three complementary two-locus homozygotes (11/22 and 22/11) were the best genotypes for AA interactions in terms of bolls per plant. Genotypes of double homozygotes, 11/22, 22/11 and 22/22, performed best for AD/DA interactions, while genotype of 11/12 performed best for DD interactions. These results indicated that (1) partial dominance and overdominance effects at single-locus level and (2) epistasis at two-locus level elucidated the genetic basis of heterosis in Upland cotton. PMID:26618635

  20. Epistasis for Fitness-Related Quantitative Traits in Arabidopsis thaliana Grown in the Field and in the Greenhouse

    PubMed Central

    Malmberg, Russell L.; Held, Stephanie; Waits, Ashleigh; Mauricio, Rodney

    2005-01-01

    The extent to which epistasis contributes to adaptation, population differentiation, and speciation is a long-standing and important problem in evolutionary genetics. Using recombinant inbred (RI) lines of Arabidopsis thaliana grown under natural field conditions, we have examined the genetic architecture of fitness-correlated traits with respect to epistasis; we identified both single-locus additive and two-locus epistatic QTL for natural variation in fruit number, germination, and seed length and width. For fruit number, we found seven significant epistatic interactions, but only two additive QTL. For seed germination, length, and width, there were from two to four additive QTL and from five to eight epistatic interactions. The epistatic interactions were both positive and negative. In each case, the magnitude of the epistatic effects was roughly double that of the effects of the additive QTL, varying from −41% to +29% for fruit number and from −5% to +4% for seed germination, length, and width. A number of the QTL that we describe participate in more than one epistatic interaction, and some loci identified as additive also may participate in an epistatic interaction; the genetic architecture for fitness traits may be a network of additive and epistatic effects. We compared the map positions of the additive and epistatic QTL for germination, seed width, and seed length from plants grown in both the field and the greenhouse. While the total number of significant additive and epistatic QTL was similar under the two growth conditions, the map locations were largely different. We found a small number of significant epistatic QTL × environment effects when we tested directly for them. Our results support the idea that epistatic interactions are an important part of natural genetic variation and reinforce the need for caution in comparing results from greenhouse-grown and field-grown plants. PMID:16157670

  1. Rift strength controls rapid plate accelerations: A global analysis of Pangea fragmentation

    NASA Astrophysics Data System (ADS)

    Brune, S.; Williams, S.; Butterworth, N. P.; Müller, D.

    2015-12-01

    Motions of Earth's plates are thought to be driven by slab pull, basal drag, and ridge push. Here we propose that plate motions during supercontinental fragmentation are decisively controlled by the non-linear decay of a resistive force: rift strength. We use state-of-the-art global tectonic reconstructions and the new geotectonic analysis tool pyGPlates to analyze the transition from rifting to sea-floor spreading of well-studied post-Pangea rift systems (Central Atlantic, South Atlantic, Iberia/Newfoundland, Australia/Antarctica, North Atlantic, South China Sea, Gulf of California). In all cases, continental extension starts with a slow phase (< 10 mm/yr, full extension velocity) followed by a rapid acceleration over periods of a few My that introduces a fast rift phase (> 10 mm/yr). The transition from slow to fast extension takes place long before crustal break-up. In fact, we find that approximately half of the present day rifted margin area was created during the slow, and the other half during the fast phase. We reproduce the transition from slow to fast rifting using numerical forward models with force boundary conditions, such that rift velocities are not imposed but instead evolve naturally in response to changing strength of the rift. These models show that the two-phase velocity behavior during rifting and the rapid speed-up are intrinsic features of continental rupture that can be robustly inferred for different crust and mantle rheologies.It has been proposed that abrupt plate accelerations can be caused by plume-lithosphere interaction, subduction initiation, and slab detachment. However, none of these mechanisms explains our result that plate speed-up systematically precedes continental break-up. We therefore propose dynamic rift weakening as a new mechanism for rapid plate motion changes.

  2. Effect of acceleration on osteoblastic and osteoclastic activities: Analysis of bone metabolism using goldfish scale as a model for bone

    NASA Astrophysics Data System (ADS)

    Suzuki, S.; Kitamura, K.; Nemoto, N.; Shimizu, S.; Wada, W.; Kondo, K.; Tabata, T.; Sodeyama, S.; Ijiri, I.; Hattori, H.

    It is well known that hypo-gravity and hyper-gravity influence bone metabolism However basic data concerning the mechanism are a few because no in vitro model system of human bone is available Human bone consists of osteoblasts osteoclasts and the bone matrix No technique for the co-culture of these components has ever been developed Fish scale is a calcified tissue that contains osteoblasts osteoclasts and bone matrix all of which are similar to those found in human bone Recently we developed a new in vitro model system using goldfish scale This system can simultaneously detect the activities of both scale osteoclasts and osteoblasts with tartrate-resistant acid phosphatase and alkaline phosphatase as the respective markers Using this system we analyzed the bone metabolism under acceleration with a custom-made G-load apparatus Osteoclastic activity in the goldfish scales was suppressed under low-acceleration 0 5-G while osteoblastic activity did not change under this acceleration Under high-acceleration 6-G however the osteoblastic activity of the scales increased In addition the osteoclastic activity of the scales decreased These results suggest that both osteoblastic and osteoclastic activities are regulated by the strength of acceleration Therefore we strongly believe that our in vitro system is useful for analysis of bone metabolism under acceleration

  3. Genome-wide association interaction analysis for Alzheimer's disease

    PubMed Central

    Gusareva, Elena S.; Carrasquillo, Minerva M.; Bellenguez, Céline; Cuyvers, Elise; Colon, Samuel; Graff-Radford, Neill R.; Petersen, Ronald C.; Dickson, Dennis W.; Mahachie Johna, Jestinah M.; Bessonov, Kyrylo; Van Broeckhoven, Christine; Williams, Julie; Amouyel, Philippe; Sleegers, Kristel; Ertekin-Taner, Nilüfer; Lambert, Jean-Charles; Van Steen, Kristel

    2015-01-01

    We propose a minimal protocol for exhaustive genome-wide association interaction analysis that involves screening for epistasis over large-scale genomic data combining strengths of different methods and statistical tools. The different steps of this protocol are illustrated on a real-life data application for Alzheimer's disease (AD) (2259 patients and 6017 controls from France). Particularly, in the exhaustive genome-wide epistasis screening we identified AD-associated interacting SNPs-pair from chromosome 6q11.1 (rs6455128, the KHDRBS2 gene) and 13q12.11 (rs7989332, the CRYL1 gene) (p = 0.006, corrected for multiple testing). A replication analysis in the independent AD cohort from Germany (555 patients and 824 controls) confirmed the discovered epistasis signal (p = 0.036). This signal was also supported by a meta-analysis approach in 5 independent AD cohorts that was applied in the context of epistasis for the first time. Transcriptome analysis revealed negative correlation between expression levels of KHDRBS2 and CRYL1 in both the temporal cortex (β = −0.19, p = 0.0006) and cerebellum (β = −0.23, p < 0.0001) brain regions. This is the first time a replicable epistasis associated with AD was identified using a hypothesis free screening approach. PMID:24958192

  4. Foreign exchange market data analysis reveals statistical features that predict price movement acceleration

    NASA Astrophysics Data System (ADS)

    Nacher, Jose C.; Ochiai, Tomoshiro

    2012-05-01

    Increasingly accessible financial data allow researchers to infer market-dynamics-based laws and to propose models that are able to reproduce them. In recent years, several stylized facts have been uncovered. Here we perform an extensive analysis of foreign exchange data that leads to the unveiling of a statistical financial law. First, our findings show that, on average, volatility increases more when the price exceeds the highest (or lowest) value, i.e., breaks the resistance line. We call this the breaking-acceleration effect. Second, our results show that the probability P(T) to break the resistance line in the past time T follows power law in both real data and theoretically simulated data. However, the probability calculated using real data is rather lower than the one obtained using a traditional Black-Scholes (BS) model. Taken together, the present analysis characterizes a different stylized fact of financial markets and shows that the market exceeds a past (historical) extreme price fewer times than expected by the BS model (the resistance effect). However, when the market does, we predict that the average volatility at that time point will be much higher. These findings indicate that any Markovian model does not faithfully capture the market dynamics.

  5. Spectral reconstruction by scatter analysis for a linear accelerator photon beam.

    PubMed

    Jalbout, Wassim T; Spyrou, Nicholas M

    2006-05-01

    Pre-existing methods for photon beam spectral reconstruction are briefly reviewed. An alternative reconstruction method by scatter analysis for linear accelerators is introduced. The method consists in irradiating a small plastic phantom at standard 100 cm SSD and inferring primary beam energy spectral information based on the measurement with a standard Farmer chamber of scatter around the phantom at several specific scatter angles: a scatter curve is measured which is indicative of the primary spectrum at hand. A Monte Carlo code is used to simulate the scatter measurement set-up and predict the relative magnitude of scatter measurements for mono-energetic primary beams. Based on mono-energetic primary scatter data, measured scatter curves are analysed and the spectrum unfolded as the sum of mono-energetic individual energy bins using the Schiff bremsstrahlung model. The method is applied to an Elekta/SL18 6 MV photon beam. The reconstructed spectrum matches the Monte Carlo calculated spectrum for the same beam within 6.2% (average error when spectra are compared bin by bin). Depth dose values calculated for the reconstructed spectrum agree with physically measured depth dose data to within 1%. Scatter analysis is preliminarily shown to have potential as a practical spectral reconstruction method requiring few measurements under standard 100 cm SSD and feasible in any radiotherapy department using a phantom and a Farmer chamber. PMID:16625037

  6. Foreign exchange market data analysis reveals statistical features that predict price movement acceleration.

    PubMed

    Nacher, Jose C; Ochiai, Tomoshiro

    2012-05-01

    Increasingly accessible financial data allow researchers to infer market-dynamics-based laws and to propose models that are able to reproduce them. In recent years, several stylized facts have been uncovered. Here we perform an extensive analysis of foreign exchange data that leads to the unveiling of a statistical financial law. First, our findings show that, on average, volatility increases more when the price exceeds the highest (or lowest) value, i.e., breaks the resistance line. We call this the breaking-acceleration effect. Second, our results show that the probability P(T) to break the resistance line in the past time T follows power law in both real data and theoretically simulated data. However, the probability calculated using real data is rather lower than the one obtained using a traditional Black-Scholes (BS) model. Taken together, the present analysis characterizes a different stylized fact of financial markets and shows that the market exceeds a past (historical) extreme price fewer times than expected by the BS model (the resistance effect). However, when the market does, we predict that the average volatility at that time point will be much higher. These findings indicate that any Markovian model does not faithfully capture the market dynamics. PMID:23004832

  7. Hyperfractionated or Accelerated Radiotherapy in Lung Cancer: An Individual Patient Data Meta-Analysis

    PubMed Central

    Mauguen, Audrey; Le Péchoux, Cécile; Saunders, Michele I.; Schild, Steven E.; Turrisi, Andrew T.; Baumann, Michael; Sause, William T.; Ball, David; Belani, Chandra P.; Bonner, James A.; Zajusz, Aleksander; Dahlberg, Suzanne E.; Nankivell, Matthew; Mandrekar, Sumithra J.; Paulus, Rebecca; Behrendt, Katarzyna; Koch, Rainer; Bishop, James F.; Dische, Stanley; Arriagada, Rodrigo; De Ruysscher, Dirk; Pignon, Jean-Pierre

    2012-01-01

    Purpose In lung cancer, randomized trials assessing hyperfractionated or accelerated radiotherapy seem to yield conflicting results regarding the effects on overall (OS) or progression-free survival (PFS). The Meta-Analysis of Radiotherapy in Lung Cancer Collaborative Group decided to address the role of modified radiotherapy fractionation. Material and Methods We performed an individual patient data meta-analysis in patients with nonmetastatic lung cancer, which included trials comparing modified radiotherapy with conventional radiotherapy. Results In non–small-cell lung cancer (NSCLC; 10 trials, 2,000 patients), modified fractionation improved OS as compared with conventional schedules (hazard ratio [HR] = 0.88, 95% CI, 0.80 to 0.97; P = .009), resulting in an absolute benefit of 2.5% (8.3% to 10.8%) at 5 years. No evidence of heterogeneity between trials was found. There was no evidence of a benefit on PFS (HR = 0.94; 95% CI, 0.86 to 1.03; P = .19). Modified radiotherapy reduced deaths resulting from lung cancer (HR = 0.89; 95% CI, 0.81 to 0.98; P = .02), and there was a nonsignificant reduction of non–lung cancer deaths (HR = 0.87; 95% CI, 0.66 to 1.15; P = .33). In small-cell lung cancer (SCLC; two trials, 685 patients), similar results were found: OS, HR = 0.87, 95% CI, 0.74 to 1.02, P = .08; PFS, HR = 0.88, 95% CI, 0.75 to 1.03, P = .11. In both NSCLC and SCLC, the use of modified radiotherapy increased the risk of acute esophageal toxicity (odds ratio [OR] = 2.44 in NSCLC and OR = 2.41 in SCLC; P < .001) but did not have an impact on the risk of other acute toxicities. Conclusion Patients with nonmetastatic NSCLC derived a significant OS benefit from accelerated or hyperfractionated radiotherapy; a similar but nonsignificant trend was observed for SCLC. As expected, there was increased acute esophageal toxicity. PMID:22753901

  8. Analysis of transmitted optical spectrum enabling accelerated testing of multijunction concentrating photovoltaic designs

    NASA Astrophysics Data System (ADS)

    Miller, David C.; Kempe, Michael D.; Kennedy, Cheryl E.; Kurtz, Sarah R.

    2011-01-01

    Concentrating photovoltaic (CPV) technology has recently gained interest based on its scalability and expected low levelized cost of electricity. The reliability of encapsulation materials used in CPV systems, however, is not well established. For example, the present qualification test for CPV modules includes only real-time ultraviolet (UV) exposure, i.e., methods for accelerated UV testing have not yet been developed. To better define the stress inherent to CPV systems, the UV and infrared spectra transmitted through representative optical systems were evaluated. Measurements of optical components are used to assess expected optical performance and quantify damaging optical exposure. Optical properties (transmittance, refractive index, reflectance, and absorptance) of candidate materials (including PMMA, soda-lime glass, borosilicate glass, and quartz refractors), components (including Ag- and Al-enabled reflectors), and encapsulants (including EVA, ionomer, PDMS, PPMS, polyolefin, and PVB) were identified. The activation spectrum was calculated for the representative optical systems using an assumed action spectrum to compare the expected damaging dose of UV radiation delivered to the cell encapsulation. The dose and flux analysis identifies the significance of IR relative to UV exposure for CPV systems. Because UV light is typically more highly attenuated, the UV dose within the encapsulation may not greatly exceed the unconcentrated global solar condition, but the thermal load scales nearly directly with the geometric concentration. Relative to a previous analysis for crystalline silicon cell technology, the analysis here is performed for III-V multijunction technology. Novel aspects here also include additional materials (such as TPU encapsulation) and additional components (transmission through silicone on glass lenses, antireflective coatings, and the front glass used with reflective systems, as well as reflection off of the cell).

  9. Evaluation and analysis of the residual radioactivity for the 15UD Pelletron accelerator facility

    SciTech Connect

    Sonkawade, R. G.

    2007-07-01

    For the assessment of radiological impact of the accelerators, it will be better to have the documented information on activation of metal parts of the accelerator components. It is very much essential to get reliable data on these subjects. During acceleration of light ion, the residual radioactivity in the accelerator facility was found near the Analyzing Magnet, single slit, Beam Profile Monitors (BPM), Faraday Cups (FC), bellows, beginning of switching magnet bellows, at the target and the ladder. Study with HPGE detector gives an insight of the formation of the short or long lived radionuclides. The different targets used in the light ion experiment were also monitored and proper decommissioning and decontamination steps were followed. This paper presents the data of residual radioactivity in the 15UD Pelletron accelerator infrastructure. (author)

  10. Numerical Analysis of MHD Accelerator with Non-Equilibrium Air Plasma

    NASA Astrophysics Data System (ADS)

    Anwari, M.; H. Qazi, H.; Sukarsan; Harada, N.

    2012-12-01

    Magnetohydrodynamic (MHD) accelerator is proposed as a next generation propulsion system. It can be used to increase the performance of a propulsion system. The objective of this study is to investigate the performance of MHD accelerator using non-equilibrium air plasma as working gas. In this study, the fundamental performance of MHD accelerator such as flow performance and electrical performance is evaluated at different levels of applied magnetic field using 1-D numerical simulation. The numerical simulation is developed based on a set of differential equations with MHD approximation. To solve this set of differential equations the MacCormack scheme is used. A specified channel designed and developed at NASA Marshall Space Flight Centre is used in the numerical simulation. The composition of the simulated air plasma consists of seven species, namely, N2, N, O2, O, NO, NO+, and e-. The performance of the non-equilibrium MHD accelerator is also compared with the equilibrium MHD accelerator.

  11. Masking Epistasis Between MYC and TGF-β Pathways in Antiangiogenesis-Mediated Colon Cancer Suppression

    PubMed Central

    2014-01-01

    Background The c-Myc oncoprotein is activated in the majority of colorectal cancers (CRCs), whereas the TGF-β pathway is frequently affected by loss-of-function mutations, for example in SMAD2/3/4 genes. The canonical model places Myc downstream of inhibitory TGF-β signaling. However, we previously demonstrated that Myc also inhibits TGF-β signaling through the miR-17~92 microRNA cluster, raising the question about functional relationships between these two pathways. Methods We engineered a series of genetically complex murine and human CRC cell lines in which Myc and TGF-β activities could be manipulated simultaneously. This was achieved through retroviral expression of the Myc–estrogen receptor fusion protein and through Smad4 short hairpin RNA knockdown. Cell lines thus modified were injected subcutaneously in immunocompromised mice, and the resultant tumors (n = 5–10 per treatment group) were analyzed for overall growth and neovascularization. Additionally, the distribution of MYC and TGF-β pathway mutations was analyzed in previously profiled human CRC samples. Results In kras-mutated/trp53-deleted murine colonocytes, either Myc activation or TGF-β inactivation increased tumor sizes and microvascular densities approximately 1.5- to 2.5-fold, chiefly through downregulation of thrombospondin-1 and related type I repeat–containing proteins. Combining Myc activation with TGF-β inactivation did not further accelerate tumorigenesis. This redundancy and the negative effect of TGF-β signaling on angiogenesis were also demonstrated using xenografts of human CRC cell lines. Furthermore, the analysis of the Cancer Genome Atlas data revealed that in CRC without microsatellite instability, overexpression of Myc and inactivation of Smads (including acquired mutations in SMAD2) are mutually exclusive, with odds ratio less than 0.1. Conclusions In human CRC, gain-of-function alterations in Myc and loss-of-function alterations in TGF-β exhibit a masking

  12. Sample distillation/graphitization system for carbon pool analysis by accelerator mass spectrometry (AMS)

    NASA Astrophysics Data System (ADS)

    Pohlman, J. W.; Knies, D. L.; Grabowski, K. S.; DeTurck, T. M.; Treacy, D. J.; Coffin, R. B.

    2000-10-01

    A facility at the Naval Research Laboratory (NRL), Washington, DC, has been developed to extract, trap, cryogenically distill and graphitize carbon from a suite of organic and inorganic carbon pools for analysis by accelerator mass spectrometry (AMS). The system was developed to investigate carbon pools associated with the formation and stability of methane hydrates. However, since the carbon compounds found in hydrate fields are ubiquitous in aquatic ecosystems, this apparatus is applicable to a number of oceanographic and environmental sample types. Targeted pools are dissolved methane, dissolved organic carbon (DOC), dissolved inorganic carbon (DIC), solid organic matrices (e.g., seston, tissue and sediments), biomarkers and short chained (C 1-C 5) hydrocarbons from methane hydrates. In most instances, the extraction, distillation and graphitization events are continuous within the system, thus, minimizing the possibility of fractionation or contamination during sample processing. A variety of methods are employed to extract carbon compounds and convert them to CO 2 for graphitization. Dissolved methane and DIC from the same sample are sparged and cryogenically separated before the methane is oxidized in a high temperature oxygen stream. DOC is oxidized to CO 2 by 1200 W ultraviolet photo-oxidation lamp, and solids oxidized in sealed, evacuated tubes. Hydrocarbons liberated from the disassociation of gas hydrates are cryogenically separated with a cryogenic temperature control unit, and biomarkers separated and concentrated by preparative capillary gas chromatography (PCGC). With this system, up to 20 samples, standards or blanks can be processed per day.

  13. Cost Based Failure Modes and Effects Analysis (FMEA) for Systems of Accelerator Magnets.

    SciTech Connect

    Spencer, Cherrill M

    2003-06-02

    The proposed Next Linear Collider (NLC) has a proposed 85% overall availability goal, the availability specifications for all its 7200 magnets and their 6167 power supplies are 97.5% each. Thus all of the electromagnets and their power supplies must be highly reliable or quickly repairable. Improved reliability or repairability comes at a higher cost. We have developed a set of analysis procedures for magnet designers to use as they decide how much effort to exert, i.e. how much money to spend, to improve the reliability of a particular style of magnet. We show these procedures being applied to a standard SLAC electromagnet design in order to make it reliable enough to meet the NLC availability specs. First, empirical data from SLAC's accelerator failure database plus design experience are used to calculate MTBF for failure modes identified through a FMEA. Availability for one particular magnet can be calculated. Next, labor and material costs to repair magnet failures are used in a Monte Carlo simulation to calculate the total cost of all failures over a 30-year lifetime. Opportunity costs are included. Engineers choose from amongst various designs by comparing lifecycle costs.

  14. Dosimetric characterization of the irradiation cavity for accelerator-based in vivo neutron activation analysis.

    PubMed

    Byun, S H; Pejović-Milić, A; McMaster, S; Matysiak, W; Aslam; Liu, Z; Watters, L M; Prestwich, W V; McNeill, F E; Chettle, D R

    2007-03-21

    A neutron irradiation cavity for in vivo activation analysis has been characterized to estimate its dosimetric specifications. The cavity is defined to confine irradiation to the hand and modifies the neutron spectrum produced by a low energy accelerator neutron source to optimize activation per dose. Neutron and gamma-ray dose rates were measured with the microdosimetric technique using a tissue-equivalent proportional counter at the hand irradiation site and inside the hand access hole. For the outside of the cavity, a spherical neutron dose equivalent meter and a Farmer dosemeter were employed instead due to the low intensity of the radiation field. The maximum dose equivalent rate at the outside of the cavity was 2.94 microSv/100 microA min, which is lower by a factor of 1/2260 than the dose rate at the hand irradiation position. The local dose contributions from a hand, an arm and the rest of a body to the effective dose rate were estimated to be 1.73, 0.782 and 2.94 microSv/100 microA min, respectively. For the standard irradiation protocol of the in vivo hand activation, 300 microA min, an effective dose of 16.3 microSv would be delivered. PMID:17455391

  15. Lorentz force detuning analysis of the Spallation Neutron Source (SNS) accelerating cavities.

    SciTech Connect

    Mitchell, R.R.; Matsumoto, K. Y.; Ciovati, G.; Davis, K.; Macha, K.; Sundelin, R. M.

    2001-01-01

    The Spallation Neutron Source (SNS) project incorporates a superconducting radio-frequency (SRF) accelerator for the final section of the pulsed mode linac. Cavities with geometrical {beta} values of {beta}=0.61 and {beta}=0.81 are utilized in the SRF section, and are constructed out of thin-walled niobium with stiffener rings welded between the cells near the iris. The welded titanium helium vessel and tuner assembly restrains the cavity beam tubes. Cavities with {beta} values less than one have relatively steep and flat side-walls making the cavities susceptible to Lorentz force detuning. In addition, the pulsed RF induces cyclic Lorentz pressures that mechanically excite the cavities, producing a dynamic Lorentz force detuning different from a continuous RF system. The amplitude of the dynamic detuning for a given cavity design is a function of the mechanical damping, stiffness of the tuner/helium vessel assembly, RF pulse profile, and the RF pulse rate. This paper presents analysis and testing results to date, and indicates areas where more investigation is required.

  16. Large scale neural circuit mapping data analysis accelerated with the graphical processing unit (GPU)

    PubMed Central

    Shi, Yulin; Veidenbaum, Alexander V.; Nicolau, Alex; Xu, Xiangmin

    2014-01-01

    Background Modern neuroscience research demands computing power. Neural circuit mapping studies such as those using laser scanning photostimulation (LSPS) produce large amounts of data and require intensive computation for post-hoc processing and analysis. New Method Here we report on the design and implementation of a cost-effective desktop computer system for accelerated experimental data processing with recent GPU computing technology. A new version of Matlab software with GPU enabled functions is used to develop programs that run on Nvidia GPUs to harness their parallel computing power. Results We evaluated both the central processing unit (CPU) and GPU-enabled computational performance of our system in benchmark testing and practical applications. The experimental results show that the GPU-CPU co-processing of simulated data and actual LSPS experimental data clearly outperformed the multi-core CPU with up to a 22x speedup, depending on computational tasks. Further, we present a comparison of numerical accuracy between GPU and CPU computation to verify the precision of GPU computation. In addition, we show how GPUs can be effectively adapted to improve the performance of commercial image processing software such as Adobe Photoshop. Comparison with Existing Method(s) To our best knowledge, this is the first demonstration of GPU application in neural circuit mapping and electrophysiology-based data processing. Conclusions Together, GPU enabled computation enhances our ability to process large-scale data sets derived from neural circuit mapping studies, allowing for increased processing speeds while retaining data precision. PMID:25277633

  17. [Preparation of Rubber Accelerator Tetramethyl Thiuram Monosulfide and Its Spectral Analysis].

    PubMed

    Wang, Zhen-xiang; Li, Hong-liang; Jia, Tai-xuan; Zhang, Nan; Jin, Xin

    2015-07-01

    In the study, rubber accelerator tetramethyl thiuram monosulfide (TMTM) was synthesized firstly. Single crystal TMTM was cultivated by solvent evaporation method. TMTM was detected and characterized by XRD single crystal diffraction, FTIR, TG-DSC. The micro-structure and intrinsic regularity were revealed. The TMTM microstructure was revealed by XRD single crystal diffraction from the diffraction data, part of bond length and bond angle. Its highly efficient performance of rubber vulcanization promotion was decided due to its orientation structure and high order. Properties of TMTM was disclosed by TG-DSC analysis from the heat effect. The results of TG-DSC and FTIR showed that single crystal TMTM possessed with little CS2. The chemical bond types in TMTM were revealed by FTIR the same as single crystal diffraction testing by different way. The decomposition temperature of TMTM was very high. It could provided reference with research on rubber vulcanizing properties by TMTM on rubber vulcanizing machine. This study can help the enterprises to designate the working standard tracing detection of TMTM industrialized production. Performance index of TMTM was judged. The project of TMTM industry standard can be declared by the enterprises, written a draft standard. It can provide the basis experimental data on completing the revision of the national ministry of industry and information technology standard system project plan. PMID:26717743

  18. Accelerator-based trace element analysis of foods and agriculture products

    NASA Astrophysics Data System (ADS)

    Lagunas-Solar, Manuel C.; Piña U, Cecilia; Solís, Corina; Mireles, Alibech

    2008-05-01

    An accelerator-based analytical method for measuring trace elements in foods and agricultural products was developed, optimized, validated and compared using reference standards. The method's initial phase is a new, rapid and effective digestion process of a small mass analyte in an aqueous media containing H2O2. Digestion is initiated by radicals formed in water with pulsed UV (PUV) induced (laser) photolysis, which rapidly react with organic matter. After digestion, trace metals are pre-concentrated as carbamates and deposited as thin targets onto Teflon filters. Conventional particle induced X-ray emission (PIXE) or X-ray fluorescence (XRF) methods are then used to analyze elements in the sample. When foods and other agricultural commodities (i.e., soils, feeds) are analyzed, the combined method named pulsed UV (PUV)/PIXE results in enhanced detection of trace elements such as Fe, Co, Ni, Cu, Zn and Pb at ∼1 mg/kg (1 ppm) levels, without lengthy, acid-based digestions. It provides improvements in digestion kinetics and processing time enhancing analytical sensitivity and element recovery. Precision and recovery yields were confirmed with food reference standards. The analysis of edible foods from contaminated agricultural areas is also reported.

  19. Linear Accelerators

    NASA Astrophysics Data System (ADS)

    Sidorin, Anatoly

    2010-01-01

    In linear accelerators the particles are accelerated by either electrostatic fields or oscillating Radio Frequency (RF) fields. Accordingly the linear accelerators are divided in three large groups: electrostatic, induction and RF accelerators. Overview of the different types of accelerators is given. Stability of longitudinal and transverse motion in the RF linear accelerators is briefly discussed. The methods of beam focusing in linacs are described.

  20. Linear Accelerators

    SciTech Connect

    Sidorin, Anatoly

    2010-01-05

    In linear accelerators the particles are accelerated by either electrostatic fields or oscillating Radio Frequency (RF) fields. Accordingly the linear accelerators are divided in three large groups: electrostatic, induction and RF accelerators. Overview of the different types of accelerators is given. Stability of longitudinal and transverse motion in the RF linear accelerators is briefly discussed. The methods of beam focusing in linacs are described.

  1. Molecular and functional analysis of mouse decay accelerating factor (CD55).

    PubMed Central

    Harris, C L; Rushmere, N K; Morgan, B P

    1999-01-01

    Molecular cloning of mouse decay accelerating factor (DAF; CD55) predicted two forms of the molecule, one transmembrane (TM) and the other glycosylphosphatidylinositol (GPI)-anchored; these are encoded by separate genes termed Daf-GPI and Daf-TM. In the present study several additional isoforms of mouse DAF, generated by alternative splicing from these genes, are described. Northern-blot analysis of RNA and reverse transcriptase-PCR from various tissues indicated that spleen and testis expressed high levels of DAF, which comprised several species. These species were cloned and sequence analysis revealed various novel forms in addition to those previously reported. Two novel forms were derived from the Daf-TM gene but the transmembrane sequence defined previously was replaced by a unique GPI-anchor addition sequence; one clone also had part of the serine/threonine/proline (STP) region deleted. A third clone, encoding a transmembrane protein, was also derived from this gene but the entire STP region was deleted. A fourth clone, derived from the Daf-GPI gene, contained a novel C-terminal sequence, suggestive of a secreted form of the protein. Two DAF cDNAs (TM and GPI-anchored) were stably expressed in Chinese hamster ovary cells. When these cells were attacked with mouse or rat complement and analysed for C3b deposition, DAF-transfected cells had greatly reduced C3b deposition compared with controls. Transfection with DAF also conferred protection from complement in a cell-lysis assay, and a soluble, recombinant form of mouse DAF inhibited complement in a haemolytic assay. PMID:10417349

  2. Analysis and design of nonlocal spin devices with electric-field-induced spin-transport acceleration

    SciTech Connect

    Takamura, Yota; Akushichi, Taiju; Shuto, Yusuke; Sugahara, Satoshi

    2015-05-07

    We apply electric-field-induced acceleration for spin transport to a four-terminal nonlocal device and theoretically analyze its Hanle-effect signals. The effect of the ferromagnetic contact widths of the spin injector and detector on the signals is carefully discussed. Although Hanle-effect signals are randomized owing to the effect of the contact widths, this can be excluded by selecting an appropriate electric field for acceleration of spin transport. Spin lifetime can be correctly extracted by nonlocal devices with electric-field acceleration even using the spin injector and detector with finite contact widths.

  3. Accelerated leukocyte telomere erosion in schizophrenia: Evidence from the present study and a meta-analysis.

    PubMed

    Rao, Shuquan; Kota, Lakshmi Narayanan; Li, Zongchang; Yao, Yao; Tang, Jinsong; Mao, Canquan; Jain, Sanjeev; Xu, Yong; Xu, Qi

    2016-08-01

    Human telomeres consist of tandem nucleotide repeats (TTAGGG) and associated proteins, and telomere length (TL) is reduced progressively with cell division over the lifespan. Telomere erosion might be accelerated or prevented to varying degrees when exposure to serious medical illnesses. In previous studies, an association between TL decrease and schizophrenia has been extensively reported; however, the results remain largely controversial. To further investigate TL in schizophrenia patients and reconcile this controversy, we first measured leucocyte TL (LTL) in our samples (52 paranoid schizophrenia, 89 non-paranoid patients and 120 controls), and then conducted a comprehensive meta-analysis of the existing results of LTL in patients of schizophrenia compared to healthy subjects. Totally, 11 studies encompassing 1243 patients of schizophrenia and 1274 controls were included in the final meta-analysis model. In our samples, significant reduction of LTL in paranoid schizophrenia was observed compared to controls (F = 50.88, P < 0.001); whereas there was no significant difference in LTL between non-paranoid schizophrenia and controls (F = 0.842, P = 0.360). For meta-analysis, random-effects model showed significant LTL decrease in patients of schizophrenia when compared to controls (Z = 2.07, P = 0.039, SMD = -0.48, 95% CI = -0.94 to -0.03). Moreover, a marginal decrease in LTL was observed in medicated patients (Z = 1.92, P = 0.055, SMD = -0.58, 95% CI = -1.18-0.01) and those patients with poor response to antipsychotics (Z = 1.76, P = 0.078, SMD = -0.60, 95% CI = -1.27-0.07). In conclusion, we observed significant reduction of LTL in individuals with schizophrenia compared with controls. However, all the studies included in the meta-analysis were cross-sectional, and better controlled long-term studies are needed to replicate this result. PMID:27174400

  4. Analysis of Transmitted Optical Spectrum Enabling Accelerated Testing of CPV Designs: Preprint

    SciTech Connect

    Miller, D. C.; Kempe, M. D.; Kennedy, C. E.; Kurtz, S. R.

    2009-07-01

    Reliability of CPV systems' materials is not well known; methods for accelerated UV testing have not been developed. UV and IR spectra transmitted through representative optical systems are evaluated.

  5. Analysis of the behavior of a discharge in a coaxial plasma jet accelerator

    NASA Astrophysics Data System (ADS)

    Voronin, A. V.; Gusev, V. K.; Gerasimenko, Ya. A.

    2013-03-01

    We analyze the behavior of the discharge in a coaxial plasma jet accelerator with a pulsed supply of the working gas released by an electric discharge from titanium hydride powder. Radiation (varying with time) from the discharge in the accelerator was detected using an optical method through a narrow slit cut along the outer electrode by a Bifo Company K008 streak camera. Stable operation of the source with the highest kinetic energy of a pure hydrogen plasma jet was attained for a relatively uniform glow of the discharge along the accelerator during the entire current pulse. Conversely, local glow of the discharge at the outlet or inlet of the accelerator considerably contaminated the discharge with impurities, and the kinetic energy of the plasma jet decreased by an order of magnitude. The highest energy of the plasma jet was attained when the polarity of the electrodes was the same as at the plasma focus.

  6. Extending PowerPack for Profiling and Analysis of High Performance Accelerator-Based Systems

    SciTech Connect

    Li, Bo; Chang, Hung-Ching; Song, Shuaiwen; Su, Chun-Yi; Meyer, Timmy; Mooring, John; Cameron, Kirk

    2014-12-01

    Accelerators offer a substantial increase in efficiency for high-performance systems offering speedups for computational applications that leverage hardware support for highly-parallel codes. However, the power use of some accelerators exceeds 200 watts at idle which means use at exascale comes at a significant increase in power at a time when we face a power ceiling of about 20 megawatts. Despite the growing domination of accelerator-based systems in the Top500 and Green500 lists of fastest and most efficient supercomputers, there are few detailed studies comparing the power and energy use of common accelerators. In this work, we conduct detailed experimental studies of the power usage and distribution of Xeon-Phi-based systems in comparison to the NVIDIA Tesla and at SandyBridge.

  7. Three-dimensional simulation analysis of the standing-wave free- electron laser two beam accelerator

    SciTech Connect

    Wang, C.; Sessler, A.

    1993-01-01

    We have modified a two-dimensional relativistic klystron code, developed by Ryne and Yu, to simulate both the standing-wave free- electron laser two-beam accelerator and the relativistic klystron two- beam accelerator. In this paper, the code is used to study a standing-wave free-electron laser with three cavities. The effect of the radius of the electron beam on the RF output power; namely, a three-dimensional effect is examined.

  8. Sensitivity analysis of an asymmetric Monte Carlo beam model of a Siemens Primus accelerator.

    PubMed

    Schreiber, Eric C; Sawkey, Daren L; Faddegon, Bruce A

    2012-01-01

    The assumption of cylindrical symmetry in radiotherapy accelerator models can pose a challenge for precise Monte Carlo modeling. This assumption makes it difficult to account for measured asymmetries in clinical dose distributions. We have performed a sensitivity study examining the effect of varying symmetric and asymmetric beam and geometric parameters of a Monte Carlo model for a Siemens PRIMUS accelerator. The accelerator and dose output were simulated using modified versions of BEAMnrc and DOSXYZnrc that allow lateral offsets of accelerator components and lateral and angular offsets for the incident electron beam. Dose distributions were studied for 40 × 40 cm² fields. The resulting dose distributions were analyzed for changes in flatness, symmetry, and off-axis ratio (OAR). The electron beam parameters having the greatest effect on the resulting dose distributions were found to be electron energy and angle of incidence, as high as 5% for a 0.25° deflection. Electron spot size and lateral offset of the electron beam were found to have a smaller impact. Variations in photon target thickness were found to have a small effect. Small lateral offsets of the flattening filter caused significant variation to the OAR. In general, the greatest sensitivity to accelerator parameters could be observed for higher energies and off-axis ratios closer to the central axis. Lateral and angular offsets of beam and accelerator components have strong effects on dose distributions, and should be included in any high-accuracy beam model. PMID:22402376

  9. Evidence of statistical epistasis between DISC1, CIT and NDEL1 impacting risk for schizophrenia: biological validation with functional neuroimaging.

    PubMed

    Nicodemus, Kristin K; Callicott, Joseph H; Higier, Rachel G; Luna, Augustin; Nixon, Devon C; Lipska, Barbara K; Vakkalanka, Radhakrishna; Giegling, Ina; Rujescu, Dan; St Clair, David; Muglia, Pierandrea; Shugart, Yin Yao; Weinberger, Daniel R

    2010-04-01

    The etiology of schizophrenia likely involves genetic interactions. DISC1, a promising candidate susceptibility gene, encodes a protein which interacts with many other proteins, including CIT, NDEL1, NDE1, FEZ1 and PAFAH1B1, some of which also have been associated with psychosis. We tested for epistasis between these genes in a schizophrenia case-control study using machine learning algorithms (MLAs: random forest, generalized boosted regression andMonteCarlo logic regression). Convergence of MLAs revealed a subset of seven SNPs that were subjected to 2-SNP interaction modeling using likelihood ratio tests for nested unconditional logistic regression models. Of the 7C2 = 21 interactions, four were significant at the α = 0.05 level: DISC1 rs1411771-CIT rs10744743 OR = 3.07 (1.37, 6.98) p = 0.007; CIT rs3847960-CIT rs203332 OR = 2.90 (1.45, 5.79) p = 0.003; CIT rs3847960-CIT rs440299 OR = 2.16 (1.04, 4.46) p = 0.038; one survived Bonferroni correction (NDEL1 rs4791707-CIT rs10744743 OR = 4.44 (2.22, 8.88) p = 0.00013). Three of four interactions were validated via functional magnetic resonance imaging (fMRI) in an independent sample of healthy controls; risk associated alleles at both SNPs predicted prefrontal cortical inefficiency during the N-back task, a schizophrenia-linked intermediate biological phenotype: rs3847960-rs440299; rs1411771-rs10744743, rs4791707-rs10744743 (SPM5 p < 0.05, corrected), although we were unable to statistically replicate the interactions in other clinical samples. Interestingly, the CIT SNPs are proximal to exons that encode theDISC1 interaction domain. In addition, the 3' UTR DISC1 rs1411771 is predicted to be an exonic splicing enhancer and the NDEL1 SNP is ~3,000 bp from the exon encoding the region of NDEL1 that interacts with the DISC1 protein, giving a plausible biological basis for epistasis signals validated by fMRI. PMID:20084519

  10. A Tandem Repeat in Decay Accelerating Factor 1 Is Associated with Severity of Murine Mercury-Induced Autoimmunity

    PubMed Central

    Gabriel, Rodney; Kono, Dwight H.; Hultman, Per; Pollard, K. Michael

    2014-01-01

    Decay accelerating factor (DAF), a complement-regulatory protein, protects cells from bystander complement-mediated lysis and negatively regulates T cells. Reduced expression of DAF occurs in several systemic autoimmune diseases including systemic lupus erythematosus, and DAF deficiency exacerbates disease in several autoimmune models, including murine mercury-induced autoimmunity (mHgIA). Daf1, located within Hmr1, a chromosome 1 locus associated in DBA/2 mice with resistance to mHgIA, could be a candidate. Here we show that reduced Daf1 transcription in lupus-prone mice was not associated with a reduction in the Daf1 transcription factor SP1. Studies of NZB mice congenic for the mHgIA-resistant DBA/2 Hmr1 locus suggested that Daf1 expression was controlled by the host genome and not the Hmr1 locus. A unique pentanucleotide repeat variant in the second intron of Daf1 in DBA/2 mice was identified and shown in F2 intercrosses to be associated with less severe disease; however, analysis of Hmr1 congenics indicated that this most likely reflected the presence of autoimmunity-predisposing genetic variants within the Hmr1 locus or that Daf1 expression is mediated by the tandem repeat in epistasis with other genetic variants present in autoimmune-prone mice. These studies argue that the effect of DAF on autoimmunity is complex and may require multiple genetic elements. PMID:24818014

  11. Application of Failure Mode and Effects Analysis to Intraoperative Radiation Therapy Using Mobile Electron Linear Accelerators

    SciTech Connect

    Ciocca, Mario; Cantone, Marie-Claire; Veronese, Ivan; Cattani, Federica; Pedroli, Guido; Molinelli, Silvia; Vitolo, Viviana; Orecchia, Roberto

    2012-02-01

    Purpose: Failure mode and effects analysis (FMEA) represents a prospective approach for risk assessment. A multidisciplinary working group of the Italian Association for Medical Physics applied FMEA to electron beam intraoperative radiation therapy (IORT) delivered using mobile linear accelerators, aiming at preventing accidental exposures to the patient. Methods and Materials: FMEA was applied to the IORT process, for the stages of the treatment delivery and verification, and consisted of three steps: 1) identification of the involved subprocesses; 2) identification and ranking of the potential failure modes, together with their causes and effects, using the risk probability number (RPN) scoring system, based on the product of three parameters (severity, frequency of occurrence and detectability, each ranging from 1 to 10); 3) identification of additional safety measures to be proposed for process quality and safety improvement. RPN upper threshold for little concern of risk was set at 125. Results: Twenty-four subprocesses were identified. Ten potential failure modes were found and scored, in terms of RPN, in the range of 42-216. The most critical failure modes consisted of internal shield misalignment, wrong Monitor Unit calculation and incorrect data entry at treatment console. Potential causes of failure included shield displacement, human errors, such as underestimation of CTV extension, mainly because of lack of adequate training and time pressures, failure in the communication between operators, and machine malfunctioning. The main effects of failure were represented by CTV underdose, wrong dose distribution and/or delivery, unintended normal tissue irradiation. As additional safety measures, the utilization of a dedicated staff for IORT, double-checking of MU calculation and data entry and finally implementation of in vivo dosimetry were suggested. Conclusions: FMEA appeared as a useful tool for prospective evaluation of patient safety in radiotherapy. The

  12. Automated combustion accelerator mass spectrometry for the analysis of biomedical samples in the low attomole range.

    PubMed

    van Duijn, Esther; Sandman, Hugo; Grossouw, Dimitri; Mocking, Johannes A J; Coulier, Leon; Vaes, Wouter H J

    2014-08-01

    The increasing role of accelerator mass spectrometry (AMS) in biomedical research necessitates modernization of the traditional sample handling process. AMS was originally developed and used for carbon dating, therefore focusing on a very high precision but with a comparably low sample throughput. Here, we describe the combination of automated sample combustion with an elemental analyzer (EA) online coupled to an AMS via a dedicated interface. This setup allows direct radiocarbon measurements for over 70 samples daily by AMS. No sample processing is required apart from the pipetting of the sample into a tin foil cup, which is placed in the carousel of the EA. In our system, up to 200 AMS analyses are performed automatically without the need for manual interventions. We present results on the direct total (14)C count measurements in <2 μL human plasma samples. The method shows linearity over a range of 0.65-821 mBq/mL, with a lower limit of quantification of 0.65 mBq/mL (corresponding to 0.67 amol for acetaminophen). At these extremely low levels of activity, it becomes important to quantify plasma specific carbon percentages. This carbon percentage is automatically generated upon combustion of a sample on the EA. Apparent advantages of the present approach include complete omission of sample preparation (reduced hands-on time) and fully automated sample analysis. These improvements clearly stimulate the standard incorporation of microtracer research in the drug development process. In combination with the particularly low sample volumes required and extreme sensitivity, AMS strongly improves its position as a bioanalysis method. PMID:25033319

  13. Field-Analysis of Vacuum Free-Space LaserAcceleration from Rough-Surface and Absorbing Thin Boundaries

    SciTech Connect

    Plettner, Thomas; /Stanford U., Ginzton Lab.

    2008-06-02

    This script presents a field-based analysis of laser acceleration of relativistic electrons in a free space that is bounded by a thin scattering or by a thin absorbing surface. The laser acceleration process is analyzed in terms of the inverse-radiation formalism and compared to the more familiar field path-integral analysis method. When the scattering boundary is modeled as a linear-index medium the predictions for laser-electron interactions from both field methods are found to agree. For the absorbing boundary both interaction pictures are also found to agree provided that the inverse radiation method is generalized to include absorption of energy from the boundary that is modeled as a linear ohmic-loss object.

  14. Can Accelerators Accelerate Learning?

    NASA Astrophysics Data System (ADS)

    Santos, A. C. F.; Fonseca, P.; Coelho, L. F. S.

    2009-03-01

    The 'Young Talented' education program developed by the Brazilian State Funding Agency (FAPERJ) [1] makes it possible for high-schools students from public high schools to perform activities in scientific laboratories. In the Atomic and Molecular Physics Laboratory at Federal University of Rio de Janeiro (UFRJ), the students are confronted with modern research tools like the 1.7 MV ion accelerator. Being a user-friendly machine, the accelerator is easily manageable by the students, who can perform simple hands-on activities, stimulating interest in physics, and getting the students close to modern laboratory techniques.

  15. PARTICLE ACCELERATOR

    DOEpatents

    Teng, L.C.

    1960-01-19

    ABS>A combination of two accelerators, a cyclotron and a ring-shaped accelerator which has a portion disposed tangentially to the cyclotron, is described. Means are provided to transfer particles from the cyclotron to the ring accelerator including a magnetic deflector within the cyclotron, a magnetic shield between the ring accelerator and the cyclotron, and a magnetic inflector within the ring accelerator.

  16. Analysis of Ion Motion and Scattering in the Extreme Regime of High Intensity Electron Beams in Plasma Wakefield Accelerators

    SciTech Connect

    Gholizadeh, Reza; Katsouleas, Tom; Muggli, Patric; Mori, Warren

    2006-11-27

    Plasma wakefield accelerator is examined in the extreme regime of nanometer transverse beam sizes, typical of designs in the multi-TeV range. We find that ion motion, synchrotron radiation, nuclear scattering and particle trapping constrain the design parameters in which high beam quality and efficiency can be maintained. For a particular example relevant to an ILC Afterburner, the analysis suggests that an intermediate mass ion such as Argon may best satisfy the constraints.

  17. Analysis of Ion Motion and Scattering in the Extreme Regime of High Intensity Electron Beams in Plasma Wakefield Accelerators

    NASA Astrophysics Data System (ADS)

    Gholizadeh, Reza; Katsouleas, Tom; Muggli, Patric; Mori, Warren

    2006-11-01

    Plasma wakefield accelerator is examined in the extreme regime of nanometer transverse beam sizes, typical of designs in the multi-TeV range. We find that ion motion, synchrotron radiation, nuclear scattering and particle trapping constrain the design parameters in which high beam quality and efficiency can be maintained. For a particular example relevant to an ILC Afterburner, the analysis suggests that an intermediate mass ion such as Argon may best satisfy the constraints.

  18. Calcium Isolation from Large-Volume Human Urine Samples for 41Ca Analysis by Accelerator Mass Spectrometry

    PubMed Central

    Miller, James J; Hui, Susanta K; Jackson, George S; Clark, Sara P; Einstein, Jane; Weaver, Connie M; Bhattacharyya, Maryka H

    2013-01-01

    Calcium oxalate precipitation is the first step in preparation of biological samples for 41Ca analysis by accelerator mass spectrometry. A simplified protocol for large-volume human urine samples was characterized, with statistically significant increases in ion current and decreases in interference. This large-volume assay minimizes cost and effort and maximizes time after 41Ca administration during which human samples, collected over a lifetime, provide 41Ca:Ca ratios that are significantly above background. PMID:23672965

  19. Simulation analysis for effects of bone loss on acceleration tolerance of human lumbar vertebra

    NASA Astrophysics Data System (ADS)

    Ma, Honglei; Zhang, Feng; Zhu, Yu; Xiao, Yanhua; Wazir, Abrar

    2014-02-01

    The purpose of the present study was to analyze and predict the changes in acceleration tolerance of human vertebra as a result of bone loss caused by long-term space flight. A human L3-L4 vertebra FEM model was constructed, in which the cancellous bone was separated, and surrounding ligaments were also taken into account. The simulation results demonstrated that bone loss has more of an effect on the acceleration tolerance in x-direction. The results serve to aid in the creation of new acceleration tolerance standards, ensuring astronauts return home safely after long-term space flight. This study shows that more attention should be focused on the bone degradation of crew members and to create new protective designs for space capsules in the future.

  20. Survey and analysis of line-frequency interference in the CEBAF accelerator

    SciTech Connect

    Tiefenback, M.G.; Li, Rui

    1995-12-31

    Feedthrough of interference from the AC power line into accelerator components is a problem which in pulsed accelerators can be reduced by operation synchronous with the AC line. This means of avoiding line-frequency effects is ineffective for continuous wave machines such as the CEBAF accelerator. We have measured line-frequency perturbations at CEBAF both in beam position and energy by using the beam position monitor system as a multiple-channel sampling oscilloscope. Comparing these data against the measured static optics (taken synchronously with the AC line) we have been able to identify point sources of interference, and resolve line-synchronous variations in the beam energy at a level near 0.001%. 3 refs., 2 figs., 1 tab.

  1. Off-normal and failure condition analysis of the MITICA negative-ion accelerator

    NASA Astrophysics Data System (ADS)

    Chitarin, Giuseppe; Agostinetti, Piero; Aprile, Daniele; Marconato, Nicolò; Marcuzzi, Diego; Serianni, Gianluigi; Veltri, Pierluigi; Zaccaria, Pierluigi

    2016-02-01

    The negative-ion accelerator for the MITICA neutral beam injector has been designed and optimized in order to reduce the thermo-mechanical stresses in all components below limits compatible with the required fatigue life. However, deviation from the expected beam performances can be caused by "off-normal" operating conditions of the accelerator. The purpose of the present work is to identify and analyse all the "off-normal" operating conditions, which could possibly become critical in terms of thermo-mechanical stresses or of degradation of the optical performances of the beam.

  2. Off-normal and failure condition analysis of the MITICA negative-ion accelerator.

    PubMed

    Chitarin, Giuseppe; Agostinetti, Piero; Aprile, Daniele; Marconato, Nicolò; Marcuzzi, Diego; Serianni, Gianluigi; Veltri, Pierluigi; Zaccaria, Pierluigi

    2016-02-01

    The negative-ion accelerator for the MITICA neutral beam injector has been designed and optimized in order to reduce the thermo-mechanical stresses in all components below limits compatible with the required fatigue life. However, deviation from the expected beam performances can be caused by "off-normal" operating conditions of the accelerator. The purpose of the present work is to identify and analyse all the "off-normal" operating conditions, which could possibly become critical in terms of thermo-mechanical stresses or of degradation of the optical performances of the beam. PMID:26932039

  3. Theoretical analysis of acceleration measurements in a model of an operating wind turbine.

    SciTech Connect

    Adams, Douglas E.; Rumsey, Mark Allen; White, Jonathan Randall

    2010-04-01

    Wind loading from turbulence and gusts can cause damage in horizontal axis wind turbines. These unsteady loads and the resulting damage initiation and propagation are difficult to predict. Unsteady loads enter at the rotor and are transmitted to the drivetrain. The current generation of wind turbine has drivetrain-mounted vibration and bearing temperature sensors, a nacelle-mounted inertial measurement unit, and a nacelle-mounted anemometer and wind vane. Some advanced wind turbines are also equipped with strain measurements at the root of the rotor. This paper analyzes additional measurements in a rotor blade to investigate the complexity of these unsteady loads. By identifying the spatial distribution, amplitude, and frequency bandwidth of these loads, design improvements could be facilitated to reduce uncertainties in reliability predictions. In addition, dynamic load estimates could be used in the future to control high-bandwidth aerodynamic actuators distributed along the rotor blade to reduce the saturation of slower pitch actuators currently used for wind turbine blades. Local acceleration measurements are made along a rotor blade to infer operational rotor states including deflection and dynamic modal contributions. Previous work has demonstrated that acceleration measurements can be experimentally acquired on an operating wind turbine. Simulations on simplified rotor blades have also been used to demonstrate that mean blade loading can be estimated based on deflection estimates. To successfully apply accelerometers in wind turbine applications for load identification, the spectral and spatial characteristics of each excitation source must be understood so that the total acceleration measurement can be decomposed into contributions from each source. To demonstrate the decomposition of acceleration measurements in conjunction with load estimation methods, a flexible body model has been created with MSC.ADAMS{copyright} The benefit of using a simulation model

  4. Predictors of Local Recurrence Following Accelerated Partial Breast Irradiation: A Pooled Analysis

    SciTech Connect

    Shah, Chirag; Wilkinson, John Ben; Lyden, Maureen; Beitsch, Peter; Vicini, Frank A.

    2012-04-01

    Purpose: To analyze a pooled set of nearly 2,000 patients treated on the American Society of Breast Surgeons (ASBS) Mammosite Registry Trial and at William Beaumont Hospital (WBH) to identify factors associated with local recurrence following accelerated partial breast irradiation (APBI). Methods and Materials: A total of 1,961 women underwent partial breast irradiation between April 1993 and November 2010 as part of the ASBS Registry Trial or at WBH. Rates of ipsilateral breast tumor recurrence (IBTR), regional recurrence (RR), distant metastases (DM), disease-free survival (DFS), cause-specific survival (CSS), and overall survival (OS) were analyzed for each group and for the pooled cohort. Clinical, pathologic, and treatment-related variables were analyzed including age, tumor stage/size, estrogen receptor status, surgical margins, and lymph node status to determine their association with IBTR. Results: The two groups weres similar, but WBH patients were more frequently node positive, had positive margins, and were less likely to be within the American Society for Radiation Oncology-unsuitable group. At 5 years, the rates of IBTR, RR, DM, DFS, CSS, and OS for the pooled group of patients were 2.9%, 0.5%, 2.4%, 89.1%, 98.5%, and 91.8%, respectively. The 5-year rate of true recurrence/marginal miss was 0.8%. Univariate analysis of IBTR found that negative estrogen receptor status (odds ratio [OR], 2.83, 95% confidence interval 1.55-5.13, p = 0.0007) was the only factor significantly associated with IBTR, while a trend was seen for age less than 50 (OR 1.80, 95% confidence interval 0.90-3.58, p = 0.10). Conclusions: Excellent 5-year outcomes were seen following APBI in over 1,900 patients. Estrogen receptor negativity was the only factor associated with IBTR, while a trend for age less than 50 was noted. Significant differences in factors associated with IBTR were noted between cohorts, suggesting that factors driving IBTR may be predicated based on the risk

  5. Predicting punching acceleration from selected strength and power variables in elite karate athletes: a multiple regression analysis.

    PubMed

    Loturco, Irineu; Artioli, Guilherme Giannini; Kobal, Ronaldo; Gil, Saulo; Franchini, Emerson

    2014-07-01

    This study investigated the relationship between punching acceleration and selected strength and power variables in 19 professional karate athletes from the Brazilian National Team (9 men and 10 women; age, 23 ± 3 years; height, 1.71 ± 0.09 m; and body mass [BM], 67.34 ± 13.44 kg). Punching acceleration was assessed under 4 different conditions in a randomized order: (a) fixed distance aiming to attain maximum speed (FS), (b) fixed distance aiming to attain maximum impact (FI), (c) self-selected distance aiming to attain maximum speed, and (d) self-selected distance aiming to attain maximum impact. The selected strength and power variables were as follows: maximal dynamic strength in bench press and squat-machine, squat and countermovement jump height, mean propulsive power in bench throw and jump squat, and mean propulsive velocity in jump squat with 40% of BM. Upper- and lower-body power and maximal dynamic strength variables were positively correlated to punch acceleration in all conditions. Multiple regression analysis also revealed predictive variables: relative mean propulsive power in squat jump (W·kg-1), and maximal dynamic strength 1 repetition maximum in both bench press and squat-machine exercises. An impact-oriented instruction and a self-selected distance to start the movement seem to be crucial to reach the highest acceleration during punching execution. This investigation, while demonstrating strong correlations between punching acceleration and strength-power variables, also provides important information for coaches, especially for designing better training strategies to improve punching speed. PMID:24276310

  6. Pedestrian movement analysis in transfer station corridor: Velocity-based and acceleration-based

    NASA Astrophysics Data System (ADS)

    Ji, Xiangfeng; Zhang, Jian; Hu, Yongkai; Ran, Bin

    2016-05-01

    In this paper, pedestrians are classified into aggressive and conservative ones by their temper. Aggressive pedestrians' walking through crowd in transfer station corridor is analyzed. Treating pedestrians as particles, this paper uses the modified social force model (MSFM) as the building block, where forces involve self-driving force, repulsive force and friction force. The proposed model in this paper is a discrete model combining the MSFM and cellular automata (CA) model, where the updating rules of the CA are redefined with MSFM. Due to the continuity of values generated by the MSFM, we use the fuzzy logic to discretize the continuous values into cells pedestrians can move in one step. With the observation that stimulus around pedestrians influences their acceleration directly, an acceleration-based movement model is presented, compared to the generally reviewed velocity-based movement model. In the acceleration-based model, a discretized version of kinematic equation is presented based on the acceleration discretized with fuzzy logic. In real life, some pedestrians would rather keep their desired speed and this is also mimicked in this paper, which is called inertia. Compared to the simple triangular membership function, a trapezoidal membership function and a piecewise linear membership function are used to capture pedestrians' inertia. With the trapezoidal and the piecewise linear membership function, many overlapping scenarios should be carefully handled and Dubois and Prade's four-index method is used to completely describe the relative relationship of fuzzy quantities. Finally, a simulation is constructed to demonstrate the effect of our model.

  7. Two-dimensional axisymmetric magnetohydrodynamic analysis of blow-by in a coaxial plasma accelerator

    NASA Astrophysics Data System (ADS)

    Cassibry, J. T.; Thio, Y. C. F.; Wu, S. T.

    2006-05-01

    When the driving magnetic pressure profile is unbalanced by the plasma density profile in a coaxial plasma accelerator, a portion of the plasma and associated current sheet may "blow by" the remaining bulk of the plasma. The fast moving plasma creates a significant back electromotive force, draining energy otherwise available for acceleration. The onset of blow-by for an unmagnetized plasma of finite length in a straight coaxial plasma accelerator was studied by exploring systematically the effects of the initial density profile, driving current, plasma temperature, inductance gradient, and electrode radii scale size on the blow-by time. In order to avoid the onset of blow-by, the principal acceleration phase needs to be less than the characteristic blow-by time, which is a function of electrode geometry, plasma conditions, and circuit parameters. For an initially uniform density profile, the total impulse at blow-by time is proportional to the current, plasma mass, jet length, and reciprocal of the electrode radius ratio.

  8. Functional Data Analysis of Spaceflight-Induced Changes in Coordination and Phase in Head Pitch Acceleration During Treadmill Walking

    NASA Technical Reports Server (NTRS)

    Miller, Christopher; Peters, Brian; Feiveson, Alan; Bloomberg, Jacob

    2011-01-01

    Astronauts returning from spaceflight experience neurovestibular disturbances during head movements and attempt to mitigate them by limiting head motion. Analyses to date of the head movements made during walking have concentrated on amplitude and variability measures extracted from ensemble averages of individual gait cycles. Phase shifts within each gait cycle can be determined by functional data analysis through the computation of time-warping functions. Large, localized variations in the timing of peaks in head kinematics may indicate changes in coordination. The purpose of this study was to determine timing changes in head pitch acceleration of astronauts during treadmill walking before and after flight. Six astronauts (5M/1F; age = 43.5+/-6.4yr) participated in the study. Subjects walked at 1.8 m/sec (4 mph) on a motorized treadmill while reading optotypes displayed on a computer screen 4 m in front of their eyes. Three-dimensional motion of the subject s head was recorded with an Inertial Measurement Unit (IMU) device. Data were recorded twice before flight and four times after landing. The head pitch acceleration was calculated by taking the time derivative of the pitch velocity data from the IMU. Data for each session with each subject were time-normalized into gait cycles, then registered to align significant features and create a mean curve. The mean curves of each postflight session for each subject were re-registered based on their preflight mean curve to create time-warping functions. The root mean squares (RMS) of these warping functions were calculated to assess the deviation of head pitch acceleration mean curves in each postflight session from the preflight mean curve. After landing, most crewmembers exhibited localized shifts within their head pitch acceleration regimes, with the greatest deviations in RMS occurring on landing day or 1 day after landing. These results show that the alteration of head pitch coordination due to spaceflight may be

  9. Bayesian Analysis of Step-Stress Accelerated Life Test with Exponential Distribution

    SciTech Connect

    Lee, J.; Pan, R.

    2012-04-01

    In this article, we propose a general Bayesian inference approach to the step-stress accelerated life test with type II censoring. We assume that the failure times at each stress level are exponentially distributed and the test units are tested in an increasing order of stress levels. We formulate the prior distribution of the parameters of life-stress function and integrate the engineering knowledge of product failure rate and acceleration factor into the prior. The posterior distribution and the point estimates for the parameters of interest are provided. Through the Markov chain Monte Carlo technique, we demonstrate a nonconjugate prior case using an industrial example. It is shown that with the Bayesian approach, the statistical precision of parameter estimation is improved and, consequently, the required number of failures could be reduced.

  10. Application of High-performance Visual Analysis Methods to Laser Wakefield Particle Acceleration Data

    SciTech Connect

    Rubel, Oliver; Prabhat, Mr.; Wu, Kesheng; Childs, Hank; Meredith, Jeremy; Geddes, Cameron G.R.; Cormier-Michel, Estelle; Ahern, Sean; Weber, Gunther H.; Messmer, Peter; Hagen, Hans; Hamann, Bernd; Bethel, E. Wes

    2008-08-28

    Our work combines and extends techniques from high-performance scientific data management and visualization to enable scientific researchers to gain insight from extremely large, complex, time-varying laser wakefield particle accelerator simulation data. We extend histogram-based parallel coordinates for use in visual information display as well as an interface for guiding and performing data mining operations, which are based upon multi-dimensional and temporal thresholding and data subsetting operations. To achieve very high performance on parallel computing platforms, we leverage FastBit, a state-of-the-art index/query technology, to accelerate data mining and multi-dimensional histogram computation. We show how these techniques are used in practice by scientific researchers to identify, visualize and analyze a particle beam in a large, time-varying dataset.

  11. Theoretical and Observational Analysis of Particle Acceleration Mechanisms at Astrophysical Shocks

    NASA Astrophysics Data System (ADS)

    Lever, Edward Lawrence

    We analytically and numerically investigate the viability of Shock Surfing as a pre-injection mechanism for Diffusive Shock Acceleration, believed to be responsible for the production of Cosmic Rays. We demonstrate mathematically and from computer simulations that four critical conditions must be satisfied for Shock Surfing to function; the shock ramp must be narrow, the shock front must be smooth, the magnetic field angle must be very nearly perpendicular and, finally, these conditions must persist without interruption over substantial time periods and spatial scales. We quantify these necessary conditions, exhibit predictive functions for velocity maxima and accelerated ion fluxes based on observable shock parameters, and show unequivocally from current observational evidence that all of these necessary conditions are violated at shocks within the heliosphere, at the heliospheric Termination Shock, and also at Supernovae.

  12. Analysis of requirements for accelerating the development of geothermal energy resources in California

    NASA Technical Reports Server (NTRS)

    Fredrickson, C. D.

    1978-01-01

    Various resource data are presented showing that geothermal energy has the potential of satisfying a singificant part of California's increasing energy needs. General factors slowing the development of geothermal energy in California are discussed and required actions to accelerate its progress are presented. Finally, scenarios for developing the most promising prospects in the state directed at timely on-line power are given. Specific actions required to realize each of these individual scenarios are identified.

  13. Continuous Wavelet Transform Analysis of Acceleration Signals Measured from a Wave Buoy

    PubMed Central

    Chuang, Laurence Zsu-Hsin; Wu, Li-Chung; Wang, Jong-Hao

    2013-01-01

    Accelerometers, which can be installed inside a floating platform on the sea, are among the most commonly used sensors for operational ocean wave measurements. To examine the non-stationary features of ocean waves, this study was conducted to derive a wavelet spectrum of ocean waves and to synthesize sea surface elevations from vertical acceleration signals of a wave buoy through the continuous wavelet transform theory. The short-time wave features can be revealed by simultaneously examining the wavelet spectrum and the synthetic sea surface elevations. The in situ wave signals were applied to verify the practicality of the wavelet-based algorithm. We confirm that the spectral leakage and the noise at very-low-frequency bins influenced the accuracies of the estimated wavelet spectrum and the synthetic sea surface elevations. The appropriate thresholds of these two factors were explored. To study the short-time wave features from the wave records, the acceleration signals recorded from an accelerometer inside a discus wave buoy are analysed. The results from the wavelet spectrum show the evidence of short-time nonlinear wave events. Our study also reveals that more surface profiles with higher vertical asymmetry can be found from short-time nonlinear wave with stronger harmonic spectral peak. Finally, we conclude that the algorithms of continuous wavelet transform are practical for revealing the short-time wave features of the buoy acceleration signals. PMID:23966188

  14. Critical analysis of high particle number emissions from accelerating compressed natural gas buses.

    PubMed

    Jayaratne, E R; Meyer, N K; Ristovski, Z D; Morawska, L; Miljevic, B

    2010-05-15

    Compressed natural gas (CNG) engines are thought to be less harmful to the environment than conventional diesel engines, especially in terms of particle emissions. Although, this is true with respect to particulate matter (PM) emissions, results of particle number (PN) emission comparisons have been inconclusive. In this study, results of on-road and dynamometer studies of buses were used to derive several important conclusions. We show that, although PN emissions from CNG buses are significantly lower than from diesel buses at low engine power, they become comparable at high power. For diesel buses, PN emissions are not significantly different between acceleration and operation at steady maximum power. However, the corresponding PN emissions from CNG buses when accelerating are an order of magnitude greater than when operating at steady maximum power. During acceleration under heavy load, PN emissions from CNG buses are an order of magnitude higher than from diesel buses. The particles emitted from CNG buses are too small to contribute to PM(10) emissions or contribute to a reduction of visibility and may consist of semivolatile nanoparticles. PMID:20384333

  15. Continuous wavelet transform analysis of acceleration signals measured from a wave buoy.

    PubMed

    Chuang, Laurence Zsu-Hsin; Wu, Li-Chung; Wang, Jong-Hao

    2013-01-01

    Accelerometers, which can be installed inside a floating platform on the sea, are among the most commonly used sensors for operational ocean wave measurements. To examine the non-stationary features of ocean waves, this study was conducted to derive a wavelet spectrum of ocean waves and to synthesize sea surface elevations from vertical acceleration signals of a wave buoy through the continuous wavelet transform theory. The short-time wave features can be revealed by simultaneously examining the wavelet spectrum and the synthetic sea surface elevations. The in situ wave signals were applied to verify the practicality of the wavelet-based algorithm. We confirm that the spectral leakage and the noise at very-low-frequency bins influenced the accuracies of the estimated wavelet spectrum and the synthetic sea surface elevations. The appropriate thresholds of these two factors were explored. To study the short-time wave features from the wave records, the acceleration signals recorded from an accelerometer inside a discus wave buoy are analysed. The results from the wavelet spectrum show the evidence of short-time nonlinear wave events. Our study also reveals that more surface profiles with higher vertical asymmetry can be found from short-time nonlinear wave with stronger harmonic spectral peak. Finally, we conclude that the algorithms of continuous wavelet transform are practical for revealing the short-time wave features of the buoy acceleration signals. PMID:23966188

  16. Development and analysis of a metal-fueled accelerator-driven burner

    SciTech Connect

    Lypsch, F.; Hill, R. N.

    1995-09-15

    The purpose of this paper is to compare the safety characteristics of an accelerator driven metal-fueled fast system to a critical core on a consistent basis to determine how these characteristics are affected solely by subcriticality of the system. To accomplish this, an accelerator proton beam/tungsten neutron source model is surrounded by a subcritical blanket using metallic fuel and sodium as coolant. The consequences of typical accident transients, namely unprotected transient overpower (TOP), loss of heat sink (LOHS), and loss of flow (LOF) were calculated for the hybrid system and compared to corresponding results for a metal-fueled fast reactor. Results indicate that the subcritical system exhibits superior performance for TOP (reactivity-induced) transients; however, only in the critical system are reactivity feedbacks able to cause passive shutdown in the LOHS and LOF events. Therefore, for a full spectrum of accident initiators considered, the overall safety behavior of accelerator-driven metal-fueled systems can neither be concluded to be worse nor to be better than advanced reactor designs which rely on passive safety features.

  17. Development and analysis of a metal-fueled accelerator-driven burner

    SciTech Connect

    Lypsch, F.; Hill, R.N.

    1994-08-01

    The purpose of this paper is to compare the safety characteristics of an accelerator driven metal fueled fast system to a critical core on a consistent basis to determine how these characteristics are affected solely by subcritically of the system. To accomplish this an accelerator proton beam/tungsten neutron source model is surrounded by a subcritical blanket using metallic fuel and sodium as coolant. The consequences of typical accident transients, namely unprotected transient overpower (TOP), loss of heat sink (LOHS), and loss of flow (LOP) were calculated for the hybrid system and compared to corresponding results for a metal-fueled fast reactor. Results indicate that the subcritical system exhibits superior performance for TOP (reactivity-induced) transits; however, only in the critical system are reactivity feedbacks able to cause passive shutdown in the LOHS ad LOP events. Therefore, for a full spectrum of accident initiators considered, the overall safety behavior of accelerator-driven metal-fueled systems can neither be concluded to be worse nor to be better than advanced reactor designs which rely on passive safety features.

  18. Neutronics analysis of three beam-filter assemblies for an accelerator-based BNCT facility

    SciTech Connect

    Bleuel, D.L.; Costes, S.V.; Donahue, R.J.; Ludewigt, B.A.

    1997-08-01

    Three moderator materials, AlF{sub 3}/Al, D{sub 2}O and LiF, have been analyzed for clinical usefulness using the reaction {sup 7}Li(p,n) as an accelerator driven neutron source. Proton energies between 2.1 MeV and 2.6 MeV have been investigated. Radiation transport in the reflector/moderator assembly is simulated using the MCNP program. Depth-dose distributions in a head phanton are calculated with the BNCT-RTPE patient treatment planning program from INEEL using the MCNP generated neutron and photon spectra as the subsequent source. Clinical efficacy is compared using the current BMRR protocol for all designs. Depth-dose distributions are compared for a fixed normal tissue tolerance dose of 12.5 Gy-Eq. Radiation analyses also include a complete anthropomorphic phantom. Results of organ and whole body dose components are presented for several designs. Results indicate that high quality accelerator beams may produce clinically favorable treatments to deep-seated tumors when compared to the BMRR beam. Also discussed are problems identified in comparing accelerator and reactor based designs using in-air figures of merit as well as some results of spectrum-averaged RBE`s.

  19. Doppler Broadening Analysis of Steel Specimens Using Accelerator Based In Situ Pair Production

    SciTech Connect

    Makarashvili, V.; Wells, D. P.; Roy, A. K.

    2009-03-10

    Positron Annihilation Spectroscopy (PAS) techniques can be utilized as a sensitive probe of defects in materials. Studying these microscopic defects is very important for a number of industries in order to predict material failure or structural integrity. We have been developing gamma-induced pair-production techniques to produce positrons in thick samples ({approx}4-40 g/cm{sup 2}, or {approx}0.5-5 cm in steel). These techniques are called 'Accelerator-based Gamma-induced Positron Annihilation Spectroscopy'(AG-PAS). We have begun testing the capabilities of this technique for imaging of defect densities in thick structural materials. As a first step, a linear accelerator (LINAC) was employed to produce photon beams by stopping 15 MeV electrons in a 1 mm thick tungsten converter. The accelerator is capable of operating with 30-60 ns pulse width, up to 200 mA peak current at 1 kHz repetition rate. The highly collimated bremsstrahlung beam impinged upon our steel tensile specimens, after traveling through a 1.2 m thick concrete wall. Annihilation radiation was detected by a well-shielded and collimated high-purity germanium detector (HPGe). Conventional Doppler broadening spectrometry (DBS) was performed to determine S, W and T parameters for our samples.

  20. Mechanical Design and Analysis of a 200 MHz, Bolt-together RFQ forthe Accelerator Driven Neutron Source

    SciTech Connect

    Virostek, Steve; Hoff, Matt; Li, Derun; Staples, John; Wells,Russell

    2007-06-20

    A high-yield neutron source to screen sea-land cargocontainers for shielded Special Nuclear Materials (SNM) has been designedat LBNL [1,2]. The Accelerator-Driven Neutron Source (ADNS) uses theD(d,n)3He reaction to create a forward directed neutron beam. Keycomponents are a high-current radio-frequency quadrupole (RFQ)accelerator and a high-power target capable of producing a neutron fluxof>107 n/(cm2 cdot s) at a distance of 2.5 m. The mechanical designand analysis of the four-module, bolt-together RFQ will be presentedhere. Operating at 200 MHz, the 5.1 m long RFQ will accelerate a 40 mAdeuteron beam to 6 MeV. At a 5 percent duty factor, the time-average d+beam current on target is 1.5 mA. Each of the 1.27 m long RFQ moduleswill consist of four solid OFHC copper vanes. A specially designed 3-DO-ring will provide vacuum sealing between both the vanes and themodules. RF connections are made with canted coil spring contacts. Aseries of 60 water-cooled pi-mode rods provides quadrupole modestabilization. A set of 80 evenly spaced fixed slug tuners is used forfinal frequency adjustment and local field perturbationcorrection.

  1. Cellular Effects and Epistasis among Three Determinants of Adaptation in Experimental Populations of Saccharomyces cerevisiae▿†

    PubMed Central

    Parreiras, Lucas S.; Kohn, Linda M.; Anderson, James B.

    2011-01-01

    Epistatic interactions in which the phenotypic effect of an allele is conditional on its genetic background have been shown to play a central part in various evolutionary processes. In a previous study (J. B. Anderson et al., Curr. Biol. 20:1383-1388, 2010; J. R. Dettman, C. Sirjusingh, L. M. Kohn, and J. B. Anderson, Nature 447:585-588, 2007), beginning with a common ancestor, we identified three determinants of fitness as mutant alleles (each designated with the letter “e”) that arose in replicate Saccharomyces cerevisiae populations propagated in two different environments, a low-glucose and a high-salt environment. In a low-glucose environment, MDS3e and MKT1e interacted positively to confer a fitness advantage. Also, PMA1e from a high-salt environment interacted negatively with MKT1e in a low-glucose environment, an example of a Dobzhansky-Muller incompatibility that confers reproductive isolation. Here we showed that the negative interaction between PMA1e and MKT1e is mediated by alterations in intracellular pH, while the positive interaction between MDS3e and MKT1e is mediated by changes in gene expression affecting glucose transporter genes. We specifically addressed the evolutionary significance of the positive interaction by showing that the presence of the MDS3 mutation is a necessary condition for the spread and fixation of the new mutations at the identical site in MKT1. The expected mutations in MKT1 rose to high frequencies in two of three experimental populations carrying MDS3e but not in any of three populations carrying the ancestral allele. These data show how positive and negative epistasis can contribute to adaptation and reproductive isolation. PMID:21856932

  2. Analysis of the dynamics of a nutating body. [numerical analysis of displacement, velocity, and acceleration of point on mechanical drives

    NASA Technical Reports Server (NTRS)

    Anderson, W. J.

    1974-01-01

    The equations for the displacement, velocity, and acceleration of a point in a nutating body are developed. These are used to derive equations for the inertial moment developed by a nutating body of arbitrary shape. Calculations made for a previously designed nutating plate transmission indicate that that device is severely speed limited because of the very high magnitude inertial moment.

  3. Plasma accelerators

    SciTech Connect

    Ruth, R.D.; Chen, P.

    1986-03-01

    In this paper we discuss plasma accelerators which might provide high gradient accelerating fields suitable for TeV linear colliders. In particular we discuss two types of plasma accelerators which have been proposed, the Plasma Beat Wave Accelerator and the Plasma Wake Field Accelerator. We show that the electric fields in the plasma for both schemes are very similar, and thus the dynamics of the driven beams are very similar. The differences appear in the parameters associated with the driving beams. In particular to obtain a given accelerating gradient, the Plasma Wake Field Accelerator has a higher efficiency and a lower total energy for the driving beam. Finally, we show for the Plasma Wake Field Accelerator that one can accelerate high quality low emittance beams and, in principle, obtain efficiencies and energy spreads comparable to those obtained with conventional techniques.

  4. Calibration of a new experimental chamber for PIXE analysis at the Accelerator Facilities Division of Atomic Energy Centre Dhaka (AECD)

    NASA Astrophysics Data System (ADS)

    Hassan, Md. Taufique; Shariff, Md. Asad; Hossein, Amzad; Abedin, Md. Joynal; Fazlul Hoque, A. K. M.; Chowdhuri, M. S.

    2015-05-01

    A new experimental chamber has been installed at the 3 MV Van de Graaff Accelerator Facilities Division in the Atomic Energy Centre, Dhaka, to perform different Ion Beam Analysis (IBA) techniques. The calibration of this new setup for Particle Induced X-ray Emission (PIXE) technique has been done using a set of thin MicroMatter standards and GUPIX (PIXE spectrum analysis software), which is explicated in this paper. The effective thicknesses of the beryllium window of the X-ray detector and of the different absorbers used were determined. For standardization, the so called instrumental constant H (product of detector solid angle and the correction factor for the setup) as function of X-ray energy were determined and stored inside the GUPIX library for further PIXE analysis.

  5. Improving the design and analysis of superconducting magnets for particle accelerators

    SciTech Connect

    Gupta, R C

    1996-11-01

    High energy particle accelerators are now the primary means of discovering the basic building blocks of matter and understanding the forces between them. In order to minimize the cost of building these machines, superconducting magnets are used in essentially all present day high energy proton and heavy ion colliders. The cost of superconducting magnets is typically in the range of 20--30% of the total cost of building such machines. The circulating particle beam goes through these magnets a large number of times (over hundreds of millions). The luminosity performance and life time of the beam in these machines depends significantly on the field quality in these magnets. Therefore, even a small error in the magnetic field shape may create a large cumulative effect in the beam trajectory to throw the particles of the magnet aperture. The superconducting accelerator magnets must, therefore, be designed and constructed so that these errors are small. In this thesis the research and development work will be described 3which has resulted in significant improvements in the field quality of the superconducting magnets for the Relativistic Heavy Ion Collider (RHIC). The design and the field quality improvements in the prototype of the main collider dipole magnet for the Superconducting Super Collider (SSC) will also be presented. RHIC will accelerate and collide two counter rotating beams of heavy ions up to 100 GeV/u and protons up to 250 GeV. It is expected that RHIC will create a hot, dense quark-gluon plasma and the conditions which, according to the Big Bang theory, existed in the early universe.

  6. SU-C-BRD-03: Analysis of Accelerator Generated Text Logs for Preemptive Maintenance

    SciTech Connect

    Able, CM; Baydush, AH; Nguyen, C; Munley, MT; Gersh, J; Ndlovu, A; Rebo, I; Booth, J; Perez, M; Sintay, B

    2014-06-15

    Purpose: To develop a model to analyze medical accelerator generated parameter and performance data that will provide an early warning of performance degradation and impending component failure. Methods: A robust 6 MV VMAT quality assurance treatment delivery was used to test the constancy of accelerator performance. The generated text log files were decoded and analyzed using statistical process control (SPC) methodology. The text file data is a single snapshot of energy specific and overall systems parameters. A total of 36 system parameters were monitored which include RF generation, electron gun control, energy control, beam uniformity control, DC voltage generation, and cooling systems. The parameters were analyzed using Individual and Moving Range (I/MR) charts. The chart limits were calculated using a hybrid technique that included the use of the standard 3σ limits and the parameter/system specification. Synthetic errors/changes were introduced to determine the initial effectiveness of I/MR charts in detecting relevant changes in operating parameters. The magnitude of the synthetic errors/changes was based on: the value of 1 standard deviation from the mean operating parameter of 483 TB systems, a small fraction (≤ 5%) of the operating range, or a fraction of the minor fault deviation. Results: There were 34 parameters in which synthetic errors were introduced. There were 2 parameters (radial position steering coil, and positive 24V DC) in which the errors did not exceed the limit of the I/MR chart. The I chart limit was exceeded for all of the remaining parameters (94.2%). The MR chart limit was exceeded in 29 of the 32 parameters (85.3%) in which the I chart limit was exceeded. Conclusion: Statistical process control I/MR evaluation of text log file parameters may be effective in providing an early warning of performance degradation or component failure for digital medical accelerator systems. Research is Supported by Varian Medical Systems, Inc.

  7. A pilot in the loop analysis of helicopter acceleration/deceleration maneuvers

    NASA Technical Reports Server (NTRS)

    Heffley, R. K.

    1982-01-01

    Helicopter flight acceleration/deceleration maneuvers are quantified and put to use in the fields of handling qualities, flight training and evaluation of simulator fidelity. The three specific cases include the normal speed change maneuver, the nap-of-the-Earth dash/quickstop, and the decelerating approach to hover. All of these maneuvers share common generic features in terms of pilot adaptation and mathematical description; yet each differs in terms of the essential feedback loop structure, implications for handling qualities requirements, and simulator fidelity criteria.

  8. On the analysis of inhomogeneous magnetic field spectrometer for laser-driven ion acceleration

    SciTech Connect

    Jung, D.; Senje, L.; McCormack, O.; Dromey, B.; Zepf, M.; Yin, L.; Albright, B. J.; Letzring, S.; Gautier, D. C.; Fernandez, J. C.; Toncian, T.; Hegelich, B. M.

    2015-03-15

    We present a detailed study of the use of a non-parallel, inhomogeneous magnetic field spectrometer for the investigation of laser-accelerated ion beams. Employing a wedged yoke design, we demonstrate the feasibility of an in-situ self-calibration technique of the non-uniform magnetic field and show that high-precision measurements of ion energies are possible in a wide-angle configuration. We also discuss the implications of a stacked detector system for unambiguous identification of different ion species present in the ion beam and explore the feasibility of detection of high energy particles beyond 100 MeV/amu in radiation harsh environments.

  9. Ferrographic analysis of wear debris generated in accelerated rolling element fatigue tests

    NASA Technical Reports Server (NTRS)

    Jones, W. R., Jr.; Parker, R. J.

    1977-01-01

    The types and quantities of wear particles generated during accelerated ball rolling contact fatigue tests were determined. Ball specimens were made of AMS 5749, a corrosion resistant, high-temperature bearing steel. The lubricant was a super-refined naphthenic mineral oil. Conditions included a maximum Hertz stress of 5.215 times 10 to the 9th power Pa and a shaft speed of 10,000 rpm. Four types of wear particles were observed; normal rubbing wear particles, fatigue spall particles, spheres, and friction polymer.

  10. Analysis of accelerator based neutron spectra for BNCT using proton recoil spectroscopy

    SciTech Connect

    Wielopolski, L.; Ludewig, H.; Powell, J.R.; Raparia, D.; Alessi, J.G.; Lowenstein, D.I.

    1999-03-01

    Boron Neutron Capture Therapy (BNCT) is a promising binary treatment modality for high-grade primary brain tumors (glioblastoma multiforme, GM) and other cancers. BNCT employs a boron-10 containing compound that preferentially accumulates in the cancer cells in the brain. Upon neutron capture by {sup 10}B energetic alpha particles and triton released at the absorption site kill the cancer cell. In order to gain penetration depth in the brain Fairchild proposed, for this purpose, the use of energetic epithermal neutrons at about 10 keV. Phase 1/2 clinical trials of BNCT for GM are underway at the Brookhaven Medical Research Reactor (BMRR) and at the MIT Reactor, using these nuclear reactors as the source for epithermal neutrons. In light of the limitations of new reactor installations, e.g. cost, safety and licensing, and limited capability for modulating the reactor based neutron beam energy spectra, alternative neutron sources are being contemplated for wider implementation of this modality in a hospital environment. For example, accelerator based neutron sources offer the possibility of tailoring the neutron beams, in terms of improved depth-dose distributions, to the individual and offer, with relative ease, the capability of modifying the neutron beam energy and port size. In previous work new concepts for compact accelerator/target configuration were published. In this work, using the Van de Graaff accelerator the authors have explored different materials for filtering and reflecting neutron beams produced by irradiating a thick Li target with 1.8 to 2.5 MeV proton beams. However, since the yield and the maximum neutron energy emerging from the Li-7(p,n)Be-7 reaction increase with increase in the proton beam energy, there is a need for optimization of the proton energy versus filter and shielding requirements to obtain the desired epithermal neutron beam. The MCNP-4A computer code was used for the initial design studies that were verified with benchmark

  11. ANALYSIS OF ACCELERATOR BASED NEUTRON SPECTRA FOR BNCT USING PROTON RECOIL SPECTROSCOPY

    SciTech Connect

    WIELOPOLSKI,L.; LUDEWIG,H.; POWELL,J.R.; RAPARIA,D.; ALESSI,J.G.; LOWENSTEIN,D.I.

    1998-11-06

    Boron Neutron Capture Therapy (BNCT) is a promising binary treatment modality for high-grade primary brain tumors (glioblastoma multiforme, GM) and other cancers. BNCT employs a boron-10 containing compound that preferentially accumulates in the cancer cells in the brain. Upon neutron capture by {sup 10}B energetic alpha particles and triton released at the absorption site kill the cancer cell. In order to gain penetration depth in the brain Fairchild proposed, for this purpose, the use of energetic epithermal neutrons at about 10 keV. Phase I/II clinical trials of BNCT for GM are underway at the Brookhaven Medical Research Reactor (BMRR) and at the MIT Reactor, using these nuclear reactors as the source for epithermal neutrons. In light of the limitations of new reactor installations, e.g. cost, safety and licensing, and limited capability for modulating the reactor based neutron beam energy spectra alternative neutron sources are being contemplated for wider implementation of this modality in a hospital environment. For example, accelerator based neutron sources offer the possibility of tailoring the neutron beams, in terms of improved depth-dose distributions, to the individual and offer, with relative ease, the capability of modifying the neutron beam energy and port size. In previous work new concepts for compact accelerator/target configuration were published. In this work, using the Van de Graaff accelerator the authors have explored different materials for filtering and reflecting neutron beams produced by irradiating a thick Li target with 1.8 to 2.5 MeV proton beams. However, since the yield and the maximum neutron energy emerging from the Li-7(p,n)Be-7 reaction increase with increase in the proton beam energy, there is a need for optimization of the proton energy versus filter and shielding requirements to obtain the desired epithermal neutron beam. The MCNP-4A computer code was used for the initial design studies that were verified with benchmark

  12. Analysis of mode scattering from an abruptly ended dielectric slab waveguide by an accelerated iteration technique.

    PubMed

    Tigelis, I G; Manenkov, A B

    2000-12-01

    A new modification of the integral equation method using an iteration technique with "accelerating" parameters is presented to solve the problem of guided-mode scattering from an abruptly ended asymmetrical slab waveguide. The optimal choice of the parameters is shown to be closely connected with the variational principle. The electric-field distribution at the terminal plane, the reflection coefficient of the guided mode, and the far-field radiation pattern are computed. Numerical results are presented for several cases of abruptly ended waveguides, including the systems with constant and variable profiles of the refractive indices. The phenomenon of the radiation pattern rotation is examined in detail. PMID:11140485

  13. ACCELERATORS: Preliminary application of turn-by-turn data analysis to the SSRF storage ring

    NASA Astrophysics Data System (ADS)

    Chen, Jian-Hui; Zhao, Zhen-Tang

    2009-07-01

    There is growing interest in utilizing the beam position monitor turn-by-turn (TBT) data to debug accelerators. TBT data can be used to determine the linear optics, coupled optics and nonlinear behaviors of the storage ring lattice. This is not only a useful complement to other methods of determining the linear optics such as LOCO, but also provides a possibility to uncover more hidden phenomena. In this paper, a preliminary application of a β function measurement to the SSRF storage ring is presented.

  14. What Factors Are Associated with Grade Acceleration? An Analysis and Comparison of Two U.S. Databases

    ERIC Educational Resources Information Center

    Wells, Ryan; Lohman, David; Marron, Maureen

    2009-01-01

    The benefits of whole-grade acceleration for the highest achieving students in K-12 education are widely acknowledged. However, much less is known about which personal, family, and school factors are correlated with student acceleration. Which children are grade accelerated in K-7 education? Have factors associated with grade acceleration changed…

  15. [Analysis and comparison of various quality protocols for radiotherapy linear accelerators].

    PubMed

    Ceruti, M; D'Ercole, L; Lisciandro, F; Nicelli, L; Rovera, G

    1997-03-01

    The main parameters determining the quality of an electron beam produced by a linear accelerator for medical use were considered in this study, particularly: flatness, symmetry and uniformity. We analyzed and compared several protocols issued by national and international associations (such as the AAPM, IPSM, ICRU, NACP), the software protocol developed for the measurement system we used (Multidata) and the measurement instructions recommended by the accelerator manufacturer (Siemens). The above associations issue quality protocols to ensure system performances suitable for medical use, to increase patient safety and to improve the treatment outcome. Radiation therapy safety and improvement depend on correct dose measurements and dose distribution in the treated volume. Once the dose value per monitor unit ratio (Gy/M.U.) is determined, controls are necessary to be sure that the value does not change in time and that the dose distribution has the same effect in the whole treated volume. Our goal is to point out the differences and the affinities in the definition of the parameters, which change slightly in the different protocols, and to study the origin of the differences found when the experimental results were compared. Another important issue is represented by the frequency of quality controls, which are definitely different from the fast checks which are often performed. In conclusion, some suggestions are provided for the choice of the quality protocol to follow. PMID:9221422

  16. Analysis of Anderson Acceleration on a Simplified Neutronics/Thermal Hydraulics System

    SciTech Connect

    Toth, Alex; Kelley, C. T.; Slattery, Stuart R; Hamilton, Steven P; Clarno, Kevin T; Pawlowski, R. P. P.

    2015-01-01

    ABSTRACT A standard method for solving coupled multiphysics problems in light water reactors is Picard iteration, which sequentially alternates between solving single physics applications. This solution approach is appealing due to simplicity of implementation and the ability to leverage existing software packages to accurately solve single physics applications. However, there are several drawbacks in the convergence behavior of this method; namely slow convergence and the necessity of heuristically chosen damping factors to achieve convergence in many cases. Anderson acceleration is a method that has been seen to be more robust and fast converging than Picard iteration for many problems, without significantly higher cost per iteration or complexity of implementation, though its effectiveness in the context of multiphysics coupling is not well explored. In this work, we develop a one-dimensional model simulating the coupling between the neutron distribution and fuel and coolant properties in a single fuel pin. We show that this model generally captures the convergence issues noted in Picard iterations which couple high-fidelity physics codes. We then use this model to gauge potential improvements with regard to rate of convergence and robustness from utilizing Anderson acceleration as an alternative to Picard iteration.

  17. Acceleration of plasma flows in the closed magnetic fields: Simulation and analysis

    SciTech Connect

    Mahajan, Swadesh M.; Shatashvili, Nana L.; Mikeladze, Solomon V.; Sigua, Ketevan I.

    2006-06-15

    Within the framework of a two-fluid description, possible pathways for the generation of fast flows (dynamical as well as steady) in the closed magnetic fields are established. It is shown that a primary plasma flow (locally sub-Alfvenic) is accelerated while interacting with ambient arcade-like closed field structures. The time scale for creating reasonably fast flows (> or approx. 100 km/s) is dictated by the initial ion skin depth, while the amplification of the flow depends on local plasma {beta}. It is shown that distances over which the flows become 'fast' are {approx}0.01R{sub 0} from the interaction surface (R{sub 0} being a characteristic length of the system); later, the fast flow localizes (with dimensions < or approx. 0.05R{sub 0}) in the upper central region of the original arcade. For fixed initial temperature, the final speed (> or approx. 500 km/s) of the accelerated flow and the modification of the field structure are independent of the time duration (lifetime) of the initial flow. In the presence of dissipation, these flows are likely to play a fundamental role in the heating of the finely structured stellar atmospheres; their relevance to the solar wind is also obvious.

  18. Acceleration gradient of a plasma wakefield accelerator

    SciTech Connect

    Uhm, Han S.

    2008-02-25

    The phase velocity of the wakefield waves is identical to the electron beam velocity. A theoretical analysis indicates that the acceleration gradient of the wakefield accelerator normalized by the wave breaking amplitude is K{sub 0}({xi})/K{sub 1}({xi}), where K{sub 0}({xi}) and K{sub 1}({xi}) are the modified Bessel functions of the second kind of order zero and one, respectively and {xi} is the beam parameter representing the beam intensity. It is also shown that the beam density must be considerably higher than the diffuse plasma density for the large radial velocity of plasma electrons that are required for a high acceleration gradient.

  19. Shielding analysis of proton therapy accelerators: a demonstration using Monte Carlo-generated source terms and attenuation lengths.

    PubMed

    Lai, Bo-Lun; Sheu, Rong-Jiun; Lin, Uei-Tyng

    2015-05-01

    Monte Carlo simulations are generally considered the most accurate method for complex accelerator shielding analysis. Simplified models based on point-source line-of-sight approximation are often preferable in practice because they are intuitive and easy to use. A set of shielding data, including source terms and attenuation lengths for several common targets (iron, graphite, tissue, and copper) and shielding materials (concrete, iron, and lead) were generated by performing Monte Carlo simulations for 100-300 MeV protons. Possible applications and a proper use of the data set were demonstrated through a practical case study, in which shielding analysis on a typical proton treatment room was conducted. A thorough and consistent comparison between the predictions of our point-source line-of-sight model and those obtained by Monte Carlo simulations for a 360° dose distribution around the room perimeter showed that the data set can yield fairly accurate or conservative estimates for the transmitted doses, except for those near the maze exit. In addition, this study demonstrated that appropriate coupling between the generated source term and empirical formulae for radiation streaming can be used to predict a reasonable dose distribution along the maze. This case study proved the effectiveness and advantage of applying the data set to a quick shielding design and dose evaluation for proton therapy accelerators. PMID:25811254

  20. Analysis of factors responsible for the accelerated creep rupture of 12% Cr martensitic steel weld joints

    NASA Astrophysics Data System (ADS)

    Kudryavtsev, A. S.; Okhapkin, K. A.; Mikhailov, M. S.; Skutin, V. S.; Zubova, G. E.; Fedotov, B. V.

    2016-06-01

    In the process of the investigation of the heat resistance of a 0.07C-12Cr-Ni-Mo-V-Nb steel of the martensitic-ferritic class, a reduction was revealed in the long-term strength of its welded joints to below the level of the strength of the base metal. To establish the causes for the accelerated failure of the welded joints, an imitation of the thermal cycles was carried out that produce the structure of the heataffected zone using a dilatometer. In the samples with the structure that corresponds to that of the heataffected zone, a local zone of softening was revealed. The investigations of the metal structure using transmission electron microscopy have shown that the reduction in the creep rupture strength was caused by structural changes under the conditions of the thermal cycle of welding upon the staying of the steel in the temperature range between the Ac 1 and Ac 3 points.

  1. Quickly changing acceleration forces (QCAFs) vibration analysis on the A300 ZERO-G.

    PubMed

    Schmidt, Werner

    2004-01-01

    Experiments that are done under microgravity, e.g. during space or parabola flights, are invariably accompanied and affected by ubiquitous vibrations of the surroundings. Vibrations induce Quickly Changing Acceleration Forces (QCAFs) that interfere with the perception of the earth gravitational field. To investigate their impact on experiments under microgravity we monitored the vibrations of the airplane A300 ZERO-G during parabola flights and analyzed them in their spectral and frequency domains. Power spectra obtained with Fast-Fourier Transforms (FFT) display a complex pattern of various vibrations whose origin, relative phases and intensities remain unidentified. During the zero-g phases (parabolas), when the engines of the airplane are throttled, the vibrations still elicit residual QCAFs of at least +/- 1 g. By means of adequate damping procedures the QCAFs could, however, be reduced by approximately 95%. PMID:15773021

  2. Accelerator mass spectrometry analysis of aroma compound absorption in plastic packaging materials

    NASA Astrophysics Data System (ADS)

    Stenström, Kristina; Erlandsson, Bengt; Hellborg, Ragnar; Wiebert, Anders; Skog, Göran; Nielsen, Tim

    1994-05-01

    Absorption of aroma compounds in plastic packaging materials may affect the taste of the packaged food and it may also change the quality of the packaging material. A method to determine the aroma compound absorption in polymers by accelerator mass spectrometry (AMS) is being developed at the Lund Pelletron AMS facility. The high sensitivity of the AMS method makes it possible to study these phenomena under realistic conditions. As a first test low density polyethylene exposed to 14C-doped ethyl acetate is examined. After converting the polymer samples with the absorbed aroma compounds to graphite, the {14C }/{13C } ratio of the samples is measured by the AMS system and the degree of aroma compound absorption is established. The results are compared with those obtained by supercritical fluid extraction coupled to gas chromatography (SFE-GC).

  3. An accelerated buoyancy adhesion assay combined with 3-D morphometric analysis for assessing osteoblast adhesion on microgrooved substrata.

    PubMed

    Sobral, J M; Malheiro, V N; Clyne, T W; Harris, J; Rezk, R; O'Neill, W; Markaki, A E

    2016-07-01

    An accelerated negative buoyancy method has been developed to assess cell adhesion strength. This method has been used in conjunction with 3-D morphometric analysis to understand the effects of surface topology on cell response. Aligned micro-grooved surface topographies (with a range of groove depths) were produced on stainless steel 316L substrates by laser ablation. An investigation was carried out on the effect of the micro-grooved surface topography on cell adhesion strength, cell and nucleus volumes, cell phenotypic expression and attachment patterns. Increased hydrophobicity and anisotropic wettability was observed on surfaces with deeper grooves. A reduction was noted in cell volume, projected areas and adhesion sites for deeper grooves, linked to lower cell proliferation and differentiation rates and also to reduced adhesion strength. The results suggest that the centrifugation assay combined with three-dimensional cell morphometric analysis has considerable potential for obtaining improved understanding of the cell/substrate interface. PMID:26773651

  4. Analysis of sonic boom measurements near shock wave extremities for flight near Mach 1.0 and for airplane accelerations

    NASA Technical Reports Server (NTRS)

    Haglund, G. T.; Kane, E. J.

    1974-01-01

    The analysis of the 14 low-altitude transonic flights showed that the prevailing meteorological consideration of the acoustic disturbances below the cutoff altitude during threshold Mach number flight has shown that a theoretical safe altitude appears to be valid over a wide range of meteorological conditions and provides a reasonable estimate of the airplane ground speed reduction to avoid sonic boom noise during threshold Mach number flight. Recent theoretical results for the acoustic pressure waves below the threshold Mach number caustic showed excellent agreement with observations near the caustic, but the predicted overpressure levels were significantly lower than those observed far from the caustic. The analysis of caustics produced by inadvertent low-magnitude accelerations during flight at Mach numbers slightly greater than the threshold Mach number showed that folds and associated caustics were produced by slight changes in the airplane ground speed. These caustic intensities ranged from 1 to 3 time the nominal steady, level flight intensity.

  5. Calculation for optimization of the experimental conditions for RBS analysis at the HUS 5SDH-2 tandem accelerator

    NASA Astrophysics Data System (ADS)

    Phong, Le Hong Khiem Ho, Vi; Nghia, Nguyen The

    2015-06-01

    The dependences of the depth and mass resolutions of analysis using Rutherford Backscattering Spectrometry (RBS) on some experimental conditions (such as the beam energy, the target tilting angle, etc.) have been investigated. A computer program for simulating the RBS spectra and for calculating the depth and mass resolution under different experimental conditions was developed. The results of calculation were experimentally checked by using some reference samples. The good agreements between calculated and experimental values have been found. The optimum analysis conditions over a wide range of RBS applications based on our calculation can be chosen. This investigation was conducted by using the RBS system at HUS 5SDH-2 Tandem accelerator at the Hanoi University of Science.

  6. Comprehensive analysis of electron beam central axis dose for a radiotherapy linear accelerator.

    PubMed

    Shiu, A S; Tung, S S; Nyerick, C E; Ochran, T G; Otte, V A; Boyer, A L; Hogstrom, K R

    1994-04-01

    This work evaluates the application of AAPM task group 25 (TG25) methodology for determination of central axis depth dose for a radiotherapy linear accelerator, whose dual scattering foil system and applicators were recently modified. The percent depth dose (%DD) and the dose output factor have been measured for square and rectangular fields at 100- and 110-cm source-to-surface distance (SSDs). At 100-cm SSD, results showed that %DD for a specific energy and field size can vary with applicator, the largest variation being for the 20-MeV, 10 x 10-cm field where a spread of +/- 2.5% or +/- 3 mm about the mean %DD is observed. The square-root method determines rectangular field %DD within 1%. Output factors for rectangular fields are calculated from square field values more accurately using a square-root method than the equivalent-square method recommended by TG25. At 110-cm SSD, the %DD calculated from that at 100-cm SSD using an inverse square factor does not agree with measured values for all fields. The maximum difference observed for the 20-MeV, 6 x 6-cm field was 5.5% or 10 mm. Output data at the 110-cm SSD show that the square-root method is suitable for determination of the air-gap correction factors of rectangular fields. In summary, the recommendations of TG25 work reasonably well for central axis electron beam dosimetry for this version of a radiotherapy linear accelerator, except in limited cases where applicator-scattered electrons apparently cause minor but clinically significant discrepancies. PMID:8058023

  7. Genetic Basis of Heterosis for Growth-Related Traits in Arabidopsis Investigated by Testcross Progenies of Near-Isogenic Lines Reveals a Significant Role of Epistasis

    PubMed Central

    Melchinger, Albrecht E.; Piepho, Hans-Peter; Utz, H. Friedrich; Muminović, Jasmina; Wegenast, Thilo; Törjék, Otto; Altmann, Thomas; Kusterer, Barbara

    2007-01-01

    Epistasis seems to play a significant role in the manifestation of heterosis. However, the power of detecting epistatic interactions among quantitative trait loci (QTL) in segregating populations is low. We studied heterosis in Arabidopsis thaliana hybrid C24 × Col-0 by testing near-isogenic lines (NILs) and their triple testcross (TTC) progenies. Our objectives were to (i) provide the theoretical basis for estimating different types of genetic effects with this experimental design, (ii) determine the extent of heterosis for seven growth-related traits, (iii) map the underlying QTL, and (iv) determine their gene action. Two substitution libraries, each consisting of 28 NILs and covering ∼61 and 39% of the Arabidopsis genome, were assayed by 110 single-nucleotide polymorphism (SNP) markers. With our novel generation means approach 38 QTL were detected, many of which confirmed heterotic QTL detected previously in the same cross with TTC progenies of recombinant inbred lines. Furthermore, many of the QTL were common for different traits and in common with the 58 QTL detected by a method that compares triplets consisting of a NIL, its recurrent parent, and their F1 cross. While the latter approach revealed mostly (75%) overdominant QTL, the former approach allowed separation of dominance and epistasis by analyzing all materials simultaneously and yielded substantial positive additive × additive effects besides directional dominance. Positive epistatic effects reduced heterosis for growth-related traits in our materials. PMID:18039884

  8. SU-E-T-144: Effective Analysis of VMAT QA Generated Trajectory Log Files for Medical Accelerator Predictive Maintenance

    SciTech Connect

    Able, CM; Baydush, AH; Nguyen, C; Munley, MT; Gersh, J; Ndlovu, A; Rebo, I; Booth, J; Perez, M; Sintay, B

    2014-06-01

    Purpose: To determine the effectiveness of SPC analysis for a model predictive maintenance process that uses accelerator generated parameter and performance data contained in trajectory log files. Methods: Each trajectory file is decoded and a total of 131 axes positions are recorded (collimator jaw position, gantry angle, each MLC, etc.). This raw data is processed and either axis positions are extracted at critical points during the delivery or positional change over time is used to determine axis velocity. The focus of our analysis is the accuracy, reproducibility and fidelity of each axis. A reference positional trace of the gantry and each MLC is used as a motion baseline for cross correlation (CC) analysis. A total of 494 parameters (482 MLC related) were analyzed using Individual and Moving Range (I/MR) charts. The chart limits were calculated using a hybrid technique that included the use of the standard 3σ limits and parameter/system specifications. Synthetic errors/changes were introduced to determine the initial effectiveness of I/MR charts in detecting relevant changes in operating parameters. The magnitude of the synthetic errors/changes was based on: TG-142 and published analysis of VMAT delivery accuracy. Results: All errors introduced were detected. Synthetic positional errors of 2mm for collimator jaw and MLC carriage exceeded the chart limits. Gantry speed and each MLC speed are analyzed at two different points in the delivery. Simulated Gantry speed error (0.2 deg/sec) and MLC speed error (0.1 cm/sec) exceeded the speed chart limits. Gantry position error of 0.2 deg was detected by the CC maximum value charts. The MLC position error of 0.1 cm was detected by the CC maximum value location charts for every MLC. Conclusion: SPC I/MR evaluation of trajectory log file parameters may be effective in providing an early warning of performance degradation or component failure for medical accelerator systems.

  9. High homocysteine and epistasis between MTHFR and APOE: association with cognitive performance in the elderly.

    PubMed

    Polito, Letizia; Poloni, Tino Emanuele; Vaccaro, Roberta; Abbondanza, Simona; Mangieri, Michela; Davin, Annalisa; Villani, Simona; Guaita, Antonio

    2016-04-01

    High total homocysteine (tHcy) is associated with cognitive impairment in the elderly. The impact of high tHcy on different cognitive domains deserves further investigation, as does the role of the C677T polymorphism of the 5,10 methylenetetrahydrofolate reductase (MTHFR) gene. A cross-sectional analysis of 903 subjects from the population-based "InveCe.Ab" study was performed. The participants had no psychosis or active neurological disorders. They underwent a neuropsychological assessment. Principal component analysis allowed cognitive performance to be condensed into two components: executive functions and memory. Novel components were evaluated for association with tHcy, controlling for potential confounders. Regression models showed that high serum tHcy was associated with lower executive functions, but not with memory. MTHFR C677T TT was associated with higher tHcy but did not affect cognitive performance per se. However, when combined with the apolipoprotein E (APOE)-ε4 allele, it was a risk factor for lower executive performance, independently of tHcy levels. In summary, high tHcy per se, or MTHFR C677T TT in combination with the APOE-ε4 allele, might be associated primarily with executive dysfunctions rather than memory loss. PMID:26774227

  10. SU-E-T-495: Neutron Induced Electronics Failure Rate Analysis for a Single Room Proton Accelerator

    SciTech Connect

    Knutson, N; DeWees, T; Klein, E

    2014-06-01

    Purpose: To determine the failure rate as a function of neutron dose of the range modulator's servo motor controller system (SMCS) while shielded with Borated Polyethylene (BPE) and unshielded in a single room proton accelerator. Methods: Two experimental setups were constructed using two servo motor controllers and two motors. Each SMCS was then placed 30 cm from the end of the plugged proton accelerator applicator. The motor was then turned on and observed from outside of the vault while being irradiated to known neutron doses determined from bubble detector measurements. Anytime the motor deviated from the programmed motion a failure was recorded along with the delivered dose. The experiment was repeated using 9 cm of BPE shielding surrounding the SMCS. Results: Ten SMCS failures were recorded in each experiment. The dose per monitor unit for the unshielded SMCS was 0.0211 mSv/MU and 0.0144 mSv/MU for the shielded SMCS. The mean dose to produce a failure for the unshielded SMCS was 63.5 ± 58.3 mSv versus 17.0 ±12.2 mSv for the shielded. The mean number of MUs between failures were 2297 ± 1891 MU for the unshielded SMCS and 2122 ± 1523 MU for the shielded. A Wilcoxon Signed Ranked test showed the dose between failures were significantly different (P value = 0.044) while the number of MUs between failures were not (P value = 1.000). Statistical analysis determined a SMCS neutron dose of 5.3 mSv produces a 5% chance of failure. Depending on the workload and location of the SMCS, this failure rate could impede clinical workflow. Conclusion: BPE shielding was shown to not reduce the average failure of the SMCS and relocation of the system outside of the accelerator vault was required to lower the failure rate enough to avoid impeding clinical work flow.

  11. A haplotype-based algorithm for multilocus linkage disequilibrium mapping of quantitative trait loci with epistasis.

    PubMed Central

    Lou, Xiang-Yang; Casella, George; Littell, Ramon C; Yang, Mark C K; Johnson, Julie A; Wu, Rongling

    2003-01-01

    For tightly linked loci, cosegregation may lead to nonrandom associations between alleles in a population. Because of its evolutionary relationship with linkage, this phenomenon is called linkage disequilibrium. Today, linkage disequilibrium-based mapping has become a major focus of recent genome research into mapping complex traits. In this article, we present a new statistical method for mapping quantitative trait loci (QTL) of additive, dominant, and epistatic effects in equilibrium natural populations. Our method is based on haplotype analysis of multilocus linkage disequilibrium and exhibits two significant advantages over current disequilibrium mapping methods. First, we have derived closed-form solutions for estimating the marker-QTL haplotype frequencies within the maximum-likelihood framework implemented by the EM algorithm. The allele frequencies of putative QTL and their linkage disequilibria with the markers are estimated by solving a system of regular equations. This procedure has significantly improved the computational efficiency and the precision of parameter estimation. Second, our method can detect marker-QTL disequilibria of different orders and QTL epistatic interactions of various kinds on the basis of a multilocus analysis. This can not only enhance the precision of parameter estimation, but also make it possible to perform whole-genome association studies. We carried out extensive simulation studies to examine the robustness and statistical performance of our method. The application of the new method was validated using a case study from humans, in which we successfully detected significant QTL affecting human body heights. Finally, we discuss the implications of our method for genome projects and its extension to a broader circumstance. The computer program for the method proposed in this article is available at the webpage http://www.ifasstat.ufl.edu/genome/~LD. PMID:12702696

  12. Sensitivity analysis in multipole-accelerated panel methods for potential flow

    NASA Technical Reports Server (NTRS)

    Leathrum, James F., Jr.

    1995-01-01

    In the design of an airframe, the effect of changing the geometry on resulting computations is necessary for design optimization. The geometry is defined in terms of a series of design variables, including design variables to define the wing planform, tail, canard, pylon, and nacelle. Design optimization in this research is based on how these design variable affect the potential flow. The potential flow is computed as a function of the geometry and location of a series of panels describing the airframe, which are in turn a function of the design variables. Multipole accelerated panel methods improve the computational complexity of the problem and thus are an attractive approach. To utilize the methods in design optimization, it was necessary to define the appropriate sensitivity derivatives. The overhead incurred from finding the sensitivity derivatives in conjunction with the original computation should be small. This research developed the background for multipole-accelerated panel methods and the framework for finding sensitivity derivatives in the methods. Potential flow panel codes are commonly used for powered-lift aerodynamic predictions for three dimensional geometries. Given an airframe which has been discretized into a series of panels to define the airframe geometry, potential is computed as a function of the influence of all panels on all other panels. This is a computationally intensive problem for which efficient solutions are desired to improve the computational time and to allow greater resolution by use of more panels. One such solution is the use of hierarchical multipole methods which entail approximations of the effects of far-field terms. Hierarchical multipole methods have become prevalent in molecular dynamics and gravitational physics, and have been introduced into the fields of capacitance calculations, computational fluid dynamics, and electromagnetics. The methods utilize multipole expansions to describe the effect of bodies (i

  13. Theoretical and experimental analysis of a linear accelerator endowed with single feed coupler with movable short-circuit

    NASA Astrophysics Data System (ADS)

    Forno, Massimo Dal; Craievich, Paolo; Penco, Giuseppe; Vescovo, Roberto

    2013-11-01

    The front-end injection systems of the FERMI@Elettra linac produce high brightness electron beams that define the performance of the Free Electron Laser. The photoinjector mainly consists of the radiofrequency (rf) gun and of two S-band rf structures which accelerate the beam. Accelerating structures endowed with a single feed coupler cause deflection and degradation of the electron beam properties, due to the asymmetry of the electromagnetic field. In this paper, a new type of single feed structure with movable short-circuit is proposed. It has the advantage of having only one waveguide input, but we propose a novel design where the dipolar component is reduced. Moreover, the racetrack geometry allows to reduce the quadrupolar component. This paper presents the microwave design and the analysis of the particle motion inside the linac. A prototype has been machined at the Elettra facility to verify the new coupler design and the rf field has been measured by adopting the bead-pull method. The results are here presented, showing good agreement with the expectations.

  14. Theoretical and experimental analysis of a linear accelerator endowed with single feed coupler with movable short-circuit

    SciTech Connect

    Forno, Massimo Dal; Craievich, Paolo; Penco, Giuseppe; Vescovo, Roberto

    2013-11-15

    The front-end injection systems of the FERMI@Elettra linac produce high brightness electron beams that define the performance of the Free Electron Laser. The photoinjector mainly consists of the radiofrequency (rf) gun and of two S-band rf structures which accelerate the beam. Accelerating structures endowed with a single feed coupler cause deflection and degradation of the electron beam properties, due to the asymmetry of the electromagnetic field. In this paper, a new type of single feed structure with movable short-circuit is proposed. It has the advantage of having only one waveguide input, but we propose a novel design where the dipolar component is reduced. Moreover, the racetrack geometry allows to reduce the quadrupolar component. This paper presents the microwave design and the analysis of the particle motion inside the linac. A prototype has been machined at the Elettra facility to verify the new coupler design and the rf field has been measured by adopting the bead-pull method. The results are here presented, showing good agreement with the expectations.

  15. Theoretical and experimental analysis of a linear accelerator endowed with single feed coupler with movable short-circuit.

    PubMed

    Dal Forno, Massimo; Craievich, Paolo; Penco, Giuseppe; Vescovo, Roberto

    2013-11-01

    The front-end injection systems of the FERMI@Elettra linac produce high brightness electron beams that define the performance of the Free Electron Laser. The photoinjector mainly consists of the radiofrequency (rf) gun and of two S-band rf structures which accelerate the beam. Accelerating structures endowed with a single feed coupler cause deflection and degradation of the electron beam properties, due to the asymmetry of the electromagnetic field. In this paper, a new type of single feed structure with movable short-circuit is proposed. It has the advantage of having only one waveguide input, but we propose a novel design where the dipolar component is reduced. Moreover, the racetrack geometry allows to reduce the quadrupolar component. This paper presents the microwave design and the analysis of the particle motion inside the linac. A prototype has been machined at the Elettra facility to verify the new coupler design and the rf field has been measured by adopting the bead-pull method. The results are here presented, showing good agreement with the expectations. PMID:24289419

  16. Comparison Study of Electromagnet and Permanent Magnet Systems for an Accelerator Using Cost-Based Failure Modes and Effects Analysis.

    SciTech Connect

    Spencer, C

    2004-02-19

    The next generation of particle accelerators will be one-of-a-kind facilities, and to meet their luminosity goals they must have guaranteed availability over their several decade lifetimes. The Next Linear Collider (NLC) is one viable option for a 1 TeV electron-positron linear collider, it has an 85% overall availability goal. We previously showed how a traditional Failure Modes and Effects Analysis (FMEA) of a SLAC electromagnet leads to reliability-enhancing design changes. Traditional FMEA identifies failure modes with high risk but does not consider the consequences in terms of cost, which could lead to unnecessarily expensive components. We have used a new methodology, ''Life Cost-Based FMEA'', which measures risk of failure in terms of cost, in order to evaluate and compare two different technologies that might be used for the 8653 NLC magnets: electromagnets or permanent magnets. The availabilities for the two different types of magnet systems have been estimated using empirical data from SLAC's accelerator failure database plus expert opinion on permanent magnet failure modes and industry standard failure data. Labor and material costs to repair magnet failures are predicted using a Monte Carlo simulation of all possible magnet failures over a 30-year lifetime. Our goal is to maximize up-time of the NLC through magnet design improvements and the optimal combination of electromagnets and permanent magnets, while reducing magnet system lifecycle costs.

  17. Structure determination of chemisorbed chirality transfer complexes: Accelerated STM analysis and exchange-correlation functional sensitivity

    NASA Astrophysics Data System (ADS)

    Groves, M. N.; Goubert, G.; Rasmussen, A. M. H.; Dong, Y.; Lemay, J.-C.; Demers-Carpentier, V.; McBreen, P. H.; Hammer, B.

    2014-11-01

    Linking STM images to atomic positions determined by DFT calculations is an important step in characterizing the intermolecular interactions at play in many surface processes including asymmetric hydrogenation on heterogeneous catalysts. An accelerated data extraction method is used to collect STM information on the geometry of complexes formed between the two substrates, 2,2,2-trifluoroacetophenone (TFAP) and 3,3,3-methyltrifluoropyruvate (MTFP), and the chiral modifier (R)-(+)-1-(1-naphthyl)ethylamine ((R)-NEA) on Pt(111). We present new experimental data for complexes formed by MTFP and the (R)-NEA-1 conformer along with a new and enlarged set of reformulated STM data that extends what was reported in previously published studies of complexed MTFP and TFAP. Atomic geometries based on DFT calculations using PBE, M06-L, and optB88-vdW exchange-correlation functionals will also be presented. It will be shown that both substrates have well-defined complexation geometries when interacting with the modifier and that the relative complexation energies are not markedly sensitive to the functional employed.

  18. Analysis of a Symmetric Terahertz Dielectric-Lined Rectangular Structure for High Gradient Acceleration

    SciTech Connect

    Marshall, T. C.; Sotnikov, G. V.; Shchelkunov, S. V.; Hirshfield, J. L.

    2009-01-22

    We study, using computational methods based on analytic theory as well as a PIC code, the wakefields set up in a seven-zone symmetric rectangular THZ structure, and find that for overall transverse x/y dimensions 2.121 mmx0.6 mm, two 5-GeV drive bunches (3 nC, with x/y/z dimensions 0.3/0.3/0.12 mm{sup 3} as available at SLAC) will set up an axial wakefield {approx}350 MV/m in the witness channel, with a transformer ratio {approx}18-20. The symmetry of the structure ensures not only that small transverse forces are imposed on the witness bunch, but also that the two components of transverse force are equal and opposite at the bunch location so as to enable dynamical stabilization in an accelerator comprising many modules. Transverse forces on the drive bunch tails may allow bunches to move {approx}0.5-1 m without suffering excessive erosion.

  19. Hyperfractionated Accelerated Radiotherapy (HART) for Anaplastic Thyroid Carcinoma: Toxicity and Survival Analysis

    SciTech Connect

    Dandekar, Prasad; Rhys-Evans, Peter; Harrington, Kevin; Nutting, Christopher; Newbold, Kate

    2009-06-01

    Purpose: Anaplastic thyroid carcinoma (ATC) is one of the most aggressive cancers, and the current protocol of hyperfractionated accelerated radiotherapy was initiated to improve survival while limiting toxicities. Methods and Materials: All patients with ATC from 1991 to 2002 were accrued and received megavoltage radiotherapy from the mastoid processes to the carina up to 60 Gy in twice-daily fractions of 1.8 and 2 Gy, 6 hours apart. Results: Thirty-one patients were accrued with a median age of 69 years, and 55% were women. Debulking was performed in 26%, and total thyroidectomy, in 6%, whereas 68% received radical radiotherapy alone. Local control data were available for 27 patients: 22% had a complete response, 26% had a partial response, 15% showed progressive disease, and 37% showed static disease. Median overall survival for all 31 patients was 70 days (95% confidence interval, 40-99). There was no significant difference in median survival between patients younger (70 days) and older than 70 years (42 days), between men (70 days) and women (49days), and between patients receiving postoperative radiotherapy (77 days) and radical radiotherapy alone (35 days). Grade III or higher skin erythema was seen in 56% patients; desquamation in 21%; dysphagia in 74%; and esophagitis in 79%. Conclusion: The current protocol failed to offer a significant survival benefit, was associated with severe toxicities, and thus was discontinued. There is a suggestion that younger patients with operable disease have longer survival, but this would require a larger study to confirm it.

  20. Fourier analysis of Solar atmospheric numerical simulations accelerated with GPUs (CUDA).

    NASA Astrophysics Data System (ADS)

    Marur, A.

    2015-12-01

    Solar dynamics from the convection zone creates a variety of waves that may propagate through the solar atmosphere. These waves are important in facilitating the energy transfer between the sun's surface and the corona as well as propagating energy throughout the solar system. How and where these waves are dissipated remains an open question. Advanced 3D numerical simulations have furthered our understanding of the processes involved. Fourier transforms to understand the nature of the waves by finding the frequency and wavelength of these waves through the simulated atmosphere, as well as the nature of their propagation and where they get dissipated. In order to analyze the different waves produced by the aforementioned simulations and models, Fast Fourier Transform algorithms will be applied. Since the processing of the multitude of different layers of the simulations (of the order of several 100^3 grid points) would be time intensive and inefficient on a CPU, CUDA, a computing architecture that harnesses the power of the GPU, will be used to accelerate the calculations.

  1. A scientific and statistical analysis of accelerated aging for pharmaceuticals. Part 1: accuracy of fitting methods.

    PubMed

    Waterman, Kenneth C; Swanson, Jon T; Lippold, Blake L

    2014-10-01

    Three competing mathematical fitting models (a point-by-point estimation method, a linear fit method, and an isoconversion method) of chemical stability (related substance growth) when using high temperature data to predict room temperature shelf-life were employed in a detailed comparison. In each case, complex degradant formation behavior was analyzed by both exponential and linear forms of the Arrhenius equation. A hypothetical reaction was used where a drug (A) degrades to a primary degradant (B), which in turn degrades to a secondary degradation product (C). Calculated data with the fitting models were compared with the projected room-temperature shelf-lives of B and C, using one to four time points (in addition to the origin) for each of three accelerated temperatures. Isoconversion methods were found to provide more accurate estimates of shelf-life at ambient conditions. Of the methods for estimating isoconversion, bracketing the specification limit at each condition produced the best estimates and was considerably more accurate than when extrapolation was required. Good estimates of isoconversion produced similar shelf-life estimates fitting either linear or nonlinear forms of the Arrhenius equation, whereas poor isoconversion estimates favored one method or the other depending on which condition was most in error. PMID:25043838

  2. Fusion-neutron-yield, activation measurements at the Z accelerator: design, analysis, and sensitivity.

    PubMed

    Hahn, K D; Cooper, G W; Ruiz, C L; Fehl, D L; Chandler, G A; Knapp, P F; Leeper, R J; Nelson, A J; Smelser, R M; Torres, J A

    2014-04-01

    We present a general methodology to determine the diagnostic sensitivity that is directly applicable to neutron-activation diagnostics fielded on a wide variety of neutron-producing experiments, which include inertial-confinement fusion (ICF), dense plasma focus, and ion beam-driven concepts. This approach includes a combination of several effects: (1) non-isotropic neutron emission; (2) the 1/r(2) decrease in neutron fluence in the activation material; (3) the spatially distributed neutron scattering, attenuation, and energy losses due to the fielding environment and activation material itself; and (4) temporally varying neutron emission. As an example, we describe the copper-activation diagnostic used to measure secondary deuterium-tritium fusion-neutron yields on ICF experiments conducted on the pulsed-power Z Accelerator at Sandia National Laboratories. Using this methodology along with results from absolute calibrations and Monte Carlo simulations, we find that for the diagnostic configuration on Z, the diagnostic sensitivity is 0.037% ± 17% counts/neutron per cm(2) and is ∼ 40% less sensitive than it would be in an ideal geometry due to neutron attenuation, scattering, and energy-loss effects. PMID:24784607

  3. Accelerated calendar and pulse life analysis of lithium-ion cells

    NASA Astrophysics Data System (ADS)

    Jungst, Rudolph G.; Nagasubramanian, Ganesan; Case, Herbert L.; Liaw, Bor Yann; Urbina, Angel; Paez, Thomas L.; Doughty, Daniel H.

    Sandia National Laboratories has been studying calendar and pulse discharge life of prototype high-power lithium-ion cells as part of the Advanced Technology Development (ATD) Program. One of the goals of ATD is to establish validated accelerated life test protocols for lithium-ion cells in the hybrid electric vehicle application. In order to accomplish this, aging experiments have been conducted on 18650-size cells containing a chemistry representative of these high-power designs. Loss of power and capacity are accompanied by increasing interfacial impedance at the cathode. These relationships are consistent within a given state-of-charge (SOC) over the range of storage temperatures and times. Inductive models have been used to construct detailed descriptions of the relationships between power fade and aging time and to relate power fade, capacity loss and impedance rise. These models can interpolate among the different experimental conditions and can also describe the error surface when fitting life prediction models to the data.

  4. Fusion-neutron-yield, activation measurements at the Z accelerator: Design, analysis, and sensitivity

    SciTech Connect

    Hahn, K. D. Ruiz, C. L.; Fehl, D. L.; Chandler, G. A.; Knapp, P. F.; Smelser, R. M.; Torres, J. A.; Cooper, G. W.; Nelson, A. J.; Leeper, R. J.

    2014-04-15

    We present a general methodology to determine the diagnostic sensitivity that is directly applicable to neutron-activation diagnostics fielded on a wide variety of neutron-producing experiments, which include inertial-confinement fusion (ICF), dense plasma focus, and ion beam-driven concepts. This approach includes a combination of several effects: (1) non-isotropic neutron emission; (2) the 1/r{sup 2} decrease in neutron fluence in the activation material; (3) the spatially distributed neutron scattering, attenuation, and energy losses due to the fielding environment and activation material itself; and (4) temporally varying neutron emission. As an example, we describe the copper-activation diagnostic used to measure secondary deuterium-tritium fusion-neutron yields on ICF experiments conducted on the pulsed-power Z Accelerator at Sandia National Laboratories. Using this methodology along with results from absolute calibrations and Monte Carlo simulations, we find that for the diagnostic configuration on Z, the diagnostic sensitivity is 0.037% ± 17% counts/neutron per cm{sup 2} and is ∼ 40% less sensitive than it would be in an ideal geometry due to neutron attenuation, scattering, and energy-loss effects.

  5. Hamiltonian Analysis of the Particle Motion in an Accelerator with the Longitudinal Magnetic Field

    SciTech Connect

    Reva, V. B.

    2006-03-20

    The particle motion at a presence of a large magnetic field directed along the particle trajectory demands the special description. This article deals with the decomposition of the Hamiltonian on the two parts: fast and slow motion. The first part describes the fast rotation around the magnetic line of longitudinal field. The second part describes the slow drift of rotation center from one magnetic line to another. The supposed method enables to write the simple Hamiltonian to each motion type and to formulate the matrix formalism for any element of an accelerator device (quadruple, skew- quadruple, drift gap, bend with a filed index). The Hamiltonian decomposition has physical clearness when the longitudinal field is larger than another fields but it is correct for the arbitrary parameters. At the small longitudinal field the coupling term in Hamiltonian between two modes is essential. The dispersion property of fast and slow modes is derived easy from Hamiltonian also. This method expands easily for nonlinear motion of such modes. This results may be used at analyzed the electron motion in the cooling device, the muon motion in the muon ionization cooler or another system with strong solenoidal coupling.

  6. Accelerated solvent extraction for gas chromatographic analysis of nicotine and cotinine in meconium samples.

    PubMed

    Sant'anna, Simone Gomes; Oliveira, Carolina Dizioli Rodrigues; Diniz, Edna Maria de Albuquerque; Yonamine, Mauricio

    2012-01-01

    Adverse effects associated with smoking during pregnancy are well documented. Although self-report surveys on drug consumption during pregnancy have been improved with new interviewing techniques, underreporting is still a concern. Therefore, a series of biological markers and specimens to diagnose fetal exposure to tobacco have been studied. In the present study, an analytical method was developed to detect nicotine and cotinine (the main nicotine metabolite) in meconium samples. Accelerated solvent extraction (ASE) followed by solid-phase extraction (SPE) were used as sample preparation techniques. The analytes were detected by gas-chromatography with nitrogen-phosphorus detection. The limits of detection were 3.0 and 30 ng/g for cotinine and nicotine, respectively. The method showed good linearity (r(2) > 0.98) in the concentration range studied (LOQ-500 ng/g). The intraday precision, given by the RSD of the method, was less than 15% for cotinine and nicotine. The method proved to be fast, practical, and sensitive. Smaller volumes of organic solvents are necessary compared to other chromatographic methods published in the scientific literature. This is the first report in which ASE was used as sample preparation technique in methods to detect xenobiotics in meconium. PMID:22290748

  7. Fusion-neutron-yield, activation measurements at the Z accelerator: Design, analysis, and sensitivity

    NASA Astrophysics Data System (ADS)

    Hahn, K. D.; Cooper, G. W.; Ruiz, C. L.; Fehl, D. L.; Chandler, G. A.; Knapp, P. F.; Leeper, R. J.; Nelson, A. J.; Smelser, R. M.; Torres, J. A.

    2014-04-01

    We present a general methodology to determine the diagnostic sensitivity that is directly applicable to neutron-activation diagnostics fielded on a wide variety of neutron-producing experiments, which include inertial-confinement fusion (ICF), dense plasma focus, and ion beam-driven concepts. This approach includes a combination of several effects: (1) non-isotropic neutron emission; (2) the 1/r2 decrease in neutron fluence in the activation material; (3) the spatially distributed neutron scattering, attenuation, and energy losses due to the fielding environment and activation material itself; and (4) temporally varying neutron emission. As an example, we describe the copper-activation diagnostic used to measure secondary deuterium-tritium fusion-neutron yields on ICF experiments conducted on the pulsed-power Z Accelerator at Sandia National Laboratories. Using this methodology along with results from absolute calibrations and Monte Carlo simulations, we find that for the diagnostic configuration on Z, the diagnostic sensitivity is 0.037% ± 17% counts/neutron per cm2 and is ˜ 40% less sensitive than it would be in an ideal geometry due to neutron attenuation, scattering, and energy-loss effects.

  8. Biological shield design and analysis of KIPT accelerator-driven subcritical facility.

    SciTech Connect

    Zhong, Z.; Gohar, Y.; Nuclear Engineering Division

    2009-12-01

    Argonne National Laboratory of the United States and Kharkov Institute of Physics and Technology of Ukraine have been collaborating on the conceptual design development of an electron accelerator-driven subcritical facility. The facility will be utilized for performing basic and applied nuclear research, producing medical isotopes, and training young nuclear specialists. This paper presents the design and analyses of the biological shield performed for the top section of the facility. The neutron source driving the subcritical assembly is generated from the interaction of a 100-kW electron beam with a natural uranium target. The electron energy is in the range of 100 to 200 MeV, and it has a uniform spatial distribution. The shield design and the associated analyses are presented including different parametric studies. In the analyses, a significant effort was dedicated to the accurate prediction of the radiation dose outside the shield boundary as a function of the shield thickness without geometrical approximations or material homogenization. The MCNPX Monte Carlo code was utilized for the transport calculation of electrons, photons, and neutrons. Weight window variance-reduction techniques were introduced, and the dose equivalent outside the shield can be calculated with reasonably good statistics.

  9. On the Performance of Point Kinetics for the Analysis of Accelerator-Driven Systems

    SciTech Connect

    Eriksson, M.; Cahalan, J.E.; Yang, W.S.

    2005-03-15

    The ability of point kinetics to describe dynamic processes in accelerator-driven systems (ADSs) is investigated. Full three-dimensional energy-space-time-dependent calculations, coupled with thermal and hydraulic feedback effects, are performed and used as a standard of comparison. Various transient accident sequences are studied. Calculations are performed in the range of k{sub eff} = 0.9594 to 0.9987 to provide insight into the dependence of the performance on the subcritical level. Numerical experiments are carried out on a minor-actinide-loaded and lead-bismuth-cooled ADS. It is shown that the point kinetics approximation is capable of providing highly accurate calculations in such systems. The results suggest better precision at lower k{sub eff} levels. It is found that subcritical operation provides features that are favorable from a point kinetics view of application. For example, reduced sensitivity to system reactivity perturbations effectively mitigates any spatial distortions. If a subcritical reactor is subject to a change in the strength of the external source, or a change in reactivity within the subcritical range, the neutron population will adjust to a new stationary level. Therefore, within the normal range of operation, the power predicted by the point kinetics method and the associated error in comparison with the exact solution tends to approach an essentially bounded value. It was found that the point kinetics model is likely to underestimate the power rise following a positive reactivity insertion in an ADS, which is similar to the behavior in critical systems. However, the effect is characteristically lowered in subcritical versus critical or near-critical reactor operation.

  10. Mediation Analysis with Survival Outcomes: Accelerated Failure Time vs. Proportional Hazards Models

    PubMed Central

    Gelfand, Lois A.; MacKinnon, David P.; DeRubeis, Robert J.; Baraldi, Amanda N.

    2016-01-01

    Objective: Survival time is an important type of outcome variable in treatment research. Currently, limited guidance is available regarding performing mediation analyses with survival outcomes, which generally do not have normally distributed errors, and contain unobserved (censored) events. We present considerations for choosing an approach, using a comparison of semi-parametric proportional hazards (PH) and fully parametric accelerated failure time (AFT) approaches for illustration. Method: We compare PH and AFT models and procedures in their integration into mediation models and review their ability to produce coefficients that estimate causal effects. Using simulation studies modeling Weibull-distributed survival times, we compare statistical properties of mediation analyses incorporating PH and AFT approaches (employing SAS procedures PHREG and LIFEREG, respectively) under varied data conditions, some including censoring. A simulated data set illustrates the findings. Results: AFT models integrate more easily than PH models into mediation models. Furthermore, mediation analyses incorporating LIFEREG produce coefficients that can estimate causal effects, and demonstrate superior statistical properties. Censoring introduces bias in the coefficient estimate representing the treatment effect on outcome—underestimation in LIFEREG, and overestimation in PHREG. With LIFEREG, this bias can be addressed using an alternative estimate obtained from combining other coefficients, whereas this is not possible with PHREG. Conclusions: When Weibull assumptions are not violated, there are compelling advantages to using LIFEREG over PHREG for mediation analyses involving survival-time outcomes. Irrespective of the procedures used, the interpretation of coefficients, effects of censoring on coefficient estimates, and statistical properties should be taken into account when reporting results. PMID:27065906

  11. Participation in the definition, conduct, and analysis of particle accelerator experiments for the first Spacelab Mission

    NASA Technical Reports Server (NTRS)

    Burch, J. L.

    1994-01-01

    The Space Experiments with Particle Accelerators (SEPAC) is a joint endeavor between NASA and the Institute of Space and Aeronautical Sciences (ISAS) in Japan. Its objectives are to use energetic electron beams to investigate beam-atmosphere interactions and beam-plasma interactions in the earth's upper atmosphere and ionosphere using the shuttle Spacelab. Two flights of SEPAC have occurred to date (Spacelab 1 on STS-9 in Nov.-Dec. 1983 and ATLAS 1 on STS-45 in Mar.-Apr. 1992). The SEPAC instrumentation is available for future missions, and the scientific results of the first two missions justify further investigations; however, at present there are no identifiable future flight opportunities. As specified in the contract, the primary purpose of this report is to review the scientific accomplishments of the ATLAS 1 SEPAC experiments, which have been documented in the published literature, with only a brief review of the earlier Spacelab 1 results. One of the main results of the Spacelab 1 SEPAC experiments was that the ejection of plasma from the magnetoplasmadynamic (MPD) arcjet was effective in maintaining vehicle charge neutralization during electron beam firings, but only for a brief period of 10 ms or so. Therefore, a xenon plasma contactor, which can provide continuous vehicle charge neutralization, was developed for the ATLAS 1 SEPAC experiments. Because of the successful operation of the plasma contactor on ATLAS 1, it was possible to perform experiments on beam-plasma interactions and beam-atmosphere interactions at the highest beam power levels of SEPAC. In addition, the ability of the plasma contactor to eject neutral xenon led to a successful experiment on the critical ionization velocity (CIV) phenomena on ATLAS 1.

  12. Instrumental photon activation analysis using the linear accelerator at the Naval Postgraduate School. Master's thesis

    SciTech Connect

    Fisher, W.A.

    1982-10-01

    Charcoal, charcoal residue, potting soil, aluminum foil, bismuth germanate, and petroleum samples have been investigated using instrumental photon activation analysis (i.e., no radiochemistry). The major and minor elements routinely observed by this nondestructive method were: C, C1, Ca, Fe, Mg, Si, and K. A compreshensive review of the principles of IPAA was also included in the study. The principles were applied to a theroetical analysis of an oil sample in which the trace element concentrations were known. It was concluded that IPAA is a highly sensitive technique which could be used to fingerprint oils.

  13. Instrumental photon activation analysis using the linear accelerator at the Naval Postgraduate School

    NASA Astrophysics Data System (ADS)

    Fisher, W. A.

    1982-10-01

    Charcoal, charcoal residue, potting soil, aluminum foil, bismuth germanate, and petroleum samples have been investigated using instrumental photon activation analysis (i.e., no radiochemistry). The major and minor elements routinely observed by this nondestructive method were: C, C1, Ca, Fe, Mg, Si, and K. A comprehensive review of the principles of IPAA was also included in the study. The principles were applied to a theoretical analysis of an oil sample in which the trace element concentrations were known. It was concluded that IPAA is a highly sensitive technique which could be used to fingerprint oils.

  14. NRG1, ERBB4 and AKT1 Epistasis Increases Schizophrenia Risk and is Biologically Validated via Functional Neuroimaging in Healthy Controls

    PubMed Central

    Nicodemus, Kristin K.; Law, Amanda J.; Radulescu, Eugenia; Luna, Augustin; Kolachana, Bhaskar; Vakkalanka, Radhakrishna; Rujescu, Dan; Giegling, Ina; Straub, Richard E.; McGee, Kate; Gold, Bert; Dean, Michael; Muglia, Pierandrea; Callicott, Joseph H.; Tan, Hao-Yang; Weinberger, Daniel R.

    2014-01-01

    CONTEXT NRG1 is a schizophrenia candidate gene and plays an important role in brain development and neural function. Schizophrenia is a complex disorder, with etiology likely due to epistasis. OBJECTIVE We sought to examine epistasis between NRG1 and selected NMDA-glutamate pathway partners implicated in its effects, including ERBB4, AKT1, DLG4, NOS1, NOS1AP. DESIGN Schizophrenia case-control sample analyzed using machine learning algorithms and logistic regression with follow-up using neuroimaging on an independent sample of healthy controls. PARTICIPANTS A referred sample of schizophrenic patients (N = 296) meeting DSM-IV criteria for schizophrenia-spectrum disorder and a volunteer sample of controls for case-control comparison (N = 365) and a separate volunteer sample of controls for neuroimaging (N = 172). MAIN OUTCOME MEASURES Epistatic association between SNPs and case-control status; epistatic association between SNPs and the BOLD physiological response during working memory measured by functional magnetic resonance imaging (fMRI). RESULTS We observed interaction between NRG1 5’ and 3’ SNPs: rs4560751-rs3802160 (likelihood ratio test (LRT) p=0.00020) and schizophrenia which was validated using fMRI of working memory in healthy controls; carriers of risk-associated genotypes showed inefficient processing in dorsolateral prefrontal cortex (DLPFC) (p=0.015, FWE corrected). We observed epistasis between NRG1 (rs10503929; Val1066Ile) and its receptor ERBB4 (rs1026882; LRT p=0.035); a three-way interaction with these two SNPs and AKT1 (rs2494734) was also observed (OR=27.13; 95% confidence interval 3.30, 223.03; LRT p=0.042). These same two- and three-way interactions were further biologically validated via fMRI: healthy individuals carrying risk genotypes for NRG1 and ERBB4, or these two together with AKT1, were disproportionately less efficient in DLPFC processing. Lower-level interactions were not observed between NRG1/ERBB4-AKT1 in association or

  15. Retrospective analysis of linear accelerator output constancy checks using process control techniques.

    PubMed

    Sanghangthum, Taweap; Suriyapee, Sivalee; Srisatit, Somyot; Pawlicki, Todd

    2013-01-01

    Shewhart control charts have previously been suggested as a process control tool for use in routine linear accelerator (linac) output verifications. However, a comprehensive approach to process control has not been investigated for linac output verifications. The purpose of this work is to investigate a comprehensive process control approach to linac output constancy quality assurance (QA). The RBA-3 dose constancy check was used to verify outputs of photon beams and electron beams delivered by a Varian Clinac 21EX linac. The data were collected during 2009 to 2010. Shewhart-type control charts, exponentially weighted moving average (EWMA) charts, and capability indices were applied to these processes. The Shewhart-type individuals chart (X-chart) was used and the number of data points used to calculate the control limits was varied. The parameters tested for the EWMA charts (smoothing parameter (λ) and the control limit width (L)) were λ = 0.05, L = 2.492; λ = 0.10, L = 2.703; and λ = 0.20, L = 2.860, as well as the number of points used to estimate the initial process mean and variation. Lastly, the number of in-control data points used to determine process capability (C(p)) and acceptability (C(pk)) were investigated, comparing the first in-control run to the longest in-control run of the process data. C(p) and C(pk) values greater than 1.0 were considered acceptable. The 95% confidence intervals were reported. The X-charts detected systematic errors (e.g., device setup errors). In-control run lengths on the X-charts varied from 5 to 30 output measurements (about one to seven months). EWMA charts showed in-control runs ranging from 9 to 33 output measurements (about two to eight months). The C(p) and C(pk) ratios are higher than 1.0 for all energies, except 12 and 20 MeV. However, 10 MV and 6, 9, and 16 MeV were in question when considering the 95% confidence limits. The X-chart should be calculated using 8-12 data points. For EWMA chart, using 4 data points

  16. GPU-Accelerated Compartmental Modeling Analysis of DCE-MRI Data from Glioblastoma Patients Treated with Bevacizumab

    PubMed Central

    Hsu, Yu-Han H.; Huang, Ziyin; Ferl, Gregory Z.; Ng, Chee M.

    2015-01-01

    The compartment model analysis using medical imaging data is the well-established but extremely time consuming technique for quantifying the changes in microvascular physiology of targeted organs in clinical patients after antivascular therapies. In this paper, we present a first graphics processing unit-accelerated method for compartmental modeling of medical imaging data. Using this approach, we performed the analysis of dynamic contrast-enhanced magnetic resonance imaging data from bevacizumab-treated glioblastoma patients in less than one minute per slice without losing accuracy. This approach reduced the computation time by more than 120-fold comparing to a central processing unit-based method that performed the analogous analysis steps in serial and more than 17-fold comparing to the algorithm that optimized for central processing unit computation. The method developed in this study could be of significant utility in reducing the computational times required to assess tumor physiology from dynamic contrast-enhanced magnetic resonance imaging data in preclinical and clinical development of antivascular therapies and related fields. PMID:25786263

  17. TRAC analysis of design basis events for the accelerator production of tritium target/blanket

    SciTech Connect

    Lin, J.C.; Elson, J.

    1997-08-01

    A two-loop primary cooling system with a residual heat removal system was designed to mitigate the heat generated in the tungsten neutron source rods inside the rungs of the ladders and the shell of the rungs. The Transient Reactor Analysis Code (TRAC) was used to analyze the thermal-hydraulic behavior of the primary cooling system during a pump coastdown transient; a cold-leg, large-break loss-of-coolant accident (LBLOCA); a hot-leg LBLOCA; and a target downcomer LBLOCA. The TRAC analysis results showed that the heat generated in the tungsten neutron source rods can be mitigated by the primary cooling system for the pump coastdown transient and all the LBLOCAs except the target downcomer LBLOCA. For the target downcomer LBLOCA, a cavity flood system is required to fill the cavity with water at a level above the large fixed headers.

  18. Accelerated Reader.

    ERIC Educational Resources Information Center

    Education Commission of the States, Denver, CO.

    This paper provides an overview of Accelerated Reader, a system of computerized testing and record-keeping that supplements the regular classroom reading program. Accelerated Reader's primary goal is to increase literature-based reading practice. The program offers a computer-aided reading comprehension and management program intended to motivate…

  19. Industrial applications of accelerator-based infrared sources: Analysis using infrared microspectroscopy

    SciTech Connect

    Bantignies, J.L.; Fuchs, G.; Wilhelm, C.; Carr, G.L.; Dumas, P.

    1997-09-01

    Infrared Microspectroscopy, using a globar source, is now widely employed in the industrial environment, for the analysis of various materials. Since synchrotron radiation is a much brighter source, an enhancement of an order of magnitude in lateral resolution can be achieved. Thus, the combination of IR microspectroscopy and synchrotron radiation provides a powerful tool enabling sample regions only few microns size to be studied. This opens up the potential for analyzing small particles. Some examples for hair, bitumen and polymer are presented.

  20. Analysis of recombination QTLs, segregation distortion, and epistasis for fitness in maize multiple populations using ultra-high-density markers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Understanding the maize genomic features would be useful for the study of genetic diversity and evolution and for maize breeding. Here, we used two maize nested association mapping (NAM) populations separately derived in China (CN-NAM) and the US (US-NAM) to explore the maize genomic features. The t...

  1. An efficient transcriptome analysis pipeline to accelerate venom peptide discovery and characterisation.

    PubMed

    Prashanth, Jutty Rajan; Lewis, Richard J

    2015-12-01

    Transcriptome sequencing is now widely adopted as an efficient means to study the chemical diversity of venoms. To improve the efficiency of analysis of these large datasets, we have optimised an analysis pipeline for cone snail venom gland transcriptomes. The pipeline combines ConoSorter with sequence architecture-based elimination and similarity searching using BLAST to improve the accuracy of sequence identification and classification, while reducing requirements for manual intervention. As a proof-of-concept, we used this approach reanalysed three previously published cone snail transcriptomes from diverse dietary groups. Our pipeline method generated similar results to the published studies with significantly less manual intervention. We additionally found undiscovered sequences in the piscovorous Conus geographus and vermivorous Conus miles and identified sequences in incorrect superfamilies in the molluscivorus Conus marmoreus and C. geographus transcriptomes. Our results indicate that this method can improve toxin detection without extending analysis time. While this method was evaluated on cone snail transcriptomes it can be easily optimised to retrieve toxins from other venomous animals. PMID:26376071

  2. Multidimensional analysis of suction feeding performance in fishes: fluid speed, acceleration, strike accuracy and the ingested volume of water.

    PubMed

    Higham, Timothy E; Day, Steven W; Wainwright, Peter C

    2006-07-01

    Suction feeding fish draw prey into the mouth using a flow field that they generate external to the head. In this paper we present a multidimensional perspective on suction feeding performance that we illustrate in a comparative analysis of suction feeding ability in two members of Centrarchidae, the largemouth bass (Micropterus salmoides) and bluegill sunfish (Lepomis macrochirus). We present the first direct measurements of maximum fluid speed capacity, and we use this to calculate local fluid acceleration and volumetric flow rate. We also calculated the ingested volume and a novel metric of strike accuracy. In addition, we quantified for each species the effects of gape magnitude, time to peak gape, and swimming speed on features of the ingested volume of water. Digital particle image velocimetry (DPIV) and high-speed video were used to measure the flow in front of the mouths of three fish from each species in conjunction with a vertical laser sheet positioned on the mid-sagittal plane of the fish. From this we quantified the maximum fluid speed (in the earthbound and fish's frame of reference), acceleration and ingested volume. Our method for determining strike accuracy involved quantifying the location of the prey relative to the center of the parcel of ingested water. Bluegill sunfish generated higher fluid speeds in the earthbound frame of reference, accelerated the fluid faster, and were more accurate than largemouth bass. However, largemouth bass ingested a larger volume of water and generated a higher volumetric flow rate than bluegill sunfish. In addition, because largemouth bass swam faster during prey capture, they generated higher fluid speeds in the fish's frame of reference. Thus, while bluegill can exert higher drag forces on stationary prey items, largemouth bass more quickly close the distance between themselves and prey. The ingested volume and volumetric flow rate significantly increased as gape increased for both species, while time to peak

  3. Angular velocities, angular accelerations, and coriolis accelerations

    NASA Technical Reports Server (NTRS)

    Graybiel, A.

    1975-01-01

    Weightlessness, rotating environment, and mathematical analysis of Coriolis acceleration is described for man's biological effective force environments. Effects on the vestibular system are summarized, including the end organs, functional neurology, and input-output relations. Ground-based studies in preparation for space missions are examined, including functional tests, provocative tests, adaptive capacity tests, simulation studies, and antimotion sickness.

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

    PubMed

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

    2015-05-01

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

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

    PubMed Central

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

    2014-01-01

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

  6. BALSA: integrated secondary analysis for whole-genome and whole-exome sequencing, accelerated by GPU.

    PubMed

    Luo, Ruibang; Wong, Yiu-Lun; Law, Wai-Chun; Lee, Lap-Kei; Cheung, Jeanno; Liu, Chi-Man; Lam, Tak-Wah

    2014-01-01

    This paper reports an integrated solution, called BALSA, for the secondary analysis of next generation sequencing data; it exploits the computational power of GPU and an intricate memory management to give a fast and accurate analysis. From raw reads to variants (including SNPs and Indels), BALSA, using just a single computing node with a commodity GPU board, takes 5.5 h to process 50-fold whole genome sequencing (∼750 million 100 bp paired-end reads), or just 25 min for 210-fold whole exome sequencing. BALSA's speed is rooted at its parallel algorithms to effectively exploit a GPU to speed up processes like alignment, realignment and statistical testing. BALSA incorporates a 16-genotype model to support the calling of SNPs and Indels and achieves competitive variant calling accuracy and sensitivity when compared to the ensemble of six popular variant callers. BALSA also supports efficient identification of somatic SNVs and CNVs; experiments showed that BALSA recovers all the previously validated somatic SNVs and CNVs, and it is more sensitive for somatic Indel detection. BALSA outputs variants in VCF format. A pileup-like SNAPSHOT format, while maintaining the same fidelity as BAM in variant calling, enables efficient storage and indexing, and facilitates the App development of downstream analyses. BALSA is available at: http://sourceforge.net/p/balsa. PMID:24949238

  7. SU-E-T-627: Failure Modes and Effect Analysis for Monthly Quality Assurance of Linear Accelerator

    SciTech Connect

    Xie, J; Xiao, Y; Wang, J; Peng, J; Lu, S; Hu, W

    2014-06-15

    Purpose: To develop and implement a failure mode and effect analysis (FMEA) on routine monthly Quality Assurance (QA) tests (physical tests part) of linear accelerator. Methods: A systematic failure mode and effect analysis method was performed for monthly QA procedures. A detailed process tree of monthly QA was created and potential failure modes were defined. Each failure mode may have many influencing factors. For each factor, a risk probability number (RPN) was calculated from the product of probability of occurrence (O), the severity of effect (S), and detectability of the failure (D). The RPN scores are in a range of 1 to 1000, with higher scores indicating stronger correlation to a given influencing factor of a failure mode. Five medical physicists in our institution were responsible to discuss and to define the O, S, D values. Results: 15 possible failure modes were identified and all RPN scores of all influencing factors of these 15 failue modes were from 8 to 150, and the checklist of FMEA in monthly QA was drawn. The system showed consistent and accurate response to erroneous conditions. Conclusion: The influencing factors of RPN greater than 50 were considered as highly-correlated factors of a certain out-oftolerance monthly QA test. FMEA is a fast and flexible tool to develop an implement a quality management (QM) frame work of monthly QA, which improved the QA efficiency of our QA team. The FMEA work may incorporate more quantification and monitoring fuctions in future.

  8. Confronting Twin Paradox Acceleration

    NASA Astrophysics Data System (ADS)

    Murphy, Thomas W.

    2016-05-01

    The resolution to the classic twin paradox in special relativity rests on the asymmetry of acceleration. Yet most students are not exposed to a satisfactory analysis of what exactly happens during the acceleration phase that results in the nonaccelerated observer's more rapid aging. The simple treatment presented here offers both graphical and quantitative solutions to the problem, leading to the correct result that the acceleration-induced age gap is 2Lβ years when the one-way distance L is expressed in light-years and velocity β ≡v/c .

  9. Analysis of coupled electromagnetic-thermal effects in superconducting accelerator magnets

    NASA Astrophysics Data System (ADS)

    Fischer, E.; Kurnyshov, R.; Shcherbakov, P.

    2008-02-01

    FAIR will built 5 magnet rings including two superconducting synchotrons. The SIS100 is the core component of the facility and will be equipped with 2 Tesla dipole magnets pulsed with 4 Tesla/s. The cable of the magnet coils is made of a hollow NbTi composite cable of about 7 mm outer diameter, cooled with two phase helium flow at 4.5 K. We calculate the heat load, the eddy and the hysteresis losses, investigate the impact of the ramping on the magnetic field, on the safety margin of the conductor and the required cooling for all different elements of the magnet including: the coil, the yoke, the bus bars and the beam pipe. This analysis is based on properties measured at cryogenic temperatures and fine detailed FEM models.

  10. Accelerating the weighted histogram analysis method by direct inversion in the iterative subspace

    PubMed Central

    Zhang, Cheng; Lai, Chun-Liang; Pettitt, B. Montgomery

    2016-01-01

    The weighted histogram analysis method (WHAM) for free energy calculations is a valuable tool to produce free energy differences with the minimal errors. Given multiple simulations, WHAM obtains from the distribution overlaps the optimal statistical estimator of the density of states, from which the free energy differences can be computed. The WHAM equations are often solved by an iterative procedure. In this work, we use a well-known linear algebra algorithm which allows for more rapid convergence to the solution. We find that the computational complexity of the iterative solution to WHAM and the closely-related multiple Bennett acceptance ratio (MBAR) method can be improved by using the method of direct inversion in the iterative subspace. We give examples from a lattice model, a simple liquid and an aqueous protein solution. PMID:27453632

  11. Finite difference method accelerated with sparse solvers for structural analysis of the metal-organic complexes

    NASA Astrophysics Data System (ADS)

    Guda, A. A.; Guda, S. A.; Soldatov, M. A.; Lomachenko, K. A.; Bugaev, A. L.; Lamberti, C.; Gawelda, W.; Bressler, C.; Smolentsev, G.; Soldatov, A. V.; Joly, Y.

    2016-05-01

    Finite difference method (FDM) implemented in the FDMNES software [Phys. Rev. B, 2001, 63, 125120] was revised. Thorough analysis shows, that the calculated diagonal in the FDM matrix consists of about 96% zero elements. Thus a sparse solver would be more suitable for the problem instead of traditional Gaussian elimination for the diagonal neighbourhood. We have tried several iterative sparse solvers and the direct one MUMPS solver with METIS ordering turned out to be the best. Compared to the Gaussian solver present method is up to 40 times faster and allows XANES simulations for complex systems already on personal computers. We show applicability of the software for metal-organic [Fe(bpy)3]2+ complex both for low spin and high spin states populated after laser excitation.

  12. Analysis of the orbit errors in the CERN accelerators using model simulation

    SciTech Connect

    Lee, M.; Kleban, S.; Clearwater, S.; Scandale, W.; Pettersson, T.; Kugler, H.; Riche, A.; Chanel, M.; Martensson, E.; Lin, In-Ho

    1987-09-01

    This paper will describe the use of the PLUS program to find various types of machine and beam errors such as, quadrupole strength, dipole strength, beam position monitors (BPMs), energy profile, and beam launch. We refer to this procedure as the GOLD (Generic Orbit and Lattice Debugger) Method which is a general technique that can be applied to analysis of errors in storage rings and transport lines. One useful feature of the Method is that it analyzes segments of a machine at a time so that the application and efficiency is independent of the size of the overall machine. Because the techniques are the same for all the types of problems it solves, the user need learn only how to find one type of error in order to use the program.

  13. LINEAR ACCELERATOR

    DOEpatents

    Colgate, S.A.

    1958-05-27

    An improvement is presented in linear accelerators for charged particles with respect to the stable focusing of the particle beam. The improvement consists of providing a radial electric field transverse to the accelerating electric fields and angularly introducing the beam of particles in the field. The results of the foregoing is to achieve a beam which spirals about the axis of the acceleration path. The combination of the electric fields and angular motion of the particles cooperate to provide a stable and focused particle beam.

  14. In silico analysis of gene expression profiles in the olfactory mucosae of aging senescence-accelerated mice.

    PubMed

    Getchell, Thomas V; Peng, Xuejun; Green, C Paul; Stromberg, Arnold J; Chen, Kuey-Chu; Mattson, Mark P; Getchell, Marilyn L

    2004-08-01

    We utilized high-density Affymetrix oligonucleotide arrays to investigate gene expression in the olfactory mucosae of near age-matched aging senescence-accelerated mice (SAM). The senescence-prone (SAMP) strain has a significantly shorter lifespan than does the senescence-resistant (SAMR) strain. To analyze our data, we applied biostatistical methods that included a correlation analysis to evaluate sources of methodologic and biological variability; a two-sided t-test to identify a subpopulation of Present genes with a biologically relevant P-value <0.05; and a false discovery rate (FDR) analysis adjusted to a stringent 5% level that yielded 127 genes with a P-value of <0.001 that were differentially regulated in near age-matched SAMPs (SAMP-Os; 13.75 months) compared to SAMRs (SAMR-Os, 12.5 months). Volcano plots related the variability in the mean hybridization signals as determined by the two-sided t-test to fold changes in gene expression. The genes were categorized into the six functional groups used previously in gene profiling experiments to identify candidate genes that may be relevant for senescence at the genomic and cellular levels in the aging mouse brain (Lee et al. [2000] Nat Genet 25:294-297) and in the olfactory mucosa (Getchell et al. [2003] Ageing Res Rev 2:211-243), which serves several functions that include chemosensory detection, immune barrier function, xenobiotic metabolism, and neurogenesis. Because SAMR-Os and SAMP-Os have substantially different median lifespans, we related the rate constant alpha in the Gompertz equation on aging to intrinsic as opposed to environmental mechanisms of senescence based on our analysis of genes modulated during aging in the olfactory mucosa. PMID:15248299

  15. The Potential of Accelerating Early Detection of Autism through Content Analysis of YouTube Videos

    PubMed Central

    Fusaro, Vincent A.; Daniels, Jena; Duda, Marlena; DeLuca, Todd F.; D’Angelo, Olivia; Tamburello, Jenna; Maniscalco, James; Wall, Dennis P.

    2014-01-01

    Abstract Autism is on the rise, with 1 in 88 children receiving a diagnosis in the United States, yet the process for diagnosis remains cumbersome and time consuming. Research has shown that home videos of children can help increase the accuracy of diagnosis. However the use of videos in the diagnostic process is uncommon. In the present study, we assessed the feasibility of applying a gold-standard diagnostic instrument to brief and unstructured home videos and tested whether video analysis can enable more rapid detection of the core features of autism outside of clinical environments. We collected 100 public videos from YouTube of children ages 1–15 with either a self-reported diagnosis of an ASD (N = 45) or not (N = 55). Four non-clinical raters independently scored all videos using one of the most widely adopted tools for behavioral diagnosis of autism, the Autism Diagnostic Observation Schedule-Generic (ADOS). The classification accuracy was 96.8%, with 94.1% sensitivity and 100% specificity, the inter-rater correlation for the behavioral domains on the ADOS was 0.88, and the diagnoses matched a trained clinician in all but 3 of 22 randomly selected video cases. Despite the diversity of videos and non-clinical raters, our results indicate that it is possible to achieve high classification accuracy, sensitivity, and specificity as well as clinically acceptable inter-rater reliability with nonclinical personnel. Our results also demonstrate the potential for video-based detection of autism in short, unstructured home videos and further suggests that at least a percentage of the effort associated with detection and monitoring of autism may be mobilized and moved outside of traditional clinical environments. PMID:24740236

  16. Acceleration switch

    DOEpatents

    Abbin, J.P. Jr.; Devaney, H.F.; Hake, L.W.

    1979-08-29

    The disclosure relates to an improved integrating acceleration switch of the type having a mass suspended within a fluid filled chamber, with the motion of the mass initially opposed by a spring and subsequently not so opposed.

  17. Acceleration switch

    DOEpatents

    Abbin, Jr., Joseph P.; Devaney, Howard F.; Hake, Lewis W.

    1982-08-17

    The disclosure relates to an improved integrating acceleration switch of the type having a mass suspended within a fluid filled chamber, with the motion of the mass initially opposed by a spring and subsequently not so opposed.

  18. ION ACCELERATOR

    DOEpatents

    Bell, J.S.

    1959-09-15

    An arrangement for the drift tubes in a linear accelerator is described whereby each drift tube acts to shield the particles from the influence of the accelerating field and focuses the particles passing through the tube. In one embodiment the drift tube is splii longitudinally into quadrants supported along the axis of the accelerator by webs from a yoke, the quadrants. webs, and yoke being of magnetic material. A magnetic focusing action is produced by energizing a winding on each web to set up a magnetic field between adjacent quadrants. In the other embodiment the quadrants are electrically insulated from each other and have opposite polarity voltages on adjacent quadrants to provide an electric focusing fleld for the particles, with the quadrants spaced sufficienily close enough to shield the particles within the tube from the accelerating electric field.

  19. LINEAR ACCELERATOR

    DOEpatents

    Christofilos, N.C.; Polk, I.J.

    1959-02-17

    Improvements in linear particle accelerators are described. A drift tube system for a linear ion accelerator reduces gap capacity between adjacent drift tube ends. This is accomplished by reducing the ratio of the diameter of the drift tube to the diameter of the resonant cavity. Concentration of magnetic field intensity at the longitudinal midpoint of the external sunface of each drift tube is reduced by increasing the external drift tube diameter at the longitudinal center region.

  20. GAMUT: GPU accelerated microRNA analysis to uncover target genes through CUDA-miRanda

    PubMed Central

    2014-01-01

    Randa implementations through multiple test datasets. Conclusions We offer a GPU-based alternative to high performance compute (HPC) that can be developed locally at a relatively small cost. The community of GPU developers in the biomedical research community, particularly for genome analysis, is still growing. With increasing shared resources, this community will be able to advance CMTI in a very significant manner. Our source code is available at https://sourceforge.net/projects/cudamiranda/. PMID:25077821

  1. Analysis of coenzyme Q10 in bee pollen using online cleanup by accelerated solvent extraction and high performance liquid chromatography.

    PubMed

    Xue, Xiaofeng; Zhao, Jing; Chen, Lanzhen; Zhou, Jinhui; Yue, Bing; Li, Yi; Wu, Liming; Liu, Fengmao

    2012-07-15

    A method for the determination of coenzyme Q10 in bee pollen has been developed applying an online cleanup of accelerated solvent extraction and using environmentally acceptable organic solvents. The extracted samples were analysed by high performance liquid chromatography with diode array detection. The optimised method employed 10 mL extraction cells, 1g sample size, absolute ethanol as extraction solvent, 80°C of extraction temperature, one extraction cycle, 5 min of static time, Cleanert Alumina-N as sorbent and 60% flush volume. The method was validated by means of an evaluation of the matrix effects, linearity, limit of detection (LOD) and quantification (LOQ), trueness, precision and stability. The assay was linear over the concentration range of 0.25-200mg/L and the LOD and LOQ were 0.16 and 0.35 mg/kg, respectively. The recoveries were above 90%. The inter- and intra-day precision was below 6.3%. The method has been successfully applied to the analysis of bee pollen samples. For 20 bee pollen products, the coenzyme Q10 content varied from not detectable to 192.8 mg/kg. PMID:25683435

  2. Accelerated Aging of BKC 44306-10 Rigid Polyurethane Foam: FT-IR Spectroscopy, Dimensional Analysis, and Micro Computed Tomography

    SciTech Connect

    Gilbertson, Robert D.; Patterson, Brian M.; Smith, Zachary

    2014-01-02

    An accelerated aging study of BKC 44306-10 rigid polyurethane foam was carried out. Foam samples were aged in a nitrogen atmosphere at three different temperatures: 50 °C, 65 °C, and 80 °C. Foam samples were periodically removed from the aging canisters at 1, 3, 6, 9, 12, and 15 month intervals when FT-IR spectroscopy, dimensional analysis, and mechanical testing experiments were performed. Micro Computed Tomography imaging was also employed to study the morphology of the foams. Over the course of the aging study the foams the decreased in size by a magnitude of 0.001 inches per inch of foam. Micro CT showed the heterogeneous nature of the foam structure likely resulting from flow effects during the molding process. The effect of aging on the compression and tensile strength of the foam was minor and no cause for concern. FT-IR spectroscopy was used to follow the foam chemistry. However, it was difficult to draw definitive conclusions about the changes in chemical nature of the materials due to large variability throughout the samples.

  3. Transient Thermo-Hydraulic Analysis of the Windowless Target System for the Lead Bismuth Eutectic Cooled Accelerator Driven System

    SciTech Connect

    Bianchi, Fosco; Ferri, Roberta; Moreau, Vincent

    2006-07-01

    The target system, whose function is to supply an external neutron source to the ADS sub-critical core to sustain the neutron chain reaction, is the most critical part of an ADS being subject to severe thermo-mechanical loading and material damage due to accelerator protons and fission neutrons. A windowless option was chosen as reference configuration for the target system of the LBE-cooled ADS within the European PDS-XADS project in order to reduce the material damage and to increase its life. This document deals with the thermo-hydraulic results of the calculations performed with STAR-CD and RELAP5 codes for studying the behaviour of the windowless target system during off-normal operating conditions. It also reports a description of modifications properly implemented in the codes needed for this analysis. The windowless target system shows a satisfactory thermo-hydraulic behaviour for the analysed accidents, except for the loss of both pumps without proton beam shut-off and the beam trips lasting more than one second. (authors)

  4. Zebrafish scales respond differently to in vitro dynamic and static acceleration: analysis of interaction between osteoblasts and osteoclasts.

    PubMed

    Kitamura, Kei-ichiro; Takahira, Koh; Inari, Masato; Satoh, Yusuke; Hayakawa, Kazuichi; Tabuchi, Yoshiaki; Ogai, Kazuhiro; Nishiuchi, Takumi; Kondo, Takashi; Mikuni-Takagaki, Yuko; Chen, Wenxi; Hattori, Atsuhiko; Suzuki, Nobuo

    2013-09-01

    Zebrafish scales consist of bone-forming osteoblasts, bone-resorbing osteoclasts, and calcified bone matrix. To elucidate the underlying molecular mechanism of the effects induced by dynamic and static acceleration, we investigated the scale osteoblast- and osteoclast-specific marker gene expression involving osteoblast-osteoclast communication molecules. Osteoblasts express RANKL, which binds to the osteoclast surface receptor, RANK, and stimulates bone resorption. OPG, on the other hand, is secreted by osteoblast as a decoy receptor for RANKL, prevents RANKL from binding to RANK and thus prevents bone resorption. Therefore, the RANK-RANKL-OPG pathway contributes to the regulation of osteoclastogenesis by osteoblasts. Semaphorin 4D, in contrast, is expressed on osteoclasts, and binding to its receptor Plexin-B1 on osteoblasts results in suppression of bone formation. In the present study, we found that both dynamic and static acceleration at 3.0×g decreased RANKL/OPG ratio and increased osteoblast-specific functional mRNA such as alkaline phosphatase, while static acceleration increased and dynamic acceleration decreased osteoclast-specific mRNA such as cathepsin K. Static acceleration increased semaphorin 4D mRNA expression, while dynamic acceleration had no effect. The results of the present study indicated that osteoclasts have predominant control over bone metabolism via semaphorin 4D expression induced by static acceleration at 3.0×g. PMID:23632157

  5. The radiation field measurement and analysis outside the shielding of A 10 MeV electron irradiation accelerator

    NASA Astrophysics Data System (ADS)

    Shang, Jing; Li, Juexin; Xu, Bing; Li, Yuxiong

    2011-10-01

    Electron accelerators are employed widely for diverse purposes in the irradiation-processing industry, from sterilizing medical products to treating gemstones. Because accelerators offer high efficiency, high power, and require little preventative maintenance, they are becoming more and more popular than using the 60Co isotope approach. However, the electron accelerator exposes potential radiation hazards. To protect workers and the public from exposure to radiation, the radiation field around the electronic accelerator must be assessed, especially that outside the shielding. Thus, we measured the radiation dose at different positions outside the shielding of a 10-MeV electron accelerator using a new data-acquisition unit named Mini-DDL (Mini-Digital Data Logging). The measurements accurately reflect the accelerator's radiation status. In this paper, we present our findings, results and compare them with our theoretical calculations. We conclude that the measurements taken outside the irradiation hall are consistent with the findings from our calculations, except in the maze outside the door of the accelerator room. We discuss the reason for this discrepancy.

  6. X-ray photoelectron spectroscopy and secondary electron yield analysis of Al and Cu samples exposed to an accelerator environment.

    SciTech Connect

    Rosenberg, R. A.; McDowell, M. W.; Ma, Q.; Harkay, K. C.; XFD; APS-USR; ASD

    2003-09-01

    It is well known that exposure to an accelerator environment can cause ''conditioning'' of the vacuum chamber surfaces. In order to understand the manner in which the surface structure might influence the production of gases and electrons in the accelerator, such surfaces should be studied both before and after exposure to accelerator conditions. Numerous studies have been performed on representative materials prior to being inserted into an accelerator, but very little has been done on materials that have ''lived'' in the accelerator for extended periods. In the present work, we mounted Al and Cu coupons at different positions in a section of the Advanced Photon Source storage ring and removed them following exposures ranging from 6 to 18 months. X-ray photoelectron spectroscopy (XPS) of the surface was performed before and after exposure. Changes were observed that depended on the location and whether the coupon was facing the chamber interior or chamber wall. These results will be presented and compared to XPS and secondary electron yield data obtained from laboratory measurements meant to simulate the accelerator conditions.

  7. GPU-accelerated nonparametric kinetic analysis of DCE-MRI data from glioblastoma patients treated with bevacizumab.

    PubMed

    Hsu, Yu-Han H; Ferl, Gregory Z; Ng, Chee M

    2013-05-01

    Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) is often used to examine vascular function in malignant tumors and noninvasively monitor drug efficacy of antivascular therapies in clinical studies. However, complex numerical methods used to derive tumor physiological properties from DCE-MRI images can be time-consuming and computationally challenging. Recent advancement of computing technology in graphics processing unit (GPU) makes it possible to build an energy-efficient and high-power parallel computing platform for solving complex numerical problems. This study develops the first reported fast GPU-based method for nonparametric kinetic analysis of DCE-MRI data using clinical scans of glioblastoma patients treated with bevacizumab (Avastin®). In the method, contrast agent concentration-time profiles in arterial blood and tumor tissue are smoothed using a robust kernel-based regression algorithm in order to remove artifacts due to patient motion and then deconvolved to produce the impulse response function (IRF). The area under the curve (AUC) and mean residence time (MRT) of the IRF are calculated using statistical moment analysis, and two tumor physiological properties that relate to vascular permeability, volume transfer constant between blood plasma and extravascular extracellular space (K(trans)) and fractional interstitial volume (ve) are estimated using the approximations AUC/MRT and AUC. The most significant feature in this method is the use of GPU-computing to analyze data from more than 60,000 voxels in each DCE-MRI image in parallel fashion. All analysis steps have been automated in a single program script that requires only blood and tumor data as the sole input. The GPU-accelerated method produces K(trans) and ve estimates that are comparable to results from previous studies but reduces computational time by more than 80-fold compared to a previously reported central processing unit-based nonparametric method. Furthermore, it is at

  8. Biomedical accelerator mass spectrometry

    NASA Astrophysics Data System (ADS)

    Freeman, Stewart P. H. T.; Vogel, John S.

    1995-05-01

    Ultrasensitive SIMS with accelerator based spectrometers has recently begun to be applied to biomedical problems. Certain very long-lived radioisotopes of very low natural abundances can be used to trace metabolism at environmental dose levels ( [greater-or-equal, slanted] z mol in mg samples). 14C in particular can be employed to label a myriad of compounds. Competing technologies typically require super environmental doses that can perturb the system under investigation, followed by uncertain extrapolation to the low dose regime. 41Ca and 26Al are also used as elemental tracers. Given the sensitivity of the accelerator method, care must be taken to avoid contamination of the mass spectrometer and the apparatus employed in prior sample handling including chemical separation. This infant field comprises the efforts of a dozen accelerator laboratories. The Center for Accelerator Mass Spectrometry has been particularly active. In addition to collaborating with groups further afield, we are researching the kinematics and binding of genotoxins in-house, and we support innovative uses of our capability in the disciplines of chemistry, pharmacology, nutrition and physiology within the University of California. The field can be expected to grow further given the numerous potential applications and the efforts of several groups and companies to integrate more the accelerator technology into biomedical research programs; the development of miniaturized accelerator systems and ion sources capable of interfacing to conventional HPLC and GMC, etc. apparatus for complementary chemical analysis is anticipated for biomedical laboratories.

  9. Plasma accelerator

    DOEpatents

    Wang, Zhehui; Barnes, Cris W.

    2002-01-01

    There has been invented an apparatus for acceleration of a plasma having coaxially positioned, constant diameter, cylindrical electrodes which are modified to converge (for a positive polarity inner electrode and a negatively charged outer electrode) at the plasma output end of the annulus between the electrodes to achieve improved particle flux per unit of power.

  10. Accelerated Achievement

    ERIC Educational Resources Information Center

    Ford, William J.

    2010-01-01

    This article focuses on the accelerated associate degree program at Ivy Tech Community College (Indiana) in which low-income students will receive an associate degree in one year. The three-year pilot program is funded by a $2.3 million grant from the Lumina Foundation for Education in Indianapolis and a $270,000 grant from the Indiana Commission…

  11. ACCELERATION INTEGRATOR

    DOEpatents

    Pope, K.E.

    1958-01-01

    This patent relates to an improved acceleration integrator and more particularly to apparatus of this nature which is gyrostabilized. The device may be used to sense the attainment by an airborne vehicle of a predetermined velocitv or distance along a given vector path. In its broad aspects, the acceleration integrator utilizes a magnetized element rotatable driven by a synchronous motor and having a cylin drical flux gap and a restrained eddy- current drag cap deposed to move into the gap. The angular velocity imparted to the rotatable cap shaft is transmitted in a positive manner to the magnetized element through a servo feedback loop. The resultant angular velocity of tae cap is proportional to the acceleration of the housing in this manner and means may be used to measure the velocity and operate switches at a pre-set magnitude. To make the above-described dcvice sensitive to acceleration in only one direction the magnetized element forms the spinning inertia element of a free gyroscope, and the outer housing functions as a gimbal of a gyroscope.

  12. Particle acceleration

    NASA Technical Reports Server (NTRS)

    Vlahos, L.; Machado, M. E.; Ramaty, R.; Murphy, R. J.; Alissandrakis, C.; Bai, T.; Batchelor, D.; Benz, A. O.; Chupp, E.; Ellison, D.

    1986-01-01

    Data is compiled from Solar Maximum Mission and Hinothori satellites, particle detectors in several satellites, ground based instruments, and balloon flights in order to answer fundamental questions relating to: (1) the requirements for the coronal magnetic field structure in the vicinity of the energization source; (2) the height (above the photosphere) of the energization source; (3) the time of energization; (4) transistion between coronal heating and flares; (5) evidence for purely thermal, purely nonthermal and hybrid type flares; (6) the time characteristics of the energization source; (7) whether every flare accelerates protons; (8) the location of the interaction site of the ions and relativistic electrons; (9) the energy spectra for ions and relativistic electrons; (10) the relationship between particles at the Sun and interplanetary space; (11) evidence for more than one acceleration mechanism; (12) whether there is single mechanism that will accelerate particles to all energies and also heat the plasma; and (13) how fast the existing mechanisms accelerate electrons up to several MeV and ions to 1 GeV.

  13. Thermal and structural analysis of the LBL 10 x 40 cm long pulse accelerator and the 12 x 48 cm common long pulse accelerator for TFTR, doublet III-D, and MFTF-B

    SciTech Connect

    Wells, R.P.

    1985-11-01

    Stress and deflection of the grid rails of the existing, Lawrence Berkeley Laboratory (LBL) designed, 10 x 40 cm Long Pulse (neutral beam) Accelerator (40LPA) and the expanded 12 x 48 cm version, Common Long Pulse Source (CLPS), have been computed for a series of assumed heat load distributions. The combined stress from self-constraint of thermal expansion and rail holder reaction forces has been calculated. A simplification of the gradient grid rail holder was analyzed and was found to work as well or better than the original 40LPA design under the most probable operating conditions. Heat flux non-uniformity over the rail surface for both accelerator designs was estimated from 40LPA grid calorimetry data for arc and beam extraction operation. The extrapolated total heat load per rail for the CLPS was less than the 1.2 kW value used in this analysis. Under worst case assumptions, the maximum equivalent stress in any of the molybdenum grid rails was less than 20% of yield. For the anticipated heat load distribution on the gradient grid, the predicted deflection of the grid rail meets the 0.0457 mm position tolerance except under extremely non-uniform heat loads.

  14. Performance analysis of GPU-accelerated filter-based source finding for HI spectral line image data

    NASA Astrophysics Data System (ADS)

    Westerlund, Stefan; Harris, Christopher

    2015-03-01

    Searching for sources of electromagnetic emission in spectral-line radio astronomy interferometric data is a computationally intensive process. Parallel programming techniques and High Performance Computing hardware may be used to improve the computational performance of a source finding program. However, it is desirable to further reduce the processing time of source finding in order to decrease the computational resources required for the task. GPU acceleration is a method that may achieve significant increases in performance for some source finding algorithms, particularly for filtering image data. This work considers the application of GPU acceleration to the task of source finding and the techniques used to achieve the best performance, such as memory management. We also examine the changes in performance, where the algorithms that were GPU accelerated achieved a speedup of around 3.2 times the 12 core per node CPU-only performance, while the program as a whole experienced a speedup of 2.0 times.

  15. Compact accelerator

    DOEpatents

    Caporaso, George J.; Sampayan, Stephen E.; Kirbie, Hugh C.

    2007-02-06

    A compact linear accelerator having at least one strip-shaped Blumlein module which guides a propagating wavefront between first and second ends and controls the output pulse at the second end. Each Blumlein module has first, second, and third planar conductor strips, with a first dielectric strip between the first and second conductor strips, and a second dielectric strip between the second and third conductor strips. Additionally, the compact linear accelerator includes a high voltage power supply connected to charge the second conductor strip to a high potential, and a switch for switching the high potential in the second conductor strip to at least one of the first and third conductor strips so as to initiate a propagating reverse polarity wavefront(s) in the corresponding dielectric strip(s).

  16. BICEP's acceleration

    SciTech Connect

    Contaldi, Carlo R.

    2014-10-01

    The recent Bicep2 [1] detection of, what is claimed to be primordial B-modes, opens up the possibility of constraining not only the energy scale of inflation but also the detailed acceleration history that occurred during inflation. In turn this can be used to determine the shape of the inflaton potential V(φ) for the first time — if a single, scalar inflaton is assumed to be driving the acceleration. We carry out a Monte Carlo exploration of inflationary trajectories given the current data. Using this method we obtain a posterior distribution of possible acceleration profiles ε(N) as a function of e-fold N and derived posterior distributions of the primordial power spectrum P(k) and potential V(φ). We find that the Bicep2 result, in combination with Planck measurements of total intensity Cosmic Microwave Background (CMB) anisotropies, induces a significant feature in the scalar primordial spectrum at scales k∼ 10{sup -3} Mpc {sup -1}. This is in agreement with a previous detection of a suppression in the scalar power [2].

  17. Development of an accelerator based system for in vivo neutron activation analysis measurements of manganese in humans

    NASA Astrophysics Data System (ADS)

    Arnold, Michelle Lynn

    2001-11-01

    Manganese is required by the human body, but as with many heavy elements, in large amounts it can be toxic, producing a neurological disorder similar to that of Parkinson's Disease. The primary industrial uses of the element are for the manufacturing of steel and alkali batteries. Environmental exposure may occur via drinking water or exhaust emissions from vehicles using gasoline with the manganese containing compound MMT as an antiknock agent (MMT has been approved for use in both Canada and the United States). Preclinical symptoms of toxicity have recently been detected in individuals occupationally exposed to airborne manganese at levels below the present threshold limit value set by the EPA. Evidence also suggests that early detection of manganese toxicity is crucial since once the symptoms have developed past a certain point, the syndrome will continue to progress even if manganese exposure ceases. The development of a system for in vivo neutron activation analysis (IVNAA) measurement of manganese levels was investigated, with the goal being to have a means of monitoring both over exposed and manganese deficient populations. The McMaster KN-accelerator was used to provide low-energy neutrons, activation within an irradiation site occurred via the 55Mn(n,gamma) 56Mn capture reaction, and the 847 keV gamma-rays emitted when 56Mn decayed were measured using one or more Nal(TI) detectors. The present data regarding manganese metabolism and storage within the body are limited, and it is unclear what the optimal measurement site would be to provide a suitable biomarker of past exposure. Therefore the feasibility of IVNAA measurements in three sites was examined---the liver, brain and hand bones. Calibration curves were derived, minimum detectable limits determined and resulting doses calculated for each site (experimentally in the case of the liver and hand bones, and through computer simulations for the brain). Detailed analytical calculations of the 7Li(p,n) 7Be

  18. Advanced concepts for acceleration

    SciTech Connect

    Keefe, D.

    1986-07-01

    Selected examples of advanced accelerator concepts are reviewed. Such plasma accelerators as plasma beat wave accelerator, plasma wake field accelerator, and plasma grating accelerator are discussed particularly as examples of concepts for accelerating relativistic electrons or positrons. Also covered are the pulsed electron-beam, pulsed laser accelerator, inverse Cherenkov accelerator, inverse free-electron laser, switched radial-line accelerators, and two-beam accelerator. Advanced concepts for ion acceleration discussed include the electron ring accelerator, excitation of waves on intense electron beams, and two-wave combinations. (LEW)

  19. Accelerators and the Accelerator Community

    SciTech Connect

    Malamud, Ernest; Sessler, Andrew

    2008-06-01

    In this paper, standing back--looking from afar--and adopting a historical perspective, the field of accelerator science is examined. How it grew, what are the forces that made it what it is, where it is now, and what it is likely to be in the future are the subjects explored. Clearly, a great deal of personal opinion is invoked in this process.

  20. An accelerated life test model for solid lubricated bearings based on dependence analysis and proportional hazard effect

    NASA Astrophysics Data System (ADS)

    Zhang, Chao; Wang, Shaoping; Bai, Guanghan

    2014-02-01

    Solid lubricated bearings are important mechanical components in space, and accelerated life tests (ALT) of them are widely conducted. ALT model is needed to give the lifetime of solid lubricated bearings with ALT data, and former accelerated life test models of solid lubricated models are mainly statistical models, while physical models can imply an understanding of the failure mechanism and are preferred whenever possible. This paper proposes a physical model, which is called copula dependent proportional hazards model. A solid lubricated bearing is considered as a system consisting of several dependent items and Clayton copula function is used to describe the dependence. Proportional hazard effect is also considered to build the model. An ALT of solid lubricated bearing is carried out and the results show that this model is effective.

  1. Damage Based Analysis (DBA): Theory, Derivation and Practical Application - Using Both an Acceleration and Pseudo-Velocity Approach

    NASA Technical Reports Server (NTRS)

    Grillo, Vince

    2016-01-01

    The objective of this presentation is to give a brief overview of the theory behind the (DBA) method, an overview of the derivation and a practical application of the theory using the Python computer language. The Theory and Derivation will use both Acceleration and Pseudo Velocity methods to derive a series of equations for processing by Python. We will take the results and compare both Acceleration and Pseudo Velocity methods and discuss implementation of the Python functions. Also, we will discuss the efficiency of the methods and the amount of computer time required for the solution. In conclusion, (DBA) offers a powerful method to evaluate the amount of energy imparted into a system in the form of both Amplitude and Duration during qualification testing and flight environments. Many forms of steady state and transient vibratory motion can be characterized using this technique. (DBA) provides a more robust alternative to traditional methods such Power Spectral Density (PSD) using a Maximax approach.

  2. Analysis of peripheral doses for base of tongue treatment by linear accelerator and helical TomoTherapy IMRT.

    PubMed

    Bennett, Brian Richard; Lamba, Michael A S; Elson, Howard R

    2010-01-01

    The purpose of this study was to compare the peripheral doses to various organs from a typical head and neck intensity-modulated radiation therapy (IMRT) treatment delivered by linear accelerator (linac) and helical TomoTherapy. Multiple human CT data sets were used to segment critical structures and organs at risk, fused and adjusted to an anthropomorphic phantom. Eighteen contours were designated for thermoluminescent dosimeter (TLD) placement. Following the RTOG IMRT Protocol 0522, treatment of the primary tumor and involved nodes (PTV70) and subclinical disease sites (PTV56) was planned utilizing IMRT to 70Gy and 56 Gy. Clinically acceptable treatment plans were produced for linac and TomoTherapy treatments. TLDs were placed and each treatment plan was delivered to the anthropomorphic phantom four times. Within 2.5 cm (one helical TomoTherapy field width) superior and inferior to the field edges, normal tissue doses were on average 45% lower using linear accelerator. Beyond 2.5 cm, the helical TomoTherapy normal tissue dose was an average of 52% lower. The majority of points proved to be statistically different using the Student's t-test with p > 0.05. Using one method of calculation, probability of a secondary malignancy was 5.88% for the linear accelerator and 4.08% for helical TomoTherapy. Helical TomoTherapy delivers more dose than a linac immediately above and below the treatment field, contributing to the higher peripheral doses adjacent to the field. At distances beyond one field width (where leakage is dominant), helical TomoTherapy doses are lower than linear accelerator doses. PMID:20717081

  3. Modal analysis of the energy loss for an accelerated electron beam passing through a laser-driven RF gun

    NASA Astrophysics Data System (ADS)

    Salah, W.

    2002-06-01

    The energy loss for an accelerated electron beam passing through a laser-driven RF gun has been studied. An analytical formula of the energy loss has been obtained using the time-dependent resonant modes of a cylindrical "pill-box" cavity. As an approximation, this formalism assumes a rigid beam pulse so the change of pulse shape dealing with space-charge force and wake field force is ignored.

  4. Simultaneous chemical fingerprint and quantitative analysis of Rhizoma Smilacis Glabrae by accelerated solvent extraction and high-performance liquid chromatography with tandem mass spectrometry.

    PubMed

    Dai, Weiquan; Zhao, Weiquan; Gao, Fangyuan; Shen, Jingjing; Lv, Diya; Qi, Yunpeng; Fan, Guorong

    2015-05-01

    Rhizoma Smilacis Glabrae (RSG) is a well-known herbal medicine with the homology of medicine and food. In this study, simultaneous chemical fingerprint and quantitative analysis of the bioactive flavonoid components of RSG were developed using accelerated solvent extraction and high-performance liquid chromatography coupled with ion trap tandem mass spectrometry. The operational parameters of accelerated solvent extraction including extraction solvent, extraction temperature, static extraction time, solid-to-liquid ratio, and extraction cycles were optimized. Hierarchical cluster analysis, similarity analysis, and principal component analysis were performed to evaluate the similarity and variation of the samples collected from several provinces in China. Subsequently, high-performance liquid chromatography fingerprints were established for the discrimination of 16 batches of RSG samples, and the major six flavonoids, namely, toxifolin, neoastilbin, astilbin, neoisoastilbin, isoastilbin, and engeletin were then quantitatively determined. The calibration curves for all the six analytes showed good linearity (r(2) > 0.999), and the limits of detection and quantification were less than 0.10 and 0.27 μg·mL(-1) , respectively. Therefore, the proposed extraction and determination methods were proved to be robust and reliable for the quality control of RSG. PMID:25678068

  5. Systematic Analysis of Long Noncoding RNAs in the Senescence-accelerated Mouse Prone 8 Brain Using RNA Sequencing.

    PubMed

    Zhang, Shuai; Qin, Chunxia; Cao, Guoqiong; Xin, Wenfeng; Feng, Chengqiang; Zhang, Wensheng

    2016-01-01

    Long noncoding RNAs (lncRNAs) may play an important role in Alzheimer's disease (AD) pathogenesis. However, despite considerable research in this area, the comprehensive and systematic understanding of lncRNAs in AD is still limited. The emergence of RNA sequencing provides a predictor and has incomparable advantage compared with other methods, including microarray. In this study, we identified lncRNAs in a 7-month-old mouse brain through deep RNA sequencing using the senescence-accelerated mouse prone 8 (SAMP8) and senescence-accelerated mouse resistant 1 (SAMR1) models. A total of 599,985,802 clean reads and 23,334 lncRNA transcripts were obtained. Then, we identified 97 significantly upregulated and 114 significantly downregulated lncRNA transcripts from all cases in SAMP8 mice relative to SAMR1 mice. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes analyses revealed that these significantly dysregulated lncRNAs were involved in regulating the development of AD from various angles, such as nerve growth factor term (GO: 1990089), mitogen-activated protein kinase signaling pathway, and AD pathway. Furthermore, the most probable AD-associated lncRNAs were predicted and listed in detail. Our study provided the systematic dissection of lncRNA profiling in SAMP8 mouse brain and accelerated the development of lncRNA biomarkers in AD. These attracting biomarkers could provide significant insights into AD therapy in the future. PMID:27483026

  6. Analysis of junction temperature and modification of luminous flux degradation for white LEDs in a thermal accelerated reliability test.

    PubMed

    Ke, Hong-Liang; Jing, Lei; Hao, Jian; Gao, Qun; Wang, Yao; Wang, Xiao-Xun; Sun, Qiang; Xu, Zhi-Jun

    2016-08-01

    An accelerated aging test is the main method in evaluation of the reliability of light-emitting diodes (LEDs), and the first goal of this study is to investigate how the junction temperature (Tj) of the LED varies during accelerated aging. The Tj measured by the forward voltage method shows an upward trend over the aging time, which gives a variation about 6°C-8°C after 3,000 h of aging under an ambient temperature of 80°C. The second goal is to investigate how the variation of Tj affects the lifetime estimation. It is verified that at a certain aging stage, as Tj increases, the normalized luminous flux linearly decreases with variation rate of microns (μ) (1/°C). Then, we propose a method to modify the luminous flux degradation with the Tj and μ to meet the requirements of a constant degradation rate in the data fitting. The experimental results show that with the proposed method, the accelerated lifetimes of samples are bigger than that of the current method with increment values from 8.8% to 21.4% in this research. PMID:27505370

  7. Inertia Coupling Analysis of a Self-Decoupled Wheel Force Transducer under Multi-Axis Acceleration Fields

    PubMed Central

    Feng, Lihang; Lin, Guoyu; Zhang, Weigong; Dai, Dong

    2015-01-01

    Wheel force transducer (WFT), which measures the three-axis forces and three-axis torques applied to the wheel, is an important instrument in the vehicle testing field and has been extremely promoted by researchers with great interests. The transducer, however, is typically mounted on the wheel of a moving vehicle, especially on a high speed car, when abruptly accelerating or braking, the mass/inertia of the transducer/wheel itself will have an extra effect on the sensor response so that the inertia/mass loads will also be detected and coupled into the signal outputs. The effect which is considered to be inertia coupling problem will decrease the sensor accuracy. In this paper, the inertia coupling of a universal WFT under multi-axis accelerations is investigated. According to the self-decoupling approach of the WFT, inertia load distribution is solved based on the principle of equivalent mass and rotary inertia, thus then inertia impact can be identified with the theoretical derivation. The verification is achieved by FEM simulation and experimental tests. Results show that strains in simulation agree well with the theoretical derivation. The relationship between the applied acceleration and inertia load for both wheel force and moment is the approximate linear, respectively. All the relative errors are less than 5% which are within acceptable and the inertia loads have the maximum impact on the signal output about 1.5% in the measurement range. PMID:25723492

  8. Inertia coupling analysis of a self-decoupled wheel force transducer under multi-axis acceleration fields.

    PubMed

    Feng, Lihang; Lin, Guoyu; Zhang, Weigong; Dai, Dong

    2015-01-01

    Wheel force transducer (WFT), which measures the three-axis forces and three-axis torques applied to the wheel, is an important instrument in the vehicle testing field and has been extremely promoted by researchers with great interests. The transducer, however, is typically mounted on the wheel of a moving vehicle, especially on a high speed car, when abruptly accelerating or braking, the mass/inertia of the transducer/wheel itself will have an extra effect on the sensor response so that the inertia/mass loads will also be detected and coupled into the signal outputs. The effect which is considered to be inertia coupling problem will decrease the sensor accuracy. In this paper, the inertia coupling of a universal WFT under multi-axis accelerations is investigated. According to the self-decoupling approach of the WFT, inertia load distribution is solved based on the principle of equivalent mass and rotary inertia, thus then inertia impact can be identified with the theoretical derivation. The verification is achieved by FEM simulation and experimental tests. Results show that strains in simulation agree well with the theoretical derivation. The relationship between the applied acceleration and inertia load for both wheel force and moment is the approximate linear, respectively. All the relative errors are less than 5% which are within acceptable and the inertia loads have the maximum impact on the signal output about 1.5% in the measurement range. PMID:25723492

  9. Will Progress in Science and Technology Avert or Accelerate Global Collapse? A Critical Analysis and Policy Recommendations

    SciTech Connect

    Huesemann, Michael H.; Huesemann, Joyce A.

    2008-12-01

    Industrial society will move towards collapse if its total environmental impact (I), expressed either in terms of energy and materials use or in terms of pollution, increases with time, i.e., dI/dt > 0. The traditional interpretation of the I=PAT equation reflects the optimistic belief that technological innovation, particularly improvements in eco-efficiency, will significantly reduce the technology (T) factor, and thereby result in a corresponding decline in impact (I). Unfortunately, this interpretation of the I=PAT equation ignores the effects of technical change on the other two factors: population (P) and per capita affluence (A). A more heuristic formulation of this equation is I=P(T)∙A(T)∙T in which the dependence of P and A on T is apparent. From historical evidence, it is clear that technological revolutions (tool-making, agricultural, and industrial) have been the primary driving forces behind successive population explosions, and that modern communication and transportation technologies have been employed to transform a large proportion of the world’s inhabitants into consumers of material- and energy-intensive products and services. In addition, factor analysis from neoclassical growth theory and the rebound effect provide evidence that science and technology have played a key role in contributing to rising living standards. While technological change has thus contributed to significant increases in both P and A, it has at the same time brought about considerable eco-efficiency improvements. Unfortunately, reductions in the T-factor have generally not been sufficiently rapid to compensate for the simultaneous increases in both P and A. As a result, total impact, in terms of energy production, mineral extraction, land-use and CO2 emissions, has in most cases increased with time, indicating that industrial society is nevertheless moving towards collapse. The belief that continued and even accelerated scientific research and technological innovation

  10. In vitro analysis of different properties of acrylic resins for ocular prosthesis submitted to accelerated aging with or without photopolymerized glaze.

    PubMed

    Santos, Daniela Micheline Dos; Nagay, Bruna Egumi; da Silva, Emily Vivianne Freitas; Bonatto, Liliane da Rocha; Sonego, Mariana Vilela; Moreno, Amália; Rangel, Elidiane Cipriano; da Cruz, Nilson Cristino; Goiato, Marcelo Coelho

    2016-12-01

    The effect of a photopolymerized glaze on different properties of acrylic resin (AR) for ocular prostheses submitted to accelerated aging was investigated. Forty discs were divided into 4 groups: N1 AR without glaze (G1); colorless AR without glaze (G2); N1 AR with glaze (G3); and colorless AR with glaze (G4). All samples were polished with sandpaper (240, 600 and 800-grit). In G1 and G2, a 1200-grit sandpaper was also used. In G3 and G4, samples were coated with MegaSeal glaze. Property analysis of color stability, microhardness, roughness, and surface energy, and assays of atomic force microscopy, scanning electron microscopy, and energy-dispersive spectroscopy were performed before and after the accelerated aging (1008h). Data were submitted to the ANOVA and Tukey Test (p<0.05). Groups with glaze exhibited statistically higher color change and roughness after aging. The surface microhardness significantly decreased in groups with glaze and increased in groups without glaze. The surface energy increased after the aging, independent of the polishing procedure. All groups showed an increase of surface irregularities. Photopolymerized glaze is an inadequate surface treatment for AR for ocular prostheses and it affected the color stability, roughness, and microhardness. The accelerated aging interfered negatively with the properties of resins. PMID:27612795

  11. Efficacy of low-level laser therapy for accelerating tooth movement during orthodontic treatment: a systematic review and meta-analysis.

    PubMed

    Ge, M K; He, W L; Chen, J; Wen, C; Yin, X; Hu, Z A; Liu, Z P; Zou, S J

    2015-07-01

    This review aimed to evaluate the efficacy of low-level laser therapy (LLLT) for accelerating tooth movement during orthodontic treatment. An extensive electronic search was conducted by two reviewers. Randomized controlled trials (RCTs) and quasi-RCTs concerning the efficacy of LLLT for accelerating tooth movement during orthodontic treatment were searched in CENTRAL, Medline, PubMed, Embase, China Biology Medicine Disc (CBM), China National Knowledge Infrastructure (CNKI), and Google Scholar. Six RCTs and three quasi-RCTs, involving 211 patients from six countries, were selected from 173 relevant studies. All nine articles were feasible for the systematic review and meta-analysis, five of which were assessed as moderate risk of bias, while the rest were assessed as high risk of bias. The mean difference and the 95 % confidence interval (95 % CI) of accumulative moved distance of teeth were observed among all the researches. The results showed that the LLLT could accelerate orthodontic tooth movement (OTM) in 7 days (mean difference 0.19, 95 % CI [0.02, 0.37], p = 0.03) and 2 months (mean difference 1.08, 95 % CI [0.16, 2.01], p = 0.02). Moreover, a relatively lower energy density (5 and 8 J/cm(2)) was seemingly more effective than 20 and 25 J/cm(2) and even higher ones. PMID:24554452

  12. Time-motion analysis of acceleration demands of 4v4 small-sided soccer games played on different pitch sizes.

    PubMed

    Hodgson, Craig; Akenhead, Richard; Thomas, Kevin

    2014-02-01

    We aimed to quantify the time-motion characteristics and technical demands of small-sided soccer games (SSGs) played on small, medium and large pitches using a high frequency non-differential global positioning system (NdGPS) that allowed assessment of acceleration and deceleration patterns. Eight male soccer players competed in SSGs comprising 4×4min quarters (3min recovery) on small (30×20m) medium (40×30m) and large (50×40m) pitch sizes. Time motion analysis using a NdGPS positioning system quantified distance covered sprinting (⩾6.7ms(-1)), high speed running (⩾5.8ms(-1)) and low (1-2ms(-2)), medium (2-3ms(-2)) and high (>3ms(-2)) acceleration. The frequency of common technical actions (passing, turning, dribbling, shooting, tackling, heading and interceptions) was performed using a hand notation system. SSGs played on medium and large pitches had a greater physical demand than on small pitches, with significantly more distance covered in all movement categories. Total distance covered in acceleration categories ranged from 230±111 (small pitch) to 356±72m (medium pitch). The small pitch imposed a greater technical demand on players (more passes, shots and tackles) compared to medium and large pitches. The study provides novel data demonstrating the acceleration patterns observed in SSGs are relatively greater than those observed during professional match play. Thus SSGs might offer a "density" type conditioning stimulus. Practitioners should be aware that changes in pitch size impact both the physical and technical demands of SSGs. PMID:24576705

  13. Accelerator system and method of accelerating particles

    NASA Technical Reports Server (NTRS)

    Wirz, Richard E. (Inventor)

    2010-01-01

    An accelerator system and method that utilize dust as the primary mass flux for generating thrust are provided. The accelerator system can include an accelerator capable of operating in a self-neutralizing mode and having a discharge chamber and at least one ionizer capable of charging dust particles. The system can also include a dust particle feeder that is capable of introducing the dust particles into the accelerator. By applying a pulsed positive and negative charge voltage to the accelerator, the charged dust particles can be accelerated thereby generating thrust and neutralizing the accelerator system.

  14. Attention's Accelerator.

    PubMed

    Reinhart, Robert M G; McClenahan, Laura J; Woodman, Geoffrey F

    2016-06-01

    How do people get attention to operate at peak efficiency in high-pressure situations? We tested the hypothesis that the general mechanism that allows this is the maintenance of multiple target representations in working and long-term memory. We recorded subjects' event-related potentials (ERPs) indexing the working memory and long-term memory representations used to control attention while performing visual search. We found that subjects used both types of memories to control attention when they performed the visual search task with a large reward at stake, or when they were cued to respond as fast as possible. However, under normal circumstances, one type of target memory was sufficient for slower task performance. The use of multiple types of memory representations appears to provide converging top-down control of attention, allowing people to step on the attentional accelerator in a variety of high-pressure situations. PMID:27056975

  15. Natural Yeast Promoter Variants Reveal Epistasis in the Generation of Transcriptional-Mediated Noise and Its Potential Benefit in Stressful Conditions

    PubMed Central

    Liu, Jian; Martin-Yken, Hélène; Bigey, Frédéric; Dequin, Sylvie; François, Jean-Marie; Capp, Jean-Pascal

    2015-01-01

    The increase in phenotypic variability through gene expression noise is proposed to be an evolutionary strategy in selective environments. Differences in promoter-mediated noise between Saccharomyces cerevisiae strains could have been selected for thanks to the benefit conferred by gene expression heterogeneity in the stressful conditions, for instance, those experienced by industrial strains. Here, we used a genome-wide approach to identify promoters conferring high noise levels in the industrial wine strain EC1118. Many promoters of genes related to environmental factors were identified, some of them containing genetic variations compared with their counterpart in the laboratory strain S288c. Each variant of eight promoters has been fused to yeast-Enhanced Green Fluorescent Protein and integrated in the genome of both strains. Some industrial variants conferred higher expression associated, as expected, with lower noise, but other variants either increased or decreased expression without modifying variability, so that they might exhibit different levels of transcriptional-mediated noise at equal mean. At different induction conditions giving similar expression for both variants of the CUP1 promoter, we indeed observed higher noise with the industrial variant. Nevertheless, this difference was only observed in the industrial strain, revealing epistasis in the generation of promoter-mediated noise. Moreover, the increased expression variability conferred by this natural yeast promoter variant provided a clear benefit in the face of an environmental stress. Thus, modulation of gene expression noise by a combination of promoter modifications and trans-influences might be a possible adaptation mechanism in yeast. PMID:25762217

  16. The common occurrence of epistasis in the determination of human pigmentation and its impact on DNA-based pigmentation phenotype prediction.

    PubMed

    Pośpiech, Ewelina; Wojas-Pelc, Anna; Walsh, Susan; Liu, Fan; Maeda, Hitoshi; Ishikawa, Takaki; Skowron, Małgorzata; Kayser, Manfred; Branicki, Wojciech

    2014-07-01

    The role of epistatic effects in the determination of complex traits is often underlined but its significance in the prediction of pigmentation phenotypes has not been evaluated so far. The prediction of pigmentation from genetic data can be useful in forensic science to describe the physical appearance of an unknown offender, victim, or missing person who cannot be identified via conventional DNA profiling. Available forensic DNA prediction systems enable the reliable prediction of several eye and hair colour categories. However, there is still space for improvement. Here we verified the association of 38 candidate DNA polymorphisms from 13 genes and explored the extent to which interactions between them may be involved in human pigmentation and their impact on forensic DNA prediction in particular. The model-building set included 718 Polish samples and the model-verification set included 307 independent Polish samples and additional 72 samples from Japan. In total, 29 significant SNP-SNP interactions were found with 5 of them showing an effect on phenotype prediction. For predicting green eye colour, interactions between HERC2 rs12913832 and OCA2 rs1800407 as well as TYRP1 rs1408799 raised the prediction accuracy expressed by AUC from 0.667 to 0.697 and increased the prediction sensitivity by >3%. Interaction between MC1R 'R' variants and VDR rs731236 increased the sensitivity for light skin by >1% and by almost 3% for dark skin colour prediction. Interactions between VDR rs1544410 and TYR rs1042602 as well as between MC1R 'R' variants and HERC2 rs12913832 provided an increase in red/non-red hair prediction accuracy from an AUC of 0.902-0.930. Our results thus underline epistasis as a common phenomenon in human pigmentation genetics and demonstrate that considering SNP-SNP interactions in forensic DNA phenotyping has little impact on eye, hair and skin colour prediction. PMID:24681889

  17. Menopause accelerates biological aging.

    PubMed

    Levine, Morgan E; Lu, Ake T; Chen, Brian H; Hernandez, Dena G; Singleton, Andrew B; Ferrucci, Luigi; Bandinelli, Stefania; Salfati, Elias; Manson, JoAnn E; Quach, Austin; Kusters, Cynthia D J; Kuh, Diana; Wong, Andrew; Teschendorff, Andrew E; Widschwendter, Martin; Ritz, Beate R; Absher, Devin; Assimes, Themistocles L; Horvath, Steve

    2016-08-16

    Although epigenetic processes have been linked to aging and disease in other systems, it is not yet known whether they relate to reproductive aging. Recently, we developed a highly accurate epigenetic biomarker of age (known as the "epigenetic clock"), which is based on DNA methylation levels. Here we carry out an epigenetic clock analysis of blood, saliva, and buccal epithelium using data from four large studies: the Women's Health Initiative (n = 1,864); Invecchiare nel Chianti (n = 200); Parkinson's disease, Environment, and Genes (n = 256); and the United Kingdom Medical Research Council National Survey of Health and Development (n = 790). We find that increased epigenetic age acceleration in blood is significantly associated with earlier menopause (P = 0.00091), bilateral oophorectomy (P = 0.0018), and a longer time since menopause (P = 0.017). Conversely, epigenetic age acceleration in buccal epithelium and saliva do not relate to age at menopause; however, a higher epigenetic age in saliva is exhibited in women who undergo bilateral oophorectomy (P = 0.0079), while a lower epigenetic age in buccal epithelium was found for women who underwent menopausal hormone therapy (P = 0.00078). Using genetic data, we find evidence of coheritability between age at menopause and epigenetic age acceleration in blood. Using Mendelian randomization analysis, we find that two SNPs that are highly associated with age at menopause exhibit a significant association with epigenetic age acceleration. Overall, our Mendelian randomization approach and other lines of evidence suggest that menopause accelerates epigenetic aging of blood, but mechanistic studies will be needed to dissect cause-and-effect relationships further. PMID:27457926

  18. Accelerator simulation using computers

    SciTech Connect

    Lee, M.; Zambre, Y.; Corbett, W.

    1992-01-01

    Every accelerator or storage ring system consists of a charged particle beam propagating through a beam line. Although a number of computer programs exits that simulate the propagation of a beam in a given beam line, only a few provide the capabilities for designing, commissioning and operating the beam line. This paper shows how a multi-track'' simulation and analysis code can be used for these applications.

  19. Accelerator simulation using computers

    SciTech Connect

    Lee, M.; Zambre, Y.; Corbett, W.

    1992-01-01

    Every accelerator or storage ring system consists of a charged particle beam propagating through a beam line. Although a number of computer programs exits that simulate the propagation of a beam in a given beam line, only a few provide the capabilities for designing, commissioning and operating the beam line. This paper shows how a ``multi-track`` simulation and analysis code can be used for these applications.

  20. Short Acceleration Times from Superdiffusive Shock Acceleration in the Heliosphere

    NASA Astrophysics Data System (ADS)

    Perri, S.; Zimbardo, G.

    2015-12-01

    The analysis of time profiles of particles accelerated at interplanetary shocks allows particle transport properties to be inferred. The frequently observed power-law decay upstream, indeed, implies a superdiffusive particle transport when the level of magnetic field variance does not change as the time interval from the shock front increases. In this context, a superdiffusive shock acceleration (SSA) theory has been developed, allowing us to make predictions of the acceleration times. In this work we estimate for a number of interplanetary shocks, including the solar wind termination shock, the acceleration times for energetic protons in the framework of SSA and we compare the results with the acceleration times predicted by standard diffusive shock acceleration. The acceleration times due to SSA are found to be much shorter than in the classical model, and also shorter than the interplanetary shock lifetimes. This decrease of the acceleration times is due to the scale-free nature of the particle displacements in the framework of superdiffusion. Indeed, very long displacements are possible, increasing the probability for particles far from the front of the shock to return, and short displacements have a high probability of occurrence, increasing the chances for particles close to the front to cross the shock many times.

  1. Superdiffusive shock acceleration and short acceleration times at interplanetary shocks

    NASA Astrophysics Data System (ADS)

    Perri, Silvia; Zimbardo, Gaetano

    2016-04-01

    The analysis of time profiles of particles accelerated at interplanetary shock waves has shown evidence for superdiffusive transport in the upstream region. Superdiffusive transport is characterized by a mean square displacement that grows faster than linearly in time and by non Gaussian statistics for the distribution of the particle jump lengths. In the superdiffusive framework it has been shown that particle time profiles upstream of a planar shock decay as power laws, at variance with exponential particle time profiles predicted in the case of diffusive transport. A large number of interplanetary shocks, including coronal mass ejection driven shocks, exhibit energetic particle time profiles that decay as power laws far upstream. In order to take this evidence into account, we have extended the standard theory of diffusive shock acceleration to the case of particle superdiffusive transport (superdiffusive shock acceleration). This has allowed us to derive both hard energy spectral indices and short acceleration times. This new theory has been tested for a number of interplanetary shock waves, observed by the Ulysses and the ACE spacecraft, and for the termination shock. The superdiffusive shock acceleration leads to a strong reduction of the acceleration times (even of about one order of magnitude) with respect to the diffusive shock acceleration. Thus, this new framework provides a substantial advancement in the understanding of the processes of particle acceleration and particle transport, which are among the main objectives of the new Solar Probe and Solar Orbiter space missions.

  2. Applications of electrostatic accelerators

    SciTech Connect

    Norton, G.A.; Klody, G.M.

    1995-10-01

    Most applications of electrostatic accelerators fit into two main groups, materials analysis and materials modification. Materials analysis includes routine use of Rutherford Backscattering for quality control applications in the semiconductor field. Particle induced x-ray emission (PDCE) is used in fields from art history through environmental sciences. X-ray imaging using 5 MeV DC electron beams and fast pulsed neutron analysis (PFNA) for plastic explosive and drug detection provide promise in the area of security. Accelerator based mass spectrometry (AMS) is having a profound effect in a wide variety of fields which rely on counting extremely rare isotopes in small samples. Materials modification provides a very significant economic impact in the field of semiconductors. Virtually all semiconductor devices now rely on ion implantation with ion beam energies ranging from a few kilovolts to several MeV. With some mention of electron beams, this talk will concentrate primarily on the applications of MeV ion beams from electrostatic accelerators.

  3. Critical Issues in Plasma Accelerator

    NASA Astrophysics Data System (ADS)

    Uesaka, M.; Hosokai, T.

    2004-10-01

    Updated achievements and critical issues in plasma accelerators are summarized. As to laser plasma accelerators, we cover the results of plasma cathodes by U.Michigan, LBNL, LOA and U.Tokyo. Although many new results of accelerated electrons have been reported, the electrons do not yet form a bunch with narrow energy spread. Several injection schemes and measurements to verify ultrashort bunch (tens fs) with narrow energy spread, low emittance and many charges are planned. E-162 experiments by UCLA / USC / SLAC and a newly proposed experiment on density transition trapping are introduced for electron beam driven plasma accelerators. Their main purpose is realization of GeV plasma accelerator, but application to pump-and-probe analysis for investigation of ultrafast quantum phenomena is also promising.

  4. Electron cyclotron harmonic wave acceleration

    NASA Technical Reports Server (NTRS)

    Karimabadi, H.; Menyuk, C. R.; Sprangle, P.; Vlahos, L.

    1987-01-01

    A nonlinear analysis of particle acceleration in a finite bandwidth, obliquely propagating electromagnetic cyclotron wave is presented. It has been suggested by Sprangle and Vlahos in 1983 that the narrow bandwidth cyclotron radiation emitted by the unstable electron distribution inside a flaring solar loop can accelerate electrons outside the loop by the interaction of a monochromatic wave propagating along the ambient magnetic field with the ambient electrons. It is shown here that electrons gyrating and streaming along a uniform, static magnetic field can be accelerated by interacting with the fundamental or second harmonic of a monochromatic, obliquely propagating cyclotron wave. It is also shown that the acceleration is virtually unchanged when a wave with finite bandwidth is considered. This acceleration mechanism can explain the observed high-energy electrons in type III bursts.

  5. Preliminary analysis of acceleration of sea level rise through the twentieth century using extended tide gauge data sets (August 2014)

    NASA Astrophysics Data System (ADS)

    Hogarth, Peter

    2014-11-01

    This work explores the potential for extending tide gauge time series from the Permanent Service for Mean Sea Level (PSMSL) using historical documents, PSMSL ancillary data, and by developing additional composite time series using near neighbor tide gauges. The aim was to increase the number, completeness, and geographical extent of records covering most or all of the twentieth century. The number of at least 75% complete century-scale time series have been approximately doubled over the original PSMSL data set. In total, over 4800 station years have been added, with 294 of these added to 10 long Southern Hemisphere records. Individual century-scale acceleration values derived from this new extended data set tend to converge on a value of 0.01 ± 0.008 mm/yr2. This result agrees closely with recent work and is statistically significant at the 1 sigma level. Possible causes of acceleration and errors are briefly discussed. Results confirm the importance of current data archeology projects involving digitization of the remaining archives of hard copy tide gauge data for sea level and climate studies.

  6. Characteristic impedance and capacitance analysis of Blumlein type pulse forming line of accelerator based on tape helix

    SciTech Connect

    Zhang Yu; Liu Jinliang; Fan Xuliang; Zhang Hongbo; Wang Shiwen; Feng Jiahuai

    2011-10-15

    In this paper, the electromagnetic dispersion theory and the classic telegraph equations were combined to calculate the important parameters of the helical Blumlein pulse forming line (BPFL) of accelerator based on tape helix. In the work band of the BPFL at several hundred ns range, electromagnetic dispersion characteristics were almost determined by the zeroth harmonic. In order to testify the dispersion theory of BPFL in this paper, filling dielectrics, such as de-ionized water, transformer oil, and air were employed in the helical BPFL, respectively. Parameters such as capacitance, inductance, characteristic impedance, and pulse duration of the BPFL were calculated. Effects of dispersion on these parameters were analyzed. Circuit simulation and electromagnetic simulation were carried out to prove these parameters of BPFL filled with these three kinds of dielectrics, respectively. The accelerator system was set up, and experimental results also corresponded to the theoretical calculations. The average theoretical errors of impedances and pulse durations were 3.5% and 3.4%, respectively, which proved the electromagnetic dispersion analyses in this paper.

  7. Analysis of Cell Division and Elongation Underlying the Developmental Acceleration of Root Growth in Arabidopsis thaliana1

    PubMed Central

    Beemster, Gerrit T.S.; Baskin, Tobias I.

    1998-01-01

    To investigate the relation between cell division and expansion in the regulation of organ growth rate, we used Arabidopsis thaliana primary roots grown vertically at 20°C with an elongation rate that increased steadily during the first 14 d after germination. We measured spatial profiles of longitudinal velocity and cell length and calculated parameters of cell expansion and division, including rates of local cell production (cells mm−1 h−1) and cell division (cells cell−1 h−1). Data were obtained for the root cortex and also for the two types of epidermal cell, trichoblasts and atrichoblasts. Accelerating root elongation was caused by an increasingly longer growth zone, while maximal strain rates remained unchanged. The enlargement of the growth zone and, hence, the accelerating root elongation rate, were accompanied by a nearly proportionally increased cell production. This increased production was caused by increasingly numerous dividing cells, whereas their rates of division remained approximately constant. Additionally, the spatial profile of cell division rate was essentially constant. The meristem was longer than generally assumed, extending well into the region where cells elongated rapidly. In the two epidermal cell types, meristem length and cell division rate were both very similar to that of cortical cells, and differences in cell length between the two epidermal cell types originated at the apex of the meristem. These results highlight the importance of controlling the number of dividing cells, both to generate tissues with different cell lengths and to regulate the rate of organ enlargement. PMID:9536070

  8. Design and analysis of a piezoelectric material based touch screen with additional pressure and its acceleration measurement functions

    NASA Astrophysics Data System (ADS)

    Chu, Xiang-Cheng; Liu, Jia-Yi; Gao, Ren-Long; Chang, Jie; Li, Long-Tu

    2013-12-01

    Touch screens are becoming more and more prevalent in everyday environments due to their convenience and humanized operation. In this paper, a piezoelectric material based touch screen is developed and investigated. Piezoelectric ceramics arrayed under the touch panel at the edges or corners are used as tactile sensors to measure the touch positioning point similarly to conventional touch screens. However, additional touch pressure and its acceleration performance can also be obtained to obtain a higher-level human-machine interface. The piezoelectric ceramics can also be added to a traditional touch screen structure, or they can be used independently to construct a novel touch screen with a high light transmittance approach to a transparent glass. The piezoelectric ceramics were processed from PZT piezoelectric ceramic powder into a round or rectangular shape. According to the varied touch position and physical press strength of a finger, or even a gloved hand or fingernail, the piezoelectric tactile sensors will have different output voltage responses. By calculating the ratio of different piezoelectric tactile sensors’ responses and summing up all piezoelectric tactile sensors’ output voltages, the touch point position, touch pressure and touch force acceleration can be detected. A prototype of such a touch screen is manufactured and its position accuracy, touch pressure and response speed are measured in detail. The experimental results show that the prototype has many advantages such as high light transmittance, low energy cost and high durability.

  9. Stochastic Analysis and Forecasts of the Patterns of Speed, Acceleration, and Levels of Material Stock Accumulation in Society.

    PubMed

    Fishman, Tomer; Schandl, Heinz; Tanikawa, Hiroki

    2016-04-01

    The recent acceleration of urbanization and industrialization of many parts of the developing world, most notably in Asia, has resulted in a fast-increasing demand for and accumulation of construction materials in society. Despite the importance of physical stocks in society, the empirical assessment of total material stock of buildings and infrastructure and reasons for its growth have been underexplored in the sustainability literature. We propose an innovative approach for explaining material stock dynamics in society and create a country typology for stock accumulation trajectories using the ARIMA (Autoregressive Integrated Moving Average) methodology, a stochastic approach commonly used in business studies and economics to inspect and forecast time series. This enables us to create scenarios for future demand and accumulation of building materials in society, including uncertainty estimates. We find that the so-far overlooked aspect of acceleration trends of material stock accumulation holds the key to explaining material stock growth, and that despite tremendous variability in country characteristics, stock accumulation is limited to only four archetypal growth patterns. The ability of nations to change their pattern will be a determining factor for global sustainability. PMID:26927731

  10. Acceleration modules in linear induction accelerators

    NASA Astrophysics Data System (ADS)

    Wang, Shao-Heng; Deng, Jian-Jun

    2014-05-01

    The Linear Induction Accelerator (LIA) is a unique type of accelerator that is capable of accelerating kilo-Ampere charged particle current to tens of MeV energy. The present development of LIA in MHz bursting mode and the successful application into a synchrotron have broadened LIA's usage scope. Although the transformer model is widely used to explain the acceleration mechanism of LIAs, it is not appropriate to consider the induction electric field as the field which accelerates charged particles for many modern LIAs. We have examined the transition of the magnetic cores' functions during the LIA acceleration modules' evolution, distinguished transformer type and transmission line type LIA acceleration modules, and re-considered several related issues based on transmission line type LIA acceleration module. This clarified understanding should help in the further development and design of LIA acceleration modules.

  11. Combined analysis of νμ disappearance and νμ→νe appearance in MINOS using accelerator and atmospheric neutrinos.

    PubMed

    Adamson, P; Anghel, I; Aurisano, A; Barr, G; Bishai, M; Blake, A; Bock, G J; Bogert, D; Cao, S V; Castromonte, C M; Cherdack, D; Childress, S; Coelho, J A B; Corwin, L; Cronin-Hennessy, D; de Jong, J K; Devan, A V; Devenish, N E; Diwan, M V; Escobar, C O; Evans, J J; Falk, E; Feldman, G J; Frohne, M V; Gallagher, H R; Gomes, R A; Goodman, M C; Gouffon, P; Graf, N; Gran, R; Grzelak, K; Habig, A; Hahn, S R; Hartnell, J; Hatcher, R; Himmel, A; Holin, A; Huang, J; Hylen, J; Irwin, G M; Isvan, Z; James, C; Jensen, D; Kafka, T; Kasahara, S M S; Koizumi, G; Kordosky, M; Kreymer, A; Lang, K; Ling, J; Litchfield, P J; Lucas, P; Mann, W A; Marshak, M L; Mayer, N; McGivern, C; Medeiros, M M; Mehdiyev, R; Meier, J R; Messier, M D; Michael, D G; Miller, W H; Mishra, S R; Moed Sher, S; Moore, C D; Mualem, L; Musser, J; Naples, D; Nelson, J K; Newman, H B; Nichol, R J; Nowak, J A; O'Connor, J; Orchanian, M; Pahlka, R B; Paley, J; Patterson, R B; Pawloski, G; Perch, A; Phan-Budd, S; Plunkett, R K; Poonthottathil, N; Qiu, X; Radovic, A; Rebel, B; Rosenfeld, C; Rubin, H A; Sanchez, M C; Schneps, J; Schreckenberger, A; Schreiner, P; Sharma, R; Sousa, A; Tagg, N; Talaga, R L; Thomas, J; Thomson, M A; Tian, X; Timmons, A; Tognini, S C; Toner, R; Torretta, D; Tzanakos, G; Urheim, J; Vahle, P; Viren, B; Weber, A; Webb, R C; White, C; Whitehead, L; Whitehead, L H; Wojcicki, S G; Zwaska, R

    2014-05-16

    We report on a new analysis of neutrino oscillations in MINOS using the complete set of accelerator and atmospheric data. The analysis combines the ν(μ) disappearance and ν(e) appearance data using the three-flavor formalism. We measure |Δm(32)(2)| = [2.28-2.46] × 10(-3) eV(2) (68% C.L.) and sin(2)θ(23) = 0.35-0.65 (90% C.L.) in the normal hierarchy, and |Δm(32)(2)| = [2.32-2.53] × 10(-3) eV(2) (68% C.L.) and sin(2)θ(23) = 0.34-0.67 (90% C.L.) in the inverted hierarchy. The data also constrain δ(CP), the θ(23} octant degeneracy and the mass hierarchy; we disfavor 36% (11%) of this three-parameter space at 68% (90%) C.L. PMID:24877929

  12. NOTE: A software tool for 2D/3D visualization and analysis of phase-space data generated by Monte Carlo modelling of medical linear accelerators

    NASA Astrophysics Data System (ADS)

    Neicu, Toni; Aljarrah, Khaled M.; Jiang, Steve B.

    2005-10-01

    A computer program has been developed for novel 2D/3D visualization and analysis of the phase-space parameters of Monte Carlo simulations of medical accelerator radiation beams. The software is written in the IDL language and reads the phase-space data generated in the BEAMnrc/BEAM Monte Carlo code format. Contour and colour-wash plots of the fluence, mean energy, energy fluence, mean angle, spectra distribution, energy fluence distribution, angular distribution, and slices and projections of the 3D ZLAST distribution can be calculated and displayed. Based on our experience of using it at Massachusetts General Hospital, the software has proven to be a useful tool for analysis and verification of the Monte Carlo generated phase-space files. The software is in the public domain.

  13. The Use of Integrated Electronic Data Capture and Analysis for Accelerator Construction and Commissioning: Pansophy from the SNS Towards the ILC

    SciTech Connect

    J. P. Ozelis; V. Bookwalter; B. Madre; C. E. Reece

    2005-05-01

    Jefferson Lab has extensively used a proprietary web-based system (Pansophy) that integrates commercial database, data analysis, document archiving and retrieval, and user interface software, as a coherent knowledge management product during the construction of the cryomodules for the SNS Superconducting Linac, providing elements of process and procedure control, data capture and review, and data mining and analysis. With near real-time and potentially global access to production data, process monitoring and performance analyses could be pursued in a timely manner, providing crucial feedback. The extensibility, portability, and accessibility of Pansophy via universally available software components provide the essential features needed in any information and project management system capable of meeting the needs of future accelerator construction efforts, requiring an unprecedented level of regional and international coordination and collaboration, to which Pansophy is well suited.

  14. Progress on plasma accelerators

    SciTech Connect

    Chen, P.

    1986-05-01

    Several plasma accelerator concepts are reviewed, with emphasis on the Plasma Beat Wave Accelerator (PBWA) and the Plasma Wake Field Accelerator (PWFA). Various accelerator physics issues regarding these schemes are discussed, and numerical examples on laboratory scale experiments are given. The efficiency of plasma accelerators is then revealed with suggestions on improvements. Sources that cause emittance growth are discussed briefly.

  15. Development and application of compact and on-chip electron linear accelerators for dynamic tracking cancer therapy and DNA damage/repair analysis

    NASA Astrophysics Data System (ADS)

    Uesaka, M.; Demachi, K.; Fujiwara, T.; Dobashi, K.; Fujisawa, H.; Chhatkuli, R. B.; Tsuda, A.; Tanaka, S.; Matsumura, Y.; Otsuki, S.; Kusano, J.; Yamamoto, M.; Nakamura, N.; Tanabe, E.; Koyama, K.; Yoshida, M.; Fujimori, R.; Yasui, A.

    2015-06-01

    We are developing compact electron linear accelerators (hereafter linac) with high RF (Radio Frequency) frequency (9.3 GHz, wavelength 32.3 mm) of X-band and applying to medicine and non-destructive testing. Especially, potable 950 keV and 3.95 MeV linac X-ray sources have been developed for on-site transmission testing at several industrial plants and civil infrastructures including bridges. 6 MeV linac have been made for pinpoint X-ray dynamic tracking cancer therapy. The length of the accelerating tube is ∼600 mm. The electron beam size at the X-ray target is less than 1 mm and X-ray spot size at the cancer is less than 3 mm. Several hardware and software are under construction for dynamic tracking therapy for moving lung cancer. Moreover, as an ultimate compact linac, we are designing and manufacturing a laser dielectric linac of ∼1 MeV with Yr fiber laser (283 THz, wavelength 1.06 pm). Since the wavelength is 1.06 μm, the length of one accelerating strcture is tens pm and the electron beam size is in sub-micro meter. Since the sizes of cell and nuclear are about 10 and 1 μm, respectively, we plan to use this “On-chip” linac for radiation-induced DNA damage/repair analysis. We are thinking a system where DNA in a nucleus of cell is hit by ∼1 μm electron or X-ray beam and observe its repair by proteins and enzymes in live cells in-situ.

  16. An Information Theoretical Study of the Epistasis Between the CNR1 1359 G/A Polymorphism and the Taq1A and Taq1B DRD2 Polymorphisms: Assessing the Susceptibility to Cannabis Addiction in a Turkish Population.

    PubMed

    Isir, Aysun Baransel; Baransel, Cesur; Nacak, Muradiye

    2016-04-01

    Addiction is a complex, multi-factorial disease, and thus, analyzing genetic variants at multiple loci and gene-gene interactions among them (epistasis) can provide crucial clues about causative factors of addiction which cannot be detected with single-nucleotide polymorphism (SNP) association studies. In this study, we discuss the interaction between the 1359 G/A polymorphism of the CNR1 gene and the DRD2 gene polymorphisms and the net effect of any possible epistasis on the cannabis addiction phenotype in a Turkish population. Using bivariate synergy and mutual information concepts as a means of capturing the magnitude of interaction between marker pairs, the present study not only confirms the A1 marker allele as a risk factor but also reveals a finer-grained association between A and B markers which manifests itself both as a preventive and a risk factor. Our results indicate that the increased phenotype of cases require an individual to be either heterozygous at both loci or homozygous at locus B with homozygous risk factor A1A1 present. We hypothesize that overlapping expressions of CB1 and D2R is the cause of CB1-D2R interactions in cases of substance abuse and the different polymorphisms of CNR1 and DRD2 genes may have decisive roles in the nature of these interactions in terms of promoting or alleviating the cannabis addiction risk factor of the individual. PMID:26833047

  17. Nonparametric Bayesian Variable Selection With Applications to Multiple Quantitative Trait Loci Mapping With Epistasis and Gene–Environment Interaction

    PubMed Central

    Zou, Fei; Huang, Hanwen; Lee, Seunggeun; Hoeschele, Ina

    2010-01-01

    The joint action of multiple genes is an important source of variation for complex traits and human diseases. However, mapping genes with epistatic effects and gene–environment interactions is a difficult problem because of relatively small sample sizes and very large parameter spaces for quantitative trait locus models that include such interactions. Here we present a nonparametric Bayesian method to map multiple quantitative trait loci (QTL) by considering epistatic and gene–environment interactions. The proposed method is not restricted to pairwise interactions among genes, as is typically done in parametric QTL analysis. Rather than modeling each main and interaction term explicitly, our nonparametric Bayesian method measures the importance of each QTL, irrespective of whether it is mostly due to a main effect or due to some interaction effect(s), via an unspecified function of the genotypes at all candidate QTL. A Gaussian process prior is assigned to this unknown function. In addition to the candidate QTL, nongenetic factors and covariates, such as age, gender, and environmental conditions, can also be included in the unspecified function. The importance of each genetic factor (QTL) and each nongenetic factor/covariate included in the function is estimated by a single hyperparameter, which enters the covariance function and captures any main or interaction effect associated with a given factor/covariate. An initial evaluation of the performance of the proposed method is obtained via analysis of simulated and real data. PMID:20551445

  18. CARAT-GxG: CUDA-Accelerated Regression Analysis Toolkit for Large-Scale Gene–Gene Interaction with GPU Computing System

    PubMed Central

    Lee, Sungyoung; Kwon, Min-Seok; Park, Taesung

    2014-01-01

    In genome-wide association studies (GWAS), regression analysis has been most commonly used to establish an association between a phenotype and genetic variants, such as single nucleotide polymorphism (SNP). However, most applications of regression analysis have been restricted to the investigation of single marker because of the large computational burden. Thus, there have been limited applications of regression analysis to multiple SNPs, including gene–gene interaction (GGI) in large-scale GWAS data. In order to overcome this limitation, we propose CARAT-GxG, a GPU computing system-oriented toolkit, for performing regression analysis with GGI using CUDA (compute unified device architecture). Compared to other methods, CARAT-GxG achieved almost 700-fold execution speed and delivered highly reliable results through our GPU-specific optimization techniques. In addition, it was possible to achieve almost-linear speed acceleration with the application of a GPU computing system, which is implemented by the TORQUE Resource Manager. We expect that CARAT-GxG will enable large-scale regression analysis with GGI for GWAS data. PMID:25574130

  19. Accelerators in Research and Industry

    NASA Astrophysics Data System (ADS)

    Norton, G. A.

    1997-10-01

    Over the last sixty years the applications of ion beam accelerators has grown from basic nuclear structure research to the manufacture, preservation, and development of a large number of products which directly affect every day life. In addition, ion beam accelerators continue to provide a unique contribution in both basic and applied research in fields from art history to zoology. Applications fit into two main groups, materials analysis and materials modification. Most materials analysis include routine use of Rutherford Backscattering (RBS) and particle induced x-ray emission (PIXE) with new developments in analysis techniques being developed for remote elemental detection of plastic explosives and drugs. Existing accelerator systems and new accelerator systems are being developed for use in the area of accelerator based mass spectrometry (AMS) which is having a profound affect on a wide variety of fields which rely on counting extremely rare isotopes in very small samples. Accelerators used for materials modification continue to have a significant economic impact in the field of semiconductors and the development of new semiconductor and other high technology products.

  20. Two-step accelerated mineral carbonation and decomposition analysis for the reduction of CO₂ emission in the eco-industrial parks.

    PubMed

    Jung, Seok; Wang, Li Pang; Dodbiba, Gjergj; Fujita, Toyohisa

    2014-07-01

    Carbon dioxide (CO₂) emissions are a leading contributor to the negative effects of global warming. Globally, research has focused on effective means of reducing and mitigating CO₂ emissions. In this study, we examined the efficacy of eco-industrial parks (EIPs) and accelerated mineral carbonation techniques in reducing CO₂ emissions in South Korea. First, we used Logarithmic Mean Divisia Index (LMDI) analysis to determine the trends in carbon production and mitigation at the existing EIPs. We found that, although CO₂ was generated as byproducts and wastes of production at these EIPs, improved energy intensity effects occurred at all EIPs, and we strongly believe that EIPs are a strong alternative to traditional industrial complexes for reducing net carbon emissions. We also examined the optimal conditions for using accelerated mineral carbonation to dispose of hazardous fly ash produced through the incineration of municipal solid wastes at these EIPs. We determined that this technique most efficiently sequestered CO₂ when micro-bubbling, low flow rate inlet gas, and ammonia additives were employed. PMID:25079989

  1. Mass transport perspective on an accelerated exclusion process: Analysis of augmented current and unit-velocity phases

    NASA Astrophysics Data System (ADS)

    Dong, Jiajia; Klumpp, Stefan; Zia, R. K. P.

    2013-02-01

    In an accelerated exclusion process (AEP), each particle can “hop” to its adjacent site if empty as well as “kick” the frontmost particle when joining a cluster of size ℓ⩽ℓmax. With various choices of the interaction range, ℓmax, we find that the steady state of AEP can be found in a homogeneous phase with augmented currents (AC) or a segregated phase with holes moving at unit velocity (UV). Here we present a detailed study on the emergence of the novel phases, from two perspectives: the AEP and a mass transport process (MTP). In the latter picture, the system in the UV phase is composed of a condensate in coexistence with a fluid, while the transition from AC to UV can be regarded as condensation. Using Monte Carlo simulations, exact results for special cases, and analytic methods in a mean field approach (within the MTP), we focus on steady state currents and cluster sizes. Excellent agreement between data and theory is found, providing an insightful picture for understanding this model system.

  2. Identification and mapping of stable QTL with main and epistasis effect on rice grain yield under upland drought stress

    PubMed Central

    2014-01-01

    Background Drought is one of the most important abiotic stresses that cause drastic reduction in rice grain yield (GY) in rainfed environments. The identification and introgression of QTL leading to high GY under drought have been advocated to be the preferred breeding strategy to improve drought tolerance of popular rice varieties. Genetic control of GY under reproductive-stage drought stress (RS) was studied in two BC1F4 mapping populations derived from crosses of Kali Aus, a drought-tolerant aus cultivar, with high-yielding popular varieties MTU1010 and IR64. The aim was to identify QTL for GY under RS that show a large and consistent effect for the trait. Bulk segregant analysis (BSA) was used to identify significant markers putatively linked with high GY under drought. Results QTL analysis revealed major-effect GY QTL: qDTY 1.2 , qDTY 2.2 and qDTY 1.3 , qDTY 2.3 (DTY; Drought grain yield) under drought consistently over two seasons in Kali Aus/2*MTU1010 and Kali Aus/2*IR64 populations, respectively. qDTY 1.2 and qDTY 2.2 explained an additive effect of 288 kg ha−1 and 567 kg ha−1 in Kali Aus/2*MTU1010, whereas qDTY 1.3 and qDTY 2.3 explained an additive effect of 198 kg ha−1 and 147 kg ha−1 in Kali Aus/2*IR64 populations, respectively. Epistatic interaction was observed for DTF (days to flowering) between regions on chromosome 2 flanked by markers RM154–RM324 and RM263–RM573 and major epistatic QTL for GY showing interaction between genomic locations on chromosome 1 at marker interval RM488–RM315 and chromosome 2 at RM324–RM263 in 2012 DS and 2013 DS RS in Kali Aus/2*IR64 mapping populations. Conclusion The QTL, qDTY 1.2 , qDTY 1.3 , qDTY 2.2 , and qDTY 2.3, identified in this study can be used to improve GY of mega varieties MTU1010 and IR64 under different degrees of severity of drought stress through marker-aided backcrossing and provide farmers with improved varieties that effectively combine high yield potential with good yield

  3. Pattern Analysis of Acute Mucosal Reactions in Patients With Head and Neck Cancer Treated With Conventional and Accelerated Irradiation

    SciTech Connect

    Wygoda, Andrzej Maciejewski, Boguslaw; Skladowski, Krzysztof; Hutnik, Marcin; Pilecki, Boleslaw; Golen, Maria; Rutkowski, Tomasz

    2009-02-01

    Purpose: To evaluate severity of acute mucosal reactions (AMR) caused by conventional (CF) and accelerated fractionation (AF) regimens using a modified Dische system and to analyze differences in incidence and severity of AMR according to frequency and regularity of scoring. Methods and Materials: Sixty-six consecutive patients (33 CF, 33 AF) with head and neck cancer irradiated with 5 fractions in 5 days per week (CF) or with 7 fractions in 7 days (AF) to a total dose of 70 Gy. A modified Dische system was used for daily quantitation of AMR during radiotherapy until complete healing. Results: Confluent mucositis (CM) was noted in 79% of patients in the CF group and 85% in the AF group. In 24% of the CF group and 18% of the AF group the CM presented a wave-like pattern. In 55% of CF and 67% of AF a classic triphasic pattern was noted. In 12 patients acute reactions did not transgress the level of spotted mucositis. The present study clearly shows that quantitation of the incidence and severity of acute mucosal effects strongly depends on frequent and regular scoring. A significant difference in the incidence of CM between the CF and AF groups was noted, mainly in weeks 4-6 of irradiation. When once-weekly irregular instead of daily scoring was evaluated, the incidence of CM was underestimated by approximately 20-36%. Conclusions: Acute mucosal reactions occur as a complex of morphologic and functional disorders with individual intensity, even among patients treated with the same fractionation regimen. In some cases they present a 'wave-like' pattern during irradiation. Therefore, precise quantitation of acute effects requires regular and frequent scoring.

  4. Analysis of tetragonal to monoclinic phase transformation caused by accelerated artificial aging and the effects of microstructure in stabilized zirconia

    NASA Astrophysics Data System (ADS)

    Lucas, Thomas J.

    This investigation addresses the issue that yttria stabilized zirconia is being used as a dental biomaterial without substantial evidence of its long-term viability. Furthermore, stabilized zirconia (SZ) undergoes low temperature degradation (LTD), which can lead to roughening of the surface. A rougher exterior can lead to increased wear of the antagonist in the oral environment. Despite the LTD concerns, SZ is now widely used in restorative dentistry, including full contour crowns. A comparison of aging methods to determine the role of artificial aging on inducing the transformation has not been extensively studied. Therefore, simulations of the transformation process were investigated by comparing different methods of accelerated aging. The rejected null hypothesis is that the temperature of aging treatment will not affect the time required to cause measurable monoclinic transformation of yttria stabilized zirconia. The transformation of SZ starts at the surface and progresses inward; however, it is unclear whether the progression is constant for different aging conditions. This investigation analyzed the depth of transformation as a function of aging conditions for stabilized zirconia in the top 5-6 mum from the surface. The rejected null hypothesis is that the transformation amount is constant throughout the first six micrometers from the surface. The effects of grain size on the amount of monoclinic transformation were also investigated. This study aimed to determine if the grain size of partially stabilized zirconia affects the amount of monoclinic transformation, surface roughness, and property degradation due to aging. The rejected null hypothesis is that the grain size will not affect the amount of monoclinic transformation, thus have no effect on surface roughening or property degradation. The final part of this study addresses the wear of enamel when opposing zirconia by observing how grain size and aging affected the wear rate of an enamel antagonist

  5. The new external ion beam analysis setup at the Demokritos Tandem accelerator and first applications in cultural heritage

    NASA Astrophysics Data System (ADS)

    Sokaras, Dimosthenis; Bistekos, Euthimios; Georgiou, Lambros; Salomon, Joseph; Bogovac, Mladen; Aloupi-Siotis, Eleni; Paschalis, Vasilis; Aslani, Ioanna; Karabagia, Sofia; Lagoyannis, Anastasios; Harissopulos, Sotirios; Kantarelou, Vasiliki; Karydas, Andreas-Germanos

    2011-03-01

    At the 5.5 MV Tandem VdG accelerator of the Institute of Nuclear Physics of N.C.S.R. "Demokritos", Athens, Greece, an external ion-beam set-up has been recently developed and installed. The aim of this development was to integrate the analytical capabilities of the PIXE, RBS and PIGE ion beam techniques in one experimental set-up, so that to attain a complete elemental and near surface structural characterization of samples in an almost non-destructive way and without any limitation concerning their size or conductive state. A careful 3D mechanical drawing optimized the set-up experimental parameters achieving probe dimensions at the millimeter range (1 mm 2) and fulfilling the special requirements imposed for optimum performance of the aforementioned techniques, including the possibility to use heavier, than protons, ion beams. For the digital pulse processing of the X-ray, γ-ray and charged particle detector signals, novel hardware and software tools were developed based on a custom FPGA configuration. The first applications were focused in the quality control of materials that have been intentionally contaminated with a particular tracer-element ("tagged" materials). The tagged materials which were developed and tested are technologically authentic replicas of ancient attic ceramics with black glazed decoration. Analytical diagnostic studies were carried out for a few representative paintings of contemporary Greek painters in order to identify and document materials/pigments and techniques and eventually to prevent trade of fakes. Finally, ancient glass beads were also examined with respect to the sodium concentration and its in-depth homogeneity.

  6. Accelerated tryptic digestion for the analysis of biopharmaceutical monoclonal antibodies in plasma by liquid chromatography with tandem mass spectrometric detection.

    PubMed

    Lesur, Antoine; Varesio, Emmanuel; Hopfgartner, Gérard

    2010-01-01

    Accelerated tryptic digestion of a therapeutic protein including microwave irradiation and thermal transfer by convection at 60 degrees C and 37 degrees C was investigated. An analytical setup was devised to follow the protein digestion rate using 1D gel electrophoresis and liquid chromatography coupled a triple quadrupole linear ion trap mass spectrometer. The formation kinetic of its tryptic peptides was monitored in the selected monitoring mode (LC-SRM/MS). Different digestion end points (e.g. 2, 5, 10, 15, 30 and 60min) as well as an overnight digestion were tested using a therapeutic human monoclonal antibody (mAb) with the goal of its LC-SRM/MS quantification in human plasma. The peptides from the human mAb were generated at different rates and were classified into three categories: (1) the fast forming peptides, (2) the slow forming peptides and (3) the peptides degrading over time. For many monitored peptides, a heating temperature of 37 degrees C with a 750rpm mixing applied for at least 30min provided equivalent results to microwave-assisted digestion and generally allowed the achievement of an equivalent peptide concentration as an overnight digestion carried out at 37 degrees C. The disappearance of the protein of the heavy and light chains can be monitored by 1D gel electrophoresis but was found not to be representative of the final tryptic peptide concentrations. For quantitative purposes a stable isotope labeled version ((13)C(4), (15)N(1)) of the therapeutic protein was used. The labeled protein as internal standard was found to be very efficient to compensate for incomplete digestion or losses during sample preparation. PMID:19939394

  7. Continuous Arc Rotation of the Couch Therapy for the Delivery of Accelerated Partial Breast Irradiation: A Treatment Planning Analysis

    SciTech Connect

    Shaitelman, Simona F.; Kim, Leonard H.; Yan Di; Martinez, Alvaro A.; Vicini, Frank A.; Grills, Inga S.

    2011-07-01

    Purpose: We present a novel form of arc therapy: continuous arc rotation of the couch (C-ARC) and compare its dosimetry with three-dimensional conformal radiotherapy (3D-CRT), intensity-modulated radiotherapy (IMRT), and volumetric-modulated arc therapy (VMAT) for accelerated partial breast irradiation (APBI). C-ARC, like VMAT, uses a modulated beam aperture and dose rate, but with the couch, not the gantry, rotating. Methods and Materials: Twelve patients previously treated with APBI using 3D-CRT were replanned with (1) C-ARC, (2) IMRT, and (3) VMAT. C-ARC plans were designed with one medial and one lateral arc through which the couch rotated while the gantry was held stationary at a tangent angle. Target dose coverage was normalized to the 3D-CRT plan. Comparative endpoints were dose to normal breast tissue, lungs, and heart and monitor units prescribed. Results: Compared with 3D-CRT, C-ARC, IMRT, and VMAT all significantly reduced the ipsilateral breast V50% by the same amount (mean, 7.8%). Only C-ARC and IMRT plans significantly reduced the contralateral breast maximum dose, the ipsilateral lung V5Gy, and the heart V5%. C-ARC used on average 40%, 30%, and 10% fewer monitor units compared with 3D-CRT, IMRT, and VMAT, respectively. Conclusions: C-ARC provides improved dosimetry and treatment efficiency, which should reduce the risks of toxicity and secondary malignancy. Its tangent geometry avoids irradiation of critical structures that is unavoidable using the en face geometry of VMAT.

  8. Analysis of accelerated failure process before the 1999 Mw7.1 Düzce earthquake based on near-fault seismograms

    NASA Astrophysics Data System (ADS)

    Wu, C.; Peng, Z.; Ben-Zion, Y.

    2011-12-01

    Laboratory and theoretical studies imply that accelerated local failure should occur at the transition from locked or slowly creeping fault to dynamic rupture. However, observing this process in natural tectonic setting has been illusive. Bouchon et al. (2011) found recently tantalizing evidence for accelerated local failure before the 1999 Mw7.4 Izmit event, by detecting in data of a near-fault instrument a family of small foreshocks that were buried in the noise. Here we use the recently developed match-filter technique to examine immediate foreshocks before the Mw7.1 Düzce earthquake, which occurred ~3 month after the Izmit event. We employ extensive waveform data set recorded by a 10-station fault zone array deployed a week after the Izmit mainshock. The data set contains many events recorded in close proximity to the hypocenter of the Düzce mainshock, over a time interval of ~3 months before and after the Düzce earthquake. Our preliminary match-filter analysis identified ~1600 small seismic events within ~2.5 days before the Düzce mainshock, although there are only 248 earthquakes listed in the catalog for the same time period. In the analysis done so far, such extensive seismic signals can only be identified both visually and by cross-correlation at a near-fault station FP (~20 km west the Düzce earthquake epicenter and ~400 m off the surface rupture of the Izmit earthquake). This is likely due to the fact that FP is the closest off-fault station to the Düzce earthquake epicenter, and the higher attenuation at nearby on-fault stations. The continuing studies will attempt to establish whether the detected seismic events are from the Düzce source region or generated locally near the station FP, and to perform more comprehensive search for immediate foreshocks using all the recorded data. Uncovering additional small events buried in the noise of the recorded waveforms can increase the available data significantly. This will offer unprecedented

  9. Accelerated partial breast irradiation using once-daily fractionation: analysis of 312 cases with four years median follow-up

    PubMed Central

    2012-01-01

    Background There are limited data on accelerated partial breast irradiation (APBI) using external beam techniques. Moreover, there are recent reports of increased fibrosis and unacceptable cosmesis with APBI using external beam with BID fractionation. We adopted a once daily regimen of APBI with fractionation similar to that shown to be effective in a Canadian randomized trial of whole breast irradiation. It is unclear whether patients with DCIS or invasive lobular carcinoma (ILC) are suitable for APBI. Methods The retrospective cohort included 310 patients with 312 tumors of T1-T2N0-N1micM0 invasive ductal carcinoma (IDC), ILC, or Tis (DCIS) treated with APBI via external beam. Most patients were treated using IMRT with 16 daily fractions of 270 cGy to a dose of 4320 cGy. The target volume included the lumpectomy cavity plus 1.0 cm to account for microscopic disease and an additional 0.5 to 1.0 cm for setup uncertainty and breathing motion. Ipsilateral breast failure (IBF) was pathologically confirmed as a local failure (LF) or an elsewhere failure (EF). Results Median follow-up was 49 months. Among the 312 cases, 213 were IDC, 31 ILC, and 68 DCIS. Median tumor size was 1.0 cm. There were 9 IBFs (2.9%) including 5 LFs and 4 EFs. The IBF rates among patients with IDC, ILC, and DCIS were 2.4%, 3.2%, and 4.4%, respectively, with no significant difference between histologies. When patients were analyzed by the ASTRO APBI consensus statement risk groups, 32% of treated cases were considered suitable, 50% cautionary, and 18% unsuitable. The IBF rates among suitable, cautionary, and unsuitable patients were 4.0%, 2.6%, and 1.8%, respectively, with no significant difference between risk groups. Acute skin reactions were rare and long-term cosmetic outcome was very good to excellent. Conclusions External beam APBI with once daily fractionation has a low rate of IBF consistent with other published APBI studies. The ASTRO risk stratification did not differentiate a subset of

  10. Analysis of physical parameters and determination of inflection point for Flattening Filter Free beams in medical linear accelerator

    PubMed Central

    Pichandi, A.; Ganesh, Kadirampatti Mani; Jerin, Amalraj; Balaji, Karunakaran; Kilara, Gurunath

    2014-01-01

    Background Medical Linear accelerators manufactured without flattening filters are increasing popular in recent days. The removal of flattening filter results in increased dose rate, reduced mean energy, reduction in head leakage and lateral scattering, which have shown advantageous when used for special treatment procedures. Aim This study aims to analyze physical parameters of FFF beams and to determine the inflection point for standardizing the beam flatness and penumbra. Materials and methods The beam profiles and depth dose patterns were measured using Radiation Field Analyzer (RFA) with 0.13 cc cylindrical ion chamber. The beam energy characteristics, head scatter factor (Sc) were obtained for 6FFF and 10FFF beams and compared with 6 MV and 10 MV photons, respectively. The symmetry and stability of unflattened regions were also analyzed. In addition, the study proposes a simple physical concept for obtaining inflection point for FFF beams and results were compared using the Akima spline interpolation method. The inflection point was used to determine the field size and penumbra of FFF beams. Results The Sc varied from 0.922 to 1.044 for 6FFF and from 0.913 to 1.044 for 10FFF with field sizes from 3 cm × 3 cm to 40 cm × 40 cm which is much less than FF beams. The obtained value of field size and penumbra for both simple physical concept and Akima spline interpolation methods is within the ±1.0 mm for the field size and ±2 mm penumbra. The results indicate that FFF beams reduce Sc compared with FF beams due to the absence of a flattening filter. Conclusion The proposed simple method to find field size and penumbra using inflection point can be accepted as it is closely approximated to mathematical results. Stability of these parameters was ascertained by repeated measurements and the study indicates good stability for FFF beam similar to that of FF beams. PMID:25184057

  11. Laser driven ion accelerator

    DOEpatents

    Tajima, Toshiki

    2006-04-18

    A system and method of accelerating ions in an accelerator to optimize the energy produced by a light source. Several parameters may be controlled in constructing a target used in the accelerator system to adjust performance of the accelerator system. These parameters include the material, thickness, geometry and surface of the target.

  12. Laser driven ion accelerator

    DOEpatents

    Tajima, Toshiki

    2005-06-14

    A system and method of accelerating ions in an accelerator to optimize the energy produced by a light source. Several parameters may be controlled in constructing a target used in the accelerator system to adjust performance of the accelerator system. These parameters include the material, thickness, geometry and surface of the target.

  13. An effective method of UV-oxidation of dissolved organic carbon in natural waters for radiocarbon analysis by accelerator mass spectrometry

    NASA Astrophysics Data System (ADS)

    Xue, Yuejun; Ge, Tiantian; Wang, Xuchen

    2015-12-01

    Radiocarbon (14C) measurement of dissolved organic carbon (DOC) is a very powerful tool to study the sources, transformation and cycling of carbon in the ocean. The technique, however, remains great challenges for complete and successful oxidation of sufficient DOC with low blanks for high precision carbon isotopic ratio analysis, largely due to the overwhelming proportion of salts and low DOC concentrations in the ocean. In this paper, we report an effective UV-Oxidation method for oxidizing DOC in natural waters for radiocarbon analysis by accelerator mass spectrometry (AMS). The UV-oxidation system and method show 95%±4% oxidation efficiency and high reproducibility for DOC in both river and seawater samples. The blanks associated with the method was also low (about 3 µg C) that is critical for 14C analysis. As a great advantage of the method, multiple water samples can be oxidized at the same time so it reduces the sample processing time substantially compared with other UV-oxidation method currently being used in other laboratories. We have used the system and method for 14C studies of DOC in rivers, estuaries, and oceanic environments and have received promise results.

  14. Variational analysis of railgun plasma-arc-armature for acceleration of solid hydrogen pellets for fusion reactor refueling

    SciTech Connect

    Choe, W.H.; Kim, K.

    1988-12-01

    This paper discusses fueling magnetically confined plasmas using a railgun plasma-arc-armature. The topics covered are: the Plasma model; Variational analysis; Current density in the plasma arc and arc voltage; and Magnetic field and the net railgun force. 5 refs., 5 figs. (LSP)

  15. Impact of integrated health system changes, accelerated due to an earthquake, on emergency department attendances and acute admissions: a Bayesian change-point analysis

    PubMed Central

    Schluter, Philip J; Hamilton, Greg J; Deely, Joanne M; Ardagh, Michael W

    2016-01-01

    Objective To chart emergency department (ED) attendance and acute admission following a devastating earthquake in 2011 which lead to Canterbury's rapidly accelerated integrated health system transformations. Design Interrupted time series analysis, modelling using Bayesian change-point methods, of ED attendance and acute admission rates over the 2008–2014 period. Setting ED department within the Canterbury District Health Board; with comparison to two other district health boards unaffected by the earthquake within New Zealand. Participants Canterbury's health system services ∼500 000 people, with around 85 000 ED attendances and 37 000 acute admissions per annum. Main outcome measures De-seasoned standardised population ED attendance and acute admission rates overall, and stratified by age and sex, compared before and after the earthquake. Results Analyses revealed five global patterns: (1) postearthquake, there was a sudden and persisting decrease in the proportion of the population attending the ED; (2) the growth rate of ED attendances per head of population did not change between the pre-earthquake and postearthquake periods; (3) postearthquake, there was a sudden and persisting decrease in the proportion of the population admitted to hospital; (4) the growth rate of hospital admissions per head of the population declined between pre-earthquake and postearthquake periods and (5) the most dramatic reduction in hospital admissions growth after the earthquake occurred among those aged 65+ years. Extrapolating from the projected and fitted deseasoned rates for December 2014, ∼676 (16.8%) of 4035 projected hospital admissions were avoided. Conclusions While both necessarily and opportunistically accelerated, Canterbury's integrated health systems transformations have resulted in a dramatic and sustained reduction in ED attendances and acute hospital admissions. This natural intervention experiment, triggered by an earthquake, demonstrated that

  16. An investigation of the neutron flux in bone-fluorine phantoms comparing accelerator based in vivo neutron activation analysis and FLUKA simulation data

    NASA Astrophysics Data System (ADS)

    Mostafaei, F.; McNeill, F. E.; Chettle, D. R.; Matysiak, W.; Bhatia, C.; Prestwich, W. V.

    2015-01-01

    We have tested the Monte Carlo code FLUKA for its ability to assist in the development of a better system for the in vivo measurement of fluorine. We used it to create a neutron flux map of the inside of the in vivo neutron activation analysis irradiation cavity at the McMaster Accelerator Laboratory. The cavity is used in a system that has been developed for assessment of fluorine levels in the human hand. This study was undertaken to (i) assess the FLUKA code, (ii) find the optimal hand position inside the cavity and assess the effects on precision of a hand being in a non-optimal position and (iii) to determine the best location for our γ-ray detection system within the accelerator beam hall. Simulation estimates were performed using FLUKA. Experimental measurements of the neutron flux were performed using Mn wires. The activation of the wires was measured inside (1) an empty bottle, (2) a bottle containing water, (3) a bottle covered with cadmium and (4) a dry powder-based fluorine phantom. FLUKA was used to simulate the irradiation cavity, and used to estimate the neutron flux in different positions both inside, and external to, the cavity. The experimental results were found to be consistent with the Monte Carlo simulated neutron flux. Both experiment and simulation showed that there is an optimal position in the cavity, but that the effect on the thermal flux of a hand being in a non-optimal position is less than 20%, which will result in a less than 10% effect on the measurement precision. FLUKA appears to be a code that can be useful for modeling of this type of experimental system.

  17. High-Intensity Proton Accelerator

    SciTech Connect

    Jay L. Hirshfield

    2011-12-27

    Analysis is presented for an eight-cavity proton cyclotron accelerator that could have advantages as compared with other accelerators because of its potentially high acceleration gradient. The high gradient is possible since protons orbit in a sequence of TE111 rotating mode cavities of equally diminishing frequencies with path lengths during acceleration that greatly exceed the cavity lengths. As the cavities operate at sequential harmonics of a basic repetition frequency, phase synchronism can be maintained over a relatively wide injection phase window without undue beam emittance growth. It is shown that use of radial vanes can allow cavity designs with significantly smaller radii, as compared with simple cylindrical cavities. Preliminary beam transport studies show that acceptable extraction and focusing of a proton beam after cyclic motion in this accelerator should be possible. Progress is also reported on design and tests of a four-cavity electron counterpart accelerator for experiments to study effects on beam quality arising from variations injection phase window width. This device is powered by four 500-MW pulsed amplifiers at 1500, 1800, 2100, and 2400 MHz that provide phase synchronous outputs, since they are driven from a with harmonics derived from a phase-locked 300 MHz source.

  18. Tidal acceleration of the moon

    NASA Technical Reports Server (NTRS)

    Williams, J. G.; Sinclair, W. S.; Yoder, C. F.

    1978-01-01

    The analysis of eight years of lunar laser ranging data yields a value for the tidally induced secular acceleration of the lunar orbital longitude of -23.8 + or - 4 arcsec/century per century. For semidiurnal tidal frequencies this corresponds to a terrestrial Q = 12 + or - 2. The error in n is dominated by noise in the data and its modeling. The error is expected to decrease significantly as future data become available and it may become possible to detect an 18.6-yr periodic modulation of the acceleration which would allow the separation of the effects of diurnal and semidiurnal tides. Comparison of the secular acceleration with values published from the analysis of classical astronomical observations does not show a significant difference which can be attributed to a changing gravitational constant.

  19. Cloning and analysis of a gene cluster from Streptomyces coelicolor that causes accelerated aerial mycelium formation in Streptomyces lividans.

    PubMed Central

    Ma, H; Kendall, K

    1994-01-01

    We describe the cloning and analysis of two overlapping DNA fragments from Streptomyces coelicolor that cause aerial mycelium to appear more rapidly than usual when introduced into Streptomyces lividans on a low-copy-number plasmid vector. Colonies of S. lividans TK64 harboring either clone produce visible aerial mycelia after only 48 h of growth, rather than the usual 72 to 96 h. From deletion and sequence analysis, this rapid aerial mycelium (Ram) phenotype appears to be due to a cluster of three genes that we have designated ramA, ramB, and ramR. Both ramA and ramB potentially encode 65-kDa proteins with homology to ATP-dependent membrane-translocating proteins. A chromosomal ramB disruption mutant of S. lividans was found to be severely defective in aerial mycelium formation. ramR could encode a 21-kDa protein with significant homology to the UhpA subset of bacterial two-component response regulator proteins. The overall organization and potential proteins encoded by the cloned DNA suggest that this is the S. coelicolor homolog of the amf gene cluster that has been shown to be important for aerial mycelium formation in Streptomyces griseus. However, despite the fact that the two regions probably have identical functions, there is relatively poor homology between the two gene clusters at the DNA sequence level. Images PMID:8206859

  20. The Analysis of Particles at Low Accelerating Voltages (≤ 10 kV) With Energy Dispersive X-Ray Spectroscopy (EDS)

    PubMed Central

    Small, J. A.

    2002-01-01

    In recent years, there have been a series of advancements in electron beam instruments and x-ray detectors which may make it possible to improve significantly the quality of results from the quantitative electron-probe analysis of individual particles. These advances include: (1) field-emission gun electron beam instruments such as scanning electron microscopes (FEG-SEMs) that have high brightness electron guns with excellent performance at low beam energies, E0 ≤ 10 keV and (2) high-resolution energy-dispersive x-ray spectrometers, like the microcalorimeter detector, that provide high-resolution (< 10 eV) parallel x-ray collection. These devices make it possible to separate low energy (< 4 keV) x-ray lines including the K lines of carbon, nitrogen and oxygen and the L and M lines for elements with atomic numbers in the range of 25 to 83. In light of these advances, this paper investigates the possibility of using accelerating voltages ≤ 10 kV, as a method to improve the accuracy of elemental analysis for micrometer-sized particles.

  1. Effect of acceleration on the chest wall.

    PubMed

    Wilson, T A; Liu, S

    1994-03-01

    The gravitational force on the rib cage has been found to be an expiratory force of approximately 8 cmH2O. The gravitational force on the abdomen is an inspiratory force of the same magnitude. Because the compliance of the rib cage is greater than the compliance of the abdomen, it follows that gravity has a net expiratory effect on lung volume and that upward accelerations augmenting the gravitational force would have an additional expiratory effect. This conclusion is contrary to observations that functional residual capacity increases during headward accelerations in centrifuges and during intervals of upward acceleration in airplanes. We report the results of two studies of the effects of accelerations that are smaller in magnitude and of shorter duration than those studied in centrifuges and airplanes. The first was an experimental study of the effect of acceleration in an elevator. In subjects who relaxed against an occluded airway, airway pressure increased during upward accelerations and decreased during downward accelerations. The second was the modeling and analysis of the effects of the accelerations that occur during walking. The analysis predicted an initial expiratory response to the acceleration spike that occurs during footfall. The prediction agreed with data in the literature on the respiratory effect of walking. In both of these studies upward accelerations had an expiratory effect. PMID:8005868

  2. The Los Alamos accelerator code group

    SciTech Connect

    Krawczyk, F.L.; Billen, J.H.; Ryne, R.D.; Takeda, Harunori; Young, L.M.

    1995-05-01

    The Los Alamos Accelerator Code Group (LAACG) is a national resource for members of the accelerator community who use and/or develop software for the design and analysis of particle accelerators, beam transport systems, light sources, storage rings, and components of these systems. Below the authors describe the LAACG`s activities in high performance computing, maintenance and enhancement of POISSON/SUPERFISH and related codes and the dissemination of information on the INTERNET.

  3. In situ X-ray pair distribution function analysis of accelerated carbonation of a synthetic calcium-silicate-hydrate gel

    SciTech Connect

    Morandeau, Antoine E.; White, Claire E.

    2015-04-21

    Calcium–silicate–hydrate (C–S–H) gel is the main binder component in hydrated ordinary Portland cement (OPC) paste, and is known to play a crucial role in the carbonation of cementitious materials, especially for more sustainable alternatives containing supplementary cementitious materials. However, the exact atomic structural changes that occur during carbonation of C–S–H gel remain unknown. Here, we investigate the local atomic structural changes that occur during carbonation of a synthetic calcium–silicate–hydrate gel exposed to pure CO₂ vapour, using in situ X-ray total scattering measurements and subsequent pair distribution function (PDF) analysis. By analysing both the reciprocal and real-space scattering data as the C–S–H carbonation reaction progresses, all phases present during the reaction (crystalline and non-crystalline) have been identified and quantified, with the results revealing the emergence of several polymorphs of crystalline calcium carbonate (vaterite and calcite) in addition to the decalcified C–S–H gel. Furthermore, the results point toward residual calcium being present in the amorphous decalcified gel, potentially in the form of an amorphous calcium carbonate phase. As a result of the quantification process, the reaction kinetics for the evolution of the individual phases have been obtained, revealing new information on the rate of growth/dissolution for each phase associated with C–S–H gel carbonation. Moreover, the investigation reveals that the use of real space diffraction data in the form of PDFs enables more accurate determination of the phases that develop during complex reaction processes such as C–S–H gel carbonation in comparison to the conventional reciprocal space Rietveld analysis approach.

  4. The direction of acceleration

    NASA Astrophysics Data System (ADS)

    Wilhelm, Thomas; Burde, Jan-Philipp; Lück, Stephan

    2015-11-01

    Acceleration is a physical quantity that is difficult to understand and hence its complexity is often erroneously simplified. Many students think of acceleration as equivalent to velocity, a ˜ v. For others, acceleration is a scalar quantity, which describes the change in speed Δ|v| or Δ|v|/Δt (as opposed to the change in velocity). The main difficulty with the concept of acceleration therefore lies in developing a correct understanding of its direction. The free iOS app AccelVisu supports students in acquiring a correct conception of acceleration by showing acceleration arrows directly at moving objects.

  5. TURBULENT SHEAR ACCELERATION

    SciTech Connect

    Ohira, Yutaka

    2013-04-10

    We consider particle acceleration by large-scale incompressible turbulence with a length scale larger than the particle mean free path. We derive an ensemble-averaged transport equation of energetic charged particles from an extended transport equation that contains the shear acceleration. The ensemble-averaged transport equation describes particle acceleration by incompressible turbulence (turbulent shear acceleration). We find that for Kolmogorov turbulence, the turbulent shear acceleration becomes important on small scales. Moreover, using Monte Carlo simulations, we confirm that the ensemble-averaged transport equation describes the turbulent shear acceleration.

  6. Bayes Analysis and Reliability Implications of Stress-Rupture Testing a Kevlar/Epoxy COPV Using Temperature and Pressure Acceleration

    NASA Technical Reports Server (NTRS)

    Phoenix, S. Leigh; Kezirian, Michael T.; Murthy, Pappu L. N.

    2009-01-01

    Composite Overwrapped Pressure Vessels (COPVs) that have survived a long service time under pressure generally must be recertified before service is extended. Flight certification is dependent on the reliability analysis to quantify the risk of stress rupture failure in existing flight vessels. Full certification of this reliability model would require a statistically significant number of lifetime tests to be performed and is impractical given the cost and limited flight hardware for certification testing purposes. One approach to confirm the reliability model is to perform a stress rupture test on a flight COPV. Currently, testing of such a Kevlar49 (Dupont)/epoxy COPV is nearing completion. The present paper focuses on a Bayesian statistical approach to analyze the possible failure time results of this test and to assess the implications in choosing between possible model parameter values that in the past have had significant uncertainty. The key uncertain parameters in this case are the actual fiber stress ratio at operating pressure, and the Weibull shape parameter for lifetime; the former has been uncertain due to ambiguities in interpreting the original and a duplicate burst test. The latter has been uncertain due to major differences between COPVs in the database and the actual COPVs in service. Any information obtained that clarifies and eliminates uncertainty in these parameters will have a major effect on the predicted reliability of the service COPVs going forward. The key result is that the longer the vessel survives, the more likely the more optimistic stress ratio model is correct. At the time of writing, the resulting effect on predicted future reliability is dramatic, increasing it by about one "nine," that is, reducing the predicted probability of failure by an order of magnitude. However, testing one vessel does not change the uncertainty on the Weibull shape parameter for lifetime since testing several vessels would be necessary.

  7. Accelerating Particles with Plasma

    SciTech Connect

    Litos, Michael; Hogan, Mark

    2014-11-05

    Researchers at SLAC explain how they use plasma wakefields to accelerate bunches of electrons to very high energies over only a short distance. Their experiments offer a possible path for the future of particle accelerators.

  8. Improved plasma accelerator

    NASA Technical Reports Server (NTRS)

    Cheng, D. Y.

    1971-01-01

    Converging, coaxial accelerator electrode configuration operates in vacuum as plasma gun. Plasma forms by periodic injections of high pressure gas that is ionized by electrical discharges. Deflagration mode of discharge provides acceleration, and converging contours of plasma gun provide focusing.

  9. Accelerated Stem Growth Rates and Improved Fiber Properties of Loblolly Pine: Functional Analysis Of CyclinD from Pinus taeda

    SciTech Connect

    Dr. John Cairney, School of Biology and Institute of Paper Science and Technology @ Georgia Tech, Georgia Institute of Technology; Dr. Gary Peter, University of Florida; Dr. Ulrika Egertsdotter, Dept. of Forestry, Virgina Tech; Dr. Armin Wagner, New Zealand Forest Research Institute Ltd.

    2005-11-30

    A sustained supply of low-cost, high quality raw materials is essential for the future success of the U.S. forest products industry. To maximize stem (trunk) growth, a fundamental understanding of the molecular mechanisms that regulate cell divisions within the cambial meristem is essential. We hypothesize that auxin levels within the cambial meristem regulate cyclin gene expression and this in turn controls cell cycle progression as occurs in all eukaryotic cells. Work with model plant species has shown that ectopic overexpression of cyclins promotes cell division thereby increasing root growth > five times. We intended to test whether ectopic overexpression of cambial cyclins in the cambial zone of loblolly pine also promotes cell division rates that enhance stem growth rates. Results generated in model annual angiosperm systems cannot be reliably extrapolated to perennial gymnosperms, thus while the generation and development of transgenic pine is time consuming, this is the necessary approach for meaningful data. We succeeded in isolating a cyclin D gene and Clustal analysis to the Arabidopsis cyclin D gene family indicates that it is more closely related to cyclin D2 than D1 or D3 Using this gene as a probe we observed a small stimulation of cyclin D expression in somatic embryo culture upon addition of auxin. We hypothesized that trees with more cells in the vascular cambial and expansion zones will have higher cyclin mRNA levels. We demonstrated that in trees under compressive stress where the rates of cambial divisions are increased on the underside of the stem relative to the top or opposite side, there was a 20 fold increase in the level of PtcyclinD1 mRNA on the compressed side of the stem relative to the opposite. This suggests that higher secondary growth rates correlate with PtcyclinD1 expression. We showed that larger diameter trees show more growth during each year and that the increased growth in loblolly pine trees correlates with more cell

  10. Cascaded proton acceleration by collisionless electrostatic shock

    SciTech Connect

    Xu, T. J.; Shen, B. F. E-mail: zhxm@siom.ac.cn; Zhang, X. M. E-mail: zhxm@siom.ac.cn; Yi, L. Q.; Wang, W. P.; Zhang, L. G.; Xu, J. C.; Zhao, X. Y.; Shi, Y.; Liu, C.; Pei, Z. K.

    2015-07-15

    A new scheme for proton acceleration by cascaded collisionless electrostatic shock (CES) is proposed. By irradiating a foil target with a moderate high-intensity laser beam, a stable CES field can be induced, which is employed as the accelerating field for the booster stage of proton acceleration. The mechanism is studied through simulations and theoretical analysis, showing that a 55 MeV seed proton beam can be further accelerated to 265 MeV while keeping a good energy spread. This scheme offers a feasible approach to produce proton beams with energy of hundreds of MeV by existing available high-intensity laser facilities.

  11. Accelerated test plan for nickel cadmium spacecraft batteries

    NASA Technical Reports Server (NTRS)

    Hennigan, T. J.

    1973-01-01

    An accelerated test matrix is outlined that includes acceptance, baseline and post-cycling tests, chemical and physical analyses, and the data analysis procedures to be used in determining the feasibility of an accelerated test for sealed, nickel cadmium cells.

  12. Sampling and analysis plan for the Bear Creek Valley Boneyard/Burnyard Accelerated Action Project, Oak Ridge Y-12 Plant, Oak Ridge, Tennessee

    SciTech Connect

    1998-03-01

    In the Bear Creek Valley Watershed Remedial Investigation, the Boneyard/Burnyard was identified as the source of the largest releases of uranium into groundwater and surface water in Bear Creek Valley. The proposed action for remediation of this site is selective excavation and removal of source material and capping of the remainder of the site. The schedule for this action has been accelerated so that this is the first remedial action planned to be implemented in the Bear Creek Valley Record of Decision. Additional data needs to support design of the remedial action were identified at a data quality objectives meeting held for this project. Sampling at the Boneyard/Burnyard will be conducted through the use of a phased approach. Initial or primary samples will be used to make in-the-field decisions about where to locate follow-up or secondary samples. On the basis of the results of surface water, soil, and groundwater analysis, up to six test pits will be dug. The test pits will be used to provide detailed descriptions of source materials and bulk samples. This document sets forth the requirements and procedures to protect the personnel involved in this project. This document also contains the health and safety plan, quality assurance project plan, waste management plan, data management plan, implementation plan, and best management practices plan for this project as appendices.

  13. Design analysis and performance evaluation of a two-dimensional camera for accelerated positron-emitter beam injection by computer simulation

    SciTech Connect

    Llacer, J.; Chatterjee, A.; Batho, E.K.; Poskanzer, J.A.

    1982-05-01

    The characteristics and design of a high-accuracy and high-sensitivity 2-dimensional camera for the measurement of the end-point of the trajectory of accelerated heavy ion beams of positron emitter isotopes are described. Computer simulation methods have been used in order to insure that the design would meet the demanding criteria of ability to obtain the location of the centroid of a point source in the X-Y plane with errors smaller than 1 mm, with an activity of 100 nanoCi, in a counting time of 5 sec or less. A computer program which can be developed into a general purpose analysis tool for a large number of positron emitter camera configurations is described in its essential parts. The validation of basic simulation results with simple measurements is reported, and the use of the program to generate simulated images which include important second order effects due to detector material, geometry, septa, etc. is demonstrated. Comparison between simulated images and initial results with the completed instrument shows that the desired specifications have been met.

  14. Far field acceleration

    SciTech Connect

    Fernow, R.C.

    1995-07-01

    Far fields are propagating electromagnetic waves far from their source, boundary surfaces, and free charges. The general principles governing the acceleration of charged particles by far fields are reviewed. A survey of proposed field configurations is given. The two most important schemes, Inverse Cerenkov acceleration and Inverse free electron laser acceleration, are discussed in detail.

  15. Angular Acceleration Without Torque?

    NASA Astrophysics Data System (ADS)

    Kaufman, Richard D.

    2012-01-01

    Hardly. Just as Robert Johns qualitatively describes angular acceleration by an internal force in his article "Acceleration Without Force?" here we will extend the discussion to consider angular acceleration by an internal torque. As we will see, this internal torque is due to an internal force acting at a distance from an instantaneous center.2

  16. Sustained linear acceleration

    NASA Technical Reports Server (NTRS)

    Fraser, T. M.

    1973-01-01

    The subjective effects of sustained acceleration are discussed, including positive, negative, forward, backward, and lateral acceleration effects. Physiological effects, such as retinal and visual response, unconsciousness and cerebral function, pulmonary response, and renal output, are studied. Human tolerance and performance under sustained acceleration are ascertained.

  17. Angular Acceleration without Torque?

    ERIC Educational Resources Information Center

    Kaufman, Richard D.

    2012-01-01

    Hardly. Just as Robert Johns qualitatively describes angular acceleration by an internal force in his article "Acceleration Without Force?" here we will extend the discussion to consider angular acceleration by an internal torque. As we will see, this internal torque is due to an internal force acting at a distance from an instantaneous center.

  18. Acceleration: It's Elementary

    ERIC Educational Resources Information Center

    Willis, Mariam

    2012-01-01

    Acceleration is one tool for providing high-ability students the opportunity to learn something new every day. Some people talk about acceleration as taking a student out of step. In actuality, what one is doing is putting a student in step with the right curriculum. Whole-grade acceleration, also called grade-skipping, usually happens between…

  19. Delineation of Interspecific Epistasis on Fiber Quality Traits in Gossypium hirsutum by ADAA Analysis of Intermated G. barbadense Chromosome Substitution Lines

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic diversity is the foundation of any crop improvement program, but the cultivated Upland cotton (Gossypium hirsutum L.) has a very narrow gene pool resulting from its origin and domestication history. G. hirsutum L., the most extensively cultivated cotton species, is characterized by agronomi...

  20. Modified first-order Horava-Lifshitz gravity: Hamiltonian analysis of the general theory and accelerating FRW cosmology in a power-law F(R) model

    SciTech Connect

    Carloni, Sante; Chaichian, Masud; Tureanu, Anca; Nojiri, Shin'ichi; Odintsov, Sergei D.; Oksanen, Markku

    2010-09-15

    We propose the most general modified first-order Horava-Lifshitz gravity, whose action does not contain time derivatives higher than the second order. The Hamiltonian structure of this theory is studied in all the details in the case of the spatially-flat Friedmann-Robertson-Walker (FRW) space-time, demonstrating many of the features of the general theory. It is shown that, with some plausible assumptions, including the projectability of the lapse function, this model is consistent. As a large class of such theories, the modified Horava-Lifshitz F(R) gravity is introduced. The study of its ultraviolet properties shows that its z=3 version seems to be renormalizable in the same way as the original Horava-Lifshitz proposal. The Hamiltonian analysis of the modified Horava-Lifshitz F(R) gravity shows that it is in general a consistent theory. The F(R) gravity action is also studied in the fixed-gauge form, where the appearance of a scalar field is particularly illustrative. Then the spatially-flat FRW cosmology for this F(R) gravity is investigated. It is shown that a special choice of parameters for this theory leads to the same equations of motion as in the case of traditional F(R) gravity. Nevertheless, the cosmological structure of the modified Horava-Lifshitz F(R) gravity turns out to be much richer than for its traditional counterpart. The emergence of multiple de Sitter solutions indicates the possibility of unification of early-time inflation with late-time acceleration within the same model. Power-law F(R) theories are also investigated in detail. It is analytically shown that they have a quite rich cosmological structure: early-/late-time cosmic acceleration of quintessence, as well as of phantom types. Also it is demonstrated that all the four known types of finite-time future singularities may occur in the power-law Horava-Lifshitz F(R) gravity. Finally, a covariant proposal for (renormalizable) F(R) gravity within the Horava-Lifshitz spirit is presented.

  1. A variable acceleration calibration system

    NASA Astrophysics Data System (ADS)

    Johnson, Thomas H.

    2011-12-01

    A variable acceleration calibration system that applies loads using gravitational and centripetal acceleration serves as an alternative, efficient and cost effective method for calibrating internal wind tunnel force balances. Two proof-of-concept variable acceleration calibration systems are designed, fabricated and tested. The NASA UT-36 force balance served as the test balance for the calibration experiments. The variable acceleration calibration systems are shown to be capable of performing three component calibration experiments with an approximate applied load error on the order of 1% of the full scale calibration loads. Sources of error are indentified using experimental design methods and a propagation of uncertainty analysis. Three types of uncertainty are indentified for the systems and are attributed to prediction error, calibration error and pure error. Angular velocity uncertainty is shown to be the largest indentified source of prediction error. The calibration uncertainties using a production variable acceleration based system are shown to be potentially equivalent to current methods. The production quality system can be realized using lighter materials and a more precise instrumentation. Further research is needed to account for balance deflection, forcing effects due to vibration, and large tare loads. A gyroscope measurement technique is shown to be capable of resolving the balance deflection angle calculation. Long term research objectives include a demonstration of a six degree of freedom calibration, and a large capacity balance calibration.

  2. Lectures in accelerator theory

    SciTech Connect

    Month, M

    1980-01-01

    Lecture I deals with the behavior of particles in the nonlinear field arising from the electromagnetic interaction of colliding beams. The case treated, that of counter-rotating proton beams crossing each other at a non-zero angle, has the simple feature that the force between the beam is one dimensional. In lecture II, an analysis of the development of traveling waves on particle beams is presented. The situation studied is that of a uniform beam current in a circular accelerator and the excitation for the coherent motion is induced by the resistivity of the vacuum chamber wall. Finally, in lecture III, a description of the current accumulation process used at the proton storage rings at CERN (The ISR) is given. Particle pulses of rather low average current are injected and stored along the length and width of the vacuum chamber. The efficiency is very high and large currents (over 40 amperes) have been achieved.

  3. Dynamics of pyroelectric accelerators

    SciTech Connect

    Ghaderi, R.; Davani, F. Abbasi

    2015-01-26

    Pyroelectric crystals are used to produce high energy electron beams. We have derived a method to model electric potential generation on LiTaO{sub 3} crystal during heating cycle. In this method, effect of heat transfer on the potential generation is investigated by some experiments. In addition, electron emission from the crystal surface is modeled by measurements and analysis. These spectral data are used to present a dynamic equation of electric potential with respect to thickness of the crystal and variation of its temperature. The dynamic equation's results for different thicknesses are compared with measured data. As a result, to attain more energetic electrons, best thickness of the crystals could be extracted from the equation. This allows for better understanding of pyroelectric crystals and help to study about current and energy of accelerated electrons.

  4. Compact Plasma Accelerator

    NASA Technical Reports Server (NTRS)

    Foster, John E.

    2004-01-01

    A plasma accelerator has been conceived for both material-processing and spacecraft-propulsion applications. This accelerator generates and accelerates ions within a very small volume. Because of its compactness, this accelerator could be nearly ideal for primary or station-keeping propulsion for spacecraft having masses between 1 and 20 kg. Because this accelerator is designed to generate beams of ions having energies between 50 and 200 eV, it could also be used for surface modification or activation of thin films.

  5. High brightness electron accelerator

    DOEpatents

    Sheffield, Richard L.; Carlsten, Bruce E.; Young, Lloyd M.

    1994-01-01

    A compact high brightness linear accelerator is provided for use, e.g., in a free electron laser. The accelerator has a first plurality of acclerating cavities having end walls with four coupling slots for accelerating electrons to high velocities in the absence of quadrupole fields. A second plurality of cavities receives the high velocity electrons for further acceleration, where each of the second cavities has end walls with two coupling slots for acceleration in the absence of dipole fields. The accelerator also includes a first cavity with an extended length to provide for phase matching the electron beam along the accelerating cavities. A solenoid is provided about the photocathode that emits the electons, where the solenoid is configured to provide a substantially uniform magnetic field over the photocathode surface to minimize emittance of the electons as the electrons enter the first cavity.

  6. Fiber Accelerating Structures

    SciTech Connect

    Hammond, Andrew P.; /Reed Coll. /SLAC

    2010-08-25

    One of the options for future particle accelerators are photonic band gap (PBG) fiber accelerators. PBG fibers are specially designed optical fibers that use lasers to excite an electric field that is used to accelerate electrons. To improve PBG accelerators, the basic parameters of the fiber were tested to maximize defect size and acceleration. Using the program CUDOS, several accelerating modes were found that maximized these parameters for several wavelengths. The design of multiple defects, similar to having closely bound fibers, was studied to find possible coupling or the change of modes. The amount of coupling was found to be dependent on distance separated. For certain distances accelerating coupled modes were found and examined. In addition, several non-periodic fiber structures were examined using CUDOS. The non-periodic fibers produced several interesting results and promised more modes given time to study them in more detail.

  7. Acceleration in astrophysics

    SciTech Connect

    Colgate, S.A.

    1993-12-31

    The origin of cosmic rays and applicable laboratory experiments are discussed. Some of the problems of shock acceleration for the production of cosmic rays are discussed in the context of astrophysical conditions. These are: The presumed unique explanation of the power law spectrum is shown instead to be a universal property of all lossy accelerators; the extraordinary isotropy of cosmic rays and the limited diffusion distances implied by supernova induced shock acceleration requires a more frequent and space-filling source than supernovae; the near perfect adiabaticity of strong hydromagnetic turbulence necessary for reflecting the accelerated particles each doubling in energy roughly 10{sup 5} to {sup 6} scatterings with negligible energy loss seems most unlikely; the evidence for acceleration due to quasi-parallel heliosphere shocks is weak. There is small evidence for the expected strong hydromagnetic turbulence, and instead, only a small number of particles accelerate after only a few shock traversals; the acceleration of electrons in the same collisionless shock that accelerates ions is difficult to reconcile with the theoretical picture of strong hydromagnetic turbulence that reflects the ions. The hydromagnetic turbulence will appear adiabatic to the electrons at their much higher Larmor frequency and so the electrons should not be scattered incoherently as they must be for acceleration. Therefore the electrons must be accelerated by a different mechanism. This is unsatisfactory, because wherever electrons are accelerated these sites, observed in radio emission, may accelerate ions more favorably. The acceleration is coherent provided the reconnection is coherent, in which case the total flux, as for example of collimated radio sources, predicts single charge accelerated energies much greater than observed.

  8. Plasma inverse transition acceleration

    SciTech Connect

    Xie, Ming

    2001-06-18

    It can be proved fundamentally from the reciprocity theorem with which the electromagnetism is endowed that corresponding to each spontaneous process of radiation by a charged particle there is an inverse process which defines a unique acceleration mechanism, from Cherenkov radiation to inverse Cherenkov acceleration (ICA) [1], from Smith-Purcell radiation to inverse Smith-Purcell acceleration (ISPA) [2], and from undulator radiation to inverse undulator acceleration (IUA) [3]. There is no exception. Yet, for nearly 30 years after each of the aforementioned inverse processes has been clarified for laser acceleration, inverse transition acceleration (ITA), despite speculation [4], has remained the least understood, and above all, no practical implementation of ITA has been found, until now. Unlike all its counterparts in which phase synchronism is established one way or the other such that a particle can continuously gain energy from an acceleration wave, the ITA to be discussed here, termed plasma inverse transition acceleration (PITA), operates under fundamentally different principle. As a result, the discovery of PITA has been delayed for decades, waiting for a conceptual breakthrough in accelerator physics: the principle of alternating gradient acceleration [5, 6, 7, 8, 9, 10]. In fact, PITA was invented [7, 8] as one of several realizations of the new principle.

  9. Accelerated Hypofractionated Intensity-Modulated Radiotherapy With Concurrent and Adjuvant Temozolomide for Patients With Glioblastoma Multiforme: A Safety and Efficacy Analysis

    SciTech Connect

    Panet-Raymond, Valerie; Souhami, Luis; Roberge, David; Kavan, Petr; Shakibnia, Lily; Muanza, Thierry; Lambert, Christine; Leblanc, Richard; Del Maestro, Rolando; Guiot, Marie-Christine; Shenouda, George

    2009-02-01

    Purpose: Despite multimodality treatments, the outcome of patients with glioblastoma multiforme remains poor. In an attempt to improve results, we have begun a program of accelerated hypofractionated intensity-modulated radiotherapy (hypo-IMRT) with concomitant and adjuvant temozolomide (TMZ). Methods and Materials: Between March 2004 and June 2006, 35 unselected patients with glioblastoma multiforme were treated with hypo-IMRT. During a 4-week period, using a concomitant boost technique, a dose of 60 Gy and 40 Gy were delivered in 20 fractions prescribed to the periphery of the gross tumor volume and planning target volume, respectively. TMZ was administered according to the regimen of Stupp et al. Results: The median follow-up was 12.6 months. Of the 35 patients, 29 (82.8%) completed the combined modality treatment, and 25 (71.4%) received a median of four cycles of adjuvant TMZ. The median overall survival was 14.4 months, and the median disease-free survival was 7.7 months. The median survival time differed significantly between patients who underwent biopsy and those who underwent partial or total resection (7.1 vs. 16.1 months, p = 0.035). The median survival was also significantly different between patients with methylated vs. unmethylated 0-6-methylguanine-DNA methyltransferase promoters (14.4 vs. 8.7 months, p = 0.049). The pattern of failure was predominantly central, within 2 cm of the initial gross tumor volume. Grade 3-4 toxicity was limited to 1 patient with nausea and emesis during adjuvant TMZ administration. Conclusion: The results of our study have shown that hypo-IMRT with concomitant and adjuvant TMZ is well tolerated with a useful 2-week shortening of radiotherapy. Despite a high number of patients with poor prognostic features (74.3% recursive partitioning analysis class V or VI), the median survival was comparable to that after standard radiotherapy fractionation schedules plus TMZ.

  10. Prediction of back-scatter radiations to a beam monitor chamber of medical linear accelerators by use of the digitized target-current-pulse analysis method.

    PubMed

    Suzuki, Yusuke; Hayashi, Naoki; Kato, Hideki; Fukuma, Hiroshi; Hirose, Yasujiro; Kawano, Makoto; Nishii, Yoshio; Nakamura, Masaru; Mukouyama, Takashi

    2013-01-01

    In small-field irradiation, the back-scattered radiation (BSR) affects the counts measured with a beam monitor chamber (BMC). In general, the effect of the BSR depends on the opened-jaw size. The effect is significantly large in small-field irradiation. Our purpose in this study was to predict the effect of BSR on LINAC output accurately with an improved target-current-pulse (TCP) technique. The pulse signals were measured with a system consisting of a personal computer and a digitizer. The pulse signals were analyzed with in-house software. The measured parameters were the number of pulses, the change in the waveform and the integrated signal values of the TCPs. The TCPs were measured for various field sizes with four linear accelerators. For comparison, Yu's method in which a universal counter was used was re-examined. The results showed that the variance of the measurements by the new method was reduced to approximately 1/10 of the variance by the previous method. There was no significant variation in the number of pulses due to a change in the field size in the Varian Clinac series. However, a change in the integrated signal value was observed. This tendency was different from the result of other investigations in the past. Our prediction method is able to define the cutoff voltage for the TCP acquired by digitizer. This functionality provides the capability of clearly classifying TCPs into signals and noise. In conclusion, our TCP analysis method can predict the effect of BSR on the BMC even for small-field irradiations. PMID:23096002

  11. Nodes and biological processes identified on the basis of network analysis in the brain of the senescence accelerated mice as an Alzheimer's disease animal model

    PubMed Central

    Cheng, Xiao-rui; Cui, Xiu-liang; Zheng, Yue; Zhang, Gui-rong; Li, Peng; Huang, Huang; Zhao, Yue-ying; Bo, Xiao-chen; Wang, Sheng-qi; Zhou, Wen-xia; Zhang, Yong-xiang

    2013-01-01

    Harboring the behavioral and histopathological signatures of Alzheimer's disease (AD), senescence accelerated mouse-prone 8 (SAMP8) mice are currently considered a robust model for studying AD. However, the underlying mechanisms, prioritized pathways and genes in SAMP8 mice linked to AD remain unclear. In this study, we provide a biological interpretation of the molecular underpinnings of SAMP8 mice. Our results were derived from differentially expressed genes in the hippocampus and cerebral cortex of SAMP8 mice compared to age-matched SAMR1 mice at 2, 6, and 12 months of age using cDNA microarray analysis. On the basis of PPI, MetaCore and the co-expression network, we constructed a distinct genetic sub-network in the brains of SAMP8 mice. Next, we determined that the regulation of synaptic transmission and apoptosis were disrupted in the brains of SAMP8 mice. We found abnormal gene expression of RAF1, MAPT, PTGS2, CDKN2A, CAMK2A, NTRK2, AGER, ADRBK1, MCM3AP, and STUB1, which may have initiated the dysfunction of biological processes in the brains of SAMP8 mice. Specifically, we found microRNAs, including miR-20a, miR-17, miR-34a, miR-155, miR-18a, miR-22, miR-26a, miR-101, miR-106b, and miR-125b, that might regulate the expression of nodes in the sub-network. Taken together, these results provide new insights into the biological and genetic mechanisms of SAMP8 mice and add an important dimension to our understanding of the neuro-pathogenesis in SAMP8 mice from a systems perspective. PMID:24194717

  12. Acceleration Environment of the International Space Station

    NASA Technical Reports Server (NTRS)

    McPherson, Kevin; Kelly, Eric; Keller, Jennifer

    2009-01-01

    Measurement of the microgravity acceleration environment on the International Space Station has been accomplished by two accelerometer systems since 2001. The Microgravity Acceleration Measurement System records the quasi-steady microgravity environment, including the influences of aerodynamic drag, vehicle rotation, and venting effects. Measurement of the vibratory/transient regime, comprised of vehicle, crew, and equipment disturbances, has been accomplished by the Space Acceleration Measurement System-II. Until the arrival of the Columbus Orbital Facility and the Japanese Experiment Module, the location of these sensors, and therefore, the measurement of the microgravity acceleration environment, has been limited to within the United States Laboratory. Japanese Aerospace Exploration Agency has developed a vibratory acceleration measurement system called the Microgravity Measurement Apparatus which will be deployed within the Japanese Experiment Module to make distributed measurements of the Japanese Experiment Module's vibratory acceleration environment. Two Space Acceleration Measurement System sensors from the United States Laboratory will be re-deployed to support vibratory acceleration data measurement within the Columbus Orbital Facility. The additional measurement opportunities resulting from the arrival of these new laboratories allows Principal Investigators with facilities located in these International Space Station research laboratories to obtain microgravity acceleration data in support of their sensitive experiments. The Principal Investigator Microgravity Services project, at NASA Glenn Research Center, in Cleveland, Ohio, has supported acceleration measurement systems and the microgravity scientific community through the processing, characterization, distribution, and archival of the microgravity acceleration data obtained from the International Space Station acceleration measurement systems. This paper summarizes the PIMS capabilities available

  13. The Dielectric Wall Accelerator

    SciTech Connect

    Caporaso, George J.; Chen, Yu-Jiuan; Sampayan, Stephen E.

    2009-01-01

    The Dielectric Wall Accelerator (DWA), a class of induction accelerators, employs a novel insulating beam tube to impress a longitudinal electric field on a bunch of charged particles. The surface flashover characteristics of this tube may permit the attainment of accelerating gradients on the order of 100 MV/m for accelerating pulses on the order of a nanosecond in duration. A virtual traveling wave of excitation along the tube is produced at any desired speed by controlling the timing of pulse generating modules that supply a tangential electric field to the tube wall. Because of the ability to control the speed of this virtual wave, the accelerator is capable of handling any charge to mass ratio particle; hence it can be used for electrons, protons and any ion. The accelerator architectures, key technologies and development challenges will be described.

  14. ACCELERATION RESPONSIVE SWITCH

    DOEpatents

    Chabrek, A.F.; Maxwell, R.L.

    1963-07-01

    An acceleration-responsive device with dual channel capabilities whereby a first circuit is actuated upon attainment of a predetermined maximum acceleration level and when the acceleration drops to a predetermined minimum acceleriltion level another circuit is actuated is described. A fluid-damped sensing mass slidably mounted in a relatively frictionless manner on a shaft through the intermediation of a ball bushing and biased by an adjustable compression spring provides inertially operated means for actuating the circuits. (AEC)

  15. Space Acceleration Measurement System

    NASA Technical Reports Server (NTRS)

    1993-01-01

    This training video, presented by the Lewis Research Center's Space Experiments Division, gives a background and detailed instructions for preparing the space acceleration measurement system (SAMS) for use. The SAMS measures, conditions, and records forces of low gravity accelerations, and is used to determine the effect of these forces on various experiments performed in microgravity. Inertial sensors are used to measure positive and negative acceleration over a specified frequency range. The video documents the SAMS' uses in different configurations during shuttle missions.

  16. Wake field accelerators

    SciTech Connect

    Wilson, P.B.

    1986-02-01

    In a wake field accelerator a high current driving bunch injected into a structure or plasma produces intense induced fields, which are in turn used to accelerate a trailing charge or bunch. The basic concepts of wake field acceleration are described. Wake potentials for closed cavities and periodic structures are derived, as are wake potentials on a collinear path with a charge distribution. Cylindrically symmetric structures excited by a beam in the form of a ring are considered. (LEW)

  17. Accelerating into the future

    NASA Astrophysics Data System (ADS)

    Murray, Cherry

    2009-05-01

    Accelerator science has traditionally been associated with high-energy physics and nuclear physics. But the use of accelerators in other areas of science, as well as in medicine and industry, is steadily growing. Accelerators are now, for example, used to treat cancer using proton therapy, which can deposit radiation onto a tumour while causing much less damage to surrounding healthy tissue than with other treatment techniques.

  18. Optically pulsed electron accelerator

    DOEpatents

    Fraser, J.S.; Sheffield, R.L.

    1985-05-20

    An optically pulsed electron accelerator can be used as an injector for a free electron laser and comprises a pulsed light source, such as a laser, for providing discrete incident light pulses. A photoemissive electron source emits electron bursts having the same duration as the incident light pulses when impinged upon by same. The photoemissive electron source is located on an inside wall of a radiofrequency-powered accelerator cell which accelerates the electron burst emitted by the photoemissive electron source.

  19. Optically pulsed electron accelerator

    DOEpatents

    Fraser, John S.; Sheffield, Richard L.

    1987-01-01

    An optically pulsed electron accelerator can be used as an injector for a free electron laser and comprises a pulsed light source, such as a laser, for providing discrete incident light pulses. A photoemissive electron source emits electron bursts having the same duration as the incident light pulses when impinged upon by same. The photoemissive electron source is located on an inside wall of a radio frequency powered accelerator cell which accelerates the electron burst emitted by the photoemissive electron source.

  20. Miniaturization Techniques for Accelerators

    SciTech Connect

    Spencer, James E.

    2003-05-27

    The possibility of laser driven accelerators [1] suggests the need for new structures based on micromachining and integrated circuit technology because of the comparable scales. Thus, we are exploring fully integrated structures including sources, optics (for both light and particle) and acceleration in a common format--an accelerator-on-chip (AOC). Tests suggest a number of preferred materials and techniques but no technical or fundamental roadblocks at scales of order 1 {micro}m or larger.

  1. Microgravity acceleration measurement and environment characterization science (17-IML-1)

    NASA Technical Reports Server (NTRS)

    1992-01-01

    The Space Acceleration Measurement System (SAMS) is a general purpose instrumentation system designed to measure the accelerations onboard the Shuttle Orbiter and Shuttle/Spacelab vehicles. These measurements are used to support microgravity experiments and investigation into the microgravity environment of the vehicle. Acceleration measurements can be made at locations remote from the SAMS main instrumentation unit by the use of up to three remote triaxial sensor heads. The prime objective for SAMS on the International Microgravity Lab (IML-1) mission will be to measure the accelerations experienced by the Fluid Experiment System (FES). The SAMS acceleration measurements for FES will be complemented by low level, low frequency acceleration measurements made by the Orbital Acceleration Research Experiment (OARE) installed on the shuttle. Secondary objectives for SAMS will be to measure accelerations at several specific locations to enable the acceleration transfer function of the Spacelab module to be analyzed. This analysis effort will be in conjunction with similar measurements analyses on other Spacelab missions.

  2. Split Course Hyperfractionated Accelerated Radio-Chemotherapy (SCHARC) for patients with advanced head and neck cancer: Influence of protocol deviations and hemoglobin on overall survival, a retrospective analysis

    PubMed Central

    Stadler, Peter; Putnik, Kurt; Kreimeyer, Thore; Sprague, Lisa D; Koelbl, Oliver; Schäfer, Christof

    2006-01-01

    Background The advantage of hyperfractionated accelerated radiation therapy for advanced head and neck cancer has been reported. Furthermore, randomized trials and meta-analyses have confirmed the survival benefit of additional chemotherapy to radiotherapy. We retrospectively analyzed the efficiency and toxicity of the Regensburg standard therapy protocol "SCHARC" and the overall survival of our patients. Methods From 1997 to 2004, 64 patients suffering from advanced head and neck cancer (88 % stage IV, 12 % stage III) were assigned to receive the SCHARC protocol. Around half of the patients were diagnosed with oro-hypopharynx carcinoma (52 %), one third with tongue and floor of mouth tumors (29 %) and one fifth (19 %) suffered from H & N cancer at other sites. The schedule consisted of one therapy block with 30 Gy in 20 fractions over a two week period with concomitant chemotherapy (d 1–5: 20 mg/m2/d DDP + 750–1000 mg/m2/d 5FU (cont. infusion). This therapy block was repeated after a fortnight break up to a cumulative dose of 60 Gy and followed by a boost up to 70 Gy (69–70.5 Gy). All patients assigned to this scheme were included in the survival evaluation. Results Forty patients (63 %) received both radiation and chemotherapy according to the protocol. The mean follow up was 2.3 years (829 d) and the median follow up was 1.9 years (678 d), respectively. The analysis of survival revealed an estimated 3 year overall survival rate of 57 %. No patient died of complications, 52 patients (80 %) had acute grade 2–3 mucositis, and 33 patients (58 %) suffered from acute grade 3 skin toxicity. Leucopenia was no major problem (mean nadir 3.4 g/nl, no patient < 1.0 g/nl) and the mean hemoglobin value decreased from 13.2 to 10.5 g/dl. Univariate analysis of survival showed a better outcome for patients with a hemoglobin nadir >10.5 g/dl and for patients who completed the protocol. Conclusion The SCHARC protocol was effective in patients diagnosed with advanced head

  3. Analysis of organochlorine pesticides in coral (Porites evermanni) samples using accelerated solvent extraction and gas chromatography/ion trap mass spectrometry.

    PubMed

    Wang, Dongli; Miao, Xiusheng; Li, Qing X

    2008-02-01

    A gas chromatography/ion trap mass spectrometry method was developed for analysis of organochlorine pesticides (OCPs) in coral samples, which were extracted with accelerated solvent extraction (ASE) and cleaned up on a sulfuric acid-modified silica gel column. The optimal ASE conditions were found to be 100 degrees C and 2000 psi, with a mixture of acetone and methylene chloride (1:1, v/v). The target analytes include hexachlorocyclohexanes (HCHs, specifically, alpha-, beta-, gamma-, and delta-HCH isomers), heptachlor, and hexachlorobenzene (HCB), o,p'-, p,p'-dichlorodiphenyltrichloroethane (o,p'-, p,p'-DDT), o,p'-, p,p'-dichlorodiphenyl-dichloroethylene (o,p'-, p,p'-DDE), and o,p'-, p,p'-dichlorodiphenyldichloroethane (o,p'-, p,p'-DDD). Standard sand samples were used as an alternative matrix spiked with OCP standards to determine the method precision and accuracy. Average recoveries of OCPs ranged from 82% to 102%, with relative standard deviations (RSDs) of 3%-6%, at a level of 10 ng/g and from 50% to 68%, with RSDs of 13%-19% at a level of 2 ng/g. The developed method was applied for analysis of OCPs in coral samples collected from Tern Island and Bikini Atoll in the Pacific Ocean. The concentrations of HCB were 7-26 pg/g dry weight in the samples from Bikini Atoll and 3-45 pg/g in those from Tern Island, and heptachlor concentrations were 208-2200 and 44-104 pg/g in the coral samples from Bikini Atoll and Tern Island, respectively. (summation operator)HCH (sum of alpha-, beta-, gamma-, and delta-HCH) were 8-82 pg/g in Bikini Atoll coral and 86-629 pg/g in Tern island coral, and (summation operator)DDT (sum of o,p'-, p,p'-DDD, o,p'-, p,p'-DDE, and o,p'- p,p'-DDT) were 80-212 pg/g in Bikini Atoll coral and 593-3165 pg/g in Tern Island coral. The results suggest that coral is a viable indicator species for pollution monitoring, which pollutants and their concentrations may be related to dated carbonate layers. PMID:17721673

  4. Particle acceleration in flares

    NASA Technical Reports Server (NTRS)

    Benz, Arnold O.; Kosugi, Takeo; Aschwanden, Markus J.; Benka, Steve G.; Chupp, Edward L.; Enome, Shinzo; Garcia, Howard; Holman, Gordon D.; Kurt, Victoria G.; Sakao, Taro

    1994-01-01

    Particle acceleration is intrinsic to the primary energy release in the impulsive phase of solar flares, and we cannot understand flares without understanding acceleration. New observations in soft and hard X-rays, gamma-rays and coherent radio emissions are presented, suggesting flare fragmentation in time and space. X-ray and radio measurements exhibit at least five different time scales in flares. In addition, some new observations of delayed acceleration signatures are also presented. The theory of acceleration by parallel electric fields is used to model the spectral shape and evolution of hard X-rays. The possibility of the appearance of double layers is further investigated.

  5. Charged particle accelerator grating

    DOEpatents

    Palmer, Robert B.

    1986-09-02

    A readily disposable and replaceable accelerator grating for a relativistic particle accelerator. The grating is formed for a plurality of liquid droplets that are directed in precisely positioned jet streams to periodically dispose rows of droplets along the borders of a predetermined particle beam path. A plurality of lasers are used to direct laser beams into the droplets, at predetermined angles, thereby to excite the droplets to support electromagnetic accelerating resonances on their surfaces. Those resonances operate to accelerate and focus particles moving along the beam path. As the droplets are distorted or destroyed by the incoming radiation, they are replaced at a predetermined frequency by other droplets supplied through the jet streams.

  6. Accelerator-based BNCT.

    PubMed

    Kreiner, A J; Baldo, M; Bergueiro, J R; Cartelli, D; Castell, W; Thatar Vento, V; Gomez Asoia, J; Mercuri, D; Padulo, J; Suarez Sandin, J C; Erhardt, J; Kesque, J M; Valda, A A; Debray, M E; Somacal, H R; Igarzabal, M; Minsky, D M; Herrera, M S; Capoulat, M E; Gonzalez, S J; del Grosso, M F; Gagetti, L; Suarez Anzorena, M; Gun, M; Carranza, O

    2014-06-01

    The activity in accelerator development for accelerator-based BNCT (AB-BNCT) both worldwide and in Argentina is described. Projects in Russia, UK, Italy, Japan, Israel, and Argentina to develop AB-BNCT around different types of accelerators are briefly presented. In particular, the present status and recent progress of the Argentine project will be reviewed. The topics will cover: intense ion sources, accelerator tubes, transport of intense beams, beam diagnostics, the (9)Be(d,n) reaction as a possible neutron source, Beam Shaping Assemblies (BSA), a treatment room, and treatment planning in realistic cases. PMID:24365468

  7. Analysis of Acceleration, Airspeed, and Gust-Velocity Data From a Four-Engine Transport Airplane Operating Over a Northwestern United States Alaska Route

    NASA Technical Reports Server (NTRS)

    Engel, Jerome N.; Copp, Martin R.

    1959-01-01

    Acceleration, airspeed, and altitude data obtained with an NACA VGH recorder from a four-engine commercial transport airplane operating over a northwestern United States-Alaska route were evaluated to determine the magnitude and frequency of occurrence of gust and maneuver accelerations., operating airspeeds, and gust velocities. The results obtained were then compared with the results previously reported in NACA Technical Note 3475 for two similar airplanes operating over transcontinental routes in the United States. No large variations in the gust experience for the three operations were noted. The results indicate that the gust-load experience of the present operation closely approximated that of the central transcontinental route in the United States with which it is compared and showed differences of about 4 to 1 when compared with that of the southern transcontinental route in the United States. In general, accelerations due to gusts occurred much more frequently than those due to operational maneuvers. At a measured normal-acceleration increment of 0.5g, accelerations due to gusts occurred roughly 35 times more frequently than those due to operational maneuvers.

  8. Generation and analysis of quasimonoenergetic electron beams by laser-plasma interaction in transitional region from the self-modulated laser wakefield to bubble acceleration regime

    SciTech Connect

    Masuda, S.; Miura, E.

    2009-09-15

    Generation of quasimonoenergetic electron beams in a transitional region from the self-modulated laser wakefield to bubble acceleration regime is reported. Quasimonoenergetic electron beams containing more than 3x10{sup 8} electrons in the monoenergetic peak with energies of 40-60 MeV have been obtained from a plasma with an electron density of 1.6x10{sup 19} cm{sup -3} produced by an 8 TW, 50 fs laser pulse. The generation of quasimonoenergetic electron beams is investigated by two-dimensional particle-in-cell simulations. Few periods of the plasma wave are located inside the laser pulse, because the laser pulse duration is longer than the wavelength of the plasma wave. Electrons trapped in the first period of the plasma wave can form the monoenergetic bunch, even though the trapped electrons interact directly with the laser field. The quasimonoenergetic electron beam can be obtained due to the small contribution of the direct acceleration by the laser field. This type of monoenergetic electron acceleration is different from that of both the self-modulated laser wakefield and bubble acceleration regimes, in which the trapped electrons in the plasma wave are located behind the laser pulse due to the pulse compression or fragmentation and free from the laser electric field. This result suggests a new regime for the quasimonoenergetic electron acceleration in the region between the self-modulation and bubble regime.

  9. Acceleration of polarized protons in circular accelerators

    SciTech Connect

    Courant, E.D.; Ruth, R.D.

    1980-09-12

    The theory of depolarization in circular accelerators is presented. The spin equation is first expressed in terms of the particle orbit and then converted to the equivalent spinor equation. The spinor equation is then solved for three different situations: (1) a beam on a flat top near a resonance, (2) uniform acceleration through an isolated resonance, and (3) a model of a fast resonance jump. Finally, the depolarization coefficient, epsilon, is calculated in terms of properties of the particle orbit and the results are applied to a calculation of depolarization in the AGS.

  10. Scaling FFAG accelerator for muon acceleration

    SciTech Connect

    Lagrange, JB.; Planche, T.; Mori, Y.

    2011-10-06

    Recent developments in scaling fixed field alternating gradient (FFAG) accelerators have opened new ways for lattice design, with straight sections, and insertions like dispersion suppressors. Such principles and matching issues are detailed in this paper. An application of these new concepts is presented to overcome problems in the PRISM project.

  11. Accelerators (4/5)

    ScienceCinema

    None

    2011-10-06

    1a) Introduction and motivation 1b) History and accelerator types 2) Transverse beam dynamics 3a) Longitudinal beam dynamics 3b) Figure of merit of a synchrotron/collider 3c) Beam control 4) Main limiting factors 5) Technical challenges Prerequisite knowledge: Previous knowledge of accelerators is not required.

  12. J-PARC Accelerator

    SciTech Connect

    Yamazaki, Yoshishige

    2008-02-21

    The Japan Proton Accelerator Research Complex (J-PARC) is under construction in Tokai site. The linac beam commissioning started last fall, while the beam commissioning of the 3-GeV Rapid-Cycling Synchrotron (RCS) will start this fall. The status of the J-PARC accelerator is reported with emphasis on the technical development accomplished for the J-PARC.

  13. Particle Acceleration in Jets

    NASA Technical Reports Server (NTRS)

    Nishikawa, Ken-Ichi

    2005-01-01

    Nonthermal radiation observed from astrophysical systems containing relativistic jets and shocks, e.g., active galactic nuclei (AGNs), gamma ray burst (GRBs), and Galactic microquasar systems usually have power-law emission spectra. Fermi acceleration is the mechanism usually assumed for the acceleration of particles in astrophysical environments.

  14. Diagnostics for induction accelerators

    SciTech Connect

    Fessenden, T.J.

    1996-04-01

    The induction accelerator was conceived by N. C. Christofilos and first realized as the Astron accelerator that operated at LLNL from the early 1960`s to the end of 1975. This accelerator generated electron beams at energies near 6 MeV with typical currents of 600 Amperes in 400 ns pulses. The Advanced Test Accelerator (ATA) built at Livermore`s Site 300 produced 10,000 Ampere beams with pulse widths of 70 ns at energies approaching 50 MeV. Several other electron and ion induction accelerators have been fabricated at LLNL and LBNL. This paper reviews the principal diagnostics developed through efforts by scientists at both laboratories for measuring the current, position, energy, and emittance of beams generated by these high current, short pulse accelerators. Many of these diagnostics are closely related to those developed for other accelerators. However, the very fast and intense current pulses often require special diagnostic techniques and considerations. The physics and design of the more unique diagnostics developed for electron induction accelerators are presented and discussed in detail.

  15. Accelerators Beyond The Tevatron?

    SciTech Connect

    Lach, Joseph

    2010-07-01

    Following the successful operation of the Fermilab superconducting accelerator three new higher energy accelerators were planned. They were the UNK in the Soviet Union, the LHC in Europe, and the SSC in the United States. All were expected to start producing physics about 1995. They did not. Why?

  16. Microscale acceleration history discriminators

    DOEpatents

    Polosky, Marc A.; Plummer, David W.

    2002-01-01

    A new class of micromechanical acceleration history discriminators is claimed. These discriminators allow the precise differentiation of a wide range of acceleration-time histories, thereby allowing adaptive events to be triggered in response to the severity (or lack thereof) of an external environment. Such devices have applications in airbag activation, and other safety and surety applications.

  17. KEK digital accelerator

    NASA Astrophysics Data System (ADS)

    Iwashita, T.; Adachi, T.; Takayama, K.; Leo, K. W.; Arai, T.; Arakida, Y.; Hashimoto, M.; Kadokura, E.; Kawai, M.; Kawakubo, T.; Kubo, Tomio; Koyama, K.; Nakanishi, H.; Okazaki, K.; Okamura, K.; Someya, H.; Takagi, A.; Tokuchi, A.; Wake, M.

    2011-07-01

    The High Energy Accelerator Research Organization KEK digital accelerator (KEK-DA) is a renovation of the KEK 500 MeV booster proton synchrotron, which was shut down in 2006. The existing 40 MeV drift tube linac and rf cavities have been replaced by an electron cyclotron resonance (ECR) ion source embedded in a 200 kV high-voltage terminal and induction acceleration cells, respectively. A DA is, in principle, capable of accelerating any species of ion in all possible charge states. The KEK-DA is characterized by specific accelerator components such as a permanent magnet X-band ECR ion source, a low-energy transport line, an electrostatic injection kicker, an extraction septum magnet operated in air, combined-function main magnets, and an induction acceleration system. The induction acceleration method, integrating modern pulse power technology and state-of-art digital control, is crucial for the rapid-cycle KEK-DA. The key issues of beam dynamics associated with low-energy injection of heavy ions are beam loss caused by electron capture and stripping as results of the interaction with residual gas molecules and the closed orbit distortion resulting from relatively high remanent fields in the bending magnets. Attractive applications of this accelerator in materials and biological sciences are discussed.

  18. Accelerators (5/5)

    ScienceCinema

    None

    2011-10-06

    1a) Introduction and motivation 1b) History and accelerator types 2) Transverse beam dynamics 3a) Longitudinal beam dynamics 3b) Figure of merit of a synchrotron/collider 3c) Beam control 4) Main limiting factors 5) Technical challenges Prerequisite knowledge: Previous knowledge of accelerators is not required.

  19. Accelerating global forest mortality

    NASA Astrophysics Data System (ADS)

    McDowell, N. G.

    2014-12-01

    Forest mortality is apparently accelerating globally. The evidence supporting this contention is now substantial, as is the evidence suggesting the acceleration has just begun and will become progressively worse in upcoming decades. I will review the data and models used to make these contentions.

  20. Accelerators (3/5)

    ScienceCinema

    None

    2011-10-06

    1a) Introduction and motivation 1b) History and accelerator types 2) Transverse beam dynamics 3a) Longitudinal beam dynamics 3b) Figure of merit of a synchrotron/collider 3c) Beam control 4) Main limiting factors 5) Technical challenges Prerequisite knowledge: Previous knowledge of accelerators is not required.